1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Yeh, H.J.C. Sayer, J.M. Liu, X. Altieri, A.S. Byrd, R.A. Lakshman, M.K. Yagi, H. Schurter, E.J. Gorenstein, D.G. Jerina, D.M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 C20 H16 O3 304.339 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE 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 Y 1 N C Y 2 N C Y 3 N C Y 4 N C Y 5 N C Y 6 N C Y 7 N C Y 8 N C Y 9 N C Y 10 N C Y 11 N C Y 12 N C Y 13 N C Y 14 N C Y 15 N C Y 16 N C N 17 R C N 18 N O N 19 R C N 20 N O N 21 R C N 22 N O N 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 H N 39 N H N 40 N O N 41 N P N 42 N O N 43 N O N 44 N O N 45 N C N 46 R C N 47 N O N 48 S C N 49 N O N 50 N C N 51 R C Y 52 N N Y 53 N C Y 54 N N Y 55 N C Y 56 N C N 57 N N Y 58 N N Y 59 N C Y 60 N N Y 61 N C 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 H N 76 N O N 77 N P N 78 N O N 79 N O N 80 N O N 81 N C N 82 R C N 83 N O N 84 S C N 85 N O N 86 N C N 87 R C N 88 N N N 89 N C N 90 N O N 91 N N N 92 N C N 93 N N N 94 N C N 95 N C 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 H N 110 N O N 111 N P N 112 N O N 113 N O N 114 N O N 115 N C N 116 R C N 117 N O N 118 S C N 119 N O N 120 N C N 121 R C Y 122 N N Y 123 N C Y 124 N N Y 125 N C N 126 N C N 127 N O N 128 N N N 129 N C N 130 N N N 131 N N Y 132 N C 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 H N 147 N O N 148 N P N 149 N O N 150 N O N 151 N O N 152 N C N 153 R C N 154 N O N 155 S C N 156 N O N 157 N C N 158 R C N 159 N N N 160 N C N 161 N O N 162 N N N 163 N C N 164 N O N 165 N C N 166 N C N 167 N C 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 182 N H Y 1 N doub Y 2 N sing N 3 N sing Y 4 N sing N 5 N sing Y 6 N doub N 7 N sing Y 8 N sing Y 9 N sing Y 10 N doub N 11 N sing Y 12 N sing N 13 N sing Y 14 N doub Y 15 N sing Y 16 N sing N 17 N sing Y 18 N doub N 19 N sing Y 20 N sing N 21 N sing Y 22 N doub Y 23 N sing Y 24 N sing N 25 N sing Y 26 N doub N 27 N sing Y 28 N sing Y 29 N doub 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 sing 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 doub 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 sing Y 67 N sing Y 68 N sing Y 69 N doub N 70 N sing Y 71 N sing Y 72 N sing Y 73 N doub N 74 N sing Y 75 N doub N 76 N sing N 77 N sing Y 78 N sing Y 79 N doub N 80 N sing Y 81 N sing N 82 N sing N 83 N sing N 84 N doub 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 sing N 107 N doub 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 doub N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N doub 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 N 139 N sing Y 140 N sing Y 141 N sing Y 142 N doub N 143 N sing Y 144 N sing N 145 N sing Y 146 N doub N 147 N doub N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N doub N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N doub 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 sing N 181 N doub N 182 N