0.041203 0.000000 0.000000 0.000000 0.025240 0.000000 0.000000 0.000000 0.015731 0.00000 0.00000 0.00000 Goodsell, D.S. Kopka, M.L. Dickerson, R.E. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 24.270 39.620 63.570 C9 H13 Br N3 O7 P 386.093 n 5-BROMO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE DNA 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 H2 O 18.015 WATER non-polymer Mg 2 24.305 MAGNESIUM ION non-polymer C18 H26 N10 O3 430.464 NETROPSIN non-polymer N 1 N BR N 2 N P N 3 N O N 4 N O N 5 N O N 6 N N N 7 N C N 8 N C N 9 N O N 10 N N N 11 N C N 12 N N N 13 N C N 14 N C N 15 N C N 16 R C N 17 N O N 18 R C N 19 S C N 20 N O N 21 N O N 22 N H N 23 N H 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 O N 36 N P N 37 N O N 38 N O N 39 N O N 40 N C N 41 R C N 42 N O N 43 S C N 44 N O N 45 N C N 46 R C Y 47 N N Y 48 N C Y 49 N N Y 50 N C Y 51 N C N 52 N N Y 53 N N Y 54 N C Y 55 N N Y 56 N C 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 H N 68 N H N 69 N H N 70 N H N 71 N O N 72 N P N 73 N O N 74 N O N 75 N O N 76 N C N 77 R C N 78 N O N 79 S C N 80 N O N 81 N C N 82 R C N 83 N N N 84 N C N 85 N O N 86 N N N 87 N C N 88 N N N 89 N C N 90 N C 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 H N 103 N H N 104 N H N 105 N O N 106 N P N 107 N O N 108 N O N 109 N O N 110 N C N 111 R C N 112 N O N 113 S C N 114 N O N 115 N C N 116 R C Y 117 N N Y 118 N C Y 119 N N Y 120 N C N 121 N C N 122 N O N 123 N N N 124 N C N 125 N N N 126 N N Y 127 N C 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 H N 141 N H N 142 N O N 143 N P N 144 N O N 145 N O N 146 N O N 147 N C N 148 R C N 149 N O N 150 S C N 151 N O N 152 N C N 153 R C N 154 N N N 155 N C N 156 N O N 157 N N N 158 N C N 159 N O N 160 N C N 161 N C N 162 N C N 163 N H N 164 N H 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 178 N O N 179 N H N 180 N H N 181 N MG N 182 N C N 183 N N N 184 N N N 185 N N N 186 N C N 187 N C N 188 N O N 189 N N Y 190 N C Y 191 N C Y 192 N C Y 193 N N N 194 N C Y 195 N C N 196 N C N 197 N O N 198 N N Y 199 N C Y 200 N C Y 201 N C Y 202 N N N 203 N C Y 204 N C N 205 N C N 206 N O N 207 N N N 208 N C N 209 N C N 210 N C N 211 N N N 212 N N N 213 N H N 214 N H N 215 N H N 216 N H 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 H N 233 N H N 234 N H N 235 N H N 236 N H N 237 N H N 238 N H N 1 N sing N 2 N doub N 3 N sing 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 doub N 12 N sing N 13 N doub N 14 N sing N 15 N