0.016389 0.009462 0.000000 0.000000 0.018924 0.000000 0.000000 0.000000 0.009722 0.00000 0.00000 0.00000 3.54356 2.42580 25.62398 1.50364 0.0 2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 9.41153 2.53737 2.59044 63.03566 0.0 2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 20.23591 4.67902 2.76514 44.01191 0.0 2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 6.96715 11.43723 0.0 1-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 7.96527 9.05267 0.0 1-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 9.51135 5.44231 1.42069 35.72801 0.0 2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 0000-0003-0105-3430 Nuthanakanti, A. 0000-0001-8328-9310 Serganov, A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 6 90.000 90.000 120.000 61.018 61.018 102.855 331643.872 C10 H14 N5 O7 P 347.221 y ADENOSINE-5'-MONOPHOSPHATE RNA linking 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 C13 H18 N4 230.309 6-methylquinoxaline non-polymer Mg 2 24.305 MAGNESIUM ION non-polymer Mn 2 54.938 MANGANESE (II) 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 O N 39 N P N 40 N O N 41 N O N 42 N O N 43 N C N 44 R C N 45 N O N 46 S C N 47 N O N 48 R C N 49 N O N 50 R C N 51 N N N 52 N C N 53 N O N 54 N N N 55 N C N 56 N N N 57 N C N 58 N C 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 H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N O N 74 N P N 75 N O N 76 N O N 77 N O N 78 N C N 79 R C N 80 N O N 81 S C N 82 N O N 83 R C N 84 N O N 85 R C Y 86 N N Y 87 N C Y 88 N N Y 89 N C N 90 N C N 91 N O N 92 N N N 93 N C N 94 N N N 95 N N Y 96 N C N 97 N H N 98 N H N 99 N H N 100 N H 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 H N 109 N H N 110 N H Y 111 N C Y 112 N C Y 113 N C N 114 N C Y 115 N C Y 116 N C Y 117 N C Y 118 N C Y 119 N C Y 120 N N Y 121 N N N 122 N H N 123 N H N 124 N H N 125 N H N 126 N H N 127 N H N 128 N H N 129 N N N 130 N C N 131 N C N 132 N N N 133 N C N 134 N C 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 MG N 147 N MN N 148 N O N 149 N P N 150 N O N 151 N O N 152 N O N 153 N C N 154 R C N 155 N O N 156 S C N 157 N O N 158 R C N 159 N O N 160 R C N 161 N N N 162 N C N 163 N O N 164 N N N 165 N C N 166 N O N 167 N C N 168 N C 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 178 N H N 179 N H N 180 N H N 181 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 N 40 N sing N 41 N sing N 42 N doub