0.008457 0.004883 0.000000 0.000000 0.009765 0.000000 0.000000 0.000000 0.004949 0.00000 0.00000 0.00000 0000-0001-7780-5278 Jones, C.P. 0000-0003-4549-1619 Ferre D'Amare, A.R. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 12 90.00 90.00 120.00 118.247 118.247 202.054 C10 H14 N5 O7 P 347.221 y ADENOSINE-5'-MONOPHOSPHATE RNA linking C12 H10 N6 O 254.247 (1M)-5-amino-1-(1,8-naphthyridin-3-yl)-1H-imidazole-4-carboxamide non-polymer C9 H14 N3 O8 P 323.197 y CYTIDINE-5'-MONOPHOSPHATE RNA linking C10 H14 N5 O8 P 363.221 y GUANOSINE-5'-MONOPHOSPHATE RNA linking H2 O 18.015 WATER non-polymer Mg 2 24.305 MAGNESIUM 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 N 38 N C Y 39 N C Y 40 N C Y 41 N C Y 42 N C Y 43 N C Y 44 N C Y 45 N C Y 46 N C Y 47 N C Y 48 N C Y 49 N C N 50 N N Y 51 N N Y 52 N N Y 53 N N Y 54 N N N 55 N N N 56 N O N 57 N H N 58 N H N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N O N 68 N P N 69 N O N 70 N O N 71 N O N 72 N C N 73 R C N 74 N O N 75 S C N 76 N O N 77 R C N 78 N O N 79 R C N 80 N N N 81 N C N 82 N O N 83 N N N 84 N C N 85 N N N 86 N C N 87 N C 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 H N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N O N 103 N P N 104 N O N 105 N O N 106 N O N 107 N C N 108 R C N 109 N O N 110 S C N 111 N O N 112 R C N 113 N O N 114 R C Y 115 N N Y 116 N C Y 117 N N Y 118 N C N 119 N C N 120 N O N 121 N N N 122 N C N 123 N N N 124 N N Y 125 N C N 126 N H N 127 N H N 128 N H N 129 N H N 130 N H N 131 N H 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 O N 141 N H N 142 N H N 143 N MG N 144 N O N 145 N P N 146 N O N 147 N O N 148 N O N 149 N C N 150 R C N 151 N O N 152 S C N 153 N O N 154 R C N 155 N O N 156 R C N 157 N N N 158 N C N 159 N O N 160 N N N 161 N C N 162 N O N 163 N C N 164 N C N 165 N H N 166 N H N 167 N H N 168 N H N 169 N H N 170 N H 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 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 Y 42 N sing Y 43 N doub Y 44 N doub Y 45 N sing Y 46 N sing Y 47 N sing Y 48 N doub Y 49 N doub Y 50 N sing N 51 N sing Y 52 N sing Y 53 N doub Y 54 N sing Y 55 N sing Y 56 N doub N 57 N sing N 58 N sing N 59 N sing N 60 N doub N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N sing 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 doub 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 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 doub N 98 N sing N 99 N doub N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N doub N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N doub N 110 N sing N 111 N sing N 112 N sing 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 Y 131 N sing Y 132 N sing Y 133 N doub N 134 N sing Y 135 N sing N 136 N sing Y 137 N doub N 138 N doub N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N doub