0.024117 0.000000 0.000000 0.000000 0.017726 0.000000 0.000000 0.000000 0.009734 0.000000 0.000000 0.000000 0000-0002-3426-9003 Pidugu, L.S. 0000-0001-7012-5376 Pozharski, E. 0000-0002-7458-8770 Drohat, A.C. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.000 90.000 90.000 41.465 56.414 102.733 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking Cl -1 35.453 CHLORIDE ION non-polymer C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C10 H14 N5 O6 P 331.222 y 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE DNA linking C9 H14 N3 O7 P 307.197 y 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O7 P 347.221 y 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE DNA linking C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking C2 H6 O2 62.068 1,2-ETHANEDIOL ETHYLENE GLYCOL non-polymer C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C3 H8 O3 92.094 GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL non-polymer C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking Na 1 22.990 SODIUM ION non-polymer C5 H13 N O5 P 1 198.134 (3R,4R)-3-hydroxy-4-[(phosphonooxy)methyl]pyrrolidinium DNA linking C4 H10 O3 106.120 DI(HYDROXYETHYL)ETHER non-polymer C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking N 1 N N N 2 S C N 3 N C N 4 N O N 5 N C N 6 N O N 7 N H N 8 N H N 9 N H N 10 N H N 11 N H N 12 N H N 13 N H N 14 N N N 15 S C N 16 N C N 17 N O N 18 N C N 19 N C N 20 N C N 21 N N N 22 N C N 23 N N N 24 N N N 25 N O N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N H N 39 N H N 40 N H N 41 N N N 42 S C N 43 N C N 44 N O N 45 N C N 46 N C N 47 N O N 48 N N N 49 N O N 50 N H N 51 N H N 52 N H N 53 N H N 54 N H N 55 N H N 56 N H N 57 N H N 58 N N N 59 S C N 60 N C N 61 N O N 62 N C N 63 N C N 64 N O N 65 N O N 66 N O N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N CL N 75 N N N 76 R C N 77 N C N 78 N O N 79 N C N 80 N S N 81 N O N 82 N H N 83 N H N 84 N H N 85 N H N 86 N H N 87 N H N 88 N H N 89 N O N 90 N P N 91 N O N 92 N O N 93 N O N 94 N C N 95 R C N 96 N O N 97 S C N 98 N O N 99 N C N 100 R C Y 101 N N Y 102 N C Y 103 N N Y 104 N C Y 105 N C N 106 N N Y 107 N N Y 108 N C Y 109 N N Y 110 N C N 111 N H N 112 N H N 113 N H N 114 N H N 115 N H N 116 N H N 117 N H N 118 N H N 119 N H N 120 N H N 121 N H N 122 N H N 123 N H N 124 N H N 125 N O N 126 N P N 127 N O N 128 N O N 129 N O N 130 N C N 131 R C N 132 N O N 133 S C N 134 N O N 135 N C N 136 R C N 137 N N N 138 N C N 139 N O N 140 N N N 141 N C N 142 N N N 143 N C N 144 N C N 145 N H N 146 N H N 147 N H N 148 N H N 149 N H N 150 N H N 151 N H N 152 N H N 153 N H N 154 N H N 155 N H N 156 N H N 157 N H N 158 N H N 159 N O N 160 N P N 161 N O N 162 N O N 163 N O N 164 N C N 165 R C N 166 N O N 167 S C N 168 N O N 169 N C N 170 R C Y 171 N N Y 172 N C Y 173 N N Y 174 N C N 175 N C N 176 N O N 177 N N N 178 N C N 179 N N N 180 N N Y 181 N C N 182 N H N 183 N H N 184 N H N 185 N H N 186 N H N 187 N H N 188 N H N 189 N H N 190 N H N 191 N H N 192 N H N 193 N H N 194 N H N 195 N H N 196 N O N 197 N P N 198 N O N 199 N O N 200 N O N 201 N C N 202 R C N 203 N O N 204 S C N 205 N O N 206 N C N 207 R C N 208 N N N 209 N C N 210 N O N 211 N N N 212 N C N 213 N O N 214 N C N 215 N C N 216 N C N 217 N H N 218 N H N 219 N H N 220 N H N 221 N H N 222 N H N 223 N H N 224 N H N 225 N H N 226 N H N 227 N H N 228 N H N 229 N H N 230 N H N 231 N H N 232 N C N 233 N O N 234 N C N 235 N O N 236 N H N 237 N H N 238 N H N 239 N H N 240 N H N 241 N H N 242 N N N 243 S C N 244 N C N 245 N O N 246 N C N 247 N C N 248 N C N 249 N O N 250 N N N 251 N O N 252 N H N 253 N H N 254 N H N 255 N H N 256 N H N 257 N H N 258 N H N 259 N H N 260 N H N 261 N H N 262 N N N 263 S C N 264 N C N 265 N O N 266 N C N 267 N C N 268 N C N 269 N O N 270 N O N 271 N O N 272 N H N 273 N H N 274 N H N 275 N H N 276 N H N 277 N H N 278 N H N 279 N H N 280 N H N 281 N N N 282 N C N 283 N C N 284 N O N 285 N O N 286 N H N 287 N H N 288 N H N 289 N H N 290 N H N 291 N C N 292 N O N 293 N C N 294 N O N 295 N C N 296 N O N 297 N H N 298 N H N 299 N H N 300 N H N 301 N H N 302 N H N 303 N H N 304 N H N 305 N N N 306 S C N 307 N C N 308 N O N 309 N C Y 310 N C Y 311 N N Y 312 N C Y 313 N C Y 314 N N N 315 N O N 316 N H N 317 N H N 318 N H N 319 N H N 320 N H N 321 N H N 322 N H N 323 N H N 324 N H N 325 N H N 326 N O N 327 N H N 328 N H N 329 N N N 330 S C N 331 N C N 332 N O N 333 S C N 334 N C N 335 N C N 336 N C N 337 N O N 338 N H N 339 N H N 340 N H N 341 N H N 342 N H N 343 N H N 344 N H N 345 N H N 346 N H N 347 N H N 348 N H N 349 N H N 350 N H N 351 N N N 352 S C N 353 N C N 354 N O N 355 N C N 356 N C N 357 N C N 358 N C N 359 N O N 360 N H N 361 N H N 362 N H N 363 N H N 364 N H N 365 N H N 366 N H N 367 N H N 368 N H N 369 N H N 370 N H N 371 N H N 372 N H N 373 N N N 374 S C N 375 N C N 376 N O N 377 N C N 378 N C N 379 N C N 380 N C N 381 N N N 382 N O N 383 N H N 384 N H N 385 N H N 386 N H N 387 N H N 388 N H N 389 N H N 390 N H N 391 N H N 392 N H N 393 N H N 394 N H