N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing 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 sing 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 doub 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 doub 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 sing N 98 N sing N 99 N sing Y 100 N sing Y 101 N sing Y 102 N doub N 103 N sing Y 104 N sing N 105 N sing Y 106 N doub N 107 N doub 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 Y 117 N doub Y 118 N sing Y 119 N sing Y 120 N doub Y 121 N sing Y 122 N doub Y 123 N doub Y 124 N sing Y 125 N sing Y 126 N sing Y 127 N doub 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 sing 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 US Proc.Natl.Acad.Sci.USA PNASA6 0040 1091-6490 119 e2122660119 e2122660119 10.1073/pnas.2122660119 35561226 SHAPE-enabled fragment-based ligand discovery for RNA. 2022 0000-0002-8963-8339 0000-0002-8630-2928 0000-0003-0105-3430 0000-0003-1658-658X 0000-0003-4796-7430 0000-0001-7891-5700 0000-0002-6748-9985 10.2210/pdb7tzt/pdb pdb_00007tzt 100 1 N PIXEL 2021-03-21 DECTRIS EIGER2 X 16M SINGLE WAVELENGTH M x-ray 1 0.9791 1.0 24-ID-C APS 0.9791 SYNCHROTRON APS BEAMLINE 24-ID-C 26798.936 RNA (79-MER) 1 syn polymer 54.938 MANGANESE (II) ION 2 syn non-polymer 24.305 MAGNESIUM ION 1 syn non-polymer 230.309 6-methylquinoxaline 1 syn non-polymer no no GCGACUCGGGGUGCCCUUCUGCGUGAAGGCUGAGAAAUACCCGUAUCACCUGAUCUGGAUAAUGCCAGCGUAGGGAAGUC GCA GCGACUCGGGGUGCCCUUCUGCGUGAAGGCUGAGAAAUACCCGUAUCACCUGAUCUGGAUAAUGCCAGCGUAGGGAAGUC GCA 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 n n n n n n n n n n n n n n n n n n n 1 2.06 40.36 large trigonal shaped crystals VAPOR DIFFUSION, HANGING DROP The RNA (0.15 mM) was incubated in a buffer containing 5 mM Tris-HCl, pH 8.0, 3 mM MgCl2, 10 mM NaCl, 0.1 M KCl, and 0.5 mM spermine with 1.0 mM compound 38. Reservoir solution was 50 mM Bis-Tris, pH 6.5, 0.5 M ammonium chloride, 15 mm MnCl2, and 28% (v/v) PEG2000 6.5-8.0 291 -0.640 1 19 A 9 A 90 -0.748 A_G9:C90_A 1 -6.541 -0.146 0.644 -0.230 3.328 1 19 A 10 A 89 -0.301 A_C10:G89_A 2 -6.459 0.122 0.514 -0.199 -2.719 1 19 A 11 A 88 0.821 A_G11:C88_A 3 -8.477 -0.217 0.091 -0.127 -5.973 1 20 A 12 A 87 -1.344 A_A12:U87_A 4 -4.890 0.002 -0.282 -0.100 -2.667 1 19 A 13 A 86 -0.454 A_C13:G86_A 5 -3.623 0.135 -0.039 -0.128 -3.253 1 20 A 14 A 85 2.775 A_U14:A85_A 6 1.173 -0.129 -0.044 -0.095 -0.329 1 19 A 15 A 51 -0.779 A_C15:G51_A 7 -4.357 