sing N 183 N sing N 184 N sing N 185 N doub N 186 N sing N 187 N sing N 188 N doub N 189 N sing N 190 N sing N 191 N sing N 192 N sing US Biochemistry BICHAW 0033 0006-2960 34 13570 13581 10.1021/bi00041a037 7577946 NMR solution structure of a nonanucleotide duplex with a dG mismatch opposite a 10S adduct derived from trans addition of a deoxyadenosine N6-amino group to (+)-(7R,8S,9S,10R)-7,8-dihydroxy-9,10-epoxy-7,8,9,10- tetrahydrobenzo[a]pyrene: an unusual syn glycosidic torsion angle at the modified dA 1995 10.2210/pdb1dxa/pdb pdb_00001dxa 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA 2780.836 DNA (5'-D(*GP*GP*TP*CP*AP*CP*GP*AP*G)-3') 1 syn polymer BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA 2716.787 DNA (5'-D(*CP*TP*CP*GP*GP*GP*AP*CP*C)-3') 1 syn polymer chemically synthesized 304.339 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE 1 syn non-polymer DEOXYRIBONUCLEIC ACID DEOXYRIBONUCLEIC ACID no no (DG)(DG)(DT)(DC)(DA)(DC)(DG)(DA)(DG) GGTCACGAG A polydeoxyribonucleotide no no (DC)(DT)(DC)(DG)(DG)(DG)(DA)(DC)(DC) CTCGGGACC B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n 8.126 1 19 A 1 B 9 -1.433 A_DG1:DC9_B 1 -5.923 -0.950 0.123 -0.293 -2.005 1 19 A 2 B 8 -1.499 A_DG2:DC8_B 2 -10.092 -1.004 0.001 -0.354 5.711 1 20 A 3 B 7 1.754 A_DT3:DA7_B 3 -8.808 0.402 -0.015 -0.104 5.815 1 19 A 4 B 6 -1.811 A_DC4:DG6_B 4 -7.584 0.730 0.226 -0.217 41.195 9 A 5 B 5 90.797 A_DA5:DG5_B 5 21.481 -0.021 -1.217 -4.454 -26.293 1 19 A 6 B 4 -2.966 A_DC6:DG4_B 6 2.338 0.560 0.661 -0.086 10.862 1 19 A 7 B 3 3.263 A_DG7:DC3_B 7 -5.893 -1.226 0.223 -0.301 7.669 1 20 A 8 B 2 4.234 A_DA8:DT2_B 8 -13.597 -0.505 -0.130 -0.145 1.349 1 19 A 9 B 1 -2.969 A_DG9:DC1_B 9 -8.773 0.195 -0.174 -0.024 3.375 39.707 A A 1 2 -0.157 B B 9 8 3.373 -0.106 0.033 -0.951 AA_DG1DG2:DC8DC9_BB 1 1.027 -1.512 39.694 -1.388 0.075 2.944 41.911 A A 2 3 4.558 B B 8 7 2.990 3.257 0.024 -0.509 AA_DG2DT3:DA7DC8_BB 2 0.263 -0.368 41.789 -1.020 -0.008 3.036 33.785 A A 3 4 8.960 B B 7 6 3.150 5.186 0.560 -0.376 AA_DT3DC4:DG6DA7_BB 3 -1.244 2.149 33.373 -1.446 -1.154 -0.086 170.390 A A 4 5 9.661 B B 6 5 2.146 18.315 -0.267 -3.791 AA_DC4DA5:DG5DG6_BB 4 -169.400 89.354 2.982 -2.011 -0.867 0.254 157.326 A A 5 6 -43.319 B B 5 4 -1.793 -80.862 -1.494 -5.703 AA_DA5DC6:DG4DG5_BB 5 127.489 -68.297 76.680 -3.108 0.447 2.216 26.648 A A 6 7 2.844 B B 4 3 2.267 1.310 -0.783 -0.554 AA_DC6DG7:DC3DG4_BB 6 0.705 -1.530 26.607 -1.437 1.825 3.197 37.098 A A 7 8 3.392 B B 3 2 3.247 2.155 -0.259 -0.387 AA_DG7DA8:DT2DC3_BB 7 2.493 -3.923 36.957 -0.893 0.736 3.196 38.338 A A 8 9 7.384 B B 2 1 3.325 4.837 0.361 -0.851 AA_DA8DG9:DC1DT2_BB 8 -0.147 0.224 38.043 -1.901 -0.567 database_2 pdbx_database_status pdbx_struct_assembly pdbx_struct_oper_list struct_conn struct_site chem_comp_atom chem_comp_bond entity pdbx_entity_src_syn repository Initial release Version format compliance Version format compliance Database references Derived calculations Other Data