1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Johnson, D.S. Stone, M.P. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 C17 H14 O7 330.289 8,9-DIHYDRO-9-HYDROXY-AFLATOXIN B1 non-polymer 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 N 1 N C N 2 R C N 3 N O N 4 R C Y 5 N C N 6 N O N 7 R C N 8 N O Y 9 N C Y 10 N C Y 11 N C N 12 N O N 13 N C Y 14 N C Y 15 N C Y 16 N O Y 17 N C N 18 N O Y 19 N C Y 20 N C N 21 N C N 22 N C N 23 N C N 24 N O 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 H N 39 N O N 40 N P N 41 N O N 42 N O N 43 N O N 44 N C N 45 R C N 46 N O N 47 S C N 48 N O N 49 N C N 50 R C Y 51 N N Y 52 N C Y 53 N N Y 54 N C Y 55 N C N 56 N N Y 57 N N Y 58 N C Y 59 N N Y 60 N C 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 H N 74 N H N 75 N O N 76 N P N 77 N O N 78 N O N 79 N O N 80 N C N 81 R C N 82 N O N 83 S C N 84 N O N 85 N C N 86 R C N 87 N N N 88 N C N 89 N O N 90 N N N 91 N C N 92 N N N 93 N C N 94 N C 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 H N 109 N O N 110 N P N 111 N O N 112 N O N 113 N O N 114 N C N 115 R C N 116 N O N 117 S C N 118 N O N 119 N C N 120 R C Y 121 N N Y 122 N C Y 123 N N Y 124 N C N 125 N C N 126 N O N 127 N N N 128 N C N 129 N N N 130 N N Y 131 N C 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 H N 145 N H N 146 N O N 147 N P N 148 N O N 149 N O N 150 N O N 151 N C N 152 R C N 153 N O N 154 S C N 155 N O N 156 N C N 157 R C N 158 N N N 159 N C N 160 N O N 161 N N N 162 N C N 163 N O N 164 N C N 165 N C N 166 N C 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 H N 179 N H N 180 N H N 181 N H N 1 N sing N 2 N sing 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 sing Y 12 N doub Y 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing Y 18 N sing Y 19 N doub N 20 N sing N 21 N sing Y 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing Y 27 N doub Y 28 N sing Y 29 N sing Y 30 N sing N 31 N doub Y 32 N sing Y 33 N doub N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 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 doub 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 Y 66 N sing Y 67 N sing Y 68 N doub N 69 N sing Y 70 N sing Y 71 N sing Y 72 N doub N 73 N sing Y 74 N doub N 75 N sing N 76 N sing Y 77 N sing Y 78 N doub N 79 N sing Y 80 N sing N 81 N sing N 82 N sing N 83 N doub 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 N 100 N sing N 101 N sing 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 doub N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N doub N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N doub 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 sing Y 139 N sing Y 140 N sing Y 141 N doub N 142 N sing Y 143 N sing N 144 N sing Y 145 N doub N 146 N doub N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N doub N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N doub 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 sing N 179 N sing N 180 N doub N 181 N sing N 182 N sing N 183 N sing N 184 N doub 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 US Biochemistry BICHAW 0033 0006-2960 34 14037 14050 10.1021/bi00043a009 7578001 Refined solution structure of 