0.123 0.108 -0.136 -4.302 1 19 A 16 A 50 2.887 A_G16:C50_A 8 -9.810 -0.208 -0.286 -0.113 -12.213 1 19 A 17 A 49 -0.401 A_G17:C49_A 9 -4.975 -0.212 -0.063 -0.152 -7.225 1 19 A 18 A 48 -0.751 A_G18:C48_A 10 -2.695 -0.180 0.251 -0.105 0.475 1 8 A 19 A 47 -18.628 A_G19:A47_A 11 2.152 0.535 0.302 1.447 7.135 1 20 A 20 A 45 9.313 A_U20:A45_A 12 6.325 0.024 0.657 -0.205 -9.304 A 35 A 24 -25.914 A_A35:C24_A 13 2.098 -4.545 -0.016 -1.745 -5.501 1 19 A 36 A 23 2.397 A_G36:C23_A 14 7.446 -0.163 -0.206 -0.102 -5.393 1 19 A 37 A 22 4.029 A_G37:C22_A 15 -1.345 -0.190 0.321 -0.137 -4.877 1 19 A 38 A 21 -2.162 A_C38:G21_A 16 8.980 0.163 0.590 -0.189 6.038 4 24 A 39 A 43 -97.356 A_U39:A43_A 17 5.262 4.096 0.604 -2.027 -17.159 A 53 A 84 165.488 A_A53:A84_A 18 15.119 6.579 0.027 -5.726 -0.661 10 11 A 56 A 83 -6.769 A_A56:G83_A 19 -5.089 -6.691 -0.671 -4.032 2.272 1 19 A 57 A 82 1.194 A_C57:G82_A 20 -7.006 0.179 -0.445 -0.136 -1.784 1 19 A 58 A 81 -0.051 A_C58:G81_A 21 2.801 0.159 -0.003 -0.140 3.234 1 20 A 59 A 80 0.440 A_U59:A80_A 22 4.755 -0.103 0.016 -0.102 -19.761 3 6 A 60 A 78 -88.529 A_G60:G78_A 23 1.109 1.081 -0.374 3.758 9.817 2 A 61 A 77 110.952 A_A61:C77_A 24 3.866 -1.131 1.323 1.177 -6.933 1 19 A 63 A 76 1.840 A_C63:G76_A 25 1.260 0.178 -0.294 -0.172 0.140 1 20 A 64 A 75 4.038 A_U64:A75_A 26 -2.845 -0.037 0.371 -0.155 -0.778 1 19 A 65 A 74 1.849 A_G65:C74_A 27 1.992 -0.190 0.358 -0.169 0.847 1 A 66 A 73 12.159 A_G66:C73_A 28 -1.655 0.028 -0.794 0.518 3.132 36.035 A A 9 10 -0.470 A A 90 89 3.120 -0.291 -0.155 -1.313 AA_G9C10:G89C90_AA 1 -0.549 0.888 36.030 -2.083 0.176 2.046 33.577 A A 10 11 24.502 A A 89 88 3.002 13.760 -0.371 -1.769 AA_C10G11:C88G89_AA 2 -0.263 0.468 30.701 -4.886 0.607 3.384 33.720 A A 11 12 2.674 A A 88 87 3.406 1.549 -0.647 -1.296 AA_G11A12:U87C88_AA 3 -2.611 4.507 33.587 -2.496 0.675 3.077 35.612 A A 12 13 3.297 A A 87 86 3.142 2.014 -0.293 -1.310 AA_A12C13:G86U87_AA 4 -2.198 3.598 35.491 -2.421 0.175 3.116 30.274 A A 13 14 4.549 A A 86 85 3.198 2.370 0.236 -1.058 AA_C13U14:A85G86_AA 5 2.638 -5.062 30.071 -2.489 0.065 2.877 42.702 A A 14 15 11.712 A A 85 51 3.127 8.476 1.053 -0.982 AA_U14C15:G51A85_AA 6 -0.293 0.405 41.890 -2.138 -1.473 2.878 29.622 A A 15 16 13.564 A A 51 50 3.319 6.872 0.780 -1.695 AA_C15G16:C50G51_AA 7 1.335 -2.635 28.801 -4.710 -1.255 3.139 36.404 A A 16 17 6.558 A A 50 49 3.265 4.081 -0.782 -1.589 AA_G16G17:C49C50_AA 8 -4.067 6.536 35.960 -3.102 0.695 