1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Schwartz, J.S. Rice, J.S. Luxon, B.A. Sayer, J.M. Xie, G. Yeh, H.J.C. Liu, X. Jerina, D.M. Gorenstein, D.G. 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 36 11069 11076 10.1021/bi971306u 9333324 Solution structure of the minor conformer of a DNA duplex containing a dG mismatch opposite a benzo[a]pyrene diol epoxide/dA adduct: glycosidic rotation from syn to anti at the modified deoxyadenosine. 1997 10.2210/pdb1bps/pdb pdb_00001bps 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 (+)-(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. 2780.836 DNA (5'-D(*GP*GP*TP*CP*(BAP)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 304.339 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE 1 syn non-polymer 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 21.053 1 19 A 1 B 18 -2.207 A_DG1:DC18_B 1 -4.302 -0.442 0.677 -0.225 12.522 1 19 A 2 B 17 -2.417 A_DG2:DC17_B 2 -9.688 -0.278 0.379 -0.190 7.231 1 20 A 3 B 16 -0.227 A_DT3:DA16_B 3 -14.102 0.032 -0.120 -0.149 13.305 1 19 A 4 B 15 -3.258 A_DC4:DG15_B 4 -4.547 0.331 0.169 -0.233 35.278 8 A 5 B 14 -13.897 A_DA5:DG14_B 5 -32.586 0.336 -0.307 1.432 -10.748 1 19 A 6 B 13 -3.106 A_DC6:DG13_B 6 -2.674 -0.053 0.228 -0.156 2.358 1 19 A 7 B 12 -1.325 A_DG7:DC12_B 7 -1.708 -0.210 -0.171 -0.177 -13.575 1 20 A 8 B 11 -0.967 A_DA8:DT11_B 8 2.197 0.147 -0.471 -0.107 4.786 1 19 A 9 B 10 -1.189 A_DG9:DC10_B 9 6.276 -0.435 -0.115 -0.223 3.295 38.704 A A 1 2 5.814 B B 18 17 3.313 3.845 -1.233 -0.669 AA_DG1DG2:DC17DC18_BB 1 -2.167 3.276 38.461 -1.487 1.590 3.189 36.311 A A 2 3 6.213 B B 17 16 3.265 3.857 0.109 -0.494 AA_DG2DT3:DA16DC17_BB 2 4.106 -6.613 35.886 -1.327 0.394 3.040 32.840 A A 3 4 8.465 B B 16 15 3.180 4.762 0.696 -0.186 AA_DT3DC4:DG15DA16_BB 3 -3.237 5.754 32.345 -1.111 -1.763 2.694 40.530 A A 4 5 5.533 B B 15 14 2.943 3.793 -1.104 1.084 AA_DC4DA5:DG14DG15_BB 4 9.751 -14.223 39.212 1.194 2.548 3.675 46.855 A A 5 6 43.475 B B 14 13 6.505 31.063 0.803 -0.911 AA_DA5DC6:DG13DG14_BB 5 -15.307 21.423 32.060 -6.021 -3.413 1.549 29.891 A A 6 7 39.052 B B 13 12 2.761 18.689 -0.468 -0.959 AA_DC6DG7:DC12DG13_BB 6 1.790 -3.741 23.364 -4.745 1.184 3.137 43.240 A A 7 8 29.996 B B 12 11 3.697 21.228 -0.019 -0.254 AA_DG7DA8:DT11DC12_BB 7 -0.733 1.036 37.883 -2.676 -0.055 2.511 22.124 A A 8 9 12.042 B B 11 10 2.795 4.585 0.115 -1.032 AA_DA8DG9:DC10DT11_BB 8 -1.440 3.782 21.602 -4.122 -0.750 database_2 pdbx_entity_src_syn pdbx_nmr_exptl pdbx_nmr_representative pdbx_nmr_software pdbx_nmr_spectrometer pdbx_struct_assembly pdbx_struct_oper_list struct_conn struct_site chem_comp_atom chem_comp_bond repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Source and taxonomy Data collection 1 0 1998-08-19 1 1 2007-10-16 1 2 2011-07-13 1 3 2021-11-03 1 4 2023-12-27 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_exptl.type _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_spectrometer.model _struct_conn.pdbx_leaving_atom_flag _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id BNL Y RCSB 1998-08-06 REL BAP 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE 32630 synthetic construct sample 32630 synthetic construct sample MINIMIZED AVERAGE STRUCTURE. THE STRUCTURE WAS DETERMINED USING DISTANCE RESTRAINTS DERIVED FROM 2D NOESY EXPERIMENTS DONE IN 99.999% D2O AND 90% H2O/ 10% D2O. 2D ROESY, TOCSY, AND EXCHANGE-ONLY EXPERIMENTS WERE USED IN THE CHEMICAL SHIFT ASSIGNMENT PROCESS. 1 1 NOESY ROESY TOCSY 2D EXCHANGE-ONLY SPECTRA 76 mM 6.8 1 atm 288 K THE FOLLOWING RESTRAINTS WERE APPLIED IN THE MOLECULAR DYNAMICS/ENERGY MINIMIZATION CALCULATIONS: (1) INTER-PROTON DISTANCE RESTRAINTS DIRECTLY DERIVED FROM RELAXATION MATRIX ANALYSIS OF NOE DATA; (2) IMINO PROTON HYDROGEN BOND RESTRAINTS FOR ALL BASE PAIRS EXCEPT THE CENTRAL DA-DG MISMATCH PAIR. THE MODIFIED DA RESIDUE OF THIS MINOR CONFORMER DISPLAYED A C2'-ENDO SUGAR PUCKER AND AN ANTI GLYCOSIDIC BOND. IT FORMED AN ANTI:ANTI BASE PAIR CONTAINING TWO HYDROGEN BONDS WITH THE OPPOSITE DG. THE MODIFIED DA RESIDUE OF THE MAJOR CONFORMER OF THIS MOLECULE [YEH ET AL. (1995) BIOCHEMISTRY 34, 13570-13581] DISPLAYED C3'-ENDO SUGAR PUCKER AND A SYN GLYCOSIDIC BOND. THE MAJOR CONFORMER MODIFIED DA RESIDUE FORMED A SYN:ANTI BASE PAIR CONTAINING NON-WATSON CRICK HYDROGEN BONDS WITH THE OPPOSITE DG. MORE REFINEMENT DETAILS CAN BE FOUND IN THE PRIMARY JOURNAL CITATION (SCHWARTZ ET AL.,1997). RELAXATION MATRIX REFINEMENT OF NOE DISTANCE RESTRAINTS AND RESTRAINED MOLECULAR DYNAMICS WITH SIMULATED ANNEALING 1 minimized average structure PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMAN refinement Amber 4.1 Luxon structure calculation MORASS 2.2 PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMAN structure calculation Amber 4.1 750 Varian UNITYPLUS 600 Varian UNITYPLUS BAP 5 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 10 n 1 DC 10 B T 11 n 2 DT 11 B C 12 n 3 DC 12 B G 13 n 4 DG 13 B G 14 n 5 DG 14 B G 15 n 6 DG 15 B A 16 n 7 DA 16 B C 17 n 8 DC 17 B C 18 n 9 DC 18 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 A DC 4 0.158 SIDE CHAIN 1 A DA 5 0.081 SIDE CHAIN 1 B DG 13 0.116 SIDE CHAIN 1 B DA 16 0.056 SIDE CHAIN 1 2.77 0.30 108.30 111.07 A A A O4' C1' N9 DG DG DG 1 1 1 N 1 -3.69 0.60 122.90 119.21 A A A C6 C5 C7 DT DT DT 3 3 3 N 1 4.61 0.30 108.30 112.91 A A A