N 395 N H N 396 N H N 397 N H N 398 N N N 399 S C N 400 N C N 401 N O N 402 N C N 403 N C N 404 N S N 405 N C N 406 N O N 407 N H N 408 N H N 409 N H N 410 N H N 411 N H N 412 N H N 413 N H N 414 N H N 415 N H N 416 N H N 417 N H N 418 N NA N 419 N P N 420 N O N 421 N O N 422 N O N 423 N C N 424 N C N 425 R C N 426 R C N 427 N C N 428 N N N 429 N O N 430 N O N 431 N H N 432 N H N 433 N H N 434 N H N 435 N H N 436 N H N 437 N H N 438 N H N 439 N H N 440 N H N 441 N H N 442 N H N 443 N H N 444 N C N 445 N O N 446 N C N 447 N O N 448 N C N 449 N C N 450 N O N 451 N H N 452 N H N 453 N H N 454 N H N 455 N H N 456 N H N 457 N H N 458 N H N 459 N H N 460 N H N 461 N N N 462 S C N 463 N C N 464 N O N 465 N C Y 466 N C Y 467 N C Y 468 N C Y 469 N C Y 470 N C Y 471 N C N 472 N O N 473 N H N 474 N H N 475 N H N 476 N H N 477 N H N 478 N H N 479 N H N 480 N H N 481 N H N 482 N H N 483 N H N 484 N N N 485 S C N 486 N C N 487 N O N 488 N C N 489 N C N 490 N C N 491 N O N 492 N H N 493 N H N 494 N H N 495 N H N 496 N H N 497 N H N 498 N H N 499 N H N 500 N H N 501 N N N 502 S C N 503 N C N 504 N O N 505 N C N 506 N O N 507 N O N 508 N H N 509 N H N 510 N H N 511 N H N 512 N H N 513 N H N 514 N H N 515 N N N 516 S C N 517 N C N 518 N O N 519 R C N 520 N O N 521 N C N 522 N O N 523 N H N 524 N H N 525 N H N 526 N H N 527 N H N 528 N H N 529 N H N 530 N H N 531 N H N 532 N N N 533 S C N 534 N C N 535 N O N 536 N C Y 537 N C Y 538 N C Y 539 N C Y 540 N N Y 541 N C Y 542 N C Y 543 N C Y 544 N C Y 545 N C N 546 N O N 547 N H N 548 N H N 549 N H N 550 N H N 551 N H N 552 N H N 553 N H N 554 N H N 555 N H N 556 N H N 557 N H N 558 N H N 559 N N N 560 S C N 561 N C N 562 N O N 563 N C Y 564 N C Y 565 N C Y 566 N C Y 567 N C Y 568 N C Y 569 N C N 570 N O N 571 N O N 572 N H N 573 N H N 574 N H N 575 N H N 576 N H N 577 N H N 578 N H N 579 N H N 580 N H N 581 N H N 582 N H N 583 N N N 584 S C N 585 N C N 586 N O N 587 N C N 588 N C N 589 N C N 590 N O N 591 N H N 592 N H N 593 N H N 594 N H N 595 N H N 596 N H N 597 N H N 598 N H N 599 N H N 600 N H N 601 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N doub N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N doub N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N doub N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N doub N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N doub N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N doub N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N doub N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N doub N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N doub N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing Y 106 N sing Y 107 N sing Y 108 N doub N 109 N sing Y 110 N sing Y 111 N sing Y 112 N doub N 113 N sing Y 114 N doub N 115 N sing N 116 N sing Y 117 N sing Y 118 N doub N 119 N sing Y 120 N sing N 121 N sing N 122 N sing N 123 N doub N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N sing N 144 N sing N 145 N sing N 146 N doub N 147 N sing N 148 N doub N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N doub N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N doub N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N sing Y 179 N sing Y 180 N sing Y 181 N doub N 182 N sing Y 183 N sing N 184 N sing Y 185 N doub N 186 N doub N 187 N sing N 188 N sing N 189 N sing N 190 N sing N 191 N doub N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N doub N 198 N sing N 199 N sing N 200 N sing N 201 N sing N 202 N sing N 203 N sing N 204 N sing N 205 N sing N 206 N sing N 207 N sing N 208 N sing N 209 N sing N 210 N sing N 211 N sing N 212 N sing N 213 N sing N 214 N sing N 215 N sing N 216 N sing N 217 N sing N 218 N sing N 219 N sing N 220 N doub N 221 N sing N 222 N sing N 223 N sing N 224 N doub N 225 N sing N 226 N sing N 227 N doub N 228 N sing N 229 N sing N 230 N sing N 231 N sing N 232 N sing N 233 N sing N 234 N sing N 235 N sing N 236 N sing N 237 N sing N 238 N sing N 239 N sing N 240 N sing N 241 N sing N 242 N sing N 243 N sing N 244 N sing N 245 N sing N 246 N sing N 247 N doub N 248 N sing N 249 N sing N 250 N sing N 251 N sing N 252 N sing N 253 N sing N 254 N sing N 255 N doub N 256 N sing N 257 N sing N 258 N sing N 259 N sing N 260 N sing N 261 N sing N 262 N sing N 263 N sing N 264 N sing N 265 N sing N 266 N doub N 267 N sing N 268 N sing N 269 N sing N 270 N sing N 271 N sing N 272 N sing N 273 N sing N 274 N doub N 275 N sing N 276 N sing N 277 N sing N 278 N sing N 279 N sing N 280 N sing N 281 N sing N 282 N sing N 283 N sing N 284 N doub N 285 N sing N 286 N sing N 287 N sing N 288 N sing N 289 N sing N 290 N sing N 291 N sing N 292 N sing N 293 N sing N 294 N sing N 295 N sing N 296 N sing N 297 N sing N 298 N sing N 299 N sing N 300 N sing N 301 N sing N 302 N sing N 303 N sing N 304 N sing N 305 N sing N 306 N doub N 307 N sing N 308 N sing N 309 N sing N 310 N sing Y 311 N sing Y 312 N doub Y 313 N doub N 314 N sing Y 315 N sing N 316 N sing Y 317 N sing N 318 N sing