2.764 32.239 A A 17 18 10.785 A A 49 48 3.065 5.955 0.058 -1.379 AA_G17G18:C48C49_AA 9 -0.940 1.703 31.685 -3.436 -0.256 2.994 38.328 A A 18 19 3.668 A A 48 47 3.143 2.405 -1.312 -0.869 AA_G18G19:A47C48_AA 10 2.559 -3.903 38.173 -1.606 2.299 1.625 -9.023 A A 19 20 -67.183 A A 47 45 3.334 8.302 -0.304 -0.395 AA_G19U20:A45A47_AA 11 -0.680 -5.501 -3.473 -18.416 -3.649 2.806 48.959 A A 35 36 7.126 A A 24 23 3.282 5.875 2.182 -1.184 AA_A35G36:C23C24_AA 12 -6.958 8.439 48.155 -1.846 -3.128 2.465 33.393 A A 36 37 15.272 A A 23 22 3.072 8.641 -0.290 -2.033 AA_G36G37:C22C23_AA 13 -5.572 9.849 31.813 -4.782 -0.297 2.761 42.169 A A 37 38 13.787 A A 22 21 3.217 9.833 -0.896 -1.844 AA_G37C38:G21C22_AA 14 -1.925 2.699 41.014 -3.501 1.061 2.671 72.889 A A 38 39 4.110 A A 21 43 3.085 4.871 -3.089 -0.958 AA_C38U39:A43G21_AA 15 9.160 -7.730 72.249 -0.946 2.864 1.341 -166.300 A A 53 56 44.822 A A 84 83 -0.330 -82.878 -2.757 -2.098 AA_A53A56:G83A84_AA 16 144.176 77.974 -1.017 1.308 -0.951 3.572 60.743 A A 56 57 -1.029 A A 83 82 3.569 -1.040 0.407 -0.719 AA_A56C57:G82G83_AA 17 -1.101 1.089 60.726 -0.657 -0.460 3.019 37.535 A A 57 58 10.774 A A 82 81 3.344 6.881 -0.501 -1.736 AA_C57C58:G81G82_AA 18 -4.480 7.015 36.658 -3.583 0.202 2.899 36.053 A A 58 59 7.057 A A 81 80 3.061 4.357 0.603 -1.314 AA_C58U59:A80G81_AA 19 0.870 -1.410 35.787 -2.687 -0.861 3.108 92.189 A A 59 60 6.928 A A 80 78 2.809 9.903 2.646 -1.975 AA_U59G60:G78A80_AA 20 23.622 -16.525 89.341 -1.547 -1.417 1.520 177.825 A A 60 61 85.963 A A 78 77 1.860 171.406 -3.260 -0.986 AA_G60A61:C77G78_AA 21 -36.648 18.380 125.104 -0.897 1.544 -1.131 161.536 A A 61 63 -70.867 A A 77 76 -0.382 -127.324 -3.580 -1.366 AA_A61C63:G76C77_AA 22 99.408 -55.329 1.138 -1.290 1.347 2.329 35.604 A A 63 64 15.145 A A 76 75 2.921 9.108 -0.530 -2.200 AA_C63U64:A75G76_AA 23 -6.803 11.313 33.796 -4.692 0.051 2.509 37.598 A A 64 65 16.631 A A 75 74 3.021 10.584 -0.689 -1.489 AA_U64G65:C74A75_AA 24 -0.442 0.694 36.127 -3.501 1.020 3.116 34.334 A A 65 66 6.801 A A 74 73 3.268 3.964 0.889 -2.223 AA_G65G66:C73C74_AA 25 8.830 -15.151 32.982 -4.385 -0.128 chem_comp_atom chem_comp_bond pdbx_initial_refinement_model repository Initial release Data collection Refinement description 1 0 2022-05-25 1 1 2023-10-18 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01GM112940 Alexander.Serganov@nyulangone.org 0000-0001-8328-9310 Alexande Serganov principal investigator/group leader N RCSB