0.016257 0.009386 0.000000 0.000000 0.018772 0.000000 0.000000 0.000000 0.009420 0.00000 0.00000 0.00000 0000-0002-5682-3685 Kondo, J. Okada, M. Tsuzuki, K. Onizuka, K. Nagasawa, R. Miyashita, E. Komatsu, K.R. Saito, H. Nagatsugi, F. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 9 90.00 90.00 120.00 61.511 61.511 106.158 C10 H14 N5 O7 P 347.221 y ADENOSINE-5'-MONOPHOSPHATE RNA linking C6 H8 Cl N7 O 229.627 3,5-DIAMINO-N-(AMINOIMINOMETHYL)-6-CHLOROPYRAZINECARBOXAMIDE AMILORIDE non-polymer C9 H14 N3 O8 P 323.197 y CYTIDINE-5'-MONOPHOSPHATE RNA linking C2 H7 As O2 137.997 CACODYLIC ACID HYDROXYDIMETHYLARSINE OXIDE non-polymer C10 H14 N5 O8 P 363.221 y GUANOSINE-5'-MONOPHOSPHATE RNA linking H2 O 18.015 WATER non-polymer Na 1 22.990 SODIUM ION non-polymer C9 H13 N2 O9 P 324.181 y URIDINE-5'-MONOPHOSPHATE RNA linking N 1 N O N 2 N P N 3 N O N 4 N O N 5 N O N 6 N C N 7 R C N 8 N O N 9 S C N 10 N O N 11 R C N 12 N O N 13 R C Y 14 N N Y 15 N C Y 16 N N Y 17 N C Y 18 N C N 19 N N Y 20 N N Y 21 N C Y 22 N N Y 23 N C N 24 N H N 25 N H 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 Y 38 N N Y 39 N C N 40 N C N 41 N N N 42 N C N 43 N N N 44 N N N 45 N O Y 46 N C N 47 N N Y 48 N N Y 49 N C N 50 N N Y 51 N C N 52 N CL N 53 N H N 54 N H N 55 N H N 56 N H N 57 N H N 58 N H N 59 N H N 60 N H N 61 N O N 62 N P N 63 N O N 64 N O N 65 N O N 66 N C N 67 R C N 68 N O N 69 S C N 70 N O N 71 R C N 72 N O N 73 R C N 74 N N N 75 N C N 76 N O N 77 N N N 78 N C N 79 N N N 80 N C N 81 N C 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 H N 90 N H N 91 N H N 92 N H N 93 N H N 94 N H N 95 N H N 96 N AS N 97 N C N 98 N C N 99 N O N 100 N O N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N O N 109 N P N 110 N O N 111 N O N 112 N O N 113 N C N 114 R C N 115 N O N 116 S C N 117 N O N 118 R C N 119 N O N 120 R C Y 121 N N Y 122 N C Y 123 N N Y 124 N C N 125 N C N 126 N O N 127 N N N 128 N C N 129 N N N 130 N N Y 131 N C N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H N 144 N H N 145 N H N 146 N O N 147 N H N 148 N H N 149 N NA N 150 N O N 151 N P N 152 N O N 153 N O N 154 N O N 155 N C N 156 R C N 157 N O N 158 S C N 159 N O N 160 R C N 161 N O N 162 R C N 163 N N N 164 N C N 165 N O N 166 N N N 167 N C N 168 N O N 169 N C N 170 N C N 171 N H N 172 N H N 173 N H N 174 N H N 175 N H N 176 N H N 177 N H N 178 N H N 179 N H N 180 N H N 181 N H N 182 N H N 183 N H N 1 N sing N 2 N sing N 3 N doub N 4 N sing N 5 N sing N 6 N sing N 7 N sing 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 sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing Y 25 N sing Y 26 N sing Y 27 N doub N 28 N sing Y 29 N sing Y 30 N sing Y 31 N doub N 32 N sing Y 33 N doub N 34 N sing N 35 N sing Y 36 N sing Y 37 N doub N 38 N sing Y 39 N sing Y 40 N doub Y 41 N sing N 42 N sing Y 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 doub N 50 N sing N 51 N sing N 52 N sing N 53 N sing Y 54 N doub N 55 N sing N 56 N sing Y 57 N sing N 58 N sing Y 59 N doub N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N doub N 66 N sing 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 sing 