doub 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 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 sing N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N doub 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 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 Y 59 N sing Y 60 N sing Y 61 N doub N 62 N sing Y 63 N sing Y 64 N sing Y 65 N doub N 66 N sing Y 67 N doub N 68 N sing N 69 N sing Y 70 N sing Y 71 N doub N 72 N sing Y 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 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 doub N 100 N sing N 101 N doub N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N doub N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N doub 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 N 131 N sing Y 132 N sing Y 133 N sing Y 134 N doub N 135 N sing Y 136 N sing N 137 N sing Y 138 N doub N 139 N doub N 140 N sing N 141 N sing N 142 N sing N 143 N sing N 144 N doub N 145 N sing N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N doub N 151 N sing 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 doub N 174 N sing N 175 N sing N 176 N sing N 177 N doub N 178 N sing N 179 N sing N 180 N doub N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N doub N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N doub N 199 N sing N 200 N sing N 201 N sing Y 202 N sing Y 203 N doub Y 204 N doub N 205 N sing Y 206 N sing N 207 N sing N 208 N sing Y 209 N sing N 210 N sing N 211 N sing N 212 N sing N 213 N sing N 214 N doub N 215 N sing N 216 N sing N 217 N sing Y 218 N sing Y 219 N doub Y 220 N doub N 221 N sing Y 222 N sing N 223 N sing N 224 N sing Y 225 N sing N 226 N sing N 227 N sing N 228 N sing N 229 N sing N 230 N doub 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 doub N 241 N sing N 242 N sing N 243 N sing N 244 N sing US Biochemistry BICHAW 0033 0006-2960 34 4983 4993 10.1021/bi00015a009 7711020 Refinement of netropsin bound to DNA: bias and feedback in electron density map interpretation. 1995 UK J.Mol.Biol. JMOBAK 0070 0022-2836 183 553 563 Binding of an Antitumor Drug to DNA. Netropsin and C-G-C-G-A-A-T-T-BrC-G-C-G 1985 10.2210/pdb101d/pdb pdb_0000101d 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 3742.288 DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(CBR)P*GP*CP*G)-3') 2 syn polymer 24.305 MAGNESIUM ION 1 syn non-polymer 430.464 NETROPSIN 1 syn non-polymer 18.015 water 36 nat water no yes (DC)(DG)(DC)(DG)(DA)(DA)(DT)(DT)(CBR)(DG)(DC)(DG) CGCGAATTCGCG