Y RCSB 2022-02-16 REL REL KXC KXC SUBJECT OF INVESTIGATION MN MANGANESE (II) ION MG MAGNESIUM ION KXC 6-methylquinoxaline 562 Escherichia coli sample 1 83 Y 2HOJ PDB experimental model MN 102 2 MN MN 101 A MN 103 2 MN MN 102 A MG 104 3 MG MG 103 A KXC 101 4 KXC KXC 104 A G 9 n 1 G 9 A C 10 n 2 C 10 A G 11 n 3 G 11 A A 12 n 4 A 12 A C 13 n 5 C 13 A U 14 n 6 U 14 A C 15 n 7 C 15 A G 16 n 8 G 16 A G 17 n 9 G 17 A G 18 n 10 G 18 A G 19 n 11 G 19 A U 20 n 12 U 20 A G 21 n 13 G 21 A C 22 n 14 C 22 A C 23 n 15 C 23 A C 24 n 16 C 24 A U 25 n 17 U 25 A n 18 26 A n 19 27 A n 20 28 A n 21 29 A C 30 n 22 C 30 A G 31 n 23 G 31 A U 32 n 24 U 32 A G 33 n 25 G 33 A A 34 n 26 A 34 A A 35 n 27 A 35 A G 36 n 28 G 36 A G 37 n 29 G 37 A C 38 n 30 C 38 A U 39 n 31 U 39 A G 40 n 32 G 40 A A 41 n 33 A 41 A G 42 n 34 G 42 A A 43 n 35 A 43 A A 44 n 36 A 44 A A 45 n 37 A 45 A U 46 n 38 U 46 A A 47 n 39 A 47 A C 48 n 40 C 48 A C 49 n 41 C 49 A C 50 n 42 C 50 A G 51 n 43 G 51 A U 52 n 44 U 52 A A 53 n 45 A 53 A U 54 n 46 U 54 A C 55 n 47 C 55 A A 56 n 48 A 56 A C 57 n 49 C 57 A C 58 n 50 C 58 A U 59 n 51 U 59 A G 60 n 52 G 60 A A 61 n 53 A 61 A U 62 n 54 U 62 A C 63 n 55 C 63 A U 64 n 56 U 64 A G 65 n 57 G 65 A G 66 n 58 G 66 A A 67 n 59 A 67 A U 68 n 60 U 68 A A 69 n 61 A 69 A A 70 n 62 A 70 A U 71 n 63 U 71 A G 72 n 64 G 72 A C 73 n 65 C 73 A C 74 n 66 C 74 A A 75 n 67 A 75 A G 76 n 68 G 76 A C 77 n 69 C 77 A G 78 n 70 G 78 A U 79 n 71 U 79 A A 80 n 72 A 80 A G 81 n 73 G 81 A G 82 n 74 G 82 A G 83 n 75 G 83 A A 84 n 76 A 84 A A 85 n 77 A 85 A G 86 n 78 G 86 A U 87 n 79 U 87 A C 88 n 80 C 88 A G 89 n 81 G 89 A C 90 n 82 C 90 A A 91 n 83 A 91 A 0.136576582032 0.129360935303 0.0255139561372 0.203406248141 -0.044277780593 0.132181880406 0.0658325078211 0.0817506027434 0.252618332053 -0.868636280827 -0.0122083471605 0.42858067413 0.139212427147 0.46613622091 -0.00000000217129811337 0.685663005776 -0.412798219492 -0.0649324666564 0.00529678218144 0.0520193013509 0.251497051157 refined -8.30212374089 16.841211741 5.43754207531 X-RAY DIFFRACTION A 9 A D 1 E X-RAY DIFFRACTION 1 all author_defined_assembly 1 monomeric none A G 40 A N7 G 32 1_555 A MN 102 C MN MN 1_555 A G 40 A O6 G 32 1_555 78.3 A A 69 A OP1 A 61 1_555 A MG 103 D MG MG 4_555 A A 91 A O3' A 83 1_555 65.4 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 P C 30 A P C 22 1 Y 1 A OP1 C 30 A OP1 C 22 1 Y 1 A OP2 C 30 A OP2 C 22 1 Y 1 A O5' C 30 A O5' C 22 1 Y 