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 sing N 86 N sing N 87 N sing N 88 N sing N 89 N doub N 90 N sing N 91 N doub N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N doub N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N doub N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N doub N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing 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 Y 134 N sing Y 135 N sing Y 136 N doub N 137 N sing Y 138 N sing N 139 N sing Y 140 N doub N 141 N doub 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 sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N doub N 155 N sing N 156 N sing N 157 N sing N 158 N sing 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 doub N 179 N sing N 180 N sing N 181 N sing N 182 N doub N 183 N sing N 184 N doub N 185 N sing N 186 N sing UK Rsc Chem Biol 2633-0679 10.1039/D6CB00055J RNA-binding Landscape of Amiloride: Large-scale Profiling and Structural Basis of U-U Mismatch Recognition 2025 10.2210/pdb23ka/pdb pdb_000023ka 100 1 N PIXEL 2025-10-19 DECTRIS EIGER X 16M SINGLE WAVELENGTH M x-ray 1 0.98 1.0 BL-17A Photon Factory 0.98 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 11285.740 RNA (35-MER) 3 syn polymer 229.627 3,5-DIAMINO-N-(AMINOIMINOMETHYL)-6-CHLOROPYRAZINECARBOXAMIDE 3 syn non-polymer 22.990 SODIUM ION 3 syn non-polymer 137.997 CACODYLIC ACID 1 syn non-polymer 18.015 water 39 nat water no no GCUUGCUCUAAGGCAUGAAAGUGCUAUGAGAUAGC GCUUGCUCUAAGGCAUGAAAGUGCUAUGAGAUAGC A,B,C polyribonucleotide 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 1 3.42 64.08 VAPOR DIFFUSION, SITTING DROP Sodium citrate tribasic dihydrate, Sodium cacodylate trihydrate, 2-Propanol 293.15 -6.154 1 19 A 1 A 35 -1.463 A_G1:C35_A 1 -11.804 -0.093 0.056 -0.417 1.505 1 19 A 2 A 34 7.728 A_C2:G34_A 2 -10.092 0.473 0.318 -0.112 15.203 1 20 A 3 A 33 -2.685 A_U3:A33_A 3 1.048 -0.027 -0.348 0.194 19.517 1 8 A 5 A 31 -17.288 A_G5:A31_A 4 -16.544 0.484 -0.113 1.394 15.795 1 19 A 6 A 30 -3.109 A_C6:G30_A 5 -20.198 0.089 -0.172 -0.209 3.596 1 20 A 7 A 29 0.620 A_U7:A29_A 6 -12.833 -0.323 0.118 -0.282 0.176 1 19 A 8 A 28 0.218 A_C8:G28_A 7 -12.375 0.639 -0.020 -0.193 17.920 4 24 A 26 A 9 -88.894 A_A26:U9_A 8 -5.238 -4.460 -0.419 -2.531 -30.259 1 20 A 11 A 27 -3.366 A_A11:U27_A 9 29.531 0.198 -0.563 -0.001 -5.735 1 28 A 12 A 25 -9.848 A_G12:U25_A 10 -4.557 -2.561 -0.191 -0.728 4.358 1 19 A 13 A 24 3.983 A_G13:C24_A 11 -6.987 -0.298 -0.108 -0.039 4.144 1 19 A 14 A 23 0.765 A_C14:G23_A 12 -11.195 0.456 -0.121 -0.179 -6.827 1 20 A 15 A 22 8.007 A_A15:U22_A 13 -9.719 0.006 -0.315 0.121 1.114 1 28 A 16 A 21 3.577 A_U16:G21_A 14 -0.023 2.478 -0.326 -0.639 12.470 A 17 A 20 -15.070 A_G17:A20_A 15 1.451 6.969 0.650 -5.163 -9.980 1 19 B 1 B 35 5.923 B_G1:C35_B 16 -3.270 -0.342 -0.048 -0.199 -4.191 1 19 B 2 B 34 -2.122 B_C2:G34_B 17 -5.449 -0.095 -0.136 -0.280 14.005 1 20 B 3 B 33 -0.174 B_U3:A33_B 18 6.538 -0.176 -0.380 -0.371 20.806 1 8 B 5 B 31 -8.865 B_G5:A31_B 19 -18.207 -0.392 -0.126 1.393 18.420 1 19 B 6 B 30 -5.239 B_C6:G30_B 20 -19.761 0.130 -0.279 -0.262 8.076 1 20 B 7 B 29 -3.525 