0.031249 0.000000 0.013252 0.000000 0.039418 0.000000 0.000000 0.000000 0.032296 0.000000 0.000000 0.000000 Chiu, T.K. Dickerson, R.E. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 112.98 90.00 32.001 25.369 33.633 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/pdb1en3/pdb pdb_00001en3 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 IMAGE PLATE 1998-11-19 MARRESEARCH SINGLE WAVELENGTH M x-ray 1 0.9500 1.0 X8C NSLS 0.9500 SYNCHROTRON NSLS BEAMLINE X8C 3045.004 DNA (5'-D(*CP*CP*AP*AP*CP*GP*TP*TP*GP*G)-3') 1 syn polymer 24.305 MAGNESIUM ION 4 syn non-polymer 18.015 water 76 nat water no no (DC)(DC)(DA)(DA)(DC)(DG)(DT)(DT)(DG)(DG) CCAACGTTGG A polydeoxyribonucleotide n n n n n n n n n n 1 2.08 37.90 VAPOR DIFFUSION, SITTING DROP INITIAL CONCENTRATION IN DROPLET: 0.24 MM DNA, 8.57 MM MAGNESIUM ACETATE, 0.11 MM STREPTONIGRIN, 10-15% MPD, 45% 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 -6.248 1 19 A 1 A 10 0.513 A_DC1:DG10_A 1 -12.791 0.200 0.141 -0.150 0.588 1 19 A 2 A 9 -1.360 A_DC2:DG9_A 2 -7.659 0.190 -0.019 -0.187 3.969 1 20 A 3 A 8 1.420 A_DA3:DT8_A 3 -7.323 -0.041 0.075 -0.162 7.371 1 20 A 4 A 7 4.883 A_DA4:DT7_A 4 -12.300 0.075 0.216 -0.181 12.456 1 19 A 5 A 6 2.054 A_DC5:DG6_A 5 -12.628 0.149 -0.129 -0.101 -12.456 1 19 A 6 A 5 2.054 A_DG6:DC5_A 6 -12.628 -0.149 -0.129 -0.101 -7.371 1 20 A 7 A 4 4.883 A_DT7:DA4_A 7 -12.300 -0.075 0.216 -0.181 -3.969 1 20 A 8 A 3 1.420 A_DT8:DA3_A 8 -7.323 0.041 0.075 -0.162 -0.588 1 19 A 9 A 2 -1.360 A_DG9:DC2_A 9 -7.659 -0.190 -0.019 -0.187 6.248 1 19 A 10 A 1 0.513 A_DG10:DC1_A 10 -12.791 -0.200 0.141 -0.150 3.129 27.688 A A 1 2 17.307 A A 10 9 3.156 8.142 -0.395 0.628 AA_DC1DC2:DG9DG10_AA 1 3.487 -7.411 26.259 -0.633 1.658 2.780 50.700 A A 2 3 -8.461 A A 9 8 3.169 -7.223 0.320 2.751 AA_DC2DA3:DT8DG9_AA 2 1.229 -1.439 50.203 3.678 -0.295 3.178 30.425 A A 3 4 15.013 A A 8 7 3.227 7.789 0.444 0.364 AA_DA3DA4:DT7DT8_AA 3 -2.092 4.032 29.361 -0.861 -1.263 3.159 30.070 A A 4 5 -2.004 A A 7 6 3.131 -1.039 0.340 -0.374 AA_DA4DC5:DG6DT7_AA 4 2.352 -4.539 29.962 -0.516 -0.192 3.672 44.742 A A 5 6 11.502 A A 6 5 3.762 8.705 0.000 -0.134 AA_DC5DG6:DC5DG6_AA 5 0.000 0.000 43.930 -1.087 0.000 3.159 30.070 A A 6 7 -2.004 A A 5 4 3.131 -1.039 -0.340 -0.374 AA_DG6DT7:DA4DC5_AA 6 -2.352 4.539 29.962 -0.516 0.192 3.178 30.425 A A 7 8 15.013 A A 4 3 3.227 7.789 -0.444 0.364 AA_DT7DT8:DA3DA4_AA 7 2.092 -4.032 29.361 -0.861 1.263 2.780 50.700 A A 8 9 -8.461 A A 3 2 3.169 -7.223 -0.320 2.751 