N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N doub N 152 N sing N 153 N sing N 154 N sing 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 doub N 176 N sing N 177 N sing N 178 N sing N 179 N doub N 180 N sing N 181 N doub N 182 N sing N 183 N sing GE Angew.Chem.Int.Ed.Engl. ACIEAY 0179 1521-3773 64 e202505971 e202505971 10.1002/anie.202505971 40310613 Machine Learning-Augmented Molecular Dynamics Simulations (MD) Reveal Insights Into the Disconnect Between Affinity and Activation of ZTP Riboswitch Ligands. 2025 0000-0002-2412-6922 10.2210/pdb8vvj/pdb pdb_00008vvj 100 1 N PIXEL 2022-02-26 DECTRIS EIGER X 16M SINGLE WAVELENGTH M x-ray 1 0.9792 1.0 24-ID-C APS 0.9792 SYNCHROTRON APS BEAMLINE 24-ID-C 20782.453 RNA (64-MER) 1 man polymer 24.305 MAGNESIUM ION 3 syn non-polymer 254.247 (1M)-5-amino-1-(1,8-naphthyridin-3-yl)-1H-imidazole-4-carboxamide 1 syn non-polymer 18.015 water 76 nat water no no GGGUCGUGACUGGCGAACAGGUGGGAAACCACCGGGGAGCGACCCUUGCCGCCCGCCUGGGCAA GGGUCGUGACUGGCGAACAGGUGGGAAACCACCGGGGAGCGACCCUUGCCGCCCGCCUGGGCAA A 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 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 sample 1 64 1660 Schaalia odontolytica 905931 in vitro transcription vector pT7-TP(deltai) Biological sequence 1 VAPOR DIFFUSION, HANGING DROP 125-300 mM lithium sulfate, 23-27% PEG 3350, 0.1 M Hepes pH 7.5 294 -33.441 11 A 12 A 28 150.469 A_G12:A28_A 1 1.018 -2.259 -1.766 6.904 4.576 1 19 A 29 A 24 -0.260 A_C29:G24_A 2 -15.319 0.086 -0.178 -0.364 -3.821 1 19 A 30 A 23 -1.246 A_C30:G23_A 3 -8.592 0.300 0.098 -0.147 3.405 1 20 A 31 A 22 -1.954 A_A31:U22_A 4 -1.435 0.311 0.250 -0.096 -3.526 1 19 A 32 A 21 2.168 A_C32:G21_A 5 -9.980 0.381 -0.048 -0.230 3.692 1 19 A 33 A 20 0.370 A_C33:G20_A 6 -7.531 0.117 0.396 -0.056 -9.619 1 28 A 35 A 11 0.668 A_G35:U11_A 7 -13.117 -2.228 -0.290 -0.500 -2.926 1 19 A 36 A 10 1.522 A_G36:C10_A 8 -7.733 -0.279 0.308 -0.189 -1.248 10 11 A 37 A 9 -5.576 A_G37:A9_A 9 -11.677 6.942 0.392 -4.712 6.417 10 11 A 38 A 8 -13.276 A_A38:G8_A 10 -8.439 -6.890 -0.421 -4.969 6.841 1 28 A 39 A 7 -3.125 A_G39:U7_A 11 -14.179 -2.560 0.161 -0.949 7.043 1 19 A 40 A 6 0.585 A_C40:G6_A 12 -14.016 0.045 -0.050 -0.231 4.695 1 19 A 41 A 5 5.338 A_G41:C5_A 13 -7.066 0.244 0.333 0.100 9.895 1 20 A 42 A 4 0.333 A_A42:U4_A 14 -12.649 -0.020 0.175 -0.003 12.280 1 19 A 43 A 3 3.731 A_C43:G3_A 15 -15.260 0.373 -0.030 0.173 2.012 1 19 A 44 A 2 3.266 A_C44:G2_A 16 -15.755 0.495 0.133 -0.113 1.938 1 19 A 45 A 1 -6.049 A_C45:G1_A 17 -16.312 0.145 0.047 -0.285 -11.786 1 20 A 46 A 64 1.734 A_U46:A64_A 18 -14.167 -0.566 0.254 -0.146 -1.645 1 20 A 47 A 63 1.185 A_U47:A63_A 19 -12.491 -0.128 0.419 0.035 3.647 1 19 A 48 A 62 4.138 A_G48:C62_A 20 -13.812 -0.248 0.168 -0.005 5.352 1 19 A 49 A 61 -1.553 A_C49:G61_A 21 -17.206 0.465 -0.114 -0.233 3.937 1 19 