B_U7:A29_B 21 -13.458 -0.080 -0.037 -0.191 -2.069 1 19 B 8 B 28 -2.794 B_C8:G28_B 22 -11.466 0.306 0.142 -0.100 -20.255 4 24 B 9 B 26 -89.457 B_U9:A26_B 23 2.950 4.396 -0.229 -2.409 -4.393 1 28 B 12 B 25 0.321 B_G12:U25_B 24 -10.970 -2.702 -0.138 -0.677 -0.709 1 19 B 13 B 24 4.466 B_G13:C24_B 25 -11.758 0.011 -0.058 -0.113 0.301 1 19 B 14 B 23 4.995 B_C14:G23_B 26 -13.033 0.097 -0.333 -0.161 -6.981 1 20 B 15 B 22 7.269 B_A15:U22_B 27 -13.162 0.402 -0.232 -0.051 -0.121 1 28 B 16 B 21 10.084 B_U16:G21_B 28 -2.527 2.544 0.051 -0.452 16.865 10 11 B 17 B 20 -10.938 B_G17:A20_B 29 0.273 7.064 0.739 -4.845 8.234 1 19 C 1 C 35 -10.899 C_G1:C35_C 30 -14.589 -0.521 -0.280 -0.039 8.461 1 19 C 2 C 34 2.607 C_C2:G34_C 31 -16.524 0.493 -0.377 -0.188 13.353 1 20 C 3 C 33 7.122 C_U3:A33_C 32 5.954 0.118 -0.415 -0.166 14.477 1 8 C 5 C 31 -15.069 C_G5:A31_C 33 -6.495 -0.305 -0.032 1.550 11.160 1 19 C 6 C 30 4.102 C_C6:G30_C 34 -11.912 0.464 0.022 -0.094 3.610 1 20 C 7 C 29 1.151 C_U7:A29_C 35 -7.907 0.176 -0.022 -0.152 4.229 1 19 C 8 C 28 0.359 C_C8:G28_C 36 -10.489 0.195 -0.074 0.000 -19.348 4 24 C 9 C 26 -90.159 C_U9:A26_C 37 0.227 4.426 -0.402 -2.497 -1.630 1 28 C 12 C 25 3.118 C_G12:U25_C 38 -8.332 -2.012 0.251 -0.581 2.057 1 19 C 13 C 24 0.566 C_G13:C24_C 39 -7.839 -0.443 -0.027 -0.117 4.072 1 19 C 14 C 23 -3.504 C_C14:G23_C 40 -8.149 -0.033 -0.274 -0.146 -4.495 1 20 C 15 C 22 4.112 C_A15:U22_C 41 -13.294 -0.170 -0.041 -0.086 0.707 1 28 C 16 C 21 3.178 C_U16:G21_C 42 -0.968 2.208 -0.070 -0.438 16.957 10 11 C 17 C 20 -15.428 C_G17:A20_C 43 2.736 6.928 0.658 -4.861 3.249 35.114 A A 1 2 -3.709 A A 35 34 3.155 -2.236 0.641 -1.929 AA_G1C2:G34C35_AA 1 -0.998 1.655 35.031 -2.870 -1.209 2.243 22.532 A A 2 3 14.882 A A 34 33 3.003 5.737 -1.221 -1.937 AA_C2U3:A33G34_AA 2 2.838 -7.363 21.615 -6.682 3.978 6.708 56.374 A A 3 5 2.760 A A 33 31 6.650 2.582 -1.423 -2.008 AA_U3G5:A31A33_AA 3 -14.297 15.279 54.619 -2.429 -0.172 3.163 30.453 A A 5 6 -0.171 A A 31 30 3.245 -0.089 0.147 -2.067 AA_G5C6:G30A31_AA 4 -5.945 11.387 29.881 -3.917 -1.455 3.065 35.386 A A 6 7 11.239 A A 30 29 3.508 6.769 0.152 -1.755 AA_C6U7:A29G30_AA 5 -5.126 8.511 34.384 -3.904 -1.020 2.911 33.575 A A 7 8 9.420 A A 29 28 3.266 5.418 -0.745 -2.169 AA_U7C8:G28A29_AA 6 -1.295 2.252 33.123 -4.600 1.089 2.623 172.115 A A 8 26 -51.405 A A 28 9 0.478 -100.912 -0.395 -4.972 AA_C8A26:U9G28_AA 7 -135.101 68.821 92.111 -2.118 -0.303 3.062 157.076 A A 26 11 -7.495 A A 9 27 2.806 -14.100 -1.910 4.139 AA_A26A11:U27U9_AA 8 -146.836 78.052 89.468 2.228 -0.233 1.688 61.941 A A 11 12 30.593 A A 27 25 2.510 30.324 3.889 -0.453 AA_A11G12:U25U27_AA 9 -5.802 5.854 54.373 -1.416 -3.966 2.893 36.119 A A 12 13 6.478 A A 25 24 3.123 4.004 0.460 -1.512 AA_G12G13:C24U25_AA 10 -3.180 5.144 35.768 -2.961 -1.157 2.910 38.450 A A 13 14 13.050 A A 24 23 3.248 8.519 -0.745 -1.457 AA_G13C14:G23C24_AA 11 -3.162 4.845 37.400 -3.224 0.756 2.736 30.354 A A 14 15 21.711 A A 23 22 3.523 11.107 0.510 -1.613 AA_C14A15:U22G23_AA 12 2.047 -4.001 28.221 -5.300 -0.564 2.880 39.387 A A 15 16 10.588 A A 22 21 3.165 7.094 0.197 -1.404 AA_A15U16:G21U22_AA 13 2.741 -4.090 38.674 -2.866 0.011 2.648 45.139 A A 16 17 14.580 A A 21 20 2.959 11.089 -2.220 -1.037 AA_U16G17:A20G21_AA 14 -0.273 0.359 43.825 -2.216 2.870 2.734 31.143 B B 1 2 10.550 B B 35 34 3.067 5.634 -0.742 -1.683 BB_G1C2:G34C35_BB 15 -0.583 1.092 30.636 -4.097 1.283 2.366 29.336 B B 2 3 24.173 B B 34 33 3.010 11.902 -0.308 -0.973 BB_C2U3:A33G34_BB 16 0.670 -1.360 26.853 -4.127 0.733 6.100 52.991 B B 3 5 14.314 B B 33 31 6.555 12.608 -0.867 -1.545 BB_U3G5:A31A33_BB 17 -9.195 10.439 50.801 -3.337 -0.199 2.952 37.146 B B 5 6 8.382 B B 31 30 3.168 5.321 0.201 -1.282 BB_G5C6:G30A31_BB 18 -1.273 2.005 36.754 -2.681 -0.475 2.908 38.521 B B 6 7 16.472 B B 30 29 3.487 10.727 0.400 -1.561 BB_C6U7:A29G30_BB 19 -2.464 3.783 36.972 -3.694 -0.912 2.752 30.923 B B 7 8 16.464 B B 29 28 3.452 8.651 -0.668 -2.256 BB_U7C8:G28A29_BB 20 -3.222 6.133 29.545 -5.858 0.647 3.251 73.173 B B 8 9 4.531 B B 28 26 3.708 5.388 -2.820 -2.187 BB_C8U9:A26G28_BB 21 8.731 -7.342 72.550 -2.021 2.667 6.269 45.524 B B 9 12 2.214 B B 26 25 6.446 1.707 -0.607 -0.433 BB_U9G12:U25A26_BB 22 6.988 -9.065 44.982 -0.854 1.987 2.862 43.133 B B 12 13 11.643 B B 25 24 3.169 8.493 0.033 -1.222 BB_G12G13:C24U25_BB 23 -4.651 6.376 42.082 -2.443 -0.473 2.866 31.495 B B 13 14 10.615 B B 24 23 3.202 5.720 0.084 -1.552 BB_G13C14:G23C24_BB 24 3.546 -6.580 30.786 -3.860 0.466 2.407 34.571 B B 14 15 27.682 B B 23 22 3.447 15.846 0.301 -1.537 BB_C14A15:U22G23_BB 25 3.126 -5.461 30.669 -4.918 -0.047 2.510 38.970 B B 15 16 21.482 B B 22 21 3.057 14.032 0.613 -1.054 BB_A15U16:G21U22_BB 26 0.765 -1.171 36.440 -3.079 -0.837 2.461 43.702 B B 16 17 14.787 B B 21 20 2.816 10.900 -1.929 -0.861 BB_U16G17:A20G21_BB 27 1.601 -2.173 42.356 -2.013 2.717 3.199 39.636 C C 1 2 1.203 C C 35 34 3.278 0.816 0.787 -1.975 CC_G1C2:G34C35_CC 28 -1.861 2.745 39.586 -3.007 -1.377 1.672 26.297 C C 2 3 33.566 C C 34 33 3.171 14.411 -0.783 -1.959 CC_C2U3:A33G34_CC 29 -3.177 7.400 21.826 -7.452 1.027 6.724 52.059 C C 3 5 3.051 C C 33 31 6.696 2.654 -1.244 -1.542 CC_U3G5:A31A33_CC 30 -12.462 14.326 50.581 -2.126 -0.315 3.070 37.308 C C 5 6 2.659 C C 31 30 3.201 1.700 0.997 -1.750 CC_G5C6:G30A31_CC 31 -1.820 2.847 37.227 -2.951 -1.790 3.123 32.632 C C 6 7 9.397 C C 30 29 3.479 5.251 -0.042 -1.932 CC_C6U7:A29G30_CC 32 -3.029 5.421 32.079 -4.367 -0.461 2.749 24.671 C C 7 8 9.983 C C 29 28 3.166 4.241 -0.711 -2.450 CC_U7C8:G28A29_CC 33 -1.840 4.332 24.241 -6.917 1.152 3.421 77.444 C C 8 9 7.512 C C 28 26 3.904 9.372 -2.963 -2.162 CC_C8U9:A26G28_CC 34 7.103 -5.693 76.685 -2.029 2.597 6.512 45.922 C C 9 12 -1.057 C C 26 25 6.542 -0.824 -0.258 -0.374 CC_U9G12:U25A26_CC 35 3.470 -4.451 45.791 -0.337 0.929 2.642 33.296 C C 12 13 14.708 C C 25 24 3.171 8.341 -0.493 -1.834 CC_G12G13:C24U25_CC 36 -1.114 1.965 32.245 -4.458 0.692 2.618 33.978 C C 13 14 17.898 C C 24 23 3.213 10.302 -0.344 -1.493 CC_G13C14:G23C24_CC 37 1.034 -1.797 32.407 -4.060 0.741 2.403 35.889 C C 14 15 26.053 C C 23 22 3.456 15.552 0.705 -1.691 CC_C14A15:U22G23_CC 38 -0.883 1.480 32.432 -4.847 -1.263 2.936 40.185 C C 15 16 10.334 C C 22 21 3.214 7.065 0.202 -1.400 CC_A15U16:G21U22_CC 39 1.203 -1.760 