A,B polydeoxyribonucleotide n n n n n n n n n n n n 2.00 38.45 2.891 1 19 A 1 B 24 -0.588 A_DC1:DG24_B 1 -17.827 0.147 -0.114 -0.208 -3.485 1 19 A 2 B 23 -3.444 A_DG2:DC23_B 2 -15.195 -0.027 0.219 -0.267 -4.972 1 19 A 3 B 22 -0.364 A_DC3:DG22_B 3 -6.435 0.096 0.286 -0.177 9.060 1 19 A 4 B 21 1.060 A_DG4:CBR21_B 4 -7.744 -0.217 0.018 0.056 6.129 1 20 A 5 B 20 7.183 A_DA5:DT20_B 5 -20.556 0.430 -0.317 -0.075 3.511 1 20 A 6 B 19 1.086 A_DA6:DT19_B 6 -18.034 -0.042 0.219 -0.078 0.306 1 20 A 7 B 18 4.024 A_DT7:DA18_B 7 -20.982 0.297 -0.043 -0.067 -14.255 1 20 A 8 B 17 7.034 A_DT8:DA17_B 8 -21.443 -0.239 0.405 -0.312 -9.615 1 19 A 9 B 16 2.726 A_CBR9:DG16_B 9 -11.260 0.246 -0.171 -0.354 6.362 1 19 A 10 B 15 -0.785 A_DG10:DC15_B 10 -2.898 -0.226 0.029 -0.252 9.834 1 19 A 11 B 14 -2.711 A_DC11:DG14_B 11 -21.915 0.749 -0.044 -0.370 -6.288 1 19 A 12 B 13 -7.468 A_DG12:DC13_B 12 10.370 0.385 -0.668 -0.273 3.577 34.297 A A 1 2 15.156 B B 24 23 3.615 8.830 -0.183 0.304 AA_DC1DG2:DC23DG24_BB 1 -3.280 5.631 33.016 -1.039 -0.268 3.195 42.837 A A 2 3 -13.357 B B 23 22 3.312 -9.673 0.953 0.420 AA_DG2DC3:DG22DC23_BB 2 2.698 -3.726 41.697 1.548 -1.034 3.134 28.476 A A 3 4 4.267 B B 22 21 3.187 2.081 -0.097 0.731 AA_DC3DG4:CBR21DG22_BB 3 6.284 -12.889 27.711 1.019 1.606 3.286 42.793 A A 4 5 7.497 B B 21 20 3.290 5.455 0.072 0.168 AA_DG4DA5:DT20CBR21_BB 4 1.938 -2.663 42.418 -0.320 0.097 3.177 34.135 A A 5 6 10.030 B B 20 19 3.248 5.814 -0.375 -0.181 AA_DA5DA6:DT19DT20_BB 5 -7.525 12.981 32.821 -1.233 -0.556 3.323 33.154 A A 6 7 -2.856 B B 19 18 3.304 -1.629 -0.205 -0.604 AA_DA6DT7:DA18DT19_BB 6 0.855 -1.500 33.104 -0.782 0.504 3.584 36.800 A A 7 8 2.976 B B 18 17 3.581 1.878 0.275 0.044 AA_DT7DT8:DA17DA18_BB 7 0.973 -1.542 36.741 -0.210 -0.290 3.276 41.760 A A 8 9 1.237 B B 17 16 3.269 0.879 0.217 0.648 AA_DT8CBR9:DG16DA17_BB 8 6.578 -9.264 41.253 0.816 0.391 3.204 27.242 A A 9 10 12.155 B B 16 15 3.089 5.641 -0.017 1.216 AA_CBR9DG10:DC15DG16_BB 9 -5.850 12.606 26.024 1.192 -1.404 3.011 47.399 A A 10 11 -13.387 B B 15 14 3.282 -10.675 -0.565 1.027 AA_DG10DC11:DG14DC15_BB 10 -2.375 2.978 46.191 2.121 0.515 3.948 38.792 A A 11 12 -13.358 B B 14 13 4.200 -8.775 0.449 0.791 AA_DC11DG12:DC13DG14_BB 11 5.297 -8.064 37.464 2.551 0.145 chem_comp_atom chem_comp_bond database_2 pdbx_struct_conn_angle struct_conn struct_conn_type struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 1995-02-27 1 1 2008-05-22 1 2 2011-07-13 1 3 2023-11-22 