0.031014 0.000000 0.015919 0.000000 0.039445 0.000000 0.000000 0.000000 0.032876 0.000000 0.000000 0.000000 Chiu, T.K. Dickerson, R.E. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 117.17 90.00 32.243 25.352 34.190 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 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 N C N 12 R C Y 13 N N Y 14 N C Y 15 N N Y 16 N C Y 17 N C N 18 N N Y 19 N N Y 20 N C Y 21 N N Y 22 N C 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 H N 36 N H N 37 N O N 38 N P N 39 N O N 40 N O N 41 N O N 42 N C N 43 R C N 44 N O N 45 S C N 46 N O N 47 N C N 48 R C N 49 N N N 50 N C N 51 N O N 52 N N N 53 N C N 54 N N N 55 N C N 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 Y 83 N N Y 84 N C Y 85 N N Y 86 N C N 87 N C N 88 N O N 89 N N N 90 N C N 91 N N N 92 N N Y 93 N C 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 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 N C N 119 R C N 120 N N N 121 N C N 122 N O N 123 N N N 124 N C N 125 N O N 126 N C N 127 N C N 128 N C 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 H N 143 N H N 144 N O N 145 N H N 146 N H N 147 N MG 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 Y 24 N sing Y 25 N sing Y 26 N doub N 27 N sing Y 28 N sing Y 29 N sing Y 30 N doub N 31 N sing Y 32 N doub N 33 N sing N 34 N sing Y 35 N sing Y 36 N doub N 37 N sing Y 38 N sing N 39 N sing N 40 N sing N 41 N doub 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 N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N doub N 65 N sing N 66 N doub N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N doub N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N doub N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N 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 Y 97 N sing Y 98 N sing Y 99 N doub N 100 N sing Y 101 N sing N 102 N sing Y 103 N doub 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 doub 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 N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N doub N 139 N sing N 140 N sing N 141 N sing N 142 N doub N 143 N sing N 144 N sing N 145 N doub N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing UK J.Mol.Biol. JMOBAK 0070 0022-2836 301 915 945 10.1006/jmbi.2000.4012 10966796 1 A crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium. 2000 UK J.Mol.Biol. JMOBAK 0070 0022-2836 292 589 608 10.1006/jmbi.1999.3075 Absence of minor groove monovalent cations in the crosslinked dodecamer CGCGAATTCGCG 1999 10.2210/pdb1en9/pdb pdb_00001en9 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100 1 AREA DETECTOR 1998-11-19 MARRESEARCH SINGLE WAVELENGTH M x-ray 1 0.9500 1.0 X8C NSLS 0.9500 SYNCHROTRON NSLS BEAMLINE X8C 3045.992 DNA (5'-D(*CP*CP*AP*GP*CP*GP*CP*TP*GP*G)-3') 1 syn polymer 24.305 MAGNESIUM ION 6 syn non-polymer 18.015 water 79 nat water no no (DC)(DC)(DA)(DG)(DC)(DG)(DC)(DT)(DG)(DG) CCAGCGCTGG A polydeoxyribonucleotide n n n n n n n n n n 1 2.06 36.88 VAPOR DIFFUSION, SITTING DROP initial concentration in droplet: 0.17 mM dna, 31.40 mM