collection Source and taxonomy Structure summary 1 0 1995-12-07 1 1 2008-03-24 1 2 2011-07-13 1 3 2022-02-16 1 4 2024-03-13 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.process_site _struct_conn.pdbx_leaving_atom_flag _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _entity.details Y BNL 1995-09-01 REL REL BAP 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE chemically synthesized sample chemically synthesized sample (+)-(7R,8S,9S,10R)-7,8-DIHYDROXY-9,10-EPOXY-7,8,9,10- TETRAHYDROBENZO[A]PYRENE IS COVALENTLY BONDED TO THE EXOCYCLIC N6 AMINO GROUP OF DEOXYADENOSINE IN THE CENTER OF THE DUPLEX THROUGH TRANS ADDITION AT THE C10 OF THE EPOXIDE. 1 TWO STARTING STRUCTURES WITH BENZO[A]PYRENE MOIETY INSIDE THE DUPLEX AND OUTSIDE THE DUPLEX, RESPECTIVELY, WERE GENERATED BY CONNECTING A STANDARD B-TYPE DNA FRAGMENT WITH A MANUALLY BUILD (+)-DE2-[BAP] FRAGMENT. SOLUTION STRUCTURES FOR THE DUPLEX WERE GENERATED BY RESTRAINTED MOLECULAR DYNAMICS AND RESTRAINTED ENERGY MINIMIZATION USING A SET OF INTER-PROTON DISTANCE RESTRAINTS AND DIHEDRAL ANGLE RESTRAINTS WHICH WERE DERIVED FROM NMR EXPERIMENTS. SOME OF STRUCTURES WITH MINIMUM RESTRAINT VIOLATIONS WERE FURTHER REFINED BY THE ITERATIVE RELAXATION MATRIX ANALYSIS (IRMA) METHOD OVER 111 WELL-SEPARATED CROSS PEAKS IN NOESY SPECTRA RECORDED IN D2O AND MIXING TIMES OF 50, 80, 120, 160 AND 200 MS. THE STRUCTURE PRESENTED HERE WAS ONE OF THE FIVE REFINED AND MINIMIZED STRUCTURES. THE FOLLOWING RESTRAINTS WERE APPLIED IN THE MOLECULAR DYNAMICS/ENERGY MINIMIZATION CALCULATIONS. THESE WERE; (1) INTER-PROTON DISTANCE RESTRAINTS DIRECTLY DERIVED FROM NOE DATA; (2) BACKBONE DIHEDRAL ANGLE RESTRAINTS FOR A STANDARD B-DNA EXCEPT THOSE IMMEDIATELY ADJACENT TO THE MODIFIED RESIDUE; (3) DIHEDRAL ANGLE RESTRAINTS FOR ALL GLYCOSIDIC BONDS, EXCEPT MODIFIED DA RESIDUE IN THE CENTER; (4) HYDROGEN BOND RESTRAINTS (BOTH DISTANCE AND PLANARITY ) FOR ALL BASE-PAIRS EXCEPT CENTRAL DA-DG MISMATCH PAIR. THESE RESTRAINTS WERE JUSTIFIED BY THE FACT THAT THE MODIFIED DUPLEX DISPLAYED CHARACTERISTIC NMR SPECTRA OF A B-DNA EXCEPT NEAR LESION SITE, WHERE THE BAP MOIETY WAS INTERCALATED. THE MODIFIED DA RESIDUE DISPLAYED C3'-ENDO SUGAR RING AND A SYN GLYCOSIDIC BOND. IT ALSO FORMED A NON-WATSON-CRICK BASE PAIR WITH THE OPPOSITE DG. ENERGY MINIMIZATION, MOLECULAR DYNAMICS BIOSYM refinement NMRCHITECT BAP 1 3 BAP BAP 10 A G 1 n 1 DG 1 A G 2 n 2 DG 2 A T 3 n 3 DT 3 A C 4 n 4 DC 4 A A 5 n 5 DA 5 A C 6 n 6 DC 6 A G 7 n 7 DG 7 A A 8 n 8 DA 8 A G 9 n 9 DG 9 A C 1 n 1 DC 1 B T 2 n 2 DT 2 B C 3 n 3 DC 3 B G 4 n 4 DG 4 B G 5 n 5 DG 5 B G 6 n 6 DG 6 B A 7 n 7 DA 7 B C 8 n 8 DC 8 B C 9 n 9 DC 9 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 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 1 A DG 2 0.096 SIDE CHAIN 1 A DT 3 0.132 SIDE CHAIN 1 A DA 5 0.082 SIDE CHAIN 1 A DA 8 0.072 SIDE CHAIN 1 B DT 2 0.115 SIDE CHAIN 1 2.49 0.30 108.30 110.79 A A A O4' C1' N9 DG DG DG 1 1 1 N 1 4.22 0.30 108.30 