39.567 -2.798 -0.165 2.485 46.139 C C 16 17 14.553 C C 21 20 2.870 11.300 -1.864 -1.084 CC_U16G17:A20G21_CC 40 1.385 -1.784 44.787 -2.189 2.477 repository Initial release 1 0 2026-05-06 Japan Japan Agency for Medical Research and Development (AMED) JP25ama121014 j.kondo@sophia.ac.jp 0000-0002-5682-3685 Jiro Kondo principal investigator/group leader N PDBJ Y PDBJ 2026-02-09 REL REL AMR AMR SUBJECT OF INVESTIGATION AMR 3,5-DIAMINO-N-(AMINOIMINOMETHYL)-6-CHLOROPYRAZINECARBOXAMIDE NA SODIUM ION CAD CACODYLIC ACID HOH water 32630 synthetic construct sample 1 35 Y N 4FNJ PDB experimental model AMR 101 2 AMR AMR 101 A NA 2 3 NA NA 102 A AMR 101 2 AMR AMR 101 B CAD 103 4 CAD CAD 102 B NA 1 3 NA NA 103 B AMR 101 2 AMR AMR 101 C NA 3 3 NA NA 102 C HOH 21 5 HOH HOH 201 A HOH 44 5 HOH HOH 202 A HOH 39 5 HOH HOH 203 A HOH 27 5 HOH HOH 204 A HOH 31 5 HOH HOH 205 A HOH 10 5 HOH HOH 206 A HOH 25 5 HOH HOH 207 A HOH 11 5 HOH HOH 208 A HOH 32 5 HOH HOH 209 A HOH 33 5 HOH HOH 210 A HOH 45 5 HOH HOH 211 A HOH 50 5 HOH HOH 212 A HOH 29 5 HOH HOH 213 A HOH 49 5 HOH HOH 214 A HOH 3 5 HOH HOH 215 A HOH 12 5 HOH HOH 201 B HOH 23 5 HOH HOH 202 B HOH 24 5 HOH HOH 203 B HOH 17 5 HOH HOH 204 B HOH 7 5 HOH HOH 205 B HOH 20 5 HOH HOH 206 B HOH 35 5 HOH HOH 207 B HOH 18 5 HOH HOH 201 C HOH 4 5 HOH HOH 202 C HOH 2 5 HOH HOH 203 C HOH 42 5 HOH HOH 204 C HOH 22 5 HOH HOH 205 C HOH 6 5 HOH HOH 206 C HOH 1 5 HOH HOH 207 C HOH 30 5 HOH HOH 208 C HOH 15 5 HOH HOH 209 C HOH 41 5 HOH HOH 210 C HOH 16 5 HOH HOH 211 C HOH 9 5 HOH HOH 212 C HOH 26 5 HOH HOH 213 C HOH 38 5 HOH HOH 214 C HOH 13 5 HOH HOH 215 C HOH 8 5 HOH HOH 216 C HOH 19 5 HOH HOH 217 C G 1 n 1 G 1 A C 2 n 2 C 2 A U 3 n 3 U 3 A U 4 n 4 U 4 A G 5 n 5 G 5 A C 6 n 6 C 6 A U 7 n 7 U 7 A C 8 n 8 C 8 A U 9 n 9 U 9 A A 10 n 10 A 10 A A 11 n 11 A 11 A G 12 n 12 G 12 A G 13 n 13 G 13 A C 14 n 14 C 14 A A 15 n 15 A 15 A U 16 n 16 U 16 A G 17 n 17 G 17 A A 18 n 18 A 18 A A 19 n 19 A 19 A A 20 n 20 A 20 A G 21 n 21 G 21 A U 22 n 22 U 22 A G 23 n 23 G 23 A C 24 n 24 C 24 A U 25 n 25 U 25 A A 26 n 26 A 26 A U 27 n 27 U 27 A G 28 n 28 G 28 A A 29 n 29 A 29 A G 30 n 30 G 30 A A 31 n 31 A 31 A U 32 n 32 U 32 A A 33 n 33 A 33 A G 34 n 34 G 34 A C 35 n 35 C 35 A G 1 n 1 G 1 B C 2 n 2 C 2 B U 3 n 3 U 3 B U 4 n 4 U 4 B G 5 n 5 G 5 B C 6 n 6 C 6 B U 7 n 7 U 7 B C 8 n 8 C 8 B U 9 n 9 U 9 B A 10 n 10 A 10 B A 11 n 11 A 11 B G 12 n 12 G 12 B G 13 n 13 G 13 B C 14 n 14 C 14 B A 15 n 15 A 15 B U 16 n 16 U 16 B G 17 n 17 G 17 B A 18 n 18 A 18 B A 19 n 19 A 19 B A 20 n 20 A 20 B G 21 n 21 G 21 B U 22 n 22 U 22 B G 23 n 23 G 23 B C 24 n 24 C 24 B U 25 n 25 U 25 B A 26 n 26 A 26 B U 27 n 27 U 27 B G 28 n 28 G 28 B A 29 n 29 A 29 B G 30 n 30 G 30 B A 31 n 31 A 31 B U 32 n 32 U 32 B A 33 n 33 A 33 B G 34 n 34 G 34 B C 35 n 35 C 35 B G 1 n 1 G 1 C C 2 n 2 C 2 C U 3 n 3 U 3 C U 4 n 4 U 4 C G 5 n 5 G 5 C C 6 n 6 C 6 C U 7 n 7 U 7 C C 8 n 8 C 8 C U 9 n 9 U 9 C A 10 n 10 A 10 C A 11 n 11 A 11 C G 12 n 12 G 12 C G 13 n 13 G 13 C C 14 n 14 C 14 C A 15 n 15 A 15 C U 16 n 16 U 16 C G 17 n 17 G 17 C A 18 n 18 A 18 C A 19 n 19 A 19 C A 20 n 20 A 20 C G 21 n 21 G 21 C U 22 n 22 U 22 