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.value _struct_conn.conn_type_id _struct_conn.id _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn_type.id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id BNL Y NDB 1994-12-14 REL MG MAGNESIUM ION NT NETROPSIN HOH water MO3 26 2 MG MG 26 A NT 25 3 NT NT 25 B HOH 27 4 HOH HOH 27 A HOH 28 4 HOH HOH 28 A HOH 33 4 HOH HOH 33 A HOH 34 4 HOH HOH 34 A HOH 35 4 HOH HOH 35 A HOH 39 4 HOH HOH 39 A HOH 44 4 HOH HOH 44 A HOH 46 4 HOH HOH 46 A HOH 48 4 HOH HOH 48 A HOH 52 4 HOH HOH 52 A HOH 53 4 HOH HOH 53 A HOH 54 4 HOH HOH 54 A HOH 59 4 HOH HOH 59 A MO3 26 4 HOH HOH 61 A HOH 29 4 HOH HOH 29 B HOH 30 4 HOH HOH 30 B HOH 31 4 HOH HOH 31 B HOH 32 4 HOH HOH 32 B HOH 36 4 HOH HOH 36 B HOH 37 4 HOH HOH 37 B HOH 38 4 HOH HOH 38 B HOH 40 4 HOH HOH 40 B HOH 41 4 HOH HOH 41 B HOH 42 4 HOH HOH 42 B HOH 43 4 HOH HOH 43 B HOH 45 4 HOH HOH 45 B HOH 47 4 HOH HOH 47 B HOH 49 4 HOH HOH 49 B HOH 50 4 HOH HOH 50 B HOH 51 4 HOH HOH 51 B HOH 55 4 HOH HOH 55 B HOH 56 4 HOH HOH 56 B HOH 57 4 HOH HOH 57 B HOH 58 4 HOH HOH 58 B MO3 26 4 HOH HOH 60 B MO3 26 4 HOH HOH 62 B C 1 n 1 DC 1 A G 2 n 2 DG 2 A C 3 n 3 DC 3 A G 4 n 4 DG 4 A A 5 n 5 DA 5 A A 6 n 6 DA 6 A T 7 n 7 DT 7 A T 8 n 8 DT 8 A C 9 n 9 CBR 9 A G 10 n 10 DG 10 A C 11 n 11 DC 11 A G 12 n 12 DG 12 A C 13 n 1 DC 13 B G 14 n 2 DG 14 B C 15 n 3 DC 15 B G 16 n 4 DG 16 B A 17 n 5 DA 17 B A 18 n 6 DA 18 B T 19 n 7 DT 19 B T 20 n 8 DT 20 B C 21 n 9 CBR 21 B G 22 n 10 DG 22 B C 23 n 11 DC 23 B G 24 n 12 DG 24 B author_defined_assembly 2 dimeric A HOH 61 E O HOH 1_555 A MG 26 C MG MG 1_555 B HOH 60 F O HOH 1_555 88.3 A HOH 61 E O HOH 1_555 A MG 26 C MG MG 1_555 B HOH 62 F O HOH 1_555 76.9 B HOH 60 F O HOH 1_555 A MG 26 C MG MG 1_555 B HOH 62 F O HOH 1_555 80.2 A CBR 9 A CBR 9 DC B CBR 21 B CBR 9 DC 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 9.68 1.10 109.80 119.48 A A A C5' C4' O4' DC DC DC 1 1 1 N 1 4.12 0.50 119.90 124.02 A A A C2 N3 C4 DC DC DC 1 1 1 N 1 -5.18 0.40 121.90 116.72 A A A N3 C4 C5 DC DC DC 1 1 1 N 1 7.40 0.70 120.20 127.60 A A A C5 C4 N4 DC DC DC 1 1 1 N 1 -10.62 1.50 119.60 108.98 A A A OP1 P OP2 DG DG DG 2 2 2 N 1 -5.50 0.80 109.40 103.90 A A A O5' C5' C4' DG DG DG 2 2 2 N 1 19.16 1.20 119.70 138.86 A A A C3' O3' P DG DG DC 2 2 3 Y 1 -2.55 0.40 121.90 119.35 A A A N3 C4 C5 DC DC DC 3 3 3 N 1 12.25 1.10 109.80 122.05 A A A C5' C4' O4' DG DG DG 4 4 4 N 1 6.79 0.30 108.30 115.09 A A A O4' C1' N9 DG DG DG 4 4 4 N 1 -4.73 0.60 125.10 120.37 A A A C6 N1 C2 DG DG