A 50 A 60 -1.306 A_C50:G60_A 22 4.837 0.153 -0.262 -0.182 -3.481 2 A 51 A 59 126.257 A_G51:G59_A 23 -45.010 -2.061 1.140 -2.284 3.124 33.642 A A 29 30 11.061 A A 24 23 3.530 6.362 -0.588 -2.023 AA_C29C30:G23G24_AA 1 -1.867 3.246 33.000 -4.562 0.703 2.380 29.053 A A 30 31 18.726 A A 23 22 3.018 9.235 -0.314 -1.598 AA_C30A31:U22G23_AA 2 -1.312 2.661 27.546 -4.907 0.382 2.740 35.881 A A 31 32 28.764 A A 22 21 3.676 17.025 0.784 -1.234 AA_A31C32:G21U22_AA 3 3.147 -5.317 31.549 -4.562 -0.800 1.943 30.958 A A 32 33 24.465 A A 21 20 2.957 12.687 0.503 -1.846 AA_C32C33:G20G21_AA 4 -1.340 2.584 28.265 -5.384 -1.146 6.391 73.230 A A 33 35 15.646 A A 20 11 6.618 18.468 2.507 -1.437 AA_C33G35:U11G20_AA 5 10.004 -8.475 70.560 -2.420 -1.443 3.022 31.186 A A 35 36 5.638 A A 11 10 3.112 3.002 -0.979 -2.293 AA_G35G36:C10U11_AA 6 -7.026 13.197 30.259 -4.810 0.547 3.248 66.942 A A 36 37 4.581 A A 10 9 3.331 5.048 -0.946 -0.653 AA_G36G37:A9C10_AA 7 2.430 -2.205 66.734 -0.791 0.954 3.362 -32.735 A A 37 38 -3.105 A A 9 8 3.338 1.738 -0.280 -0.683 AA_G37A38:G8A9_AA 8 6.352 11.343 -32.083 0.902 0.637 3.299 57.288 A A 38 39 -0.058 A A 8 7 3.442 -0.056 1.209 -1.104 AA_A38G39:U7G8_AA 9 -6.467 6.757 56.953 -1.148 -1.626 3.282 44.035 A A 39 40 -0.102 A A 7 6 3.278 -0.077 -0.184 -1.480 AA_G39C40:G6U7_AA 10 -0.409 0.545 44.033 -1.967 0.207 2.337 31.507 A A 40 41 20.844 A A 6 5 3.172 11.056 -0.310 -1.907 AA_C40G41:C5G6_AA 11 -4.104 7.738 29.269 -5.315 -0.098 2.724 32.887 A A 41 42 14.871 A A 5 4 3.114 8.330 -0.571 -1.085 AA_G41A42:U4C5_AA 12 1.357 -2.422 31.814 -3.210 1.219 2.733 33.615 A A 42 43 17.550 A A 4 3 3.210 10.002 0.444 -1.217 AA_A42C43:G3U4_AA 13 1.252 -2.197 32.109 -3.626 -0.577 2.558 36.237 A A 43 44 22.010 A A 3 2 3.338 13.385 -0.126 -1.560 AA_C43C44:G2G3_AA 14 -0.661 1.086 33.745 -4.266 0.116 2.757 32.260 A A 44 45 11.335 A A 2 1 3.195 6.253 0.036 -1.969 AA_C44C45:G1G2_AA 15 2.774 -5.029 31.545 -4.567 0.389 3.392 39.149 A A 45 46 9.423 A A 1 64 3.474 6.277 1.333 -1.061 AA_C45U46:A64G1_AA 16 4.408 -6.618 38.420 -2.381 -1.429 2.837 32.297 A A 46 47 8.684 A A 64 63 3.066 4.813 0.276 -1.295 AA_U46U47:A63A64_AA 17 -0.894 1.613 31.933 -3.103 -0.639 2.657 29.303 A A 47 48 12.042 A A 63 62 3.039 6.049 0.389 -1.616 AA_U47G48:C62A63_AA 18 0.564 -1.122 28.680 -4.344 -0.663 3.452 36.217 A A 48 49 -4.500 A A 62 61 3.306 -2.793 -0.738 -1.573 AA_G48C49:G61C62_AA 19 -2.234 3.598 36.046 -2.124 0.862 2.409 31.706 A A 49 50 22.158 A A 61 60 3.415 11.821 -0.233 -2.063 AA_C49C50:G60G61_AA 20 1.788 -3.351 29.420 -5.790 0.730 0.222 177.691 A A 50 51 30.400 A A 60 59 -0.122 60.653 -2.018 -2.649 AA_C50G51:G59G60_AA 21 -162.453 81.422 138.986 -1.328 1.001 citation citation_author repository Initial release Database references 1 0 2025-06-11 1 1 2025-08-06 _citation.journal_volume _citation.title _citation_author.identifier_ORCID _citation_author.name United States National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) adrian.ferre@gmail.com 0000-0003-4549-1619 Adrian Ferre-D'Amare principal investigator/group leader Structure of the same RNA with a related synthetic ligand N RCSB N RCSB 2024-01-31 REL REL A1AD3 A1AD3 SUBJECT OF INVESTIGATION MG MAGNESIUM ION A1AD3 (1M)-5-amino-1-(1,8-naphthyridin-3-yl)-1H-imidazole-4-carboxamide HOH water Y N 4XWF Ions, ligands removed PDB experimental model MG 2 2 MG MG 101 A MG 3 2 MG MG 102 A MO6 1 2 MG MG 103 A A12 1 3 A1AD3 A1AD3 104 A HOH 50 4 HOH HOH 201 A HOH 71 4 HOH HOH 202 A HOH 72 4 HOH HOH 203 A HOH 30 4 HOH HOH 204 A HOH 60 4 HOH HOH 205 A HOH 59 4 HOH HOH 206 A HOH 45 4 HOH HOH 207 A HOH 46 4 HOH HOH 208 A HOH 65 4 HOH HOH 209 A HOH 39 4 HOH HOH 210 A HOH 17 4 HOH HOH 211 A HOH 44 4 HOH HOH 212 A HOH 4 4 HOH HOH 213 A HOH 61 4 HOH HOH 214 A HOH 47 4 HOH HOH 215 A HOH 68 4 HOH HOH 216 A HOH 26 4 HOH HOH 217 A HOH 62 4 HOH HOH 218 A HOH 52 4 HOH HOH 219 A HOH 64 4 HOH HOH 220 A HOH 37 4 HOH HOH 221 A HOH 7 4 HOH HOH 222 A HOH 63 4 HOH HOH 223 A HOH 36 4 HOH HOH 224 A HOH 13 4 HOH HOH 225 A MO6 1 4 HOH HOH 226 A HOH 22 4 HOH HOH 227 A HOH 15 4 HOH HOH 228 A HOH 18 4 HOH HOH 229 A HOH 12 4 HOH HOH 230 A MO6 1 4 HOH HOH 231 A HOH 31 4 HOH HOH 232 A HOH 49 4 HOH HOH 233 A HOH 24 4 HOH HOH 234 A HOH 10 4 HOH HOH 235 A HOH 3 4 HOH HOH 236 A HOH 33 4 HOH HOH 237 A MO6 1 4 HOH HOH 238 A HOH 32 4 HOH HOH 239 A HOH 11 4 HOH HOH 240 A HOH 2 4 HOH HOH 241 A HOH 14 4 HOH HOH 242 A HOH 67 4 HOH HOH 243 A HOH 48 4 HOH HOH 244 A HOH 25 4 HOH HOH 245 A HOH 70 4 HOH HOH 246 A HOH 6 4 HOH HOH 247 A HOH 28 4 HOH HOH 248 A HOH 19 4 HOH HOH 249 A HOH 27 4 HOH HOH 250 A MO6 1 4 HOH HOH 251 A HOH 5 4 HOH HOH 252 A HOH 41 4 HOH HOH 253 A HOH 35 4 HOH HOH 254 A HOH 38 4 HOH HOH 255 A HOH 56 4 HOH HOH 256 A HOH 16 4 HOH HOH 257 A HOH 53 4 HOH HOH 258 A MO6 1 4 HOH HOH 259 A HOH 69 4 HOH HOH 260 A HOH 21 4 HOH HOH 261 A HOH 54 4 HOH HOH 262 A HOH 23 4 HOH HOH 263 A HOH 57 4 HOH HOH 264 A HOH 8 4 HOH HOH 265 A HOH 74 4 HOH HOH 266 A HOH 1 4 HOH HOH 267 A HOH 29 4 HOH HOH 268 A HOH 58 4 HOH HOH 269 A HOH 43 4 HOH HOH 270 A HOH 40 4 HOH HOH 271 A HOH 66 4 HOH HOH 272 A HOH 42 4 HOH HOH 273 A HOH 55 4 HOH HOH 274 A HOH 73 4 HOH HOH 275 A MO6 1 4 HOH HOH 276 A G 1 n 1 G 1 A G 2 n 2 G 2 A G 3 n 3 G 3 A U 4 n 4 U 4 A C 5 n 5 C 5 A G 6 n 6 G 6 A U 7 n 7 U 7 A G 8 n 8 G 8 A A 9 n 9 A 9 A C 10 n 10 C 10 A U 11 n 11 U 11 A G 12 n 12 G 12 A G 13 n 13 G 13 A C 14 n 14 C 14 A G 15 n 15 G 15 A A 16 n 16 A 16 A A 17 n 17 A 17 A C 18 n 18 C 18 A A 19 n 19 A 19 A G 20 n 20 G 20 A G 21 n 21 G 21 A U 22 n 22 U 22 A G 23 n 23 G 23 A G 24 n 24 G 24 A G 25 n 25 G 25 A A 26 n 26 A 26 A A 27 n 27 A 27 A A 28 n 28 A 28 A C 29 n 29 C 29 A C 30 n 30 C 30 A A 31 n 31 A 31 A C 32 n 32 C 32 A C 33 n 33 C 