C G 23 n 23 G 23 C C 24 n 24 C 24 C U 25 n 25 U 25 C A 26 n 26 A 26 C U 27 n 27 U 27 C G 28 n 28 G 28 C A 29 n 29 A 29 C G 30 n 30 G 30 C A 31 n 31 A 31 C U 32 n 32 U 32 C A 33 n 33 A 33 C G 34 n 34 G 34 C C 35 n 35 C 35 C author_defined_assembly 1 monomeric author_defined_assembly 1 monomeric author_defined_assembly 1 monomeric none A G 13 A O6 G 13 1_555 A NA 102 E NA NA 1_555 A HOH 205 K O HOH 1_555 65.4 B A 10 B O3' A 10 1_555 B NA 103 H NA NA 1_555 B A 10 B O2' A 10 1_555 63.0 B A 10 B O3' A 10 1_555 B NA 103 H NA NA 1_555 B G 12 B O6 G 12 1_555 132.1 B A 10 B O2' A 10 1_555 B NA 103 H NA NA 1_555 B G 12 B O6 G 12 1_555 76.4 C A 10 C O2' A 10 1_555 C NA 102 J NA NA 1_555 C G 12 C O6 G 12 1_555 67.5 C A 10 C O2' A 10 1_555 C NA 102 J NA NA 1_555 C HOH 207 M O HOH 1_555 177.3 C G 12 C O6 G 12 1_555 C NA 102 J NA NA 1_555 C HOH 207 M O HOH 1_555 111.0 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 7.79 1.10 110.50 118.29 B B B O3' P OP1 U G G 27 28 28 Y 0.2192 0.1820 0.1858 2.59 37.60 1413 13903 10.16 99.83 0.51 1 FREE R-VALUE 2.04 MOLECULAR REPLACEMENT 27.60 0.90 1.10 ML FLAT BULK SOLVENT MODEL 2.59 37.60 39 2333 53 2241 0 0.009 2557 1.591 3975 14.402 1251 0.089 522 0.011 111 0.3130 0.3324 2.69 128 1228 99.00 0.4398 0.3730 2.79 150 1282 100.00 0.3948 0.3234 2.92 140 1244 100.00 0.3517 0.2588 3.07 146 1266 100.00 0.2562 0.2029 3.27 142 1215 100.00 0.2454 0.2023 3.52 136 1254 100.00 0.2153 0.1623 3.87 144 1263 100.00 0.1716 0.1522 4.43 136 1256 100.00 0.1393 0.1246 5.58 139 1265 100.00 0.1649 0.1335 37.60 152 1217 100.00 2.59 37.60 23KA 13907 0.065 1 23.51 10.5 99.9 0.343 2.59 2.69 1026 1 refinement PHENIX (1.20.1_4487: ???) data extraction PDB_EXTRACT data reduction XDS data scaling XSCALE phasing PHASER N pre-miR-6074 internal loop in complex with amiloride (Form 2) 1 N N 1 N N 1 N N 2 N N 3 N N 2 N N 4 N N 3 N N 2 N N 3 N N 5 N N 5 N N 5 N N covale 1.308 none A U 3 A O2' U 3 1_555 A AMR 101 D N6 AMR 1_555 metalc 3.080 A G 13 A O6 G 13 1_555 A NA 102 E NA NA 1_555 metalc 2.958 A NA 102 E NA NA 1_555 A HOH 205 K O HOH 1_555 metalc 2.771 B A 10 B O3' A 10 1_555 B NA 103 H NA NA 1_555 metalc 2.466 B A 10 B O2' A 10 1_555 B NA 103 H NA NA 1_555 metalc 2.445 B G 12 B O6 G 12 1_555 B NA 103 H NA NA 1_555 metalc 2.811 C A 10 C O2' A 10 1_555 C NA 102 J NA NA 1_555 metalc 2.628 C G 12 C O6 G 12 1_555 C NA 102 J NA NA 1_555 metalc 2.615 C NA 102 J NA NA 1_555 C HOH 207 M O HOH 1_555 hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 A C 35 A N3 C 35 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 A C 35 A O2 C 35 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 A C 35 A N4 C 35 1_555 hydrog WATSON-CRICK A C 2 A N3 C 2 1_555 A G 34 A N1 G 34 1_555 hydrog WATSON-CRICK A C 2 A N4 C 2 1_555 A G 34 A O6 G 34 1_555 hydrog WATSON-CRICK A C 2 A O2 C 2 1_555 A G 34 A N2 G 34 1_555 hydrog WATSON-CRICK A U 3 A N3 U 3 1_555 A A 33 A N1 A 33 1_555 hydrog WATSON-CRICK A U 3 A O4 U 3 1_555 A A 33 A N6 A 33 1_555 hydrog TYPE_8_PAIR A G 5 A N1 G 5 1_555 A A 31 A N1 A 31 1_555 hydrog TYPE_8_PAIR A G 5 A O6 G 5 1_555 A A 31 A N6 A 31 1_555 hydrog WATSON-CRICK A C 6 A