DG 4 4 4 N 1 4.66 0.60 123.90 128.56 A A A N1 C2 N3 DG DG DG 4 4 4 N 1 3.87 0.50 111.50 115.37 A A A C5 C6 N1 DG DG DG 4 4 4 N 1 -5.28 0.70 119.90 114.62 A A A N3 C2 N2 DG DG DG 4 4 4 N 1 -3.69 0.60 128.60 124.91 A A A C5 C6 O6 DG DG DG 4 4 4 N 1 4.00 0.60 118.60 122.60 A A A C6 N1 C2 DA DA DA 5 5 5 N 1 -3.15 0.50 129.30 126.15 A A A N1 C2 N3 DA DA DA 5 5 5 N 1 8.68 1.20 119.70 128.38 A A A C3' O3' P DA DA DA 5 5 6 Y 1 -5.52 0.70 108.00 102.48 A A A O4' C1' N9 DA DA DA 6 6 6 N 1 3.96 0.60 118.60 122.56 A A A C6 N1 C2 DA DA DA 6 6 6 N 1 -3.05 0.50 117.70 114.65 A A A C5 C6 N1 DA DA DA 6 6 6 N 1 10.09 1.20 119.70 129.79 A A A C3' O3' P DA DA DT 6 6 7 Y 1 -13.42 1.50 119.60 106.18 A A A OP1 P OP2 DT DT DT 7 7 7 N 1 8.52 1.20 110.70 119.22 A A A O5' P OP2 DT DT DT 7 7 7 N 1 -7.65 0.80 109.40 101.75 A A A O5' C5' C4' DT DT DT 7 7 7 N 1 -5.93 0.80 105.90 99.97 A A A O4' C1' C2' DT DT DT 7 7 7 N 1 -6.60 0.60 127.20 120.60 A A A C2 N3 C4 DT DT DT 7 7 7 N 1 5.63 0.60 115.20 120.83 A A A N3 C4 C5 DT DT DT 7 7 7 N 1 14.71 1.20 119.70 134.41 A A A C3' O3' P DT DT DT 7 7 8 Y 1 3.94 0.60 114.60 118.54 A A A N1 C2 N3 DT DT DT 8 8 8 N 1 -4.60 0.60 127.20 122.60 A A A C2 N3 C4 DT DT DT 8 8 8 N 1 3.62 0.60 115.20 118.82 A A A N3 C4 C5 DT DT DT 8 8 8 N 1 -3.82 0.60 119.90 116.08 A A A N3 C4 O4 DT DT DT 8 8 8 N 1 24.02 1.20 119.70 143.72 A A A C3' O3' P DT DT CBR 8 8 9 Y 1 15.63 1.20 119.70 135.33 A A A C3' O3' P CBR CBR DG 9 9 10 Y 1 -10.73 1.50 119.60 108.87 A A A OP1 P OP2 DG DG DG 10 10 10 N 1 18.33 1.60 120.90 139.23 A A A P O5' C5' DG DG DG 10 10 10 N 1 2.75 0.30 108.30 111.05 A A A O4' C1' N9 DG DG DG 10 10 10 N 1 -4.76 0.60 125.10 120.34 A A A C6 N1 C2 DG DG DG 10 10 10 N 1 4.01 0.60 123.90 127.91 A A A N1 C2 N3 DG DG DG 10 10 10 N 1 3.89 0.50 111.50 115.39 A A A C5 C6 N1 DG DG DG 10 10 10 N 1 12.06 1.20 119.70 131.76 A A A C3' O3' P DG DG DC 10 10 11 Y 1 -9.99 1.50 119.60 109.61 A A A OP1 P OP2 DC DC DC 11 11 11 N 1 -4.85 0.70 108.00 103.15 A A A O4' C1' N1 DC DC DC 11 11 11 N 1 -13.02 1.50 119.60 106.58 A A A OP1 P OP2 DG DG DG 12 12 12 N 1 -8.18 0.80 109.40 101.22 A A A O5' C5' C4' DG DG DG 12 12 12 N 1 3.71 0.50 106.80 110.51 A A A O4' C1' C2' DG DG DG 12 12 12 N 1 3.33 0.50 111.90 115.23 A A A C2 N3 C4 DG DG DG 12 12 12 N 1 -4.92 0.80 109.40 104.48 B B B O5' C5' C4' DC DC DC 13 13 13 N 1 -2.46 0.40 121.90 119.44 B B B N3 C4 C5 DC DC DC 13 13 13 N 1 3.81 0.60 118.90 122.71 B B B N1 C2 O2 DC DC DC 13 13 13 N 1 -6.26 0.80 109.40 103.14 B B B O5' C5' C4' DG