8,9-dihydro-8-(N7-guanyl)-9-hydroxyaflatoxin B1 opposite CpA in the complementary strand of an oligodeoxynucleotide duplex as determined by 1H NMR. 1995 10.2210/pdb1ag5/pdb pdb_00001ag5 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXYAFLATOXIN B1 OPPOSITE CPA IN THE COMPLEMENTARY STRAND 2964.957 DNA (5'-D(*CP*CP*AP*TP*CP*GP*AP*TP*CP*C)-3') 1 syn polymer 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXYAFLATOXIN B1 OPPOSITE CPA IN THE COMPLEMENTARY STRAND 3438.259 DNA (5'-D(*GP*GP*AP*TP*CP*AP*GP*AP*TP*GP*G)-3') 1 syn polymer 330.289 8,9-DIHYDRO-9-HYDROXY-AFLATOXIN B1 1 syn non-polymer no no (DC)(DC)(DA)(DT)(DC)(DG)(DA)(DT)(DC)(DC) CCATCGATCC A polydeoxyribonucleotide no no (DG)(DG)(DA)(DT)(DC)(DA)(DG)(DA)(DT)(DG)(DG) GGATCAGATGG B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n n -15.320 1 19 A 1 B 21 -6.402 A_DC1:DG21_B 1 -5.238 0.215 0.354 -0.082 0.788 1 19 A 2 B 20 0.769 A_DC2:DG20_B 2 -13.495 1.003 0.027 -0.410 -1.042 1 20 A 3 B 19 2.120 A_DA3:DT19_B 3 -7.412 0.455 -0.043 0.032 17.221 1 20 A 4 B 18 -11.882 A_DT4:DA18_B 4 -6.158 -0.390 -0.311 0.125 10.197 1 19 A 5 B 17 -1.772 A_DC5:DG17_B 5 -9.914 0.550 -0.018 -0.211 -13.205 1 19 A 6 B 15 0.584 A_DG6:DC15_B 6 6.362 0.584 -0.357 -0.072 -10.433 1 20 A 7 B 14 5.244 A_DA7:DT14_B 7 -12.968 0.213 -0.287 -0.037 -3.044 1 20 A 8 B 13 8.202 A_DT8:DA13_B 8 -12.497 0.358 -0.047 -0.130 -4.721 1 19 A 9 B 12 2.722 A_DC9:DG12_B 9 1.525 0.795 -0.081 -0.192 5.230 1 19 A 10 B 11 -3.207 A_DC10:DG11_B 10 -1.993 0.634 -0.124 -0.197 2.998 32.665 A A 1 2 4.780 B B 21 20 2.976 2.685 0.987 0.570 AA_DC1DC2:DG20DG21_BB 1 -0.449 0.799 32.555 0.588 -1.826 2.338 33.795 A A 2 3 28.317 B B 20 19 2.950 15.849 -0.896 -0.657 AA_DC2DA3:DT19DG20_BB 2 -0.697 1.244 29.937 -3.336 1.445 1.587 20.246 A A 3 4 42.248 B B 19 18 2.691 13.558 -0.884 -0.520 AA_DA3DT4:DA18DT19_BB 3 1.494 -4.654 14.997 -6.129 3.028 3.017 36.242 A A 4 5 4.669 B B 18 17 3.136 2.898 0.546 -0.687 AA_DT4DC5:DG17DA18_BB 4 -3.141 5.061 35.997 -1.488 -1.294 2.122 39.616 A A 6 7 33.126 B B 15 14 3.022 21.343 0.630 -0.851 AA_DG6DA7:DT14DC15_BB 5 -0.519 0.806 33.567 -3.399 -0.982 2.615 29.024 A A 7 8 8.218 B B 14 13 2.724 4.103 0.422 -0.416 AA_DA7DT8:DA13DT14_BB 6 -1.544 3.093 28.698 -1.572 -1.121 2.915 32.398 A A 8 9 8.261 B B 13 12 3.058 4.594 -0.092 -0.796 AA_DT8DC9:DG12DA13_BB 7 0.951 -1.710 32.065 -2.170 0.318 3.191 36.721 A A 9 10 -11.483 B B 12 11 3.054 -7.188 1.330 -1.353 AA_DC9DC10:DG11DG12_BB 8 -1.727 2.759 35.994 -1.200 -2.339 atom_site chem_comp entity entity_poly entity_poly_seq ndb_struct_conf_na ndb_struct_na_base_pair ndb_struct_na_base_pair_step pdbx_database_status pdbx_entity_nonpoly pdbx_entity_src_syn pdbx_nonpoly_scheme pdbx_poly_seq_scheme pdbx_struct_assembly pdbx_struct_mod_residue pdbx_struct_oper_list pdbx_validate_rmsd_angle struct_asym struct_conn struct_ref chem_comp_atom chem_comp_bond database_2 pdbx_nmr_software struct_conn repository Initial release Version format compliance Version format compliance Atomic model Data collection Database references Derived calculations Non-polymer description Other Polymer sequence Source and taxonomy Structure summary Data collection Database references Derived calculations 1 0 1997-09-17 1 1 