magnesium acetate 0.28 mM streptonigrin, 10-15% MPD, 30% final MPD concentration in reservoir. Solutions were unbuffered, VAPOR DIFFUSION, SITTING DROP, temperature 275.0K 275.0 magnesium acetate 1 streptonigrin 1 MPD 1 MPD 2 -8.229 1 19 A 1 A 10 0.408 A_DC1:DG10_A 1 -12.065 0.200 0.147 -0.109 -1.257 1 19 A 2 A 9 -0.804 A_DC2:DG9_A 2 -8.207 0.238 0.004 -0.151 1.348 1 20 A 3 A 8 1.245 A_DA3:DT8_A 3 -6.641 0.034 0.046 -0.136 8.349 1 19 A 4 A 7 -1.007 A_DG4:DC7_A 4 -7.152 -0.156 0.183 -0.087 11.736 1 19 A 5 A 6 -1.736 A_DC5:DG6_A 5 -16.742 0.338 0.013 -0.185 -11.736 1 19 A 6 A 5 -1.736 A_DG6:DC5_A 6 -16.742 -0.338 0.013 -0.185 -8.349 1 19 A 7 A 4 -1.007 A_DC7:DG4_A 7 -7.152 0.156 0.183 -0.087 -1.348 1 20 A 8 A 3 1.245 A_DT8:DA3_A 8 -6.641 -0.034 0.046 -0.136 1.257 1 19 A 9 A 2 -0.804 A_DG9:DC2_A 9 -8.207 -0.238 0.004 -0.151 8.229 1 19 A 10 A 1 0.408 A_DG10:DC1_A 10 -12.065 -0.200 0.147 -0.109 3.175 28.527 A A 1 2 14.553 A A 10 9 3.186 7.081 -0.337 0.621 AA_DC1DC2:DG9DG10_AA 1 3.545 -7.286 27.428 -0.342 1.486 2.879 51.275 A A 2 3 -6.984 A A 9 8 3.213 -6.032 0.136 2.865 AA_DC2DA3:DT8DG9_AA 2 0.040 -0.046 50.943 3.698 -0.154 3.180 22.829 A A 3 4 22.749 A A 8 7 3.222 8.758 0.502 0.736 AA_DA3DG4:DC7DT8_AA 3 -2.646 6.873 20.938 -1.341 -2.235 3.250 38.413 A A 4 5 -5.843 A A 7 6 3.332 -3.838 -0.670 0.661 AA_DG4DC5:DG6DC7_AA 4 0.161 -0.245 38.228 1.487 1.039 3.639 42.736 A A 5 6 11.898 A A 6 5 3.731 8.616 0.000 -0.113 AA_DC5DG6:DC5DG6_AA 5 0.000 0.000 41.898 -1.138 0.000 3.250 38.413 A A 6 7 -5.843 A A 5 4 3.332 -3.838 0.670 0.661 AA_DG6DC7:DG4DC5_AA 6 -0.161 0.245 38.228 1.487 -1.039 3.180 22.829 A A 7 8 22.749 A A 4 3 3.222 8.758 -0.502 0.736 AA_DC7DT8:DA3DG4_AA 7 2.646 -6.873 20.938 -1.341 2.235 2.879 51.275 A A 8 9 -6.984 A A 3 2 3.213 -6.032 -0.136 2.865 AA_DT8DG9:DC2DA3_AA 8 -0.040 0.046 50.943 3.698 0.154 3.175 28.527 A A 9 10 14.553 A A 2 1 3.186 7.081 0.337 0.621 AA_DG9DG10:DC1DC2_AA 9 -3.545 7.286 27.428 -0.342 -1.486 chem_comp_atom chem_comp_bond database_2 pdbx_struct_conn_angle struct_conn struct_site pdbx_initial_refinement_model repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Refinement description 1 0 2000-09-25 1 1 2008-04-27 1 2 2011-07-13 1 3 2024-02-07 1 4 2024-04-03 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id NDB Y NDB 2000-03-20 REL REL MG MAGNESIUM ION HOH water 5DNB BDJ019 PDB experimental model MO3 111 2 MG MG 111 A MO4 116 2 MG MG 116 A MO5 112 2 MG MG 112 A MO6 113 2 MG MG 113 A MO6 114 2 MG MG 114 A MO6 115 2 MG MG 115 A HOH 201 3 HOH HOH 201 A HOH 202 3 HOH HOH 202 A HOH 203 3 HOH HOH 203 A HOH 204 3 HOH HOH 204 A HOH 206 3 HOH HOH 206 A HOH 207 3 HOH HOH 207 A HOH 208 3 HOH HOH 208 A HOH 209 3 HOH HOH 209 A HOH 210 3 HOH HOH 210 A HOH 211 3 HOH HOH 211 A HOH 212 3 HOH HOH 212 A HOH 213 3 HOH HOH 213 A HOH 214 3 HOH HOH 214 A HOH 215 3 HOH HOH 215 A HOH 216 3 HOH HOH 216 A HOH 217 3 HOH HOH 217 A HOH 218 3 HOH HOH 218 A HOH 219 3 HOH HOH 219 A HOH 220 3 HOH HOH 220 A HOH 221 3 HOH HOH 221 A HOH 222 3 HOH HOH 222 A HOH 224 3 HOH HOH 224 A HOH 225 3 HOH HOH 225 A HOH 226 