33 A G 34 n 34 G 34 A G 35 n 35 G 35 A G 36 n 36 G 36 A G 37 n 37 G 37 A A 38 n 38 A 38 A G 39 n 39 G 39 A C 40 n 40 C 40 A G 41 n 41 G 41 A A 42 n 42 A 42 A C 43 n 43 C 43 A C 44 n 44 C 44 A C 45 n 45 C 45 A U 46 n 46 U 46 A U 47 n 47 U 47 A G 48 n 48 G 48 A C 49 n 49 C 49 A C 50 n 50 C 50 A G 51 n 51 G 51 A C 52 n 52 C 52 A C 53 n 53 C 53 A C 54 n 54 C 54 A G 55 n 55 G 55 A C 56 n 56 C 56 A C 57 n 57 C 57 A U 58 n 58 U 58 A G 59 n 59 G 59 A G 60 n 60 G 60 A G 61 n 61 G 61 A C 62 n 62 C 62 A A 63 n 63 A 63 A A 64 n 64 A 64 A 5.7901 -3.3329 -4.0624 3.8376 1.6129 3.5545 -1.3544 -0.2080 -1.5250 1.0463 0.5493 -0.1844 0.8359 0.5367 0.6067 0.2215 0.0467 0.0986 0.7126 -0.0457 1.0835 refined 49.6759 -11.4142 18.6035 X-RAY DIFFRACTION 0.4653 0.4925 -0.2795 2.7769 -0.4167 2.4350 -0.0895 -0.0732 -0.1812 -0.0596 0.0050 -0.2399 0.1694 0.2158 -0.0507 0.1887 0.0325 -0.0016 0.2966 -0.0044 0.3752 refined 31.6836 -3.3884 19.4617 X-RAY DIFFRACTION 1.8541 -1.7439 -0.2990 2.3544 0.6066 2.9443 -0.1297 0.0231 -0.2493 -0.1615 -0.0547 0.6933 0.1278 -0.4605 0.1045 0.3029 -0.1098 -0.0094 0.4533 0.0071 0.5519 refined 78.8135 -4.8521 11.6280 X-RAY DIFFRACTION X-RAY DIFFRACTION 1 chain 'A' and (resid 1 through 10 ) X-RAY DIFFRACTION 2 chain 'A' and (resid 11 through 45 ) X-RAY DIFFRACTION 3 chain 'A' and (resid 46 through 64 ) author_and_software_defined_assembly PISA 2 dimeric isothermal titration calorimetry 6090 -86 19320 A U 11 A OP1 U 11 1_555 A MG 102 C MG MG 4_655 A C 29 A OP2 C 29 1_555 163.2 A U 11 A OP1 U 11 1_555 A MG 102 C MG MG 4_655 A A1AD3 104 E O03 A1AD3 1_555 21.0 A C 29 A OP2 C 29 1_555 A MG 102 C MG MG 4_655 A A1AD3 104 E O03 A1AD3 1_555 145.5 A U 11 A OP1 U 11 1_555 A MG 102 C MG MG 4_655 A HOH 225 F O HOH 4_655 20.2 A C 29 A OP2 C 29 1_555 A MG 102 C MG MG 4_655 A HOH 225 F O HOH 4_655 144.9 A A1AD3 104 E O03 A1AD3 1_555 A MG 102 C MG MG 4_655 A HOH 225 F O HOH 4_655 4.0 A U 11 A OP1 U 11 1_555 A MG 102 C MG MG 4_655 A HOH 228 F O HOH 1_555 18.5 A C 29 A OP2 C 29 1_555 A MG 102 C MG MG 4_655 A HOH 228 F O HOH 1_555 147.3 A A1AD3 104 E O03 A1AD3 1_555 A MG 102 C MG MG 4_655 A HOH 228 F O HOH 1_555 2.8 A HOH 225 F O HOH 4_655 A MG 102 C MG MG 4_655 A HOH 228 F O HOH 1_555 2.9 A U 11 A OP1 U 11 1_555 A MG 102 C MG MG 4_655 A HOH 242 F O HOH 4_655 22.6 A C 29 A OP2 C 29 1_555 A MG 102 C MG MG 4_655 A HOH 242 F O HOH 4_655 143.0 A A1AD3 104 E O03 A1AD3 1_555 A MG 102 C MG MG 4_655 A HOH 242 F O HOH 4_655 3.1 A HOH 225 F O HOH 4_655 A MG 102 C MG MG 4_655 A HOH 242 F O HOH 4_655 2.9 A HOH 228 F O HOH 1_555 A MG 102 C MG MG 4_655 A HOH 242 F O HOH 4_655 4.3 A G 15 A OP2 G 15 1_555 A MG 101 B MG MG 1_555 A A 19 A OP2 A 19 1_555 151.2 A G 15 A OP2 G 15 1_555 A MG 101 B MG MG 1_555 A HOH 217 F O HOH 1_555 71.9 A A 19 A OP2 A 19 1_555 A MG 101 B MG MG 1_555 A HOH 217 F O HOH 1_555 89.2 A G 15 A OP2 G 