AA_DT8DG9:DC2DA3_AA 8 -1.229 1.439 50.203 3.678 0.295 3.129 27.688 A A 9 10 17.307 A A 2 1 3.156 8.142 0.395 0.628 AA_DG9DG10:DC1DC2_AA 9 -3.487 7.411 26.259 -0.633 -1.658 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 MO6 112 2 MG MG 112 A MO6 114 2 MG MG 114 A MO6 113 2 MG MG 113 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 205 3 HOH HOH 205 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 223 3 HOH HOH 223 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 229 3 HOH HOH 229 A HOH 230 3 HOH HOH 230 A HOH 231 3 HOH HOH 231 A HOH 232 3 HOH HOH 232 A HOH 233 3 HOH HOH 233 A HOH 234 3 HOH HOH 234 A HOH 235 3 HOH HOH 235 A HOH 238 3 HOH HOH 238 A HOH 239 3 HOH HOH 239 A HOH 240 3 HOH HOH 240 A HOH 242 3 HOH HOH 242 A HOH 243 3 HOH HOH 243 A HOH 245 3 HOH HOH 245 A HOH 247 3 HOH HOH 247 A HOH 248 3 HOH HOH 248 A HOH 250 3 HOH HOH 250 A HOH 251 3 HOH HOH 251 A HOH 252 3 HOH HOH 252 A HOH 254 3 HOH HOH 254 A HOH 256 3 HOH HOH 256 A HOH 259 3 HOH HOH 259 A HOH 262 3 HOH HOH 262 A HOH 266 3 HOH HOH 266 A HOH 1210 3 HOH HOH 1210 A HOH 1271 3 HOH HOH 1271 A HOH 1281 3 HOH HOH 1281 A HOH 1317 3 HOH HOH 1317 A MO3 111 3 HOH HOH 1318 A MO3 111 3 HOH HOH 1319 A MO3 111 3 HOH HOH 1320 A MO6 112 3 HOH HOH 1321 A MO6 112 3 HOH HOH 1322 A MO6 112 3 HOH HOH 1323 A MO6 112 3 HOH HOH 1324 A MO6 112 3 HOH HOH 1325 A MO6 112 3 HOH HOH 1326 A MO6 114 3 HOH HOH 1327 A MO6 114 3 HOH HOH 1328 A MO6 114 3 HOH HOH 1329 A MO6 114 3 HOH HOH 1330 A MO6 114 3 HOH HOH 1331 A MO6 114 3 HOH HOH 1332 A MO6 113 3 HOH HOH 1333 A MO6 113 3 HOH HOH 1334 A MO6 113 3 HOH HOH 1335 A MO6 113 3 HOH HOH 1336 A MO6 113 3 HOH HOH 1337 A MO6 113 3 HOH HOH 1338 A C 1 n 1 DC 1 A C 2 n 2 DC 2 A A 3 n 3 DA 3 A A 4 n 4 DA 4 A C 5 n 5 DC 5 A G 6 n 6 DG 6 A T 7 n 7 DT 7 A T 8 n 8 DT 8 A G 9 n 9 DG 9 A G 10 n 10 DG 10 A 0.1391000 0.1545000 592 5 12786 author_defined_assembly 2 dimeric A HOH 1318 F O HOH 1_555 A MG 111 B MG MG 1_555 A HOH 1318 F O HOH 2_655 179.8 A HOH 1318 F O HOH 1_555 A MG 111 B MG MG 1_555 A HOH 1319 F O HOH 1_555 89.8 A HOH 1318 F O HOH 2_655 A MG 111 B MG MG 1_555 A HOH 1319 F O HOH 1_555 90.1 A HOH 1318 F O HOH 1_555 A MG 111 B MG MG 1_555 A HOH 1319 F O HOH 2_655 90.1 A HOH 1318 F O HOH 2_655 A MG 111 B MG MG 1_555 A HOH 1319 F O HOH 2_655 89.8 A HOH 1319 F O HOH 1_555 A MG 111 B MG MG 1_555 A HOH 1319 F O HOH 2_655 90.0 A HOH 1318 F O HOH 1_555 A MG 111 B MG MG 1_555 A HOH 1320 F O HOH 1_555 89.7 A HOH 1318 F O HOH 2_655 A MG 111 B MG MG 1_555 