2008-03-24 1 2 2011-07-13 2 0 2019-01-30 2 1 2024-04-10 _atom_site.B_iso_or_equiv _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.group_PDB _atom_site.label_asym_id _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.type_symbol _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.type _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly_seq.mon_id _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.tilt _pdbx_database_status.process_site _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.pdb_mon_id _struct_ref.pdbx_align_begin _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _struct_conn.pdbx_leaving_atom_flag Y BNL 1997-04-01 REL AFN 8,9-DIHYDRO-9-HYDROXY-AFLATOXIN B1 32630 synthetic construct sample 1 10 32630 synthetic construct sample 1 11 THIS STRUCTURE PROVIDED THE BEST-FIT FOR THE NOE DATA BASED ON THE RELAXATION MATRIX ANALYSIS USING CORMA 1 1 NOESY 2QF-COSY AND TOCSY : NOESY 2QF-COSY AND 6.9 278 K REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. NOE-RESTRAINED MOLECULAR DYNAMICS/SIMULATED ANNEALING BRUNGER refinement X-PLOR 3.1 structure solution Felix structure solution X-PLOR structure solution MARDIGRAS structure solution CORMA 500 Bruker AMX500 X 6 3 AFN AFN 11 A C 1 n 1 DC 1 A C 2 n 2 DC 2 A A 3 n 3 DA 3 A T 4 n 4 DT 4 A C 5 n 5 DC 5 A X 6 n 6 DG 6 A A 7 n 7 DA 7 A T 8 n 8 DT 8 A C 9 n 9 DC 9 A C 10 n 10 DC 10 A G 11 n 1 DG 11 B G 12 n 2 DG 12 B A 13 n 3 DA 13 B T 14 n 4 DT 14 B C 15 n 5 DC 15 B A 16 n 6 DA 16 B G 17 n 7 DG 17 B A 18 n 8 DA 18 B T 19 n 9 DT 19 B G 20 n 10 DG 20 B G 21 n 11 DG 21 B author_defined_assembly 2 dimeric 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 identity operation 0.0000000000 0.0000000000 0.0000000000 1 2.37 0.30 108.30 110.67 A A A O4' C1' N1 DC DC DC 1 1 1 N 1 3.50 0.30 108.30 111.80 A A A O4' C1' N1 DC DC DC 2 2 2 N 1 3.77 0.50 113.80 117.57 A A A N7 C8 N9 DA DA DA 3 3 3 N 1 3.76 0.30 108.30 112.06 A A A O4' C1' N1 DT DT DT 4 4 4 N 1 2.85 0.30 108.30 111.15 A A A O4' C1' N1 DC DC DC 5 5 5 N 1 3.49 0.30 108.30 111.79 A A A O4' C1' N9 DG DG DG 6 6 6 N 1 4.31 0.50 113.10 117.41 A A A N7 C8 N9 DG DG DG 6 6 6 N 1 -2.74 0.40 106.40 103.66 A A A C8 N9 C4 DG DG DG 6 6 6 N 1 2.87 0.30 108.30 111.17 A A A O4' C1' N9 DA DA DA 7 7 7 N 1 3.71 0.50 113.80 117.51 A A A N7 C8 N9 DA DA DA 7 7 7 N 1 3.76 0.30 108.30 112.06 A A A O4' C1' N1 DT DT DT 8 8 8 N 1 3.14 0.30 108.30 111.44 A A A O4' C1' N1 DC DC DC 9 9 9 N 1 3.05 0.30 108.30 111.35 A A A O4' C1' N1 DC DC DC 10 10 10 N 1 2.11 0.30 108.30 110.41 B B B O4' C1' N9 DG DG DG 11 11 11 N 1 4.62 0.50 113.10 117.72 B B B N7 C8 N9 DG DG DG 11 11 11 N 1 -2.87 0.40 106.40 103.53 B B B C8 N9 C4 DG DG DG 11 11 11 N 1 3.07 0.30 108.30 111.37 B B B O4' C1' N9 DG DG DG 12 12 12 N 1 4.52 0.50 113.10 117.62 B B B N7 C8 N9 DG DG DG 12 12 12 N 1 -2.72 0.40 106.40 103.68 B B B C8 N9 C4 DG DG DG 12 12 12 N 1 3.27 0.30 108.30 111.57 B B B O4' C1' N9 DA DA DA 13 13 13 N 1 3.68 0.50 113.80 117.48 B B B N7 C8 N9 DA DA DA 13 13 13 N 1 4.26 0.30 108.30 112.56 B B B O4' C1' N1 DT DT DT 14 14 14 N 1 2.47 0.30 108.30 110.77 B B B O4' C1' N1 DC DC DC 15 15 15 N 1 2.66 0.30 108.30 110.96 B B B O4' C1' N9 DA DA DA 16 16 16 N 1 3.70 0.50 113.80 