15 1_555 A MG 101 B MG MG 1_555 A HOH 234 F O HOH 1_555 107.2 A A 19 A OP2 A 19 1_555 A MG 101 B MG MG 1_555 A HOH 234 F O HOH 1_555 95.1 A HOH 217 F O HOH 1_555 A MG 101 B MG MG 1_555 A HOH 234 F O HOH 1_555 93.3 A G 15 A OP2 G 15 1_555 A MG 101 B MG MG 1_555 A HOH 245 F O HOH 1_555 75.9 A A 19 A OP2 A 19 1_555 A MG 101 B MG MG 1_555 A HOH 245 F O HOH 1_555 79.1 A HOH 217 F O HOH 1_555 A MG 101 B MG MG 1_555 A HOH 245 F O HOH 1_555 78.1 A HOH 234 F O HOH 1_555 A MG 101 B MG MG 1_555 A HOH 245 F O HOH 1_555 169.7 A G 15 A OP2 G 15 1_555 A MG 101 B MG MG 1_555 A HOH 267 F O HOH 1_555 99.7 A A 19 A OP2 A 19 1_555 A MG 101 B MG MG 1_555 A HOH 267 F O HOH 1_555 91.7 A HOH 217 F O HOH 1_555 A MG 101 B MG MG 1_555 A HOH 267 F O HOH 1_555 161.8 A HOH 234 F O HOH 1_555 A MG 101 B MG MG 1_555 A HOH 267 F O HOH 1_555 104.7 A HOH 245 F O HOH 1_555 A MG 101 B MG MG 1_555 A HOH 267 F O HOH 1_555 84.2 A HOH 226 F O HOH 1_555 A MG 103 D MG MG 1_555 A HOH 231 F O HOH 1_555 178.2 A HOH 226 F O HOH 1_555 A MG 103 D MG MG 1_555 A HOH 238 F O HOH 1_555 91.0 A HOH 231 F O HOH 1_555 A MG 103 D MG MG 1_555 A HOH 238 F O HOH 1_555 88.4 A HOH 226 F O HOH 1_555 A MG 103 D MG MG 1_555 A HOH 251 F O HOH 1_555 88.5 A HOH 231 F O HOH 1_555 A MG 103 D MG MG 1_555 A HOH 251 F O HOH 1_555 89.8 A HOH 238 F O HOH 1_555 A MG 103 D MG MG 1_555 A HOH 251 F O HOH 1_555 92.0 A HOH 226 F O HOH 1_555 A MG 103 D MG MG 1_555 A HOH 259 F O HOH 1_555 91.4 A HOH 231 F O HOH 1_555 A MG 103 D MG MG 1_555 A HOH 259 F O HOH 1_555 90.3 A HOH 238 F O HOH 1_555 A MG 103 D MG MG 1_555 A HOH 259 F O HOH 1_555 85.9 A HOH 251 F O HOH 1_555 A MG 103 D MG MG 1_555 A HOH 259 F O HOH 1_555 177.9 A HOH 226 F O HOH 1_555 A MG 103 D MG MG 1_555 A HOH 276 F O HOH 1_555 89.5 A HOH 231 F O HOH 1_555 A MG 103 D MG MG 1_555 A HOH 276 F O HOH 1_555 91.2 A HOH 238 F O HOH 1_555 A MG 103 D MG MG 1_555 A HOH 276 F O HOH 1_555 175.1 A HOH 251 F O HOH 1_555 A MG 103 D MG MG 1_555 A HOH 276 F O HOH 1_555 92.9 A HOH 259 F O HOH 1_555 A MG 103 D MG MG 1_555 A HOH 276 F O HOH 1_555 89.2 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 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 4_655 -x+1,-y,z crystal symmetry operation 118.2470000000 0.0000000000 0.0000000000 0.3339 0.3118 0.3126 2.15 101.03 2937 85958 3.42 99.90 0.43 1 FREE R-VALUE 1.34 MOLECULAR REPLACEMENT 39.31 0.90 1.11 ML FLAT BULK SOLVENT MODEL 2.15 101.03 70 1474 28 1376 0 0.005 1567 0.918 2448 12.233 766 0.039 319 0.007 67 0.4777 0.4117 2.19 141 3963 100.00 0.3203 0.3983 2.22 138 3931 100.00 0.3814 0.4150 2.26 140 3927 100.00 0.3957 0.3719 2.31 138 3983 100.00 0.3597 0.3517 2.35 143 3956 100.00 0.3633 0.3441 2.41 139 3977 100.00 0.4166 0.3558 2.46 145 3957 100.00 0.4112 0.3574 2.52 144 3947 100.00 0.4002 0.3671 2.59 139 3923 100.00 0.3836 0.3748 2.67 141 3943 100.00 0.4328 0.3913 2.75 