A HOH 1320 F O HOH 1_555 90.4 A HOH 1319 F O HOH 1_555 A MG 111 B MG MG 1_555 A HOH 1320 F O HOH 1_555 87.3 A HOH 1319 F O HOH 2_655 A MG 111 B MG MG 1_555 A HOH 1320 F O HOH 1_555 177.4 A HOH 1318 F O HOH 1_555 A MG 111 B MG MG 1_555 A HOH 1320 F O HOH 2_655 90.4 A HOH 1318 F O HOH 2_655 A MG 111 B MG MG 1_555 A HOH 1320 F O HOH 2_655 89.7 A HOH 1319 F O HOH 1_555 A MG 111 B MG MG 1_555 A HOH 1320 F O HOH 2_655 177.3 A HOH 1319 F O HOH 2_655 A MG 111 B MG MG 1_555 A HOH 1320 F O HOH 2_655 87.3 A HOH 1320 F O HOH 1_555 A MG 111 B MG MG 1_555 A HOH 1320 F O HOH 2_655 95.3 A HOH 1321 A F O HOH 1_555 A MG 112 A C MG MG 1_555 A HOH 1322 A F O HOH 1_555 176.9 A HOH 1321 A F O HOH 1_555 A MG 112 A C MG MG 1_555 A HOH 1323 A F O HOH 1_555 90.6 A HOH 1322 A F O HOH 1_555 A MG 112 A C MG MG 1_555 A HOH 1323 A F O HOH 1_555 90.8 A HOH 1321 A F O HOH 1_555 A MG 112 A C MG MG 1_555 A HOH 1324 A F O HOH 1_555 89.4 A HOH 1322 A F O HOH 1_555 A MG 112 A C MG MG 1_555 A HOH 1324 A F O HOH 1_555 89.3 A HOH 1323 A F O HOH 1_555 A MG 112 A C MG MG 1_555 A HOH 1324 A F O HOH 1_555 175.8 A HOH 1321 A F O HOH 1_555 A MG 112 A C MG MG 1_555 A HOH 1325 A F O HOH 1_555 92.5 A HOH 1322 A F O HOH 1_555 A MG 112 A C MG MG 1_555 A HOH 1325 A F O HOH 1_555 90.3 A HOH 1323 A F O HOH 1_555 A MG 112 A C MG MG 1_555 A HOH 1325 A F O HOH 1_555 86.4 A HOH 1324 A F O HOH 1_555 A MG 112 A C MG MG 1_555 A HOH 1325 A F O HOH 1_555 89.4 A HOH 1321 A F O HOH 1_555 A MG 112 A C MG MG 1_555 A HOH 1326 A F O HOH 1_555 87.7 A HOH 1322 A F O HOH 1_555 A MG 112 A C MG MG 1_555 A HOH 1326 A F O HOH 1_555 89.6 A HOH 1323 A F O HOH 1_555 A MG 112 A C MG MG 1_555 A HOH 1326 A F O HOH 1_555 90.9 A HOH 1324 A F O HOH 1_555 A MG 112 A C MG MG 1_555 A HOH 1326 A F O HOH 1_555 93.3 A HOH 1325 A F O HOH 1_555 A MG 112 A C MG MG 1_555 A HOH 1326 A F O HOH 1_555 177.3 A HOH 1333 A F O HOH 1_555 A MG 113 A E MG MG 1_555 A HOH 1334 A F O HOH 1_555 178.0 A HOH 1333 A F O HOH 1_555 A MG 113 A E MG MG 1_555 A HOH 1335 A F O HOH 1_555 92.6 A HOH 1334 A F O HOH 1_555 A MG 113 A E MG MG 1_555 A HOH 1335 A F O HOH 1_555 88.9 A HOH 1333 A F O HOH 1_555 A MG 113 A E MG MG 1_555 A HOH 1336 A F O HOH 1_555 90.7 A HOH 1334 A F O HOH 1_555 A MG 113 A E MG MG 1_555 A HOH 1336 A F O HOH 1_555 87.8 A HOH 1335 A F O HOH 1_555 A MG 113 A E MG MG 1_555 A HOH 1336 A F O HOH 1_555 176.0 A HOH 1333 A F O HOH 1_555 A MG 113 A E MG MG 1_555 A HOH 1337 A F O HOH 1_555 90.7 A HOH 1334 A F O HOH 1_555 A MG 113 A E MG MG 