3 HOH HOH 226 A HOH 227 3 HOH HOH 227 A HOH 228 3 HOH HOH 228 A HOH 232 3 HOH HOH 232 A HOH 235 3 HOH HOH 235 A HOH 237 3 HOH HOH 237 A HOH 239 3 HOH HOH 239 A HOH 240 3 HOH HOH 240 A HOH 241 3 HOH HOH 241 A HOH 242 3 HOH HOH 242 A HOH 243 3 HOH HOH 243 A HOH 245 3 HOH HOH 245 A HOH 250 3 HOH HOH 250 A HOH 251 3 HOH HOH 251 A HOH 252 3 HOH HOH 252 A HOH 255 3 HOH HOH 255 A HOH 256 3 HOH HOH 256 A HOH 257 3 HOH HOH 257 A HOH 1114 3 HOH HOH 1114 A HOH 1116 3 HOH HOH 1116 A HOH 1228 3 HOH HOH 1228 A HOH 1233 3 HOH HOH 1233 A HOH 1239 3 HOH HOH 1239 A HOH 1244 3 HOH HOH 1244 A HOH 1250 3 HOH HOH 1250 A HOH 1277 3 HOH HOH 1277 A MO3 111 3 HOH HOH 1278 A MO3 111 3 HOH HOH 1279 A MO3 111 3 HOH HOH 1280 A MO4 116 3 HOH HOH 1281 A MO4 116 3 HOH HOH 1282 A MO4 116 3 HOH HOH 1283 A MO4 116 3 HOH HOH 1284 A MO5 112 3 HOH HOH 1285 A MO5 112 3 HOH HOH 1286 A MO5 112 3 HOH HOH 1287 A MO5 112 3 HOH HOH 1288 A MO5 112 3 HOH HOH 1289 A MO6 113 3 HOH HOH 1290 A MO6 113 3 HOH HOH 1291 A MO6 113 3 HOH HOH 1292 A MO6 113 3 HOH HOH 1293 A MO6 113 3 HOH HOH 1294 A MO6 113 3 HOH HOH 1295 A MO6 114 3 HOH HOH 1296 A MO6 114 3 HOH HOH 1297 A MO6 114 3 HOH HOH 1298 A MO6 114 3 HOH HOH 1299 A MO6 114 3 HOH HOH 1300 A MO6 114 3 HOH HOH 1301 A MO6 115 3 HOH HOH 1302 A MO6 115 3 HOH HOH 1303 A MO6 115 3 HOH HOH 1304 A MO6 115 3 HOH HOH 1305 A MO6 115 3 HOH HOH 1306 A MO6 115 3 HOH HOH 1307 A C 1 n 1 DC 1 A C 2 n 2 DC 2 A A 3 n 3 DA 3 A G 4 n 4 DG 4 A C 5 n 5 DC 5 A G 6 n 6 DG 6 A C 7 n 7 DC 7 A T 8 n 8 DT 8 A G 9 n 9 DG 9 A G 10 n 10 DG 10 A 0.1380000 0.1490000 632 5 12512 author_defined_assembly 2 dimeric A HOH 1278 H O HOH 1_555 A MG 111 B MG MG 1_555 A HOH 1278 H O HOH 2_655 98.4 A HOH 1278 H O HOH 1_555 A MG 111 B MG MG 1_555 A HOH 1279 H O HOH 1_555 85.4 A HOH 1278 H O HOH 2_655 A MG 111 B MG MG 1_555 A HOH 1279 H O HOH 1_555 176.2 A HOH 1278 H O HOH 1_555 A MG 111 B MG MG 1_555 A HOH 1279 H O HOH 2_655 176.2 A HOH 1278 H O HOH 2_655 A MG 111 B MG MG 1_555 A HOH 1279 H O HOH 2_655 85.4 A HOH 1279 H O HOH 1_555 A MG 111 B MG MG 1_555 A HOH 1279 H O HOH 2_655 90.8 A HOH 1278 H O HOH 1_555 A MG 111 B MG MG 1_555 A HOH 1280 H O HOH 1_555 91.0 A HOH 1278 H O HOH 2_655 A MG 111 B MG MG 1_555 A HOH 1280 H O HOH 1_555 88.0 A HOH 1279 H O HOH 1_555 A MG 111 B MG MG 1_555 A HOH 1280 H O HOH 1_555 91.6 A HOH 1279 H O HOH 2_655 A MG 111 B MG MG 1_555 A HOH 1280 H O HOH 1_555 89.5 A HOH 1278 H O HOH 1_555 A MG 111 B MG MG 1_555 A HOH 1280 H O HOH 2_655 88.0 A HOH 1278 H O HOH 2_655 A MG 111 B MG MG 1_555 A HOH 1280 H O HOH 2_655 91.0 A HOH 1279 H O HOH 1_555 A MG 111 B MG MG 1_555 A HOH 1280 H O HOH 2_655 89.5 A HOH 1279 H O HOH 2_655 A MG 111 B MG MG 1_555 A HOH 1280 H O HOH 2_655 91.6 A HOH 1280 H O HOH 1_555 A MG 111 B MG MG 1_555 A HOH 1280 H O HOH 2_655 178.4 A HOH 1285 C H O HOH 1_555 A MG 112 C D MG MG 1_555 A HOH 1286 C H O HOH 1_555 91.6 A HOH 1285 C H O HOH 1_555 A MG 112 C D MG MG 1_555 A HOH 1287 C H O HOH 1_555 88.7 A HOH 1286 C H O HOH 1_555 A MG 112 C D MG MG 1_555 A HOH 1287 C H O HOH 1_555 179.6 A HOH 1285 C H O HOH 1_555 A MG 