139 3989 100.00 0.4642 0.4005 2.85 139 3936 100.00 0.3202 0.3646 2.97 140 3961 100.00 0.3585 0.3069 3.10 138 3943 100.00 0.3075 0.2866 3.26 139 3954 100.00 0.3026 0.2706 3.47 133 3942 100.00 0.2808 0.2634 3.74 146 3935 100.00 0.3110 0.2972 4.11 138 3955 100.00 0.3522 0.3021 4.71 137 3966 100.00 0.2788 0.2691 5.93 140 3964 100.00 0.2858 0.2702 101.03 140 3969 100.00 2.15 101.03 8VVJ 85958 .997 .2546 1 12.41 39.1 99.89 2.508 2.15 2.227 4513 .831 1 refinement PHENIX (1.19.2_4158: ???) data reduction XDS data scaling XDS phasing PHASER N Structure of S. odontolytica ZTP riboswitch bound to m-1-pyridinyl-AICA 1 N N 2 N N 2 N N 2 N N 3 N N 4 N N metalc 2.062 A U 11 A OP1 U 11 1_555 A MG 102 C MG MG 4_655 metalc 2.246 A G 15 A OP2 G 15 1_555 A MG 101 B MG MG 1_555 metalc 2.165 A A 19 A OP2 A 19 1_555 A MG 101 B MG MG 1_555 metalc 1.919 A C 29 A OP2 C 29 1_555 A MG 102 C MG MG 4_655 metalc 2.033 A MG 101 B MG MG 1_555 A HOH 217 F O HOH 1_555 metalc 2.334 A MG 101 B MG MG 1_555 A HOH 234 F O HOH 1_555 metalc 2.504 A MG 101 B MG MG 1_555 A HOH 245 F O HOH 1_555 metalc 2.333 A MG 101 B MG MG 1_555 A HOH 267 F O HOH 1_555 metalc 1.825 A MG 102 C MG MG 1_555 A A1AD3 104 E O03 A1AD3 1_555 metalc 1.888 A MG 102 C MG MG 1_555 A HOH 225 F O HOH 4_655 metalc 2.189 A MG 102 C MG MG 1_555 A HOH 228 F O HOH 1_555 metalc 2.212 A MG 102 C MG MG 1_555 A HOH 242 F O HOH 4_655 metalc 2.178 A MG 103 D MG MG 1_555 A HOH 226 F O HOH 1_555 metalc 2.164 A MG 103 D MG MG 1_555 A HOH 231 F O HOH 1_555 metalc 2.162 A MG 103 D MG MG 1_555 A HOH 238 F O HOH 1_555 metalc 2.185 A MG 103 D MG MG 1_555 A HOH 251 F O HOH 1_555 metalc 2.179 A MG 103 D MG MG 1_555 A HOH 259 F O HOH 1_555 metalc 2.172 A MG 103 D MG MG 1_555 A HOH 276 F O HOH 1_555 hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 A C 45 A N3 C 45 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 A C 45 A O2 C 45 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 A C 45 A N4 C 45 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 A C 44 A N3 C 44 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 A C 44 A O2 C 44 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 A C 44 A N4 C 44 1_555 hydrog WATSON-CRICK A G 3 A N1 G 3 1_555 A C 43 A N3 C 43 1_555 hydrog WATSON-CRICK A G 3 A N2 G 3 1_555 A C 43 A O2 C 43 1_555 hydrog WATSON-CRICK A G 3 A O6 G 3 1_555 A C 43 A N4 C 43 1_555 hydrog WATSON-CRICK A U 4 A N3 U 4 1_555 A A 42 A N1 A 42 1_555 hydrog WATSON-CRICK A U 4 A O4 U 4 1_555 A A 42 A N6 A 42 1_555 hydrog WATSON-CRICK A C 5 A N3 C 5 1_555 A G 41 A N1 G 41 1_555 hydrog WATSON-CRICK A C 5 A N4 C 5 1_555 A G 41 A O6 G 41 1_555 hydrog WATSON-CRICK A C 5 A O2 C 5 1_555 A G 41 A N2 G 41 1_555 hydrog WATSON-CRICK A G 6 A N1 G 6 1_555 A C 40 A N3 C 40 1_555 hydrog WATSON-CRICK A G 6 A N2 G 6 1_555 A C 40 A O2 C 40 1_555 hydrog WATSON-CRICK A G 6 