1_555 A HOH 1337 A F O HOH 1_555 90.7 A HOH 1335 A F O HOH 1_555 A MG 113 A E MG MG 1_555 A HOH 1337 A F O HOH 1_555 87.8 A HOH 1336 A F O HOH 1_555 A MG 113 A E MG MG 1_555 A HOH 1337 A F O HOH 1_555 94.4 A HOH 1333 A F O HOH 1_555 A MG 113 A E MG MG 1_555 A HOH 1338 A F O HOH 1_555 88.9 A HOH 1334 A F O HOH 1_555 A MG 113 A E MG MG 1_555 A HOH 1338 A F O HOH 1_555 89.8 A HOH 1335 A F O HOH 1_555 A MG 113 A E MG MG 1_555 A HOH 1338 A F O HOH 1_555 90.6 A HOH 1336 A F O HOH 1_555 A MG 113 A E MG MG 1_555 A HOH 1338 A F O HOH 1_555 87.2 A HOH 1337 A F O HOH 1_555 A MG 113 A E MG MG 1_555 A HOH 1338 A F O HOH 1_555 178.3 A HOH 1333 B F O HOH 1_555 A MG 113 B E MG MG 1_555 A HOH 1334 B F O HOH 1_555 179.6 A HOH 1333 B F O HOH 1_555 A MG 113 B E MG MG 1_555 A HOH 1335 B F O HOH 1_555 90.8 A HOH 1334 B F O HOH 1_555 A MG 113 B E MG MG 1_555 A HOH 1335 B F O HOH 1_555 89.3 A HOH 1333 B F O HOH 1_555 A MG 113 B E MG MG 1_555 A HOH 1336 B F O HOH 1_555 89.8 A HOH 1334 B F O HOH 1_555 A MG 113 B E MG MG 1_555 A HOH 1336 B F O HOH 1_555 90.1 A HOH 1335 B F O HOH 1_555 A MG 113 B E MG MG 1_555 A HOH 1336 B F O HOH 1_555 178.6 A HOH 1333 B F O HOH 1_555 A MG 113 B E MG MG 1_555 A HOH 1337 B F O HOH 1_555 91.7 A HOH 1334 B F O HOH 1_555 A MG 113 B E MG MG 1_555 A HOH 1337 B F O HOH 1_555 87.9 A HOH 1335 B F O HOH 1_555 A MG 113 B E MG MG 1_555 A HOH 1337 B F O HOH 1_555 89.2 A HOH 1336 B F O HOH 1_555 A MG 113 B E MG MG 1_555 A HOH 1337 B F O HOH 1_555 89.6 A HOH 1333 B F O HOH 1_555 A MG 113 B E MG MG 1_555 A HOH 1338 B F O HOH 1_555 89.7 A HOH 1334 B F O HOH 1_555 A MG 113 B E MG MG 1_555 A HOH 1338 B F O HOH 1_555 90.7 A HOH 1335 B F O HOH 1_555 A MG 113 B E MG MG 1_555 A HOH 1338 B F O HOH 1_555 91.7 A HOH 1336 B F O HOH 1_555 A MG 113 B E MG MG 1_555 A HOH 1338 B F O HOH 1_555 89.5 A HOH 1337 B F O HOH 1_555 A MG 113 B E MG MG 1_555 A HOH 1338 B F O HOH 1_555 178.3 A HOH 1327 B F O HOH 1_555 A MG 114 B D MG MG 1_555 A HOH 1328 B F O HOH 1_555 176.7 A HOH 1327 B F O HOH 1_555 A MG 114 B D MG MG 1_555 A HOH 1329 B F O HOH 1_555 92.1 A HOH 1328 B F O HOH 1_555 A MG 114 B D MG MG 1_555 A HOH 1329 B F O HOH 1_555 89.6 A HOH 1327 B F O HOH 1_555 A MG 114 B D MG MG 1_555 A HOH 1330 B F O HOH 1_555 88.5 A HOH 1328 B F O HOH 1_555 A MG 114 B D MG MG 1_555 A HOH 1330 B F O HOH 1_555 90.3 A HOH 1329 B F O HOH 1_555 A MG 114 B D MG MG 1_555 A HOH 1330 B F O HOH 1_555 172.4 A HOH 1327 B F O HOH 1_555 A MG 114 B D MG MG 1_555 A HOH 1331 B F O HOH 1_555 91.6 