O4' C1' N1 DC DC DC 4 4 4 N 1 5.31 0.30 108.30 113.61 A A A O4' C1' N9 DA DA DA 5 5 5 N 1 2.21 0.30 108.30 110.51 A A A O4' C1' N1 DC DC DC 6 6 6 N 1 3.34 0.30 108.30 111.64 A A A O4' C1' N9 DG DG DG 7 7 7 N 1 5.12 0.30 108.30 113.42 A A A O4' C1' N9 DG DG DG 9 9 9 N 1 4.34 0.30 108.30 112.64 B B B O4' C1' N1 DT DT DT 11 11 11 N 1 -4.75 0.60 122.90 118.15 B B B C6 C5 C7 DT DT DT 11 11 11 N 1 6.49 0.30 108.30 114.79 B B B O4' C1' N9 DG DG DG 13 13 13 N 1 3.12 0.30 108.30 111.42 B B B O4' C1' N9 DG DG DG 14 14 14 N 1 3.37 0.30 108.30 111.67 B B B O4' C1' N1 DC DC DC 18 18 18 N MINOR CONFORMER OF A BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA IN DUPLEX DNA 1 N N 2 N N 3 N N covale 1.471 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 18 B N3 DC 9 1_555 hydrog WATSON-CRICK A DG 1 A N2 DG 1 1_555 B DC 18 B O2 DC 9 1_555 hydrog WATSON-CRICK A DG 1 A O6 DG 1 1_555 B DC 18 B N4 DC 9 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 B DC 17 B N3 DC 8 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B DC 17 B O2 DC 8 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B DC 17 B N4 DC 8 1_555 hydrog WATSON-CRICK A DT 3 A N3 DT 3 1_555 B DA 16 B N1 DA 7 1_555 hydrog WATSON-CRICK A DT 3 A O4 DT 3 1_555 B DA 16 B N6 DA 7 1_555 hydrog WATSON-CRICK A DC 4 A N3 DC 4 1_555 B DG 15 B N1 DG 6 1_555 hydrog WATSON-CRICK A DC 4 A N4 DC 4 1_555 B DG 15 B O6 DG 6 1_555 hydrog WATSON-CRICK A DC 4 A O2 DC 4 1_555 B DG 15 B N2 DG 6 1_555 hydrog TYPE_8_PAIR A DA 5 A N1 DA 5 1_555 B DG 14 B N1 DG 5 1_555 hydrog TYPE_8_PAIR A DA 5 A N6 DA 5 1_555 B DG 14 B O6 DG 5 1_555 hydrog WATSON-CRICK A DC 6 A N3 DC 6 1_555 B DG 13 B N1 DG 4 1_555 hydrog WATSON-CRICK A DC 6 A N4 DC 6 1_555 B DG 13 B O6 DG 4 1_555 hydrog WATSON-CRICK A DC 6 A O2 DC 6 1_555 B DG 13 B N2 DG 4 1_555 hydrog WATSON-CRICK A DG 7 A N1 DG 7 1_555 B DC 12 B N3 DC 3 1_555 hydrog WATSON-CRICK A DG 7 A N2 DG 7 1_555 B DC 12 B O2 DC 3 1_555 hydrog WATSON-CRICK A DG 7 A O6 DG 7 1_555 B DC 12 B N4 DC 3 1_555 hydrog WATSON-CRICK A DA 8 A N1 DA 8 1_555 B DT 11 B N3 DT 2 1_555 hydrog WATSON-CRICK A DA 8 A N6 DA 8 1_555 B DT 11 B O4 DT 2 1_555 hydrog WATSON-CRICK A DG 9 A N1 DG 9 1_555 B DC 10 B N3 DC 1 1_555 hydrog WATSON-CRICK A DG 9 A N2 DG 9 1_555 B DC 10 B O2 DC 1 1_555 hydrog WATSON-CRICK A DG 9 A O6 DG 9 1_555 B DC 10 B N4 DC 1 1_555 DNA DEOXYRIBONUCLEIC ACID, BENZO[A]PYRENE DIOL EPOXIDE ADDUCT, DUPLEX DNA, DNA 1BPS PDB 1 1BPS 1BPS PDB 2 1BPS 1 9 1BPS 1 9 1BPS A 1 1 9 10 18 1BPS 10 18 1BPS B 2 1 9 BINDING SITE FOR RESIDUE BAP A 10 A BAP 10 Software 5 A DC 4 A DC 4 5 1_555 A DA 5 A DA 5 5 1_555 A DC 6 A DC 6 5 1_555 B DG 13 B DG 4 5 1_555 B DG 14 B DG 5 5 1_555 1 P 1