112 C D MG MG 1_555 A HOH 1288 C H O HOH 1_555 89.2 A HOH 1286 C H O HOH 1_555 A MG 112 C D MG MG 1_555 A HOH 1288 C H O HOH 1_555 89.8 A HOH 1287 C H O HOH 1_555 A MG 112 C D MG MG 1_555 A HOH 1288 C H O HOH 1_555 90.5 A HOH 1285 C H O HOH 1_555 A MG 112 C D MG MG 1_555 A HOH 1289 C H O HOH 1_555 96.7 A HOH 1286 C H O HOH 1_555 A MG 112 C D MG MG 1_555 A HOH 1289 C H O HOH 1_555 89.5 A HOH 1287 C H O HOH 1_555 A MG 112 C D MG MG 1_555 A HOH 1289 C H O HOH 1_555 90.2 A HOH 1288 C H O HOH 1_555 A MG 112 C D MG MG 1_555 A HOH 1289 C H O HOH 1_555 174.1 A HOH 1285 D H O HOH 1_555 A MG 112 D D MG MG 1_555 A HOH 1286 D H O HOH 1_555 177.1 A HOH 1285 D H O HOH 1_555 A MG 112 D D MG MG 1_555 A HOH 1287 D H O HOH 1_555 93.0 A HOH 1286 D H O HOH 1_555 A MG 112 D D MG MG 1_555 A HOH 1287 D H O HOH 1_555 85.0 A HOH 1285 D H O HOH 1_555 A MG 112 D D MG MG 1_555 A HOH 1288 D H O HOH 1_555 88.3 A HOH 1286 D H O HOH 1_555 A MG 112 D D MG MG 1_555 A HOH 1288 D H O HOH 1_555 89.5 A HOH 1287 D H O HOH 1_555 A MG 112 D D MG MG 1_555 A HOH 1288 D H O HOH 1_555 89.2 A HOH 1285 D H O HOH 1_555 A MG 112 D D MG MG 1_555 A HOH 1289 D H O HOH 1_555 92.4 A HOH 1286 D H O HOH 1_555 A MG 112 D D MG MG 1_555 A HOH 1289 D H O HOH 1_555 89.8 A HOH 1287 D H O HOH 1_555 A MG 112 D D MG MG 1_555 A HOH 1289 D H O HOH 1_555 89.4 A HOH 1288 D H O HOH 1_555 A MG 112 D D MG MG 1_555 A HOH 1289 D H O HOH 1_555 178.5 A HOH 1285 E H O HOH 1_555 A MG 112 E D MG MG 1_555 A HOH 1286 E H O HOH 1_555 90.5 A HOH 1285 E H O HOH 1_555 A MG 112 E D MG MG 1_555 A HOH 1287 E H O HOH 1_555 89.4 A HOH 1286 E H O HOH 1_555 A MG 112 E D MG MG 1_555 A HOH 1287 E H O HOH 1_555 179.8 A HOH 1285 E H O HOH 1_555 A MG 112 E D MG MG 1_555 A HOH 1288 E H O HOH 1_555 88.2 A HOH 1286 E H O HOH 1_555 A MG 112 E D MG MG 1_555 A HOH 1288 E H O HOH 1_555 89.6 A HOH 1287 E H O HOH 1_555 A MG 112 E D MG MG 1_555 A HOH 1288 E H O HOH 1_555 90.5 A HOH 1285 E H O HOH 1_555 A MG 112 E D MG MG 1_555 A HOH 1289 E H O HOH 1_555 96.6 A HOH 1286 E H O HOH 1_555 A MG 112 E D MG MG 1_555 A HOH 1289 E H O HOH 1_555 88.5 A HOH 1287 E H O HOH 1_555 A MG 112 E D MG MG 1_555 A HOH 1289 E H O HOH 1_555 91.3 A HOH 1288 E H O HOH 1_555 A MG 112 E D MG MG 1_555 A HOH 1289 E H O HOH 1_555 174.9 A HOH 1290 C H O HOH 1_555 A MG 113 C E MG MG 1_555 A HOH 1291 C H O HOH 1_555 177.3 A HOH 1290 C H O HOH 1_555 A MG 113 C E MG MG 1_555 A HOH 1292 C H O HOH 1_555 89.1 A HOH 1291 C H O HOH 1_555 A MG 113 C E MG MG 1_555 A HOH 1292 C H O HOH 1_555 93.4 A HOH 1290 C H O HOH 1_555 A MG 113 C E MG MG 1_555 A HOH 1293 C H O HOH 1_555 89.9 A HOH 1291 C H O HOH 1_555 A MG 113 C E MG MG 1_555 A HOH 1293 C H O HOH 1_555 87.7 A HOH 1292 C H O HOH 1_555 A MG 113 C E MG MG 1_555 A HOH 1293 C H O HOH 1_555 173.8 A HOH 1290 C H O HOH 1_555 A MG 113 C E MG MG 1_555 A HOH 1294 C H O HOH 1_555 93.0 A HOH 1291 C H O HOH 1_555 A MG 113 C E MG MG 1_555 A HOH 1294 C H O HOH 1_555 88.4 A HOH 1292 C H O HOH 1_555 A MG 113 C E MG MG 1_555 A HOH 1294 C H O HOH 1_555 82.5 A HOH 1293 C H O HOH 1_555 A MG 113 C E MG MG 1_555 A HOH 