DG DG 14 14 14 N 1 4.28 0.60 106.00 110.28 B B B O4' C4' C3' DG DG DG 14 14 14 N 1 -6.08 1.00 110.10 104.02 B B B C1' O4' C4' DG DG DG 14 14 14 N 1 13.89 1.20 119.70 133.59 B B B C3' O3' P DG DG DC 14 14 15 Y 1 1.92 0.30 108.30 110.22 B B B O4' C1' N1 DC DC DC 15 15 15 N 1 21.88 1.20 119.70 141.58 B B B C3' O3' P DC DC DG 15 15 16 Y 1 -5.55 0.80 102.40 96.85 B B B C3' C2' C1' DG DG DG 16 16 16 N 1 2.70 0.30 108.30 111.00 B B B O4' C1' N9 DG DG DG 16 16 16 N 1 -4.94 0.60 125.10 120.16 B B B C6 N1 C2 DG DG DG 16 16 16 N 1 3.99 0.50 111.50 115.49 B B B C5 C6 N1 DG DG DG 16 16 16 N 1 -11.36 1.50 119.60 108.24 B B B OP1 P OP2 DA DA DA 17 17 17 N 1 11.98 1.20 110.70 122.68 B B B O5' P OP2 DA DA DA 17 17 17 N 1 6.85 0.60 118.60 125.45 B B B C6 N1 C2 DA DA DA 17 17 17 N 1 -5.55 0.50 129.30 123.75 B B B N1 C2 N3 DA DA DA 17 17 17 N 1 -4.08 0.50 117.70 113.62 B B B C5 C6 N1 DA DA DA 17 17 17 N 1 3.93 0.60 118.60 122.53 B B B N1 C6 N6 DA DA DA 17 17 17 N 1 10.06 1.20 110.70 120.76 B B B O5' P OP1 DA DA DA 18 18 18 N 1 12.06 1.20 115.70 127.76 B B B C5' C4' C3' DA DA DA 18 18 18 N 1 5.20 0.60 118.60 123.80 B B B C6 N1 C2 DA DA DA 18 18 18 N 1 -5.83 0.50 129.30 123.47 B B B N1 C2 N3 DA DA DA 18 18 18 N 1 -3.61 0.50 117.70 114.09 B B B C5 C6 N1 DA DA DA 18 18 18 N 1 7.44 0.60 118.60 126.04 B B B N1 C6 N6 DA DA DA 18 18 18 N 1 -5.70 0.80 109.40 103.70 B B B O5' C5' C4' DT DT DT 19 19 19 N 1 -7.79 1.00 110.10 102.31 B B B C1' O4' C4' DT DT DT 19 19 19 N 1 -4.53 0.60 127.20 122.67 B B B C2 N3 C4 DT DT DT 19 19 19 N 1 -6.18 0.60 119.90 113.72 B B B N3 C4 O4 DT DT DT 19 19 19 N 1 22.28 1.20 119.70 141.98 B B B C3' O3' P DT DT DT 19 19 20 Y 1 11.71 1.90 104.00 115.71 B B B O3' P O5' DT DT DT 19 20 20 Y 1 -6.32 1.00 110.10 103.78 B B B C1' O4' C4' DT DT DT 20 20 20 N 1 -4.92 0.60 127.20 122.28 B B B C2 N3 C4 DT DT DT 20 20 20 N 1 5.17 0.60 115.20 120.37 B B B N3 C4 C5 DT DT DT 20 20 20 N 1 -6.56 0.60 119.90 113.34 B B B N3 C4 O4 DT DT DT 20 20 20 N 1 10.47 1.20 119.70 130.17 B B B C3' O3' P DT DT CBR 20 20 21 Y 1 7.41 1.20 119.70 127.11 B B B C3' O3' P CBR CBR DG 21 21 22 Y 1 -8.07 0.80 102.40 94.33 B B B C3' C2' C1' DG DG DG 22 22 22 N 1 4.53 0.30 108.30 112.83 B B B O4' C1' N9 DG DG DG 22 22 22 N 1 -4.89 0.70 119.90 115.01 B B B N3 C2 N2 DG DG DG 22 22 22 N 1 -4.41 0.60 128.60 124.19 B B B C5 C6 O6 DG DG DG 22 22 22 N 1 -6.20 0.70 108.00 101.80 B B B O4' C1' N1 DC DC DC 23 23 23 N 1 4.41 0.50 119.90 124.31 B B B C2 N3 C4 DC DC DC 23 23 23 N 1 -4.25 0.40 121.90 