1 A N1 U 46 A N1 U 38 1 Y 1 A C2 U 46 A C2 U 38 1 Y 1 A O2 U 46 A O2 U 38 1 Y 1 A N3 U 46 A N3 U 38 1 Y 1 A C4 U 46 A C4 U 38 1 Y 1 A O4 U 46 A O4 U 38 1 Y 1 A C5 U 46 A C5 U 38 1 Y 1 A C6 U 46 A C6 U 38 1 Y 1 A C2 U 54 A C2 U 46 1 Y 1 A O2 U 54 A O2 U 46 1 Y 1 A N3 U 54 A N3 U 46 1 Y 1 A C4 U 54 A C4 U 46 1 Y 1 A O4 U 54 A O4 U 46 1 Y 1 A C5 U 54 A C5 U 46 1 Y 1 A C6 U 54 A C6 U 46 1 Y 1 A N1 C 55 A N1 C 47 1 Y 1 A C2 C 55 A C2 C 47 1 Y 1 A O2 C 55 A O2 C 47 1 Y 1 A N3 C 55 A N3 C 47 1 Y 1 A C4 C 55 A C4 C 47 1 Y 1 A N4 C 55 A N4 C 47 1 Y 1 A C5 C 55 A C5 C 47 1 Y 1 A C6 C 55 A C6 C 47 1 Y 1 A N1 U 62 A N1 U 54 1 Y 1 A C2 U 62 A C2 U 54 1 Y 1 A O2 U 62 A O2 U 54 1 Y 1 A N3 U 62 A N3 U 54 1 Y 1 A C4 U 62 A C4 U 54 1 Y 1 A O4 U 62 A O4 U 54 1 Y 1 A C5 U 62 A C5 U 54 1 Y 1 A C6 U 62 A C6 U 54 1 Y 1 A N1 KXC 104 E N1 KXC 1 1 N 1 A C1 KXC 104 E C1 KXC 1 1 N 1 A C2 KXC 104 E C2 KXC 1 1 N 1 A N4 KXC 104 E N4 KXC 1 1 N 1 A C3 KXC 104 E C3 KXC 1 1 N 1 A C13 KXC 104 E C13 KXC 1 1 N 1 A U 26 A U 18 1 Y 1 A C 27 A C 19 1 Y 1 A U 28 A U 20 1 Y 1 A G 29 A G 21 1 Y 1 A A O2 N6 C A 24 35 2.19 115.66 0.2570 0.2434 0.2445 2.96 47.00 4715 7902 4715 9.93 98.19 0.3197 1 FREE R-VALUE 1.36 MOLECULAR REPLACEMENT 36.9635 0.9000 1.1100 2HOJ GeoStd + Monomer Library + CDL v1.2 FLAT BULK SOLVENT MODEL 2.96 47.00 0 1669 14 1655 0 0.0020 1863 0.6046 2901 0.0326 390 0.0048 76 16.6256 935 0.4597 0.3918 3.15 137 1265 93.97 0.3902 0.3215 3.39 150 1338 98.61 0.2664 0.2914 3.73 143 1299 97.90 0.3005 0.2604 4.27 152 1315 99.12 0.2515 0.2382 5.38 156 1328 100.00 0.2074 0.2030 47.00 133 1357 99.53 97.50 2.93 50.0 7TZT 4715 0.995 0.130 0.044 1 304.8 10.0 99.9 3.612 2.93 2.98 5.5 238 0.637 1.140 1 10.6 100 refinement PHENIX 1.14-3260 data scaling HKL-2000 data reduction HKL-2000 phasing PHASER 1.14_3260 model building Coot 0.8.9.1 153 trigonal P 32 1 2 P 32 2 (x,y,z+1/6) x,y,z -y,x-y,z+2/3 -x+y,-x,z+1/3 -y,-x,-z+1/3 -x+y,y,-z+2/3 x,x-y,-z N Crystal structure of the E. coli thiM riboswitch in complex with N1,N1-dimethyl-N2-(quinoxalin-6-ylmethyl)ethane-1,2-diamine (linked compound 37) 1 N N 2 N N 2 N N 3 N N 4 N N metalc 2.045 A G 40 A N7 G 32 1_555 A MN 102 C MN MN 1_555 metalc 2.786 A G 40 A O6 G 32 1_555 A MN 102 C MN MN 1_555 metalc 2.026 A A 41 A N7 A 33 1_555 A MN 101 B MN MN 1_555 metalc 2.372 A A 69 A OP1 A 61 1_555 A MG 103 D MG MG 4_555 metalc 2.245 A A 91 A O3' A 83 1_555 A MG 103 D MG MG 1_555 hydrog WATSON-CRICK A G 9 