1294 C H O HOH 1_555 91.4 A HOH 1290 C H O HOH 1_555 A MG 113 C E MG MG 1_555 A HOH 1295 C H O HOH 1_555 88.5 A HOH 1291 C H O HOH 1_555 A MG 113 C E MG MG 1_555 A HOH 1295 C H O HOH 1_555 90.3 A HOH 1292 C H O HOH 1_555 A MG 113 C E MG MG 1_555 A HOH 1295 C H O HOH 1_555 94.4 A HOH 1293 C H O HOH 1_555 A MG 113 C E MG MG 1_555 A HOH 1295 C H O HOH 1_555 91.7 A HOH 1294 C H O HOH 1_555 A MG 113 C E MG MG 1_555 A HOH 1295 C H O HOH 1_555 176.6 A HOH 1296 H O HOH 1_555 A MG 114 F MG MG 1_555 A HOH 1297 H O HOH 1_555 177.6 A HOH 1296 H O HOH 1_555 A MG 114 F MG MG 1_555 A HOH 1298 H O HOH 1_555 90.8 A HOH 1297 H O HOH 1_555 A MG 114 F MG MG 1_555 A HOH 1298 H O HOH 1_555 91.3 A HOH 1296 H O HOH 1_555 A MG 114 F MG MG 1_555 A HOH 1299 H O HOH 1_555 88.3 A HOH 1297 H O HOH 1_555 A MG 114 F MG MG 1_555 A HOH 1299 H O HOH 1_555 89.6 A HOH 1298 H O HOH 1_555 A MG 114 F MG MG 1_555 A HOH 1299 H O HOH 1_555 178.0 A HOH 1296 H O HOH 1_555 A MG 114 F MG MG 1_555 A HOH 1300 H O HOH 1_555 90.7 A HOH 1297 H O HOH 1_555 A MG 114 F MG MG 1_555 A HOH 1300 H O HOH 1_555 90.4 A HOH 1298 H O HOH 1_555 A MG 114 F MG MG 1_555 A HOH 1300 H O HOH 1_555 87.5 A HOH 1299 H O HOH 1_555 A MG 114 F MG MG 1_555 A HOH 1300 H O HOH 1_555 90.7 A HOH 1296 H O HOH 1_555 A MG 114 F MG MG 1_555 A HOH 1301 H O HOH 1_555 88.1 A HOH 1297 H O HOH 1_555 A MG 114 F MG MG 1_555 A HOH 1301 H O HOH 1_555 90.9 A HOH 1298 H O HOH 1_555 A MG 114 F MG MG 1_555 A HOH 1301 H O HOH 1_555 88.4 A HOH 1299 H O HOH 1_555 A MG 114 F MG MG 1_555 A HOH 1301 H O HOH 1_555 93.3 A HOH 1300 H O HOH 1_555 A MG 114 F MG MG 1_555 A HOH 1301 H O HOH 1_555 175.7 A HOH 1302 H O HOH 1_555 A MG 115 G MG MG 1_555 A HOH 1303 H O HOH 1_555 178.6 A HOH 1302 H O HOH 1_555 A MG 115 G MG MG 1_555 A HOH 1304 H O HOH 1_555 91.3 A HOH 1303 H O HOH 1_555 A MG 115 G MG MG 1_555 A HOH 1304 H O HOH 1_555 88.2 A HOH 1302 H O HOH 1_555 A MG 115 G MG MG 1_555 A HOH 1305 H O HOH 1_555 91.2 A HOH 1303 H O HOH 1_555 A MG 115 G MG MG 1_555 A HOH 1305 H O HOH 1_555 89.3 A HOH 1304 H O HOH 1_555 A MG 115 G MG MG 1_555 A HOH 1305 H O HOH 1_555 177.5 A HOH 1302 H O HOH 1_555 A MG 115 G MG MG 1_555 A HOH 1306 H O HOH 1_555 88.9 A HOH 1303 H O HOH 1_555 A MG 115 G MG MG 1_555 A HOH 1306 H O HOH 1_555 89.7 A HOH 1304 H O HOH 1_555 A MG 115 G MG MG 1_555 A HOH 1306 H O HOH 1_555 89.1 A HOH 1305 H O HOH 1_555 A MG 115 G MG MG 1_555 A HOH 1306 H O HOH 1_555 90.5 A HOH 1302 H O HOH 1_555 A MG 115 G MG MG 1_555 A HOH 1307 H O HOH 1_555 89.7 A HOH 1303 H O HOH 1_555 A MG 115 G MG MG 1_555 A HOH 1307 H O HOH 1_555 91.6 A HOH 1304 H O HOH 1_555 A MG 115 G MG MG 1_555 A HOH 1307 H O HOH 1_555 92.5 A HOH 1305 H O HOH 1_555 A MG 115 G MG MG 1_555 A HOH 1307 H O HOH 1_555 87.9 A HOH 1306 H O HOH 1_555 A MG 115 G MG MG 1_555 A HOH 1307 H O HOH 1_555 177.9 A HOH 1281 D H O HOH 1_555 A MG 116 D C MG MG 1_555 A HOH 1282 D H O HOH 1_555 95.4 A HOH 1281 D H O HOH 1_555 A MG 116 D C MG MG 1_555 A HOH 1283 D H O HOH 1_555 90.5 A HOH 1282 D H O HOH 1_555 A MG 116 D C MG MG 1_555 A HOH 1283 D H O HOH 1_555 92.3 A HOH 1281 D H