117.65 B B B N3 C4 C5 DC DC DC 23 23 23 N 1 16.38 1.60 120.90 137.28 B B B P O5' C5' DG DG DG 24 24 24 N 1 -4.68 0.70 108.00 103.32 B B B O4' C1' N9 DG DG DG 24 24 24 N 1 -5.94 0.90 116.20 110.26 B B B N1 C2 N2 DG DG DG 24 24 24 N 1 4.26 0.70 119.90 124.16 B B B N3 C2 N2 DG DG DG 24 24 24 N 1 A A C2' C1' DC DC 1 1 -0.069 0.010 1.518 1.449 N 1 A A O4' C1' DC DC 1 1 0.068 0.011 1.420 1.488 N 1 A A O4' C4' DC DC 1 1 -0.071 0.010 1.446 1.375 N 1 A A N7 C8 DG DG 2 2 -0.038 0.006 1.305 1.267 N 1 A A C2' C1' DC DC 3 3 -0.067 0.010 1.518 1.451 N 1 A A C4' C3' DG DG 4 4 0.061 0.010 1.529 1.590 N 1 A A C2' C1' DA DA 6 6 -0.090 0.010 1.518 1.428 N 1 A A O4' C1' DT DT 7 7 0.067 0.011 1.420 1.487 N 1 A A O4' C4' DT DT 7 7 -0.064 0.010 1.446 1.382 N 1 A A O4' C1' DT DT 8 8 0.072 0.011 1.420 1.492 N 1 A A O3' C3' DT DT 8 8 -0.038 0.006 1.419 1.381 N 1 A A C2' C1' DC DC 11 11 -0.069 0.010 1.518 1.449 N 1 A A O4' C1' DC DC 11 11 0.083 0.011 1.420 1.503 N 1 B B C5' C4' DG DG 14 14 0.050 0.007 1.512 1.562 N 1 B B O4' C1' DG DG 14 14 0.068 0.011 1.420 1.488 N 1 B B O3' C3' DC DC 15 15 -0.039 0.006 1.419 1.380 N 1 B B N7 C8 DA DA 17 17 -0.056 0.007 1.311 1.255 N 1 B B O3' C3' DT DT 19 19 -0.063 0.006 1.419 1.356 N 1 B B C2' C1' DT DT 20 20 -0.069 0.010 1.518 1.449 N 1 B B O4' C4' DG DG 24 24 -0.071 0.010 1.446 1.375 N 0.252 0.163 2.250 8.000 2430 1 2.000 TR isotropic TR isotropic 2.250 8.000 33 556 37 486 0 4.282 6.000 4.990 6.000 5.693 6.000 5.227 6.000 0.024 0.030 0.040 0.040 0.026 0.040 0.057 0.050 0.014 0.020 0.161 0.150 0.093 0.100 0.097 0.100 fix fix refinement NUCLSQ REFINEMENT OF NETROPSIN BOUND TO DNA: BIAS AND FEEDBACK IN ELECTRON DENSITY MAP INTERPRETATION 1 N N 1 N N 2 N N 3 N N 4 N N 4 N N covale 1.624 both A DT 8 A O3' DT 8 1_555 A CBR 9 A P CBR 9 1_555 covale 1.551 both A CBR 9 A O3' CBR 9 1_555 A DG 10 A P DG 10 1_555 covale 1.578 both B DT 20 B O3' DT 8 1_555 B CBR 21 B P CBR 9 1_555 covale 1.595 both B CBR 21 B O3' CBR 9 1_555 B DG 22 B P DG 10 1_555 metalc 2.164 A MG 26 C MG MG 1_555 A HOH 61 E O HOH 1_555 metalc 2.101 A MG 26 C MG MG 1_555 B HOH 60 F O HOH 1_555 metalc 2.110 A MG 26 C MG MG 1_555 B HOH 62 F O HOH 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 24 B N1 DG 12 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 24 B O6 DG 12 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 24 B N2 DG 12 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 B DC 23 B N3 DC 11 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B DC 23 