N 319 N sing N 320 N sing N 321 N sing N 322 N sing N 323 N sing N 324 N sing N 325 N sing N 326 N sing N 327 N sing N 328 N sing N 329 N doub N 330 N sing N 331 N sing N 332 N sing N 333 N sing N 334 N sing N 335 N sing N 336 N sing N 337 N sing N 338 N sing N 339 N sing N 340 N sing N 341 N sing N 342 N sing N 343 N sing N 344 N sing N 345 N sing N 346 N sing N 347 N sing N 348 N sing N 349 N sing N 350 N doub N 351 N sing N 352 N sing N 353 N sing N 354 N sing N 355 N sing N 356 N sing N 357 N sing N 358 N sing N 359 N sing N 360 N sing N 361 N sing N 362 N sing N 363 N sing N 364 N sing N 365 N sing N 366 N sing N 367 N sing N 368 N sing N 369 N sing N 370 N sing N 371 N doub N 372 N sing N 373 N sing N 374 N sing N 375 N sing N 376 N sing N 377 N sing N 378 N sing N 379 N sing N 380 N sing N 381 N sing N 382 N sing N 383 N sing N 384 N sing N 385 N sing N 386 N sing N 387 N sing N 388 N sing N 389 N sing N 390 N sing N 391 N sing N 392 N sing N 393 N sing N 394 N sing N 395 N doub N 396 N sing N 397 N sing N 398 N sing N 399 N sing N 400 N sing N 401 N sing N 402 N sing N 403 N sing N 404 N sing N 405 N sing N 406 N sing N 407 N sing N 408 N sing N 409 N sing N 410 N sing N 411 N sing N 412 N sing N 413 N sing N 414 N sing N 415 N doub N 416 N sing N 417 N sing N 418 N sing N 419 N sing N 420 N sing N 421 N sing N 422 N sing N 423 N sing N 424 N sing N 425 N sing N 426 N sing N 427 N sing N 428 N sing N 429 N sing N 430 N sing N 431 N sing N 432 N sing N 433 N sing N 434 N sing N 435 N sing N 436 N sing N 437 N sing N 438 N sing N 439 N sing N 440 N sing N 441 N sing N 442 N sing N 443 N sing N 444 N sing N 445 N sing N 446 N sing N 447 N sing N 448 N sing N 449 N sing N 450 N sing N 451 N sing N 452 N sing N 453 N sing N 454 N sing N 455 N doub N 456 N sing N 457 N sing N 458 N sing N 459 N sing Y 460 N doub Y 461 N sing Y 462 N sing N 463 N sing Y 464 N doub N 465 N sing Y 466 N doub N 467 N sing Y 468 N sing N 469 N sing N 470 N sing N 471 N sing N 472 N sing N 473 N sing N 474 N sing N 475 N sing N 476 N sing N 477 N sing N 478 N doub N 479 N sing N 480 N sing N 481 N sing N 482 N sing N 483 N sing N 484 N sing N 485 N sing N 486 N sing N 487 N sing N 488 N sing N 489 N sing N 490 N sing N 491 N sing N 492 N sing N 493 N sing N 494 N sing N 495 N doub N 496 N sing N 497 N sing N 498 N sing N 499 N sing N 500 N sing N 501 N sing N 502 N sing N 503 N sing N 504 N sing N 505 N sing N 506 N sing N 507 N sing N 508 N doub N 509 N sing N 510 N sing N 511 N sing N 512 N sing N 513 N sing N 514 N sing N 515 N sing N 516 N sing N 517 N sing N 518 N sing N 519 N sing N 520 N sing N 521 N sing N 522 N sing N 523 N sing N 524 N doub N 525 N sing N 526 N sing N 527 N sing N 528 N sing Y 529 N doub Y 530 N sing Y 531 N sing N 532 N sing Y 533 N doub Y 534 N sing Y 535 N sing N 536 N sing Y 537 N sing Y 538 N doub N 539 N sing Y 540 N doub N 541 N sing Y 542 N sing N 543 N sing N 544 N sing N 545 N sing N 546 N sing N 547 N sing N 548 N sing N 549 N sing N 550 N sing N 551 N sing N 552 N doub N 553 N sing N 554 N sing N 555 N sing N 556 N sing Y 557 N doub Y 558 N sing Y 559 N sing N 560 N sing Y 561 N doub N 562 N sing Y 563 N doub N 564 N sing Y 565 N sing N 566 N sing N 567 N sing N 568 N sing N 569 N sing N 570 N sing N 571 N sing N 572 N sing N 573 N sing N 574 N sing N 575 N sing N 576 N doub N 577 N sing N 578 N sing N 579 N sing N 580 N sing N 581 N sing N 582 N sing N 583 N sing N 584 N sing N 585 N sing N 586 N sing N 587 N sing UK J.Mol.Biol. JMOBAK 0070 1089-8638 433 167097 167097 10.1016/j.jmb.2021.167097 34107280 Structural Insights into the Mechanism of Base Excision by MBD4. 2021 10.2210/pdb7kzg/pdb pdb_00007kzg 100 1 N PIXEL 2020-10-24 DECTRIS PILATUS 6M Si(111) and Si(220) double crystal SINGLE WAVELENGTH M x-ray 1 0.9795 1.0 BL9-2 SSRL 0.9795 SYNCHROTRON SSRL BEAMLINE BL9-2 20560.615 Methyl-CpG-binding domain protein 4 3.2.2.- glycosylase domain (UNP residues 426-580) 1 man polymer 3524.307 DNA (5'-D(*CP*CP*AP*GP*CP*GP*(NR1)P*GP*CP*AP*GP*C)-3') 1 syn polymer 3695.390 DNA (5'-D(*GP*CP*TP*GP*CP*GP*CP*GP*CP*TP*GP*G)-3') 1 syn polymer 92.094 GLYCEROL 4 syn non-polymer 106.120 DI(HYDROXYETHYL)ETHER 1 syn non-polymer 62.068 1,2-ETHANEDIOL 1 syn non-polymer 22.990 SODIUM ION 1 syn non-polymer 35.453 CHLORIDE ION 1 syn non-polymer 18.015 water 235 nat water Methyl-CpG-binding endonuclease 1,Methyl-CpG-binding protein MBD4,Mismatch-specific DNA N-glycosylase no no MGSSHHHHHHSSGLVPRGSALSPPRRKAFKKWTPPRSPFNLVQETLFHDPWKLLIATIFLNRTSGKMAIPVLWKFLEKYP SAEVARTADWRDVSELLKPLGLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSYRIFCVNEWKQVHPEDHKLNKY HDWLWENHEKLSLS MGSSHHHHHHSSGLVPRGSALSPPRRKAFKKWTPPRSPFNLVQETLFHDPWKLLIATIFLNRTSGKMAIPVLWKFLEKYP SAEVARTADWRDVSELLKPLGLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSYRIFCVNEWKQVHPEDHKLNKY HDWLWENHEKLSLS A polypeptide(L) no yes (DC)(DC)(DA)(DG)(DC)(DG)(NR1)(DG)(DC)(DA)(DG)(DC) CCAGCGXGCAGC C polydeoxyribonucleotide no no (DG)(DC)(DT)(DG)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DG) GCTGCGCGCTGG D polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n Human sample 1 174 MBD4, MED1 9606 Homo sapiens 562 Escherichia coli Biological sequence 1 2.16 43.12 VAPOR DIFFUSION, SITTING DROP 7.5 PEG1000, HEPES 293 -22.369 1 19 C 1 D 12 -0.425 C_DC1:DG12_D 1 -6.172 0.224 0.240 -0.108 -1.963 1 19 C 2 D 11 3.081 C_DC2:DG11_D 2 3.383 0.164 -0.340 -0.227 10.535 1 20 C 3 D 10 -0.414 C_DA3:DT10_D 3 -8.928 -0.162 0.275 -0.147 2.873 1 19 C 4 D 9 0.480 C_DG4:DC9_D 4 -11.028 -0.079 0.226 -0.134 -4.732 1 19 C 5 D 8 0.500 C_DC5:DG8_D 5 -7.229 0.108 -0.005 -0.146 8.943 1 19 C 6 D 7 1.088 C_DG6:DC7_D 6 -8.879 -0.213 0.360 -0.097 -12.618 1 19 C 8 D 5 0.612 C_DG8:DC5_D 7 -7.486 -0.358 -0.244 -0.109 -1.502 1 19 C 9 D 4 -2.992 C_DC9:DG4_D 8 -3.341 0.154 0.165 -0.091 7.936 1 20 C 10 D 3 -0.370 C_DA10:DT3_D 9 -12.686 0.093 0.107 -0.128 13.203 1 19 C 11 D 2 3.111 C_DG11:DC2_D 10 -7.751 -0.291 0.317 -0.146 10.115 1 19 C 12 D 1 6.090 C_DC12:DG1_D 11 -12.114 0.352 -0.148 -0.272 3.108 32.836 C C 1 2 11.092 D D 12 11 2.898 6.177 0.988 0.605 CC_DC1DC2:DG11DG12_DD 1 7.784 -13.978 31.336 0.073 -0.492 3.342 32.548 C C 2 3 3.097 D D 11 10 3.172 1.729 -0.979 1.290 CC_DC2DA3:DT10DG11_DD 2 -4.814 8.623 32.154 2.000 0.904 3.427 35.537 C C 3 4 5.698 D D 10 9 3.478 3.473 -0.054 -0.377 CC_DA3DG4:DC9DT10_DD 3 -0.123 0.202 35.373 -1.154 0.069 3.484 35.319 C C 4 5 1.530 D D 9 8 3.459 0.926 0.527 -0.433 CC_DG4DC5:DG8DC9_DD 4 4.036 -6.666 35.083 -0.859 -0.234 3.178 35.530 C C 5 6 9.219 D D 8 7 3.093 5.581 -0.448 0.592 CC_DC5DG6:DC7DG8_DD 5 -5.642 9.320 34.660 0.178 -0.066 3.058 27.257 C C 8 9 7.338 D D 5 4 3.074 3.438 -0.315 -0.055 CC_DG8DC9:DG4DC5_DD 6 -3.782 8.072 26.782 -0.930 -0.225 3.243 37.068 C C 9 10 6.037 D D 4 3 3.144 3.823 0.605 0.661 CC_DC9DA10:DT3DG4_DD 7 4.510 -7.122 36.609 0.536 -0.358 3.095 32.162 C C 10 11 9.524 D D 3 2 3.174 5.248 0.383 0.021 CC_DA10DG11:DC2DT3_DD 8 -2.697 4.894 31.630 -0.869 -1.158 3.343 35.313 C C 11 12 2.538 D D 2 1 3.361 1.535 0.192 -0.264 CC_DG11DC12:DG1DC2_DD 9 4.732 -7.825 34.972 -0.669 0.404 chem_comp_atom chem_comp_bond pdbx_initial_refinement_model repository Initial release Data collection Refinement description 1 0 2021-11-10 1 1 2023-10-18 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01-GM072711, R35-GM136225 N RCSB Y RCSB 2020-12-10 REL REL NR1 NR1 SUBJECT OF INVESTIGATION GOL GLYCEROL PEG DI(HYDROXYETHYL)ETHER EDO 1,2-ETHANEDIOL NA SODIUM ION CL CHLORIDE ION HOH water 9606 Human Homo sapiens sample 1 12 9606 Human Homo sapiens sample 1 12 Y 4DK9 PDB entry 4DK9 PDB experimental model GOL 701 4 GOL GOL 701 A PEG 801 5 PEG PEG 702 A EDO 1001 6 EDO EDO 703 A GOL 1101 4 GOL GOL 704 A NA 1 7 NA NA 705 A CL 2 8 CL CL 706 A GOL 101 4 GOL GOL 101 C GOL 101 4 GOL GOL 101 D HOH 201 9 HOH HOH 801 A HOH 166 9 HOH HOH 802 A HOH 409 9 HOH HOH 803 A HOH 279 9 HOH HOH 804 A HOH 54 9 HOH HOH 805 A HOH 334 9 HOH HOH 806 A HOH 128 9 HOH HOH 807 A HOH 17 9 HOH HOH 808 A HOH 348 9 HOH HOH 809 A HOH 240 9 HOH HOH 810 A HOH 142 9 HOH HOH 811 A HOH 365 9 HOH HOH 812 A HOH 82 9 HOH HOH 813 A HOH 170 9 HOH HOH 814 A HOH 243 9 HOH HOH 815 A HOH 108 9 HOH HOH 816 A HOH 87 9 HOH HOH 817 A HOH 5 9 HOH HOH 818 A HOH 327 9 HOH HOH 819 A HOH 189 9 HOH HOH 820 A HOH 29 9 HOH HOH 821 A HOH 313 9 HOH HOH 822 A HOH 226 9 HOH HOH 823 A HOH 208 9 HOH HOH 824 A HOH 130 9 HOH HOH 825 A HOH 277 9 HOH HOH 826 A HOH 311 9 HOH HOH 827 A HOH 389 9 HOH HOH 828 A HOH 269 9 HOH HOH 829 A HOH 219 9 HOH HOH 830 A HOH 282 9 HOH HOH 831 A HOH 214 9 HOH HOH 832 A HOH 329 9 HOH HOH 833 A HOH 229 9 HOH HOH 834 A HOH 85 9 HOH HOH 835 A HOH 6 9 HOH HOH 836 A HOH 207 9 HOH HOH 837 A HOH 216 9 HOH HOH 838 A HOH 62 9 HOH HOH 839 A HOH 182 9 HOH HOH 840 A HOH 413 9 HOH HOH 841 A HOH 281 9 HOH HOH 842 A HOH 174 9 HOH HOH 843 A HOH 25 9 HOH HOH 844 A HOH 116 9 HOH HOH 845 A HOH 268 9 HOH HOH 846 A HOH 28 9 HOH HOH 847 A HOH 185 9 HOH HOH 848 A HOH 378 9 HOH HOH 849 A HOH 248 9 HOH HOH 850 A HOH 165 9 HOH HOH 851 A HOH 416 9 HOH HOH 852 A HOH 232 9 HOH HOH 853 A HOH 18 9 HOH HOH 854 A HOH 203 9 HOH HOH 855 A HOH 186 9 HOH HOH 856 A HOH 20 9 HOH HOH 857 A HOH 302 9 HOH HOH 858 A HOH 131 9 HOH HOH 859 A HOH 202 9 HOH HOH 860 A HOH 307 9 HOH HOH 861 A HOH 239 9 HOH HOH 862 A HOH 370 9 HOH HOH 863 A HOH 183 9 HOH HOH 864 A HOH 249 9 HOH HOH 865 A HOH 428 9 HOH HOH 866 A HOH 59 9 HOH HOH 867 A HOH 244 9 HOH HOH 868 A HOH 264 9 HOH HOH 869 A HOH 414 9 HOH HOH 870 A HOH 61 9 HOH HOH 871 A HOH 280 9 HOH HOH 872 A HOH 396 9 HOH HOH 873 A HOH 181 9 HOH HOH 874 A HOH 316 9 HOH HOH 875 A HOH 192 9 HOH HOH 876 A HOH 285 9 HOH HOH 877 A HOH 305 9 HOH HOH 878 A HOH 123 9 HOH HOH 879 A HOH 218 9 HOH HOH 880 A HOH 231 9 HOH HOH 881 A HOH 71 9 HOH HOH 882 A HOH 180 9 HOH HOH 883 A HOH 380 9 HOH HOH 884 A HOH 27 9 HOH HOH 885 A HOH 19 9 HOH HOH 886 A HOH 317 9 HOH HOH 887 A HOH 266 9 HOH HOH 888 A HOH 12 9 HOH HOH 889 A HOH 118 9 HOH HOH 890 A HOH 288 9 HOH HOH 891 A HOH 275 9 HOH HOH 892 A HOH 146 9 HOH HOH 893 A HOH 224 9 HOH HOH 894 A HOH 241 9 HOH HOH 895 A HOH 