112.52 A A A O4' C1' N9 DG DG DG 2 2 2 N 1 -6.04 0.80 102.40 96.36 A A A C3' C2' C1' DA DA DA 5 5 5 N 1 4.22 0.30 108.30 112.52 A A A O4' C1' N9 DA DA DA 5 5 5 N 1 4.26 0.30 108.30 112.56 A A A O4' C1' N1 DC DC DC 6 6 6 N 1 2.06 0.30 108.30 110.36 A A A O4' C1' N9 DA DA DA 8 8 8 N 1 3.87 0.30 108.30 112.17 A A A O4' C1' N9 DG DG DG 9 9 9 N 1 -5.12 0.80 102.40 97.28 B B B C3' C2' C1' DC DC DC 1 1 1 N 1 5.17 0.30 108.30 113.47 B B B O4' C1' N1 DC DC DC 1 1 1 N 1 2.92 0.30 108.30 111.22 B B B O4' C1' N1 DC DC DC 3 3 3 N 1 1.94 0.30 108.30 110.24 B B B O4' C1' N9 DG DG DG 4 4 4 N 1 3.37 0.30 108.30 111.67 B B B O4' C1' N9 DG DG DG 5 5 5 N 1 3.36 0.30 108.30 111.67 B B B O4' C1' N9 DG DG DG 6 6 6 N 1 2.91 0.30 108.30 111.21 B B B O4' C1' N9 DA DA DA 7 7 7 N 1 2.37 0.30 108.30 110.67 B B B O4' C1' N1 DC DC DC 8 8 8 N 1 2.29 0.30 108.30 110.59 B B B O4' C1' N1 DC DC DC 9 9 9 N BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA IN DUPLEX DNA 1 N N 2 N N 3 N N covale 1.470 none A DA 5 A N6 DA 5 1_555 A BAP 10 C C4' BAP 1_555 hydrog WATSON-CRICK A DG 1 A N1 DG 1 1_555 B DC 9 B N3 DC 9 1_555 hydrog WATSON-CRICK A DG 1 A N2 DG 1 1_555 B DC 9 B O2 DC 9 1_555 hydrog WATSON-CRICK A DG 1 A O6 DG 1 1_555 B DC 9 B N4 DC 9 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 B DC 8 B N3 DC 8 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B DC 8 B O2 DC 8 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B DC 8 B N4 DC 8 1_555 hydrog WATSON-CRICK A DT 3 A N3 DT 3 1_555 B DA 7 B N1 DA 7 1_555 hydrog WATSON-CRICK A DT 3 A O4 DT 3 1_555 B DA 7 B N6 DA 7 1_555 hydrog WATSON-CRICK A DC 4 A N3 DC 4 1_555 B DG 6 B N1 DG 6 1_555 hydrog WATSON-CRICK A DC 4 A N4 DC 4 1_555 B DG 6 B O6 DG 6 1_555 hydrog WATSON-CRICK A DC 4 A O2 DC 4 1_555 B DG 6 B N2 DG 6 1_555 hydrog TYPE_9_PAIR A DA 5 A N6 DA 5 1_555 B DG 5 B O6 DG 5 1_555 hydrog TYPE_9_PAIR A DA 5 A N7 DA 5 1_555 B DG 5 B N1 DG 5 1_555 hydrog WATSON-CRICK A DC 6 A N3 DC 6 1_555 B DG 4 B N1 DG 4 1_555 hydrog WATSON-CRICK A DC 6 A N4 DC 6 1_555 B DG 4 B O6 DG 4 1_555 hydrog WATSON-CRICK A DC 6 A O2 DC 6 1_555 B DG 4 B N2 DG 4 1_555 hydrog WATSON-CRICK A DG 7 A N1 DG 7 1_555 B DC 3 B N3 DC 3 1_555 hydrog WATSON-CRICK A DG 7 A N2 DG 7 1_555 B DC 3 B O2 DC 3 1_555 hydrog WATSON-CRICK A DG 7 A O6 DG 7 1_555 B DC 3 B N4 DC 3 1_555 hydrog WATSON-CRICK A DA 8 A N1 DA 8 1_555 B DT 2 B N3 DT 2 1_555 hydrog WATSON-CRICK A DA 8 A N6 DA 8 1_555 B DT 2 B O4 DT 2 1_555 hydrog WATSON-CRICK A DG 9 A N1 DG 9 1_555 B DC 1 B N3 DC 1 1_555 hydrog WATSON-CRICK A DG 9 A N2 DG 9 1_555 B DC 1 B O2 DC 1 1_555 hydrog WATSON-CRICK A DG 9 A O6 DG 9 1_555 B DC 1 B N4 DC 1 1_555 DNA DOUBLE HELIX, BENZO[A]PYRENE DIOL EPOXIDE ADDUCT, DUPLEX DNA, NON-WATSON-CRICK BASE PAIR, DNA 1DXA PDB 1 1DXA 1DXA PDB 2 1DXA 1 9 1DXA 1 9 1DXA A 1 1 9 1 9 1DXA 1 9 1DXA B 2 1 9 BINDING SITE FOR RESIDUE BAP A 10 A BAP 10 Software 4 A DA 5 A DA 5 4 1_555 A DC 6 A DC 6 4 1_555 B DG 4 B DG 4 4 1_555 B DG 5 B DG 5 4 1_555 1 P 1