B O2 DC 11 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B DC 23 B N4 DC 11 1_555 hydrog WATSON-CRICK A DC 3 A N3 DC 3 1_555 B DG 22 B N1 DG 10 1_555 hydrog WATSON-CRICK A DC 3 A N4 DC 3 1_555 B DG 22 B O6 DG 10 1_555 hydrog WATSON-CRICK A DC 3 A O2 DC 3 1_555 B DG 22 B N2 DG 10 1_555 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 B CBR 21 B N3 CBR 9 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B CBR 21 B O2 CBR 9 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 B CBR 21 B N4 CBR 9 1_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 B DT 20 B N3 DT 8 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 B DT 20 B O4 DT 8 1_555 hydrog WATSON-CRICK A DA 6 A N1 DA 6 1_555 B DT 19 B N3 DT 7 1_555 hydrog WATSON-CRICK A DA 6 A N6 DA 6 1_555 B DT 19 B O4 DT 7 1_555 hydrog WATSON-CRICK A DT 7 A N3 DT 7 1_555 B DA 18 B N1 DA 6 1_555 hydrog WATSON-CRICK A DT 7 A O4 DT 7 1_555 B DA 18 B N6 DA 6 1_555 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 B DA 17 B N1 DA 5 1_555 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 B DA 17 B N6 DA 5 1_555 hydrog WATSON-CRICK A CBR 9 A N3 CBR 9 1_555 B DG 16 B N1 DG 4 1_555 hydrog WATSON-CRICK A CBR 9 A N4 CBR 9 1_555 B DG 16 B O6 DG 4 1_555 hydrog WATSON-CRICK A CBR 9 A O2 CBR 9 1_555 B DG 16 B N2 DG 4 1_555 hydrog WATSON-CRICK A DG 10 A N1 DG 10 1_555 B DC 15 B N3 DC 3 1_555 hydrog WATSON-CRICK A DG 10 A N2 DG 10 1_555 B DC 15 B O2 DC 3 1_555 hydrog WATSON-CRICK A DG 10 A O6 DG 10 1_555 B DC 15 B N4 DC 3 1_555 hydrog WATSON-CRICK A DC 11 A N3 DC 11 1_555 B DG 14 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 11 A N4 DC 11 1_555 B DG 14 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 11 A O2 DC 11 1_555 B DG 14 B N2 DG 2 1_555 hydrog WATSON-CRICK A DG 12 A N1 DG 12 1_555 B DC 13 B N3 DC 1 1_555 hydrog WATSON-CRICK A DG 12 A N2 DG 12 1_555 B DC 13 B O2 DC 1 1_555 hydrog WATSON-CRICK A DG 12 A O6 DG 12 1_555 B DC 13 B N4 DC 1 1_555 DNA B-DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, MODIFIED, DNA 101D PDB 1 101D 1 12 101D 1 12 101D A 1 1 12 13 24 101D 13 24 101D B 1 1 12 BINDING SITE FOR RESIDUE NT B 25 B NT 25 Software 9 BINDING SITE FOR RESIDUE MG A 26 A MG 26 Software 3 A DA 6 A DA 6 9 1_555 A DT 7 A DT 7 9 1_555 A DT 8 A DT 8 9 1_555 B DA 17 B DA 5 9 1_555 B DA 18 B DA 6 9 1_555 B DT 19 B DT 7 9 1_555 B DT 20 B DT 8 9 1_555 B CBR 21 B CBR 9 9 1_555 B DG 22 B DG 10 9 1_555 A HOH 61 E HOH 3 1_555 B HOH 60 F HOH 3 1_555 B HOH 62 F HOH 3 1_555 19 P 21 21 21