A N1 G 1 1_555 A C 90 A N3 C 82 1_555 hydrog WATSON-CRICK A G 9 A N2 G 1 1_555 A C 90 A O2 C 82 1_555 hydrog WATSON-CRICK A G 9 A O6 G 1 1_555 A C 90 A N4 C 82 1_555 hydrog WATSON-CRICK A C 10 A N3 C 2 1_555 A G 89 A N1 G 81 1_555 hydrog WATSON-CRICK A C 10 A N4 C 2 1_555 A G 89 A O6 G 81 1_555 hydrog WATSON-CRICK A C 10 A O2 C 2 1_555 A G 89 A N2 G 81 1_555 hydrog WATSON-CRICK A G 11 A N1 G 3 1_555 A C 88 A N3 C 80 1_555 hydrog WATSON-CRICK A G 11 A N2 G 3 1_555 A C 88 A O2 C 80 1_555 hydrog WATSON-CRICK A G 11 A O6 G 3 1_555 A C 88 A N4 C 80 1_555 hydrog WATSON-CRICK A A 12 A N1 A 4 1_555 A U 87 A N3 U 79 1_555 hydrog WATSON-CRICK A A 12 A N6 A 4 1_555 A U 87 A O4 U 79 1_555 hydrog WATSON-CRICK A C 13 A N3 C 5 1_555 A G 86 A N1 G 78 1_555 hydrog WATSON-CRICK A C 13 A N4 C 5 1_555 A G 86 A O6 G 78 1_555 hydrog WATSON-CRICK A C 13 A O2 C 5 1_555 A G 86 A N2 G 78 1_555 hydrog WATSON-CRICK A U 14 A N3 U 6 1_555 A A 85 A N1 A 77 1_555 hydrog WATSON-CRICK A U 14 A O4 U 6 1_555 A A 85 A N6 A 77 1_555 hydrog WATSON-CRICK A C 15 A N3 C 7 1_555 A G 51 A N1 G 43 1_555 hydrog WATSON-CRICK A C 15 A N4 C 7 1_555 A G 51 A O6 G 43 1_555 hydrog WATSON-CRICK A C 15 A O2 C 7 1_555 A G 51 A N2 G 43 1_555 hydrog WATSON-CRICK A G 16 A N1 G 8 1_555 A C 50 A N3 C 42 1_555 hydrog WATSON-CRICK A G 16 A N2 G 8 1_555 A C 50 A O2 C 42 1_555 hydrog WATSON-CRICK A G 16 A O6 G 8 1_555 A C 50 A N4 C 42 1_555 hydrog G-A MISPAIR A G 16 A N2 G 8 1_555 A A 84 A N3 A 76 1_555 hydrog WATSON-CRICK A G 17 A N1 G 9 1_555 A C 49 A N3 C 41 1_555 hydrog WATSON-CRICK A G 17 A N2 G 9 1_555 A C 49 A O2 C 41 1_555 hydrog WATSON-CRICK A G 17 A O6 G 9 1_555 A C 49 A N4 C 41 1_555 hydrog G-A MISPAIR A G 17 A N2 G 9 1_555 A A 56 A N3 A 48 1_555 hydrog WATSON-CRICK A G 18 A N1 G 10 1_555 A C 48 A N3 C 40 1_555 hydrog WATSON-CRICK A G 18 A N2 G 10 1_555 A C 48 A O2 C 40 1_555 hydrog WATSON-CRICK A G 18 A O6 G 10 1_555 A C 48 A N4 C 40 1_555 hydrog TYPE_4_PAIR A G 19 A N2 G 11 1_555 A G 42 A N3 G 34 1_555 hydrog TYPE_4_PAIR A G 19 A N3 G 11 1_555 A G 42 A N2 G 34 1_555 hydrog TYPE_8_PAIR A G 19 A N1 G 11 1_555 A A 47 A N1 A 39 1_555 hydrog TYPE_8_PAIR A G 19 A O6 G 11 1_555 A A 47 A N6 A 39 1_555 hydrog WATSON-CRICK A U 20 A N3 U 12 1_555 A A 45 A N1 A 37 1_555 hydrog WATSON-CRICK A U 20 A O4 U 12 1_555 A A 45 A N6 A 37 1_555 hydrog WATSON-CRICK A G 21 A N1 G 13 1_555 A C 38 A N3 C 30 1_555 hydrog WATSON-CRICK A G 21 A N2 G 13 1_555 A C 38 A