117.50 B B B N7 C8 N9 DA DA DA 16 16 16 N 1 2.60 0.30 108.30 110.90 B B B O4' C1' N9 DG DG DG 17 17 17 N 1 4.48 0.50 113.10 117.58 B B B N7 C8 N9 DG DG DG 17 17 17 N 1 -2.67 0.40 106.40 103.73 B B B C8 N9 C4 DG DG DG 17 17 17 N 1 2.93 0.30 108.30 111.23 B B B O4' C1' N9 DA DA DA 18 18 18 N 1 3.79 0.50 113.80 117.59 B B B N7 C8 N9 DA DA DA 18 18 18 N 1 3.36 0.30 108.30 111.66 B B B O4' C1' N1 DT DT DT 19 19 19 N 1 2.59 0.30 108.30 110.89 B B B O4' C1' N9 DG DG DG 20 20 20 N 1 4.56 0.50 113.10 117.66 B B B N7 C8 N9 DG DG DG 20 20 20 N 1 -2.76 0.40 106.40 103.64 B B B C8 N9 C4 DG DG DG 20 20 20 N 1 2.97 0.30 108.30 111.27 B B B O4' C1' N9 DG DG DG 21 21 21 N 1 4.59 0.50 113.10 117.69 B B B N7 C8 N9 DG DG DG 21 21 21 N 1 -2.96 0.40 106.40 103.44 B B B C8 N9 C4 DG DG DG 21 21 21 N model building X-PLOR 3.1 refinement X-PLOR 3.1 phasing X-PLOR 3.1 THE SOLUTION STRUCTURE OF AN AFLATOXIN B1 EPOXIDE ADDUCT AT THE N7 POSITION OF GUANINE OPPOSITE AN ADENINE IN THE COMPLEMENTARY STRAND OF AN OLIGODEOXYNUCLEOTIDE DUPLEX, NMR, MINIMIZED AVERAGE STRUCTURE 1 N N 2 N N 3 N N covale 1.486 none sing A DG 6 A N7 DG 6 1_555 A AFN 11 C C8A AFN 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 21 B N1 DG 11 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 21 B O6 DG 11 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 21 B N2 DG 11 1_555 hydrog WATSON-CRICK A DC 2 A N3 DC 2 1_555 B DG 20 B N1 DG 10 1_555 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 B DG 20 B O6 DG 10 1_555 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 B DG 20 B N2 DG 10 1_555 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 B DT 19 B N3 DT 9 1_555 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 B DT 19 B O4 DT 9 1_555 hydrog WATSON-CRICK A DT 4 A N3 DT 4 1_555 B DA 18 B N1 DA 8 1_555 hydrog WATSON-CRICK A DT 4 A O4 DT 4 1_555 B DA 18 B N6 DA 8 1_555 hydrog WATSON-CRICK A DC 5 A N3 DC 5 1_555 B DG 17 B N1 DG 7 1_555 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 B DG 17 B O6 DG 7 1_555 hydrog WATSON-CRICK A DC 5 A O2 DC 5 1_555 B DG 17 B N2 DG 7 1_555 hydrog WATSON-CRICK A DG 6 A N1 DG 6 1_555 B DC 15 B N3 DC 5 1_555 hydrog WATSON-CRICK A DG 6 A N2 DG 6 1_555 B DC 15 B O2 DC 5 1_555 hydrog WATSON-CRICK A DG 6 A O6 DG 6 1_555 B DC 15 B N4 DC 5 1_555 hydrog WATSON-CRICK A DA 7 A N1 DA 7 1_555 B DT 14 B N3 DT 4 1_555 hydrog WATSON-CRICK A DA 7 A N6 DA 7 1_555 B DT 14 B O4 DT 4 1_555 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 B DA 13 B N1 DA 3 1_555 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 B DA 13 B N6 DA 3 1_555 hydrog WATSON-CRICK A DC 9 A N3 DC 9 1_555 B DG 12 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 9 A N4 DC 9 1_555 B DG 12 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 9 A O2 DC 9 1_555 B DG 12 B N2 DG 2 1_555 hydrog WATSON-CRICK A DC 10 A N3 DC 10 1_555 B DG 11 B N1 DG 1 1_555 hydrog WATSON-CRICK A DC 10 A N4 DC 10 1_555 B DG 11 B O6 DG 1 1_555 hydrog WATSON-CRICK A DC 10 A O2 DC 10 1_555 B DG 11 B N2 DG 1 1_555 DNA AFLATOXIN B1, N7-GUANINE ADDUCT, INTERCALATION, DNA DUPLEX, DEOXYRIBONUCLEIC ACID, DNA 1AG5 PDB 1 1 1AG5 1AG5 PDB 2 1 1AG5 1 10 1AG5 1 10 1AG5 A 1 1 10 11 21 1AG5 11 21 1AG5 B 2 1 11 1 P 1