330 9 HOH HOH 896 A HOH 265 9 HOH HOH 897 A HOH 296 9 HOH HOH 898 A HOH 401 9 HOH HOH 899 A HOH 267 9 HOH HOH 900 A HOH 395 9 HOH HOH 901 A HOH 205 9 HOH HOH 902 A HOH 433 9 HOH HOH 903 A HOH 303 9 HOH HOH 904 A HOH 26 9 HOH HOH 905 A HOH 412 9 HOH HOH 906 A HOH 86 9 HOH HOH 907 A HOH 238 9 HOH HOH 908 A HOH 337 9 HOH HOH 909 A HOH 344 9 HOH HOH 910 A HOH 233 9 HOH HOH 911 A HOH 217 9 HOH HOH 912 A HOH 272 9 HOH HOH 913 A HOH 261 9 HOH HOH 914 A HOH 49 9 HOH HOH 915 A HOH 8 9 HOH HOH 916 A HOH 278 9 HOH HOH 917 A HOH 379 9 HOH HOH 918 A HOH 38 9 HOH HOH 919 A HOH 430 9 HOH HOH 920 A HOH 289 9 HOH HOH 921 A HOH 391 9 HOH HOH 922 A HOH 394 9 HOH HOH 923 A HOH 377 9 HOH HOH 924 A HOH 111 9 HOH HOH 925 A HOH 420 9 HOH HOH 926 A HOH 4 9 HOH HOH 927 A HOH 376 9 HOH HOH 928 A HOH 427 9 HOH HOH 929 A HOH 109 9 HOH HOH 930 A HOH 415 9 HOH HOH 931 A HOH 408 9 HOH HOH 932 A HOH 228 9 HOH HOH 933 A HOH 252 9 HOH HOH 934 A HOH 210 9 HOH HOH 935 A HOH 339 9 HOH HOH 936 A HOH 331 9 HOH HOH 937 A HOH 392 9 HOH HOH 938 A HOH 423 9 HOH HOH 939 A HOH 431 9 HOH HOH 940 A HOH 21 9 HOH HOH 941 A HOH 422 9 HOH HOH 942 A HOH 295 9 HOH HOH 943 A HOH 169 9 HOH HOH 944 A HOH 406 9 HOH HOH 945 A HOH 373 9 HOH HOH 946 A HOH 79 9 HOH HOH 947 A HOH 140 9 HOH HOH 948 A HOH 432 9 HOH HOH 949 A HOH 271 9 HOH HOH 950 A HOH 67 9 HOH HOH 951 A HOH 374 9 HOH HOH 952 A HOH 429 9 HOH HOH 953 A HOH 294 9 HOH HOH 954 A HOH 225 9 HOH HOH 955 A HOH 325 9 HOH HOH 956 A HOH 407 9 HOH HOH 957 A HOH 381 9 HOH HOH 958 A HOH 69 9 HOH HOH 959 A HOH 345 9 HOH HOH 960 A HOH 312 9 HOH HOH 961 A HOH 333 9 HOH HOH 962 A HOH 375 9 HOH HOH 963 A HOH 351 9 HOH HOH 964 A HOH 418 9 HOH HOH 965 A HOH 230 9 HOH HOH 966 A HOH 291 9 HOH HOH 967 A HOH 332 9 HOH HOH 968 A HOH 257 9 HOH HOH 969 A HOH 310 9 HOH HOH 201 C HOH 300 9 HOH HOH 202 C HOH 251 9 HOH HOH 203 C HOH 234 9 HOH HOH 204 C HOH 176 9 HOH HOH 205 C HOH 45 9 HOH HOH 206 C HOH 260 9 HOH HOH 207 C HOH 1 9 HOH HOH 208 C HOH 425 9 HOH HOH 209 C HOH 145 9 HOH HOH 210 C HOH 112 9 HOH HOH 211 C HOH 223 9 HOH HOH 212 C HOH 258 9 HOH HOH 213 C HOH 114 9 HOH HOH 214 C HOH 91 9 HOH HOH 215 C HOH 299 9 HOH HOH 216 C HOH 372 9 HOH HOH 217 C HOH 178 9 HOH HOH 218 C HOH 41 9 HOH HOH 219 C HOH 206 9 HOH HOH 220 C HOH 301 9 HOH HOH 221 C HOH 259 9 HOH HOH 222 C HOH 298 9 HOH HOH 223 C HOH 157 9 HOH HOH 224 C HOH 384 9 HOH HOH 225 C HOH 255 9 HOH HOH 226 C HOH 107 9 HOH HOH 227 C HOH 322 9 HOH HOH 201 D HOH 236 9 HOH HOH 202 D HOH 198 9 HOH HOH 203 D HOH 212 9 HOH HOH 204 D HOH 199 9 HOH HOH 205 D HOH 403 9 HOH HOH 206 D HOH 37 9 HOH HOH 207 D HOH 175 9 HOH HOH 208 D HOH 361 9 HOH HOH 209 D HOH 177 9 HOH HOH 210 D HOH 184 9 HOH HOH 211 D HOH 235 9 HOH HOH 212 D HOH 426 9 HOH HOH 213 D HOH 213 9 HOH HOH 214 D HOH 138 9 HOH HOH 215 D HOH 92 9 HOH HOH 216 D HOH 102 9 HOH HOH 217 D HOH 362 9 HOH HOH 218 D HOH 323 9 HOH HOH 219 D HOH 274 9 HOH HOH 220 D HOH 262 9 HOH HOH 221 D HOH 359 9 HOH HOH 222 D HOH 399 9 HOH HOH 223 D HOH 254 9 HOH HOH 224 D HOH 93 9 HOH HOH 225 D HOH 129 9 HOH HOH 226 D HOH 172 9 HOH HOH 227 D HOH 400 9 HOH HOH 228 D HOH 358 9 HOH HOH 229 D HOH 324 9 HOH HOH 230 D HOH 388 9 HOH HOH 231 D HOH 382 9 HOH HOH 232 D HOH 367 9 HOH HOH 233 D HOH 404 9 HOH HOH 234 D HOH 134 9 HOH HOH 235 D HOH 293 9 HOH HOH 236 D HOH 220 9 HOH HOH 237 D HOH 309 9 HOH HOH 238 D HOH 110 9 HOH HOH 239 D n 1 407 A n 2 408 A n 3 409 A n 4 410 A n 5 411 A n 6 412 A n 7 413 A n 8 414 A n 9 415 A n 10 416 A n 11 417 A n 12 418 A n 13 419 A n 14 420 A n 15 421 A n 16 422 A n 17 423 A n 18 424 A n 19 425 A n 20 426 A n 21 427 A n 22 428 A n 23 429 A n 24 430 A n 25 431 A n 26 432 A n 27 433 A n 28 434 A n 29 435 A n 30 436 A LYS 437 n 31 LYS 437 A TRP 438 n 32 TRP 438 A THR 439 n 33 THR 439 A PRO 440 n 34 PRO 440 A PRO 441 n 35 PRO 441 A ARG 442 n 36 ARG 442 A SER 443 n 37 SER 443 A PRO 444 n 38 PRO 444 A PHE 445 n 39 PHE 445 A ASN 446 n 40 ASN 446 A LEU 447 n 41 LEU 447 A VAL 448 n 42 VAL 448 A GLN 449 n 43 GLN 449 A GLU 450 n 44 GLU 450 A THR 451 n 45 THR 451 A LEU 452 n 46 LEU 452 A PHE 453 n 47 PHE 453 A HIS 454 n 48 HIS 454 A ASP 455 n 49 ASP 455 A PRO 456 n 50 PRO 456 A TRP 457 n 51 TRP 457 A LYS 458 n 52 LYS 458 A LEU 459 n 53 LEU 459 A LEU 460 n 54 LEU 460 A ILE 461 n 55 ILE 461 A ALA 462 n 56 ALA 462 A THR 463 n 57 THR 463 A ILE 464 n 58 ILE 464 A PHE 465 n 59 PHE 465 A LEU 466 n 60 LEU 466 A ASN 467 n 61 ASN 467 A ARG 468 n 62 ARG 468 A THR 469 n 63 THR 469 A SER 470 n 64 SER 470 A GLY 471 n 65 GLY 471 A LYS 472 n 66 LYS 472 A MET 473 n 67 MET 473 A ALA 474 n 68 ALA 474 A ILE 475 n 69 ILE 475 A PRO 476 n 70 PRO 476 A VAL 477 n 71 VAL 477 A LEU 478 n 72 LEU 478 A TRP 479 n 73 TRP 479 A LYS 480 n 74 LYS 480 A PHE 481 n 75 PHE 481 A LEU 482 n 76 LEU 482 A GLU 483 n 77 GLU 483 A LYS 484 n 78 LYS 484 A TYR 485 n 79 TYR 485 A PRO 486 n 80 PRO 486 A SER 487 n 81 SER 487 A ALA 488 n 82 ALA 488 A GLU 489 n 83 GLU 489 A VAL 490 n 84 VAL 490 A ALA 491 n 85 ALA 491 A ARG 492 n 86 ARG 492 A THR 493 n 87 THR 493 A ALA 494 n 88 ALA 494 A ASP 495 n 89 ASP 495 A TRP 