A O6 G 6 1_555 A C 40 A N4 C 40 1_555 hydrog TYPE_28_PAIR A U 7 A N3 U 7 1_555 A G 39 A O6 G 39 1_555 hydrog TYPE_28_PAIR A U 7 A O2 U 7 1_555 A G 39 A N1 G 39 1_555 hydrog TYPE_11_PAIR A G 8 A N2 G 8 1_555 A A 38 A N7 A 38 1_555 hydrog TYPE_11_PAIR A G 8 A N3 G 8 1_555 A A 38 A N6 A 38 1_555 hydrog TYPE_11_PAIR A A 9 A N6 A 9 1_555 A G 37 A N3 G 37 1_555 hydrog TYPE_11_PAIR A A 9 A N7 A 9 1_555 A G 37 A N2 G 37 1_555 hydrog WATSON-CRICK A C 10 A N3 C 10 1_555 A G 36 A N1 G 36 1_555 hydrog WATSON-CRICK A C 10 A N4 C 10 1_555 A G 36 A O6 G 36 1_555 hydrog WATSON-CRICK A C 10 A O2 C 10 1_555 A G 36 A N2 G 36 1_555 hydrog TYPE_28_PAIR A U 11 A N3 U 11 1_555 A G 35 A O6 G 35 1_555 hydrog TYPE_28_PAIR A U 11 A O2 U 11 1_555 A G 35 A N1 G 35 1_555 hydrog G-A MISPAIR A G 12 A N2 G 12 1_555 A A 28 A N3 A 28 1_555 hydrog WATSON-CRICK A G 20 A N1 G 20 1_555 A C 33 A N3 C 33 1_555 hydrog WATSON-CRICK A G 20 A N2 G 20 1_555 A C 33 A O2 C 33 1_555 hydrog WATSON-CRICK A G 20 A O6 G 20 1_555 A C 33 A N4 C 33 1_555 hydrog WATSON-CRICK A G 21 A N1 G 21 1_555 A C 32 A N3 C 32 1_555 hydrog WATSON-CRICK A G 21 A N2 G 21 1_555 A C 32 A O2 C 32 1_555 hydrog WATSON-CRICK A G 21 A O6 G 21 1_555 A C 32 A N4 C 32 1_555 hydrog WATSON-CRICK A U 22 A N3 U 22 1_555 A A 31 A N1 A 31 1_555 hydrog WATSON-CRICK A U 22 A O4 U 22 1_555 A A 31 A N6 A 31 1_555 hydrog WATSON-CRICK A G 23 A N1 G 23 1_555 A C 30 A N3 C 30 1_555 hydrog WATSON-CRICK A G 23 A N2 G 23 1_555 A C 30 A O2 C 30 1_555 hydrog WATSON-CRICK A G 23 A O6 G 23 1_555 A C 30 A N4 C 30 1_555 hydrog WATSON-CRICK A G 24 A N1 G 24 1_555 A C 29 A N3 C 29 1_555 hydrog WATSON-CRICK A G 24 A N2 G 24 1_555 A C 29 A O2 C 29 1_555 hydrog WATSON-CRICK A G 24 A O6 G 24 1_555 A C 29 A N4 C 29 1_555 hydrog WATSON-CRICK A U 46 A N3 U 46 1_555 A A 64 A N1 A 64 1_555 hydrog WATSON-CRICK A U 46 A O4 U 46 1_555 A A 64 A N6 A 64 1_555 hydrog WATSON-CRICK A U 47 A N3 U 47 1_555 A A 63 A N1 A 63 1_555 hydrog WATSON-CRICK A U 47 A O4 U 47 1_555 A A 63 A N6 A 63 1_555 hydrog WATSON-CRICK A G 48 A N1 G 48 1_555 A C 62 A N3 C 62 1_555 hydrog WATSON-CRICK A G 48 A N2 G 48 1_555 A C 62 A O2 C 62 1_555 hydrog WATSON-CRICK A G 48 A O6 G 48 1_555 A C 62 A N4 C 62 1_555 hydrog WATSON-CRICK A C 49 A N3 C 49 1_555 A G 61 A N1 G 61 1_555 hydrog WATSON-CRICK A C 49 A N4 C 49 1_555 A G 61 A O6 G 61 1_555 hydrog WATSON-CRICK A C 49 A O2 C 49 1_555 A G 61 A N2 G 61 1_555 hydrog WATSON-CRICK A C 50 A N3 C 50 1_555 A G 60 A N1 G 60 1_555 hydrog WATSON-CRICK A C 50 A N4 C 50 1_555 A G 60 A O6 G 60 1_555 hydrog WATSON-CRICK A C 50 A O2 C 50 1_555 A G 60 A N2 G 60 1_555 hydrog G-G MISPAIR A G 51 A O6 G 51 1_555 A G 59 A N1 G 59 1_555 hydrog G-G MISPAIR A G 51 A O6 G 51 1_555 A G 60 A N1 G 60 1_555 RNA riboswitch, drug, synthetic, aptamer, RNA 8VVJ PDB 1 1 8VVJ 1 64 8VVJ 1 64 8VVJ A 1 1 64 177 P 6 2 2