A HOH 1328 B F O HOH 1_555 A MG 114 B D MG MG 1_555 A HOH 1331 B F O HOH 1_555 85.3 A HOH 1329 B F O HOH 1_555 A MG 114 B D MG MG 1_555 A HOH 1331 B F O HOH 1_555 94.3 A HOH 1330 B F O HOH 1_555 A MG 114 B D MG MG 1_555 A HOH 1331 B F O HOH 1_555 93.2 A HOH 1327 B F O HOH 1_555 A MG 114 B D MG MG 1_555 A HOH 1332 B F O HOH 1_555 89.4 A HOH 1328 B F O HOH 1_555 A MG 114 B D MG MG 1_555 A HOH 1332 B F O HOH 1_555 93.6 A HOH 1329 B F O HOH 1_555 A MG 114 B D MG MG 1_555 A HOH 1332 B F O HOH 1_555 87.3 A HOH 1330 B F O HOH 1_555 A MG 114 B D MG MG 1_555 A HOH 1332 B F O HOH 1_555 85.1 A HOH 1331 B F O HOH 1_555 A MG 114 B D MG MG 1_555 A HOH 1332 B F O HOH 1_555 178.0 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 18.8703476042 0.0000000000 30.9639250848 1 A MG 111 B MG 1 A HOH 217 F HOH 1 A HOH 219 F HOH 1 A DA 3 A 0.072 SIDE CHAIN 1 A DC 5 0.064 SIDE CHAIN 1 A DT 7 A 0.075 SIDE CHAIN 1 A DG 9 0.069 SIDE CHAIN 1 -7.80 0.80 109.40 101.60 A A A O5' C5' C4' DA DA DA 3 3 3 B B B N 1 -16.33 2.50 109.70 93.37 A A A C4' C3' O3' DA DA DA 3 3 3 B N 1 3.83 0.50 103.90 107.73 A A A C5 N7 C8 DA DA DA 3 3 3 N 1 -2.55 0.40 105.80 103.25 A A A N9 C4 C5 DA DA DA 3 3 3 N 1 16.32 1.40 114.30 130.62 A A A N9 C1' C2' DA DA DA 4 4 4 N 1 6.31 0.50 129.30 135.61 A A A N1 C2 N3 DA DA DA 4 4 4 N 1 -3.92 0.50 110.60 106.68 A A A C2 N3 C4 DA DA DA 4 4 4 N 1 -3.24 0.50 117.00 113.76 A A A C4 C5 C6 DA DA DA 4 4 4 N 1 4.35 0.50 110.70 115.05 A A A C4 C5 N7 DA DA DA 4 4 4 N 1 -4.95 0.50 103.90 98.95 A A A C5 N7 C8 DA DA DA 4 4 4 N 1 4.22 0.50 113.80 118.02 A A A N7 C8 N9 DA DA DA 4 4 4 N 1 -5.99 0.40 105.80 99.81 A A A C8 N9 C4 DA DA DA 4 4 4 N 1 3.95 0.60 118.60 122.55 A A A N1 C6 N6 DA DA DA 4 4 4 N 1 11.82 1.80 126.30 138.12 A A A C4 N9 C1' DA DA DA 4 4 4 N 1 -6.66 1.00 110.10 103.44 A A A C1' O4' C4' DC DC DC 5 5 5 N 1 -7.57 0.70 108.00 100.43 A A A O4' C1' N1 DC DC DC 5 5 5 N 1 3.32 0.40 120.30 123.62 A A A C6 N1 C2 DC DC DC 5 5 5 N 1 -8.90 0.70 119.20 110.30 A A A N1 C2 N3 DC DC DC 5 5 5 N 1 6.66 0.50 119.90 126.56 A A A C2 N3 C4 DC DC DC 5 5 5 N 1 7.96 0.70 121.90 129.86 A A A N3 C2 O2 DC DC DC 5 5 5 N 1 9.45 1.20 119.70 129.15 A A A C3' O3' P DC DC DG 5 5 6 Y 1 -4.49 0.60 125.10 120.61 A A A C6 N1 C2 DG DG DG 6 6 6 N 1 -2.91 0.40 110.80 107.89 A A A C4 C5 N7 DG DG DG 6 6 6 N 1 3.90 0.50 104.30 108.20 A A A C5 N7 C8 DG DG DG 6 6 6 N 1 -3.10 0.50 113.10 110.00 A A A N7 C8 N9 DG DG DG 6 6 6 N 1 -3.44 0.40 106.40 102.96 A A A C8 N9 C4 DG DG DG 6 6 6 N 1 