496 n 90 TRP 496 A ARG 497 n 91 ARG 497 A ASP 498 n 92 ASP 498 A VAL 499 n 93 VAL 499 A SER 500 n 94 SER 500 A GLU 501 n 95 GLU 501 A LEU 502 n 96 LEU 502 A LEU 503 n 97 LEU 503 A LYS 504 n 98 LYS 504 A PRO 505 n 99 PRO 505 A LEU 506 n 100 LEU 506 A GLY 507 n 101 GLY 507 A LEU 508 n 102 LEU 508 A TYR 509 n 103 TYR 509 A ASP 510 n 104 ASP 510 A LEU 511 n 105 LEU 511 A ARG 512 n 106 ARG 512 A ALA 513 n 107 ALA 513 A LYS 514 n 108 LYS 514 A THR 515 n 109 THR 515 A ILE 516 n 110 ILE 516 A VAL 517 n 111 VAL 517 A LYS 518 n 112 LYS 518 A PHE 519 n 113 PHE 519 A SER 520 n 114 SER 520 A ASP 521 n 115 ASP 521 A GLU 522 n 116 GLU 522 A TYR 523 n 117 TYR 523 A LEU 524 n 118 LEU 524 A THR 525 n 119 THR 525 A LYS 526 n 120 LYS 526 A GLN 527 n 121 GLN 527 A TRP 528 n 122 TRP 528 A LYS 529 n 123 LYS 529 A TYR 530 n 124 TYR 530 A PRO 531 n 125 PRO 531 A ILE 532 n 126 ILE 532 A GLU 533 n 127 GLU 533 A LEU 534 n 128 LEU 534 A HIS 535 n 129 HIS 535 A GLY 536 n 130 GLY 536 A ILE 537 n 131 ILE 537 A GLY 538 n 132 GLY 538 A LYS 539 n 133 LYS 539 A TYR 540 n 134 TYR 540 A GLY 541 n 135 GLY 541 A ASN 542 n 136 ASN 542 A ASP 543 n 137 ASP 543 A SER 544 n 138 SER 544 A TYR 545 n 139 TYR 545 A ARG 546 n 140 ARG 546 A ILE 547 n 141 ILE 547 A PHE 548 n 142 PHE 548 A CYS 549 n 143 CYS 549 A VAL 550 n 144 VAL 550 A ASN 551 n 145 ASN 551 A GLU 552 n 146 GLU 552 A TRP 553 n 147 TRP 553 A LYS 554 n 148 LYS 554 A GLN 555 n 149 GLN 555 A VAL 556 n 150 VAL 556 A HIS 557 n 151 HIS 557 A PRO 558 n 152 PRO 558 A GLU 559 n 153 GLU 559 A ASP 560 n 154 ASP 560 A HIS 561 n 155 HIS 561 A LYS 562 n 156 LYS 562 A LEU 563 n 157 LEU 563 A ASN 564 n 158 ASN 564 A LYS 565 n 159 LYS 565 A TYR 566 n 160 TYR 566 A HIS 567 n 161 HIS 567 A ASP 568 n 162 ASP 568 A TRP 569 n 163 TRP 569 A LEU 570 n 164 LEU 570 A TRP 571 n 165 TRP 571 A GLU 572 n 166 GLU 572 A ASN 573 n 167 ASN 573 A HIS 574 n 168 HIS 574 A GLU 575 n 169 GLU 575 A LYS 576 n 170 LYS 576 A LEU 577 n 171 LEU 577 A SER 578 n 172 SER 578 A LEU 579 n 173 LEU 579 A SER 580 n 174 SER 580 A DC 1 n 1 DC 1 C DC 2 n 2 DC 2 C DA 3 n 3 DA 3 C DG 4 n 4 DG 4 C DC 5 n 5 DC 5 C DG 6 n 6 DG 6 C NR1 7 n 7 NR1 7 C DG 8 n 8 DG 8 C DC 9 n 9 DC 9 C DA 10 n 10 DA 10 C DG 11 n 11 DG 11 C DC 12 n 12 DC 12 C DG 1 n 1 DG 1 D DC 2 n 2 DC 2 D DT 3 n 3 DT 3 D DG 4 n 4 DG 4 D DC 5 n 5 DC 5 D DG 6 n 6 DG 6 D DC 7 n 7 DC 7 D DG 8 n 8 DG 8 D DC 9 n 9 DC 9 D DT 10 n 10 DT 10 D DG 11 n 11 DG 11 D DG 12 n 12 DG 12 D 2.8541 -0.3262 1.1918 1.7901 1.0428 2.4986 0.0405 -0.3053 0.4972 0.0811 -0.0588 0.0725 -0.2435 -0.1931 -0.0090 0.1740 0.0092 0.0014 0.1887 -0.0048 0.2067 refined 5.2152 17.8493 17.2520 X-RAY DIFFRACTION 2.6252 1.2101 0.0878 5.3048 0.2265 2.8507 -0.0495 -0.1089 -0.0707 -0.0713 0.0566 0.0913 -0.0359 -0.0554 -0.0097 0.0891 0.0134 -0.0076 0.1224 0.0073 0.0858 refined 13.5999 6.3229 17.8962 X-RAY DIFFRACTION 1.9625 2.7472 1.7774 4.6381 0.9449 5.9029 0.2776 -0.3949 0.2455 0.5196 -0.1977 0.2983 0.0392 -0.1175 -0.0487 0.1974 0.0363 0.0423 0.1380 -0.0031 0.1248 refined 12.6385 6.3150 27.6359 X-RAY DIFFRACTION 4.1394 0.0939 -0.1297 4.2376 0.3020 4.0078 0.0480 -0.2630 0.0939 0.4924 -0.0139 -0.3454 -0.1282 0.1189 -0.0461 0.1675 -0.0081 -0.0427 0.1465 -0.0344 0.1384 refined 27.0575 9.6175 24.2087 X-RAY DIFFRACTION 2.9258 3.4221 0.0977 4.6707 1.4244 6.7458 0.0116 -0.5645 -0.1898 0.3461 0.0183 -0.2502 -0.0470 0.2441 0.0004 0.2219 0.0524 -0.0272 0.1754 0.0227 0.1393 refined 20.5953 -2.7904 25.9434 X-RAY DIFFRACTION 2.9918 2.7884 -1.4205 6.6237 -2.6464 3.5648 -0.0491 -0.0022 -0.0596 -0.1549 -0.0025 -0.3047 0.1108 0.2386 0.0649 0.0946 0.0173 -0.0091 0.1252 -0.0066 0.1125 refined 24.1258 4.0818 17.0816 X-RAY DIFFRACTION 6.1921 0.6781 1.1835 4.0923 -0.7450 5.3699 0.0633 0.3987 0.1783 -0.0389 -0.0502 -0.2372 -0.0989 0.2918 0.0111 0.1260 0.0138 0.0096 0.1339 0.0170 0.0965 refined 21.9162 11.2481 7.3057 X-RAY DIFFRACTION 4.3894 -0.9887 1.2424 4.7256 1.7208 2.3708 0.1279 0.1070 0.0982 -0.1734 -0.0716 0.2604 0.0861 -0.2487 -0.0564 0.1183 -0.0038 -0.0108 0.1316 0.0283 0.1102 refined 10.8090 12.0586 8.4688 X-RAY DIFFRACTION 4.4192 0.9096 6.2183 1.7264 1.7025 8.9246 -0.2711 0.1245 0.3632 -0.2687 0.0109 -0.2531 -0.6149 0.1464 0.2642 0.2115 -0.0003 0.0142 0.1609 0.0534 0.1952 refined 8.2334 19.8378 5.0226 X-RAY DIFFRACTION 6.6421 2.7686 -2.5301 4.3344 -5.2253 6.4312 0.0357 0.2777 -0.2377 -0.4710 0.0062 -0.1475 0.8883 0.1085 -0.0810 0.2497 0.0542 -0.0586 0.1450 -0.0112 0.1114 refined 5.1894 8.2673 3.5574 X-RAY DIFFRACTION 4.3170 -2.5226 2.0210 4.3940 -2.3753 6.5312 0.1364 -0.0789 -0.1001 -0.2237 0.0919 0.3761 0.1930 -0.4175 -0.2399 0.1458 -0.0165 -0.0178 0.1738 0.0141 0.1767 refined -1.5395 13.1762 8.2296 X-RAY DIFFRACTION 0.9869 -0.6334 0.4698 0.9025 1.6322 7.7713 0.1776 0.1420 0.7818 -1.2478 -0.2863 -0.4741 -1.0180 0.7334 -0.0745 0.4208 0.0419 0.0628 0.4764 0.1405 0.4796 refined -2.8324 25.4258 6.9829 X-RAY DIFFRACTION 0.8671 0.9272 -0.1055 3.0846 -1.3707 3.0575 -0.2906 0.2325 -0.4928 -0.4437 0.2056 0.0501 0.5880 -0.2762 0.1519 0.2158 -0.0344 0.0177 0.1630 -0.0099 0.2825 