O HOH 1_555 A MG 116 D C MG MG 1_555 A HOH 1284 D H O HOH 1_555 90.7 A HOH 1282 D H O HOH 1_555 A MG 116 D C MG MG 1_555 A HOH 1284 D H O HOH 1_555 90.4 A HOH 1283 D H O HOH 1_555 A MG 116 D C MG MG 1_555 A HOH 1284 D H O HOH 1_555 177.0 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 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 2_656 -x+1,y,-z+1 crystal symmetry operation 16.6307462069 0.0000000000 30.4173245290 1 A MG 111 B MG 1 A HOH 228 H HOH 1 A DA 3 A 0.073 SIDE CHAIN 1 A DC 7 A 0.065 SIDE CHAIN 1 A DG 9 0.071 SIDE CHAIN 1 -4.97 0.80 102.40 97.43 A A A C3' C2' C1' DC DC DC 2 2 2 B N 1 -5.02 0.80 109.40 104.38 A A A O5' C5' C4' DA DA DA 3 3 3 B B B N 1 7.81 1.20 115.70 123.51 A A A C5' C4' C3' DA DA DA 3 3 3 A A N 1 -5.83 0.80 109.40 103.57 A A A O5' C5' C4' DG DG DG 6 6 6 B B N 1 10.07 1.60 120.90 130.97 A A A P O5' C5' DG DG DG 6 6 6 C N 1 6.79 1.10 109.80 116.59 A A A C5' C4' O4' DG DG DG 6 6 6 A A A N 1 13.83 1.40 114.30 128.13 A A A N9 C1' C2' DG DG DG 6 6 6 A A N 1 -12.37 0.70 108.00 95.63 A A A O4' C1' N9 DG DG DG 6 6 6 A A N 1 3.21 0.40 110.80 114.01 A A A C4 C5 N7 DG DG DG 6 6 6 N 1 -2.68 0.40 105.40 102.72 A A A N9 C4 C5 DG DG DG 6 6 6 N 1 -4.13 0.60 130.40 126.27 A A A C6 C5 N7 DG DG DG 6 6 6 N 1 4.53 0.60 119.90 124.43 A A A N1 C6 O6 DG DG DG 6 6 6 N 1 11.07 1.20 119.70 130.77 A A A C3' O3' P DG DG DC 6 6 7 B B B Y 1 13.20 1.10 110.50 123.70 A A A O3' P OP1 DG DC DC 6 7 7 C C C Y 1 9.28 1.50 119.60 128.88 A A A OP1 P OP2 DC DC DC 7 7 7 C C C N 1 -37.24 0.90 105.70 68.46 A A A O5' P OP2 DC DC DC 7 7 7 C C C N 1 -5.87 0.80 109.40 103.53 A A A O5' C5' C4' DC DC DC 7 7 7 A A A N 1 -12.14 1.60 120.90 108.76 A A A P O5' C5' DC DC DC 7 7 7 C C C N 1 -2.97 0.40 104.50 101.53 A A A O4' C4' C3' DC DC DC 7 7 7 A N 1 -6.96 1.00 110.10 103.14 A A A C1' O4' C4' DC DC DC 7 7 7 A N 1 7.46 1.20 115.70 123.16 A A A C5' C4' C3' DG DG DG 9 9 9 A N 1 2.27 0.30 108.30 110.57 A A A O4' C1' N9 DG DG DG 10 10 10 N 1 A A O3' P DG DC 4 5 -0.083 0.012 1.607 1.524 Y 1 A A O4' C1' DG DG 6 6 0.105 0.011 1.420 1.525 A A N 1 A A C5 C7 DT DT 8 8 0.036 0.006 1.496 1.532 N REFINEMENT STARTED IN X-PLOR 3.843 WITH DNA MODEL FROM BDJ019. AFTER ALL DATA HAS BEEN ADDED AND REFINED BY SIMULATED ANNEALING IN X-PLOR 3.843, REFINEMENT CONTINUED BY CONJUGATE GRADIENT LEAST-SQUARES IN SHELXL-97. THE TOP 50 MOST DISAGREEABLE REFLECTIONS WERE REJECTED TOWARDS THE LATTER STAGES OF REFINEMENT BUT THESE ARE STILL INCLUDED IN THE RELEASED DATA. 0.1509000 0.1405000 0.1405000 0.985 8.0 16139 654 13087 13087 5024 5 93.3 random 1 THROUGHOUT 0 0 MOLECULAR REPLACEMENT BDJ019 Parkinson et al. SHELX swat option 9 113 271.4 0.985 8.0 51 484 48 385 0 0.018 0.053 0.041 0.006 0.023 0.039 5.82 0.985 8.0 1EN9 13087 13087 -1.0 0.0310000 1 32.8 4.87 93.3 0.1220000 0.985 1.016 6.9 1253 89.5 model building X-PLOR refinement SHELXL-97 data reduction DENZO data scaling SCALEPACK phasing X-PLOR 1A CRYSTAL STRUCTURES OF B-DNA REVEAL SEQUENCE-SPECIFIC BINDING AND GROOVE-SPECIFIC BENDING OF DNA BY MAGNESIUM AND CALCIUM. 