5.52 0.40 105.40 110.92 A A A N9 C4 C5 DG DG DG 6 6 6 N 1 -3.92 0.60 123.70 119.78 A A A C5 C6 N1 DT DT DT 7 7 7 N 1 -5.16 0.80 109.40 104.24 A A A O5' C5' C4' DT DT DT 8 8 8 B B B N 1 A A C4 C5 DC DC 2 2 -0.061 0.008 1.425 1.364 N 1 A A N3 C4 DA DA 3 3 -0.052 0.006 1.344 1.292 N 1 A A C5 N7 DA DA 3 3 -0.046 0.006 1.388 1.342 N 1 A A N7 C8 DA DA 3 3 -0.072 0.007 1.311 1.239 N 1 A A C8 N9 DA DA 3 3 0.068 0.008 1.373 1.441 N 1 A A C1' N9 DA DA 4 4 -0.220 0.014 1.468 1.248 N 1 A A C4 C5 DA DA 4 4 0.047 0.007 1.383 1.430 N 1 A A C5 C6 DA DA 4 4 0.072 0.009 1.406 1.478 N 1 A A C5 N7 DA DA 4 4 -0.114 0.006 1.388 1.274 N 1 A A N7 C8 DA DA 4 4 0.077 0.007 1.311 1.388 N 1 A A C1' N1 DC DC 5 5 0.143 0.013 1.488 1.631 N 1 A A C2 O2 DC DC 5 5 -0.078 0.009 1.240 1.162 N 1 A A N1 C2 DC DC 5 5 0.085 0.010 1.397 1.482 N 1 A A N1 C6 DC DC 5 5 -0.099 0.006 1.367 1.268 N 1 A A N3 C4 DC DC 5 5 -0.057 0.007 1.335 1.278 N 1 A A N3 C4 DG DG 6 6 0.055 0.007 1.350 1.405 N 1 A A C5 N7 DG DG 6 6 -0.042 0.006 1.388 1.346 N 1 A A C8 N9 DG DG 6 6 0.044 0.007 1.374 1.418 N 1 A A C2 N2 DG DG 6 6 -0.064 0.010 1.341 1.277 N 1 A A C5 C7 DT DT 7 7 0.042 0.006 1.496 1.538 N 1 A A N1 C2 DT DT 8 8 -0.048 0.008 1.376 1.328 N 1 A A C5 C7 DT DT 8 8 0.038 0.006 1.496 1.534 N 1 A A C4 C5 DG DG 9 9 0.052 0.007 1.379 1.431 N 1 A A C5 N7 DG DG 9 9 -0.037 0.006 1.388 1.351 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. 0.1592000 0.1409000 0.1409000 0.985 8.0 17441 631 13464 13464 2945 5 95 RANDOM 1 THROUGHOUT 0 0 MOLECULAR REPLACEMENT BDJ019 PARKINSON ET AL. SWAT 0.814695 0.4550 14 114.0 272.84 0.985 8.0 61 457 32 364 0 0.018 0.049 0.019 0.006 0.026 0.072 5.3 0.985 8.0 1EN3 13464 13464 -1.0 0.0470000 1 21.6 5.75 95.0 0.1230000 0.985 1.016 7.4 90.7 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 3 N N metalc 2.047 A MG 111 B MG MG 1_555 A HOH 1318 F O HOH 1_555 metalc 2.046 A MG 111 B MG MG 1_555 A HOH 1318 F O HOH 2_655 metalc 2.090 A MG 111 B MG MG 1_555 A HOH 1319 F O HOH 1_555 metalc 2.091 A MG 111 B MG MG 1_555 A HOH 1319 F O HOH 2_655 metalc 2.120 A MG 111 B MG MG 1_555 A HOH 1320 F O HOH 1_555 metalc 2.120 A MG 111 B MG MG 1_555 A HOH 1320 F O HOH 2_655 metalc 2.075 A A A MG 112 C MG MG 1_555 A HOH 1321 F O HOH 1_555 metalc 2.076 A A A MG 112 C MG MG 1_555 A HOH 1322 F O HOH 1_555 metalc 2.065 A A A MG 112 C MG MG 1_555 A HOH 1323 F O HOH 1_555 metalc 2.065 A A A MG 112 C MG MG 1_555 A HOH 1324 F O HOH 1_555 metalc 2.094 A A A MG 112 C MG MG 1_555 A HOH 1325 F O