refined 9.1692 -8.2703 13.8219 X-RAY DIFFRACTION 4.8715 0.3596 0.4272 1.6413 0.3788 1.3961 -0.1781 0.0831 -0.0641 -0.4198 0.3362 0.5416 0.4838 -0.2357 -0.0208 0.2816 -0.0621 -0.0373 0.1844 0.1037 0.3253 refined 7.9730 -9.9898 16.5287 X-RAY DIFFRACTION A 437 A 455 X-RAY DIFFRACTION 1 chain 'A' and (resid 437 through 455 ) A 456 A 470 X-RAY DIFFRACTION 2 chain 'A' and (resid 456 through 470 ) A 471 A 484 X-RAY DIFFRACTION 3 chain 'A' and (resid 471 through 484 ) A 485 A 495 X-RAY DIFFRACTION 4 chain 'A' and (resid 485 through 495 ) A 496 A 508 X-RAY DIFFRACTION 5 chain 'A' and (resid 496 through 508 ) A 509 A 525 X-RAY DIFFRACTION 6 chain 'A' and (resid 509 through 525 ) A 526 A 538 X-RAY DIFFRACTION 7 chain 'A' and (resid 526 through 538 ) A 539 A 548 X-RAY DIFFRACTION 8 chain 'A' and (resid 539 through 548 ) A 549 A 555 X-RAY DIFFRACTION 9 chain 'A' and (resid 549 through 555 ) A 556 A 560 X-RAY DIFFRACTION 10 chain 'A' and (resid 556 through 560 ) A 561 A 573 X-RAY DIFFRACTION 11 chain 'A' and (resid 561 through 573 ) A 574 A 580 X-RAY DIFFRACTION 12 chain 'A' and (resid 574 through 580 ) C 1 C 12 X-RAY DIFFRACTION 13 chain 'C' and (resid 1 through 12 ) D 1 D 12 X-RAY DIFFRACTION 14 chain 'D' and (resid 1 through 12 ) author_and_software_defined_assembly PISA 3 trimeric gel filtration 4780 -44 10490 A ILE 532 A O ILE 126 1_555 A NA 705 H NA NA 1_555 A LEU 534 A O LEU 128 1_555 102.1 A ILE 532 A O ILE 126 1_555 A NA 705 H NA NA 1_555 A ILE 537 A O ILE 131 1_555 94.3 A LEU 534 A O LEU 128 1_555 A NA 705 H NA NA 1_555 A ILE 537 A O ILE 131 1_555 97.1 A ILE 532 A O ILE 126 1_555 A NA 705 H NA NA 1_555 A HOH 927 L O HOH 1_555 89.8 A LEU 534 A O LEU 128 1_555 A NA 705 H NA NA 1_555 A HOH 927 L O HOH 1_555 84.0 A ILE 537 A O ILE 131 1_555 A NA 705 H NA NA 1_555 A HOH 927 L O HOH 1_555 175.4 A ILE 532 A O ILE 126 1_555 A NA 705 H NA NA 1_555 C DA 10 B OP1 DA 10 1_555 168.9 A LEU 534 A O LEU 128 1_555 A NA 705 H NA NA 1_555 C DA 10 B OP1 DA 10 1_555 88.5 A ILE 537 A O ILE 131 1_555 A NA 705 H NA NA 1_555 C DA 10 B OP1 DA 10 1_555 87.6 A HOH 927 L O HOH 1_555 A NA 705 H NA NA 1_555 C DA 10 B OP1 DA 10 1_555 87.9 A ILE 532 A O ILE 126 1_555 A NA 705 H NA NA 1_555 C HOH 211 M O HOH 1_555 87.4 A LEU 534 A O LEU 128 1_555 A NA 705 H NA NA 1_555 C HOH 211 M O HOH 1_555 165.0 A ILE 537 A O ILE 131 1_555 A NA 705 H NA NA 1_555 C HOH 211 M O HOH 1_555 93.8 A HOH 927 L O HOH 1_555 A NA 705 H NA NA 1_555 C HOH 211 M O HOH 1_555 84.4 C DA 10 B OP1 DA 10 1_555 A NA 705 H NA NA 1_555 C HOH 211 M O HOH 1_555 81.5 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 1 A CE LYS 472 A CE LYS 66 1 Y 1 A NZ LYS 472 A NZ LYS 66 1 Y 1 A CE LYS 480 A CE LYS 74 1 Y 1 A NZ LYS 480 A NZ LYS 74 1 Y 1 A CE LYS 484 A CE LYS 78 1 Y 1 A NZ LYS 484 A NZ LYS 78 1 Y 1 A ND1 HIS 561 A ND1 HIS 155 1 Y 1 A CD2 HIS 561 A CD2 HIS 155 1 Y 1 A CE1 HIS 561 A CE1 HIS 155 1 Y 1 A NE2 HIS 561 A NE2 HIS 155 1 Y 1 A CD LYS 576 A CD LYS 170 1 Y 1 A CE LYS 576 A CE LYS 170 1 Y 1 A NZ LYS 576 A NZ LYS 170 1 Y 1 A OG SER 578 A OG SER 172 1 Y 1 A OG SER 580 A OG SER 174 1 Y 1 A MET 407 A MET 1 1 Y 1 A GLY 408 A GLY 2 1 Y 1 A SER 409 A SER 3 1 Y 1 A SER 410 A SER 4 1 Y 1 A HIS 411 A HIS 5 1 Y 1 A HIS 412 A HIS 6 1 Y 1 A HIS 413 A HIS 7 1 Y 1 A HIS 414 A HIS 8 1 Y 1 A HIS 415 A HIS 9 1 Y 1 A HIS 416 A HIS 10 1 Y 1 A SER 417 A SER 11 1 Y 1 A SER 418 A SER 12 1 Y 1 A GLY 419 A GLY 13 1 Y 1 A LEU 420 A LEU 14 1 Y 1 A VAL 421 A VAL 15 1 Y 1 A PRO 422 A PRO 16 1 Y 1 A ARG 423 A ARG 17 1 Y 1 A GLY 424 A GLY 18 1 Y 1 A SER 425 A SER 19 1 Y 1 A ALA 426 A ALA 20 1 Y 1 A LEU 427 A LEU 21 1 Y 1 A SER 428 A SER 22 1 Y 1 A PRO 429 A PRO 23 1 Y 1 A PRO 430 A PRO 24 1 Y 1 A ARG 431 A ARG 25 1 Y 1 A ARG 432 A ARG 26 1 Y 1 A LYS 433 A LYS 27 1 Y 1 A ALA 434 A ALA 28 1 Y 1 A PHE 435 A PHE 29 1 Y 1 A LYS 436 A LYS 30 1 Y 1 9.40 1.20 119.70 129.10 C C C C3' O3' P DG DG NR1 6 6 7 Y 1 A ASN 551 -88.48 46.94 94.180 27.4813 9.490 0.2046 0.1681 0.1699 1.6800 37.9800 1429 26617 28046 5.1000 99.3700 0.1700 1 THROUGHOUT 1.330 MOLECULAR REPLACEMENT 19.0200 0.9000 1.1100 PDB entry 4DK9 ML FLAT BULK SOLVENT MODEL 1.6800 37.9800 242 1968 37.81 38.93 37 478 1211 168 0.2662 0.0000 0.2613 1.7400 143 2600 2743 10 99.0000 0.2728 0.0000 0.2354 1.8100 146 2632 2778 10 100.0000 0.2229 0.0000 0.2161 1.8900 132 2596 2728 10 98.0000 0.2260 0.0000 0.1917 1.9900 146 2621 2767 10 100.0000 0.2179 0.0000 0.1739 2.1200 125 2659 2784 10 100.0000 0.2007 0.0000 0.1720 2.2800 154 2650 2804 10 100.0000 0.1906 0.0000 0.1616 2.5100 151 2635 2786 10 99.0000 0.2058 0.0000 0.1587 2.8700 140 2690 2830 10 100.0000 0.1970 0.0000 0.1526 3.6200 146 2682 2828 10 99.0000 0.1871 0.0000 0.1508 37.9800 146 2852 2998 10 99.0000 1.680 37.980 7KZG 28121 0.994 0.091 0.333 1 10.200 367050 13.100 251 99.600 1.680 1.710 19077 1429 0.416 1.723 6.403 1 1.500 13.300 100.000 9.050 37.980 2643 230 0.973 0.030 0.097 1 35.300 11.500 99.100 refinement PHENIX 1.17.1_3660 data reduction Wolfgang Kabsch Wolfgang.Kabsch@mpimf-heidelberg.mpg.de