1 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 3 N N metalc 2.135 A MG 111 B MG MG 1_555 A HOH 1278 H O HOH 1_555 metalc 2.135 A MG 111 B MG MG 1_555 A HOH 1278 H O HOH 2_655 metalc 2.086 A MG 111 B MG MG 1_555 A HOH 1279 H O HOH 1_555 metalc 2.086 A MG 111 B MG MG 1_555 A HOH 1279 H O HOH 2_655 metalc 2.062 A MG 111 B MG MG 1_555 A HOH 1280 H O HOH 1_555 metalc 2.061 A MG 111 B MG MG 1_555 A HOH 1280 H O HOH 2_655 metalc 2.096 C C A MG 112 D MG MG 1_555 A HOH 1285 H O HOH 1_555 metalc 2.071 D D A MG 112 D MG MG 1_555 A HOH 1285 H O HOH 1_555 metalc 2.093 E E A MG 112 D MG MG 1_555 A HOH 1285 H O HOH 1_555 metalc 2.076 C C A MG 112 D MG MG 1_555 A HOH 1286 H O HOH 1_555 metalc 2.094 D D A MG 112 D MG MG 1_555 A HOH 1286 H O HOH 1_555 metalc 2.090 E E A MG 112 D MG MG 1_555 A HOH 1286 H O HOH 1_555 metalc 2.082 C C A MG 112 D MG MG 1_555 A HOH 1287 H O HOH 1_555 metalc 2.104 D D A MG 112 D MG MG 1_555 A HOH 1287 H O HOH 1_555 metalc 2.068 E E A MG 112 D MG MG 1_555 A HOH 1287 H O HOH 1_555 metalc 2.093 C C A MG 112 D MG MG 1_555 A HOH 1288 H O HOH 1_555 metalc 2.085 D D A MG 112 D MG MG 1_555 A HOH 1288 H O HOH 1_555 metalc 2.098 E E A MG 112 D MG MG 1_555 A HOH 1288 H O HOH 1_555 metalc 2.066 C C A MG 112 D MG MG 1_555 A HOH 1289 H O HOH 1_555 metalc 2.063 D D A MG 112 D MG MG 1_555 A HOH 1289 H O HOH 1_555 metalc 2.068 E E A MG 112 D MG MG 1_555 A HOH 1289 H O HOH 1_555 metalc 2.083 C C A MG 113 E MG MG 1_555 A HOH 1290 H O HOH 1_555 metalc 2.090 C C A MG 113 E MG MG 1_555 A HOH 1291 H O HOH 1_555 metalc 2.077 C C A MG 113 E MG MG 1_555 A HOH 1292 H O HOH 1_555 metalc 2.087 C C A MG 113 E MG MG 1_555 A HOH 1293 H O HOH 1_555 metalc 2.108 C C A MG 113 E MG MG 1_555 A HOH 1294 H O HOH 1_555 metalc 2.081 C C A MG 113 E MG MG 1_555 A HOH 1295 H O HOH 1_555 metalc 2.080 A MG 114 F MG MG 1_555 A HOH 1296 H O HOH 1_555 metalc 2.058 A MG 114 F MG MG 1_555 A HOH 1297 H O HOH 1_555 metalc 2.091 A MG 114 F MG MG 1_555 A HOH 1298 H O HOH 1_555 metalc 2.065 A MG 114 F MG MG 1_555 A HOH 1299 H O HOH 1_555 metalc 2.076 A MG 114 F MG MG 1_555 A HOH 1300 H O HOH 1_555 metalc 2.081 A MG 114 F MG MG 1_555 A HOH 1301 H O HOH 1_555 metalc 2.081 A MG 115 G MG MG 1_555 A HOH 1302 H O HOH 1_555 metalc 2.087 A MG 115 G MG MG 1_555 A HOH 1303 H O HOH 1_555 metalc 2.079 A MG 115 G MG MG 1_555 A HOH 1304 H O HOH 1_555 metalc 2.076 A MG 115 G MG MG 1_555 A HOH 1305 H O HOH 1_555 metalc 2.090 A MG 115 G MG MG 1_555 A HOH 1306 H O HOH 1_555 metalc 2.082 A MG 115 G MG MG 1_555 A HOH 1307 H O HOH 1_555 metalc 2.068 D D A MG 116 C MG MG 1_555 A HOH 1281 H O HOH 1_555 metalc 2.047 D D A MG 116 C MG MG 1_555 A HOH 1282 H O HOH 1_555 metalc 2.075 D D A MG 116 C MG MG 1_555 A HOH 1283 H O HOH 1_555 metalc 2.085 D D A MG 116 C MG MG 1_555 A HOH 1284 H O HOH 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 A DG 10 A N1 DG 10 2_656 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 A DG 10 A O6 DG 10 2_656 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 A DG 10 A N2 DG 10 2_656 hydrog WATSON-CRICK A DC 2 A N3 DC 2 1_555 A DG 9 A N1 DG 9 2_656 