N3 C 6 1_555 A G 30 A N1 G 30 1_555 hydrog WATSON-CRICK A C 6 A N4 C 6 1_555 A G 30 A O6 G 30 1_555 hydrog WATSON-CRICK A C 6 A O2 C 6 1_555 A G 30 A N2 G 30 1_555 hydrog WATSON-CRICK A U 7 A N3 U 7 1_555 A A 29 A N1 A 29 1_555 hydrog WATSON-CRICK A U 7 A O4 U 7 1_555 A A 29 A N6 A 29 1_555 hydrog WATSON-CRICK A C 8 A N3 C 8 1_555 A G 28 A N1 G 28 1_555 hydrog WATSON-CRICK A C 8 A N4 C 8 1_555 A G 28 A O6 G 28 1_555 hydrog WATSON-CRICK A C 8 A O2 C 8 1_555 A G 28 A N2 G 28 1_555 hydrog REVERSED HOOGSTEEN A U 9 A N3 U 9 1_555 A A 26 A N7 A 26 1_555 hydrog REVERSED HOOGSTEEN A U 9 A O2 U 9 1_555 A A 26 A N6 A 26 1_555 hydrog WATSON-CRICK A A 11 A N1 A 11 1_555 A U 27 A N3 U 27 1_555 hydrog WATSON-CRICK A A 11 A N6 A 11 1_555 A U 27 A O4 U 27 1_555 hydrog TYPE_28_PAIR A G 12 A N1 G 12 1_555 A U 25 A O2 U 25 1_555 hydrog TYPE_28_PAIR A G 12 A O6 G 12 1_555 A U 25 A N3 U 25 1_555 hydrog G-U MISPAIR A G 12 A N2 G 12 1_555 A U 27 A O4 U 27 1_555 hydrog WATSON-CRICK A G 13 A N1 G 13 1_555 A C 24 A N3 C 24 1_555 hydrog WATSON-CRICK A G 13 A N2 G 13 1_555 A C 24 A O2 C 24 1_555 hydrog WATSON-CRICK A G 13 A O6 G 13 1_555 A C 24 A N4 C 24 1_555 hydrog WATSON-CRICK A C 14 A N3 C 14 1_555 A G 23 A N1 G 23 1_555 hydrog WATSON-CRICK A C 14 A N4 C 14 1_555 A G 23 A O6 G 23 1_555 hydrog WATSON-CRICK A C 14 A O2 C 14 1_555 A G 23 A N2 G 23 1_555 hydrog WATSON-CRICK A A 15 A N1 A 15 1_555 A U 22 A N3 U 22 1_555 hydrog WATSON-CRICK A A 15 A N6 A 15 1_555 A U 22 A O4 U 22 1_555 hydrog TYPE_28_PAIR A U 16 A N3 U 16 1_555 A G 21 A O6 G 21 1_555 hydrog TYPE_28_PAIR A U 16 A O2 U 16 1_555 A G 21 A N1 G 21 1_555 hydrog G-A MISPAIR A G 17 A N2 G 17 1_555 A A 20 A N7 A 20 1_555 hydrog WATSON-CRICK B G 1 B N1 G 1 1_555 B C 35 B N3 C 35 1_555 hydrog WATSON-CRICK B G 1 B N2 G 1 1_555 B C 35 B O2 C 35 1_555 hydrog WATSON-CRICK B G 1 B O6 G 1 1_555 B C 35 B N4 C 35 1_555 hydrog WATSON-CRICK B C 2 B N3 C 2 1_555 B G 34 B N1 G 34 1_555 hydrog WATSON-CRICK B C 2 B N4 C 2 1_555 B G 34 B O6 G 34 1_555 hydrog WATSON-CRICK B C 2 B O2 C 2 1_555 B G 34 B N2 G 34 1_555 hydrog WATSON-CRICK B U 3 B N3 U 3 1_555 B A 33 B N1 A 33 1_555 hydrog WATSON-CRICK B U 3 B O4 U 3 1_555 B A 33 B N6 A 33 1_555 hydrog TYPE_8_PAIR B G 5 B N1 G 5 1_555 B A 31 B N1 A 31 1_555 hydrog TYPE_8_PAIR B G 5 B O6 G 5 1_555 B A 31 B N6 A 31 1_555 hydrog WATSON-CRICK B C 6 B N3 C 6 1_555 B G 30 B N1 G 30 1_555 hydrog WATSON-CRICK B C 6 B N4 C 6 1_555 B G 30 B O6 G 30 1_555 hydrog WATSON-CRICK B C 6 B O2 C 6 1_555 B G 30 B N2 G 30 1_555 hydrog WATSON-CRICK B U 7 B N3 U 7 1_555 B A 29 B N1 A 29 1_555 hydrog WATSON-CRICK B U 7 B O4 U 7 1_555 B A 29 B N6 A 29 1_555 hydrog WATSON-CRICK B C 8 B N3 C 8 1_555 B G 28 B N1 G 28 1_555 hydrog WATSON-CRICK B C 8 B N4 C 8 1_555 B G 28 B O6 G 28 1_555 hydrog WATSON-CRICK B C 8 B O2 C 8 1_555 B G 28 B N2 G 28 1_555 hydrog REVERSED HOOGSTEEN B U 9 B N3 U 9 1_555 B A 26 B N7 A 26 1_555 hydrog REVERSED HOOGSTEEN B U 9 B O2 U 9 1_555 B A 26 B N6 A 26 1_555 hydrog TYPE_28_PAIR B G 12 B N1 G 12 1_555 B U 25 B O2 U 25 1_555 hydrog TYPE_28_PAIR B G 12 B O6 G 12 1_555 B U 25 B N3 U 25 1_555 hydrog WATSON-CRICK