http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/ XDS package data scaling Phil Evans 13/12/18 http://www.mrc-lmb.cam.ac.uk/harry/pre/aimless.html Aimless program 0.7.4 phasing Randy J. Read cimr-phaser@lists.cam.ac.uk http://www-structmed.cimr.cam.ac.uk/phaser/ PHASER program data extraction PDB deposit@deposit.rcsb.org Oct. 31, 2020 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.27 N Human MBD4 glycosylase domain bound to DNA containing oxacarbenium-ion analog 1-aza-2'-deoxyribose 1 N N 2 N N 3 N N 4 N N 5 N N 6 N N 4 N N 7 N N 8 N N 4 N N 4 N N 9 N N 9 N N 9 N N A VAL 448 A VAL 42 HELX_P A PHE 453 A PHE 47 1 AA1 6 A ASP 455 A ASP 49 HELX_P A LEU 466 A LEU 60 1 AA2 12 A SER 470 A SER 64 HELX_P A TYR 485 A TYR 79 1 AA3 16 A SER 487 A SER 81 HELX_P A ARG 492 A ARG 86 1 AA4 6 A ASP 495 A ASP 89 HELX_P A LYS 504 A LYS 98 1 AA5 10 A PRO 505 A PRO 99 HELX_P A GLY 507 A GLY 101 5 AA6 3 A LEU 508 A LEU 102 HELX_P A LYS 526 A LYS 120 1 AA7 19 A TYR 530 A TYR 124 HELX_P A LEU 534 A LEU 128 5 AA8 5 A GLY 538 A GLY 132 HELX_P A CYS 549 A CYS 143 1 AA9 12 A GLU 552 A GLU 146 HELX_P A VAL 556 A VAL 150 5 AB1 5 A ASP 560 A ASP 154 HELX_P A HIS 574 A HIS 168 1 AB2 15 covale 1.556 both C DG 6 B O3' DG 6 1_555 C NR1 7 B P NR1 7 1_555 covale 1.559 both C NR1 7 B O3' NR1 7 1_555 C DG 8 B P DG 8 1_555 metalc 2.390 A ILE 532 A O ILE 126 1_555 A NA 705 H NA NA 1_555 metalc 2.379 A LEU 534 A O LEU 128 1_555 A NA 705 H NA NA 1_555 metalc 2.373 A ILE 537 A O ILE 131 1_555 A NA 705 H NA NA 1_555 metalc 2.557 A NA 705 H NA NA 1_555 A HOH 927 L O HOH 1_555 metalc 2.679 A NA 705 H NA NA 1_555 C DA 10 B OP1 DA 10 1_555 metalc 2.422 A NA 705 H NA NA 1_555 C HOH 211 M O HOH 1_555 hydrog WATSON-CRICK C DC 1 B N3 DC 1 1_555 D DG 12 C N1 DG 12 1_555 hydrog WATSON-CRICK C DC 1 B N4 DC 1 1_555 D DG 12 C O6 DG 12 1_555 hydrog WATSON-CRICK C DC 1 B O2 DC 1 1_555 D DG 12 C N2 DG 12 1_555 hydrog WATSON-CRICK C DC 2 B N3 DC 2 1_555 D DG 11 C N1 DG 11 1_555 hydrog WATSON-CRICK C DC 2 B N4 DC 2 1_555 D DG 11 C O6 DG 11 1_555 hydrog WATSON-CRICK C DC 2 B O2 DC 2 1_555 D DG 11 C N2 DG 11 1_555 hydrog WATSON-CRICK C DA 3 B N1 DA 3 1_555 D DT 10 C N3 DT 10 1_555 hydrog WATSON-CRICK C DA 3 B N6 DA 3 1_555 D DT 10 C O4 DT 10 1_555 hydrog WATSON-CRICK C DG 4 B N1 DG 4 1_555 D DC 9 C N3 DC 9 1_555 hydrog WATSON-CRICK C DG 4 B N2 DG 4 1_555 D DC 9 C O2 DC 9 1_555 hydrog WATSON-CRICK C DG 4 B O6 DG 4 1_555 D DC 9 C N4 DC 9 1_555 hydrog WATSON-CRICK C DC 5 B N3 DC 5 1_555 D DG 8 C N1 DG 8 1_555 hydrog WATSON-CRICK C DC 5 B N4 DC 5 1_555 D DG 8 C O6 DG 8 1_555 hydrog WATSON-CRICK C DC 5 B O2 DC 5 1_555 D DG 8 C N2 DG 8 1_555 hydrog WATSON-CRICK C DG 6 B N1 DG 6 1_555 D DC 7 C N3 DC 7 1_555 hydrog WATSON-CRICK C DG 6 B N2 DG 6 1_555 D DC 7 C O2 DC 7 1_555 hydrog WATSON-CRICK C DG 6 B O6 DG 6 1_555 D DC 7 C N4 DC 7 1_555 hydrog WATSON-CRICK C DG 8 B N1 DG 8 1_555 D DC 5 C N3 DC 5 1_555 hydrog WATSON-CRICK C DG 8 B N2 DG 8 1_555 D DC 5 C O2 DC 5 1_555 hydrog WATSON-CRICK C DG 8 B O6 DG 8 1_555 D DC 5 C N4 DC 5 1_555 hydrog WATSON-CRICK C DC 9 B N3 DC 9 1_555 D DG 4 C N1 DG 4 1_555 hydrog WATSON-CRICK C DC 9 B N4 DC 9 1_555 D DG 4 C O6 DG 4 1_555 hydrog WATSON-CRICK C DC 9 B O2 DC 9 1_555 D DG 4 C N2 DG 4 1_555 hydrog WATSON-CRICK C DA 10 B N1 DA 10 1_555 D DT 3 C N3 DT 3 1_555 hydrog WATSON-CRICK C DA 10 B N6 DA 10 1_555 D DT 3 C O4 DT 3 1_555 hydrog WATSON-CRICK C DG 11 B N1 DG 11 1_555 D DC 2 C N3 DC 2 1_555 hydrog WATSON-CRICK C DG 11 B N2 DG 11 1_555 D DC 2 C O2 DC 2 1_555 hydrog WATSON-CRICK C DG 11 B O6 DG 11 1_555 D DC 2 C N4 DC 2 1_555 hydrog WATSON-CRICK C DC 12 B N3 DC 12 1_555 D DG 1 C N1 DG 1 1_555 hydrog WATSON-CRICK C DC 12 B N4 DC 12 1_555 D DG 1 C O6 DG 1 1_555 hydrog WATSON-CRICK C DC 12 B O2 DC 12 1_555 D DG 1 C N2 DG 1 1_555 HYDROLASE/DNA protein-DNA complex, HYDROLASE-DNA complex MBD4_HUMAN UNP 1 426 O95243 ALSPPRRKAFKKWTPPRSPFNLVQETLFHDPWKLLIATIFLNRTSGKMAIPVLWKFLEKYPSAEVARTADWRDVSELLKP LGLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSYRIFCVNEWKQVHPEDHKLNKYHDWLWENHEKLSLS 7KZG PDB 2 1 7KZG 7KZG PDB 3 1 7KZG 426 580 7KZG 426 580 O95243 A 1 20 174 1 12 7KZG 1 12 7KZG C 2 1 12 1 12 7KZG 1 12 7KZG D 3 1 12 1 expression tag MET 407 7KZG A O95243 UNP 1 1 expression tag GLY 408 7KZG A O95243 UNP 2 1 expression tag SER 409 7KZG A O95243 UNP 3 1 expression tag SER 410 7KZG A O95243 UNP 4 1 expression tag HIS 411 7KZG A O95243 UNP 5 1 expression tag HIS 412 7KZG A O95243 UNP 6 1 expression tag HIS 413 7KZG A O95243 UNP 7 1 expression tag HIS 414 7KZG A O95243 UNP 8 1 expression tag HIS 415 7KZG A O95243 UNP 9 1 expression tag HIS 416 7KZG A O95243 UNP 10 1 expression tag SER 417 7KZG A O95243 UNP 11 1 expression tag SER 418 7KZG A O95243 UNP 12 1 expression tag GLY 419 7KZG A O95243 UNP 13 1 expression tag LEU 420 7KZG A O95243 UNP 14 1 expression tag VAL 421 7KZG A O95243 UNP 15 1 expression tag PRO 422 7KZG A O95243 UNP 16 1 expression tag ARG 423 7KZG A O95243 UNP 17 1 expression tag GLY 424 7KZG A O95243 UNP 18 1 expression tag SER 425 7KZG A O95243 UNP 19 19 P 21 21 21