HOH 1_555 metalc 2.071 A A A MG 112 C MG MG 1_555 A HOH 1326 F O HOH 1_555 metalc 2.080 A A A MG 113 E MG MG 1_555 A HOH 1333 F O HOH 1_555 metalc 2.077 B B A MG 113 E MG MG 1_555 A HOH 1333 F O HOH 1_555 metalc 2.073 A A A MG 113 E MG MG 1_555 A HOH 1334 F O HOH 1_555 metalc 2.086 B B A MG 113 E MG MG 1_555 A HOH 1334 F O HOH 1_555 metalc 2.064 A A A MG 113 E MG MG 1_555 A HOH 1335 F O HOH 1_555 metalc 2.088 B B A MG 113 E MG MG 1_555 A HOH 1335 F O HOH 1_555 metalc 2.073 A A A MG 113 E MG MG 1_555 A HOH 1336 F O HOH 1_555 metalc 2.084 B B A MG 113 E MG MG 1_555 A HOH 1336 F O HOH 1_555 metalc 2.131 A A A MG 113 E MG MG 1_555 A HOH 1337 F O HOH 1_555 metalc 2.084 B B A MG 113 E MG MG 1_555 A HOH 1337 F O HOH 1_555 metalc 2.091 A A A MG 113 E MG MG 1_555 A HOH 1338 F O HOH 1_555 metalc 2.082 B B A MG 113 E MG MG 1_555 A HOH 1338 F O HOH 1_555 metalc 2.065 B B A MG 114 D MG MG 1_555 A HOH 1327 F O HOH 1_555 metalc 2.052 B B A MG 114 D MG MG 1_555 A HOH 1328 F O HOH 1_555 metalc 2.062 B B A MG 114 D MG MG 1_555 A HOH 1329 F O HOH 1_555 metalc 2.087 B B A MG 114 D MG MG 1_555 A HOH 1330 F O HOH 1_555 metalc 2.087 B B A MG 114 D MG MG 1_555 A HOH 1331 F O HOH 1_555 metalc 2.107 B B A MG 114 D MG MG 1_555 A HOH 1332 F 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 DA 4 A N1 DA 4 1_555 A DT 7 A N3 DT 7 2_656 hydrog WATSON-CRICK A DA 4 A N6 DA 4 1_555 A DT 7 A O4 DT 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 DT 7 A N3 DT 7 1_555 A DA 4 A N1 DA 4 2_656 hydrog WATSON-CRICK A DT 7 A O4 DT 7 1_555 A DA 4 A N6 DA 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 1EN3 PDB 1 1EN3 1 10 1EN3 1 10 1EN3 A 1 1 10 BINDING SITE FOR RESIDUE MG A 111 A MG 111 Software 6 BINDING SITE FOR RESIDUE MG A 112 A MG 112 Software 6 BINDING SITE FOR RESIDUE MG A 114 A MG 114 Software 6 BINDING SITE FOR RESIDUE MG A 113 A MG 113 Software 6 A HOH 1318 F HOH 6 1_555 A HOH 1318 F HOH 6 2_655 A HOH 1319 F HOH 6 1_555 A HOH 1319 F HOH 6 2_655 A HOH 1320 F HOH 6 2_655 A HOH 1320 F HOH 6 1_555 A HOH 1321 F HOH 6 1_555 A HOH 1322 F HOH 6 1_555 A HOH 1323 F HOH 6 1_555 A HOH 1324 F HOH 6 1_555 A HOH 1325 F HOH 6 1_555 A HOH 1326 F HOH 6 1_555 A HOH 1327 F HOH 6 1_555 A HOH 1328 F HOH 6 1_555 A HOH 1329 F HOH 6 1_555 A HOH 1330 F HOH 6 1_555 A HOH 1331 F HOH 6 1_555 A HOH 1332 F HOH 6 1_555 A HOH 1333 F HOH 6 1_555 A HOH 1334 F HOH 6 1_555 A HOH 1335 F HOH 6 1_555 A HOH 1336 F HOH 6 1_555 A HOH 1337 F HOH 6 1_555 A HOH 1338 F HOH 6 1_555 5 monoclinic C 1 2 1