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 A DG 9 A O6 DG 9 2_656 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 A DG 9 A N2 DG 9 2_656 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 A DT 8 A N3 DT 8 2_656 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 A DT 8 A O4 DT 8 2_656 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 A DC 7 A N3 DC 7 2_656 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 A DC 7 A O2 DC 7 2_656 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 A DC 7 A N4 DC 7 2_656 hydrog WATSON-CRICK A DC 5 A N3 DC 5 1_555 A DG 6 A N1 DG 6 2_656 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 A DG 6 A O6 DG 6 2_656 hydrog WATSON-CRICK A DC 5 A O2 DC 5 1_555 A DG 6 A N2 DG 6 2_656 hydrog WATSON-CRICK A DG 6 A N1 DG 6 1_555 A DC 5 A N3 DC 5 2_656 hydrog WATSON-CRICK A DG 6 A N2 DG 6 1_555 A DC 5 A O2 DC 5 2_656 hydrog WATSON-CRICK A DG 6 A O6 DG 6 1_555 A DC 5 A N4 DC 5 2_656 hydrog WATSON-CRICK A DC 7 A N3 DC 7 1_555 A DG 4 A N1 DG 4 2_656 hydrog WATSON-CRICK A DC 7 A N4 DC 7 1_555 A DG 4 A O6 DG 4 2_656 hydrog WATSON-CRICK A DC 7 A O2 DC 7 1_555 A DG 4 A N2 DG 4 2_656 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 A DA 3 A N1 DA 3 2_656 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 A DA 3 A N6 DA 3 2_656 hydrog WATSON-CRICK A DG 9 A N1 DG 9 1_555 A DC 2 A N3 DC 2 2_656 hydrog WATSON-CRICK A DG 9 A N2 DG 9 1_555 A DC 2 A O2 DC 2 2_656 hydrog WATSON-CRICK A DG 9 A O6 DG 9 1_555 A DC 2 A N4 DC 2 2_656 hydrog WATSON-CRICK A DG 10 A N1 DG 10 1_555 A DC 1 A N3 DC 1 2_656 hydrog WATSON-CRICK A DG 10 A N2 DG 10 1_555 A DC 1 A O2 DC 1 2_656 hydrog WATSON-CRICK A DG 10 A O6 DG 10 1_555 A DC 1 A N4 DC 1 2_656 DNA divalent cations, DNA sequence-specific binding, shelxdna, B-DNA, DNA 1EN9 PDB 1 1EN9 1 10 1EN9 1 10 1EN9 A 1 1 10 BINDING SITE FOR RESIDUE MG A 111 A MG 111 Software 6 BINDING SITE FOR RESIDUE MG A 116 A MG 116 Software 6 BINDING SITE FOR RESIDUE MG A 112 A MG 112 Software 6 BINDING SITE FOR RESIDUE MG A 113 A MG 113 Software 6 BINDING SITE FOR RESIDUE MG A 114 A MG 114 Software 6 BINDING SITE FOR RESIDUE MG A 115 A MG 115 Software 6 A HOH 1278 H HOH 6 2_655 A HOH 1278 H HOH 6 1_555 A HOH 1279 H HOH 6 1_555 A HOH 1279 H HOH 6 2_655 A HOH 1280 H HOH 6 2_655 A HOH 1280 H HOH 6 1_555 A HOH 1116 H HOH 6 1_555 A HOH 1281 H HOH 6 1_555 A HOH 1282 H HOH 6 1_555 A HOH 1283 H HOH 6 1_555 A HOH 1284 H HOH 6 1_555 A HOH 1291 H HOH 6 1_556 A HOH 1114 H HOH 6 1_555 A HOH 1285 H HOH 6 1_555 A HOH 1286 H HOH 6 1_555 A HOH 1287 H HOH 6 1_555 A HOH 1288 H HOH 6 1_555 A HOH 1289 H HOH 6 1_555 A HOH 1290 H HOH 6 1_555 A HOH 1291 H HOH 6 1_555 A HOH 1292 H HOH 6 1_555 A HOH 1293 H HOH 6 1_555 A HOH 1294 H HOH 6 1_555 A HOH 1295 H HOH 6 1_555 A HOH 1296 H HOH 6 1_555 A HOH 1297 H HOH 6 1_555 A HOH 1298 H HOH 6 1_555 A HOH 1299 H HOH 6 1_555 A HOH 1300 H HOH 6 1_555 A HOH 1301 H HOH 6 1_555 A HOH 1302 H HOH 6 1_555 A HOH 1303 H HOH 6 1_555 A HOH 1304 H HOH 6 1_555 A HOH 1305 H HOH 6 1_555 A HOH 1306 H HOH 6 1_555 A HOH 1307 H HOH 6 1_555 5 monoclinic C 1 2 1