O2 C 30 1_555 hydrog WATSON-CRICK A G 21 A O6 G 13 1_555 A C 38 A N4 C 30 1_555 hydrog G-U MISPAIR A G 21 A N2 G 13 1_555 A U 71 A O2 U 63 1_555 hydrog WATSON-CRICK A C 22 A N3 C 14 1_555 A G 37 A N1 G 29 1_555 hydrog WATSON-CRICK A C 22 A N4 C 14 1_555 A G 37 A O6 G 29 1_555 hydrog WATSON-CRICK A C 22 A O2 C 14 1_555 A G 37 A N2 G 29 1_555 hydrog WATSON-CRICK A C 23 A N3 C 15 1_555 A G 36 A N1 G 28 1_555 hydrog WATSON-CRICK A C 23 A N4 C 15 1_555 A G 36 A O6 G 28 1_555 hydrog WATSON-CRICK A C 23 A O2 C 15 1_555 A G 36 A N2 G 28 1_555 hydrog C-A MISPAIR A C 24 A N3 C 16 1_555 A A 35 A N6 A 27 1_555 hydrog REVERSED HOOGSTEEN A U 39 A N3 U 31 1_555 A A 43 A N7 A 35 1_555 hydrog REVERSED HOOGSTEEN A U 39 A O2 U 31 1_555 A A 43 A N6 A 35 1_555 hydrog A-A MISPAIR A A 53 A N7 A 45 1_555 A A 84 A N6 A 76 1_555 hydrog TYPE_11_PAIR A A 56 A N6 A 48 1_555 A G 83 A N3 G 75 1_555 hydrog TYPE_11_PAIR A A 56 A N7 A 48 1_555 A G 83 A N2 G 75 1_555 hydrog WATSON-CRICK A C 57 A N3 C 49 1_555 A G 82 A N1 G 74 1_555 hydrog WATSON-CRICK A C 57 A N4 C 49 1_555 A G 82 A O6 G 74 1_555 hydrog WATSON-CRICK A C 57 A O2 C 49 1_555 A G 82 A N2 G 74 1_555 hydrog WATSON-CRICK A C 58 A N3 C 50 1_555 A G 81 A N1 G 73 1_555 hydrog WATSON-CRICK A C 58 A N4 C 50 1_555 A G 81 A O6 G 73 1_555 hydrog WATSON-CRICK A C 58 A O2 C 50 1_555 A G 81 A N2 G 73 1_555 hydrog WATSON-CRICK A U 59 A N3 U 51 1_555 A A 80 A N1 A 72 1_555 hydrog WATSON-CRICK A U 59 A O4 U 51 1_555 A A 80 A N6 A 72 1_555 hydrog G-G MISPAIR A G 60 A O6 G 52 1_555 A G 72 A N1 G 64 1_555 hydrog TYPE_6_PAIR A G 60 A N1 G 52 1_555 A G 78 A O6 G 70 1_555 hydrog TYPE_6_PAIR A G 60 A N2 G 52 1_555 A G 78 A N7 G 70 1_555 hydrog A-C MISPAIR A A 61 A N6 A 53 1_555 A C 77 A O2 C 69 1_555 hydrog WATSON-CRICK A C 63 A N3 C 55 1_555 A G 76 A N1 G 68 1_555 hydrog WATSON-CRICK A C 63 A N4 C 55 1_555 A G 76 A O6 G 68 1_555 hydrog WATSON-CRICK A C 63 A O2 C 55 1_555 A G 76 A N2 G 68 1_555 hydrog WATSON-CRICK A U 64 A N3 U 56 1_555 A A 75 A N1 A 67 1_555 hydrog WATSON-CRICK A U 64 A O4 U 56 1_555 A A 75 A N6 A 67 1_555 hydrog WATSON-CRICK A G 65 A N1 G 57 1_555 A C 74 A N3 C 66 1_555 hydrog WATSON-CRICK A G 65 A N2 G 57 1_555 A C 74 A O2 C 66 1_555 hydrog WATSON-CRICK A G 65 A O6 G 57 1_555 A C 74 A N4 C 66 1_555 hydrog G-C PAIR A G 66 A N2 G 58 1_555 A C 73 A O2 C 65 1_555 RNA thiM TPP riboswitch, RNA 7TZT PDB 1 1 7TZT 9 91 7TZT 9 91 7TZT A 1 1 83 153 P 32 1 2 P 32 2 (x,y,z+1/6)