B G 13 B N1 G 13 1_555 B C 24 B N3 C 24 1_555 hydrog WATSON-CRICK B G 13 B N2 G 13 1_555 B C 24 B O2 C 24 1_555 hydrog WATSON-CRICK B G 13 B O6 G 13 1_555 B C 24 B N4 C 24 1_555 hydrog WATSON-CRICK B C 14 B N3 C 14 1_555 B G 23 B N1 G 23 1_555 hydrog WATSON-CRICK B C 14 B N4 C 14 1_555 B G 23 B O6 G 23 1_555 hydrog WATSON-CRICK B C 14 B O2 C 14 1_555 B G 23 B N2 G 23 1_555 hydrog WATSON-CRICK B A 15 B N1 A 15 1_555 B U 22 B N3 U 22 1_555 hydrog WATSON-CRICK B A 15 B N6 A 15 1_555 B U 22 B O4 U 22 1_555 hydrog TYPE_28_PAIR B U 16 B N3 U 16 1_555 B G 21 B O6 G 21 1_555 hydrog TYPE_28_PAIR B U 16 B O2 U 16 1_555 B G 21 B N1 G 21 1_555 hydrog TYPE_11_PAIR B G 17 B N2 G 17 1_555 B A 20 B N7 A 20 1_555 hydrog TYPE_11_PAIR B G 17 B N3 G 17 1_555 B A 20 B N6 A 20 1_555 hydrog WATSON-CRICK C G 1 C N1 G 1 1_555 C C 35 C N3 C 35 1_555 hydrog WATSON-CRICK C G 1 C N2 G 1 1_555 C C 35 C O2 C 35 1_555 hydrog WATSON-CRICK C G 1 C O6 G 1 1_555 C C 35 C N4 C 35 1_555 hydrog WATSON-CRICK C C 2 C N3 C 2 1_555 C G 34 C N1 G 34 1_555 hydrog WATSON-CRICK C C 2 C N4 C 2 1_555 C G 34 C O6 G 34 1_555 hydrog WATSON-CRICK C C 2 C O2 C 2 1_555 C G 34 C N2 G 34 1_555 hydrog WATSON-CRICK C U 3 C N3 U 3 1_555 C A 33 C N1 A 33 1_555 hydrog WATSON-CRICK C U 3 C O4 U 3 1_555 C A 33 C N6 A 33 1_555 hydrog TYPE_8_PAIR C G 5 C N1 G 5 1_555 C A 31 C N1 A 31 1_555 hydrog TYPE_8_PAIR C G 5 C O6 G 5 1_555 C A 31 C N6 A 31 1_555 hydrog WATSON-CRICK C C 6 C N3 C 6 1_555 C G 30 C N1 G 30 1_555 hydrog WATSON-CRICK C C 6 C N4 C 6 1_555 C G 30 C O6 G 30 1_555 hydrog WATSON-CRICK C C 6 C O2 C 6 1_555 C G 30 C N2 G 30 1_555 hydrog WATSON-CRICK C U 7 C N3 U 7 1_555 C A 29 C N1 A 29 1_555 hydrog WATSON-CRICK C U 7 C O4 U 7 1_555 C A 29 C N6 A 29 1_555 hydrog WATSON-CRICK C C 8 C N3 C 8 1_555 C G 28 C N1 G 28 1_555 hydrog WATSON-CRICK C C 8 C N4 C 8 1_555 C G 28 C O6 G 28 1_555 hydrog WATSON-CRICK C C 8 C O2 C 8 1_555 C G 28 C N2 G 28 1_555 hydrog REVERSED HOOGSTEEN C U 9 C N3 U 9 1_555 C A 26 C N7 A 26 1_555 hydrog REVERSED HOOGSTEEN C U 9 C O2 U 9 1_555 C A 26 C N6 A 26 1_555 hydrog TYPE_28_PAIR C G 12 C N1 G 12 1_555 C U 25 C O2 U 25 1_555 hydrog TYPE_28_PAIR C G 12 C O6 G 12 1_555 C U 25 C N3 U 25 1_555 hydrog WATSON-CRICK C G 13 C N1 G 13 1_555 C C 24 C N3 C 24 1_555 hydrog WATSON-CRICK C G 13 C N2 G 13 1_555 C C 24 C O2 C 24 1_555 hydrog WATSON-CRICK C G 13 C O6 G 13 1_555 C C 24 C N4 C 24 1_555 hydrog WATSON-CRICK C C 14 C N3 C 14 1_555 C G 23 C N1 G 23 1_555 hydrog WATSON-CRICK C C 14 C N4 C 14 1_555 C G 23 C O6 G 23 1_555 hydrog WATSON-CRICK C C 14 C O2 C 14 1_555 C G 23 C N2 G 23 1_555 hydrog WATSON-CRICK C A 15 C N1 A 15 1_555 C U 22 C N3 U 22 1_555 hydrog WATSON-CRICK C A 15 C N6 A 15 1_555 C U 22 C O4 U 22 1_555 hydrog TYPE_28_PAIR C U 16 C N3 U 16 1_555 C G 21 C O6 G 21 1_555 hydrog TYPE_28_PAIR C U 16 C O2 U 16 1_555 C G 21 C N1 G 21 1_555 hydrog TYPE_11_PAIR C G 17 C N2 G 17 1_555 C A 20 C N7 A 20 1_555 hydrog TYPE_11_PAIR C G 17 C N3 G 17 1_555 C A 20 C N6 A 20 1_555 RNA pre-miR-6074, RNA 23KA PDB 1 1 23KA 1 35 23KA 1 35 23KA A 1 1 35 1 35 23KA 1 35 23KA B 1 1 35 1 35 23KA 1 35 23KA C 1 1 35 145 P 32