1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Li, Z. Kim, H.Y. Tamura, P.J. Harris, C.M. Harris, T.M. 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 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 C18 H16 O3 280.318 8,9,10,11-TETRAHYDRO-BENZO[A]ANTHRACENE-8,9,10-TRIOL non-polymer US Biochemistry BICHAW 0033 0006-2960 38 14820 14832 10.1021/bi991607z 10555964 Role of a polycyclic aromatic hydrocarbon bay region ring in modulating DNA adduct structure: the non-bay region (8S,9R,10S, 11R)-N(6)-[11-(8,9,10,11-tetrahydro-8,9, 10-trihydroxybenz[a]anthracenyl)]-2' -deoxyadenosyl adduct in codon 61 of the human N-ras protooncogene 1999 10.2210/pdb1djd/pdb pdb_00001djd 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 3416.263 DNA(5'-D(*CT*GT*GT*AT*CT*AT*AT*GT*AT*AT*G)-3') 1 syn polymer 3291.145 DNA(5'-D(*CT*TT*TT*CT*TT*TT*GT*TT*CT*CT*G)-3') 1 syn polymer 280.318 8,9,10,11-TETRAHYDRO-BENZO[A]ANTHRACENE-8,9,10-TRIOL 1 syn non-polymer no no (DC)(DG)(DG)(DA)(DC)(DA)(DA)(DG)(DA)(DA)(DG) CGGACAAGAAG A polydeoxyribonucleotide no no (DC)(DT)(DT)(DC)(DT)(DT)(DG)(DT)(DC)(DC)(DG) CTTCTTGTCCG B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n n n -6.085 1 19 A 1 B 22 -0.142 A_DC1:DG22_B 1 -6.767 0.173 0.036 -0.126 10.110 1 19 A 2 B 21 -3.796 A_DG2:DC21_B 2 -2.142 -0.124 0.208 -0.108 16.065 1 19 A 3 B 20 -0.594 A_DG3:DC20_B 3 -7.424 -0.198 0.103 -0.072 -3.027 1 20 A 4 B 19 1.149 A_DA4:DT19_B 4 -4.077 0.131 0.078 -0.129 17.830 1 19 A 5 B 18 1.855 A_DC5:DG18_B 5 6.796 0.177 0.477 -0.105 -24.992 A 6 B 17 -43.998 A_DA6:DT17_B 6 24.351 2.729 0.572 0.822 7.687 1 20 A 7 B 16 -2.788 A_DA7:DT16_B 7 -2.553 0.243 0.675 0.063 7.594 1 19 A 8 B 15 -3.364 A_DG8:DC15_B 8 -5.843 -0.143 0.074 -0.123 12.324 1 20 A 9 B 14 0.767 A_DA9:DT14_B 9 -9.549 0.127 -0.016 -0.076 10.109 1 20 A 10 B 13 4.197 A_DA10:DT13_B 10 -9.671 0.098 -0.074 -0.099 18.448 1 19 A 11 B 12 -2.985 A_DG11:DC12_B 11 -1.954 -0.139 0.260 -0.110 2.467 29.538 A A 1 2 19.082 B B 22 21 2.725 9.561 -0.316 -0.365 AA_DC1DG2:DC21DG22_BB 1 0.172 -0.343 27.979 -2.374 0.651 3.149 37.445 A A 2 3 1.185 B B 21 20 3.142 0.761 0.688 -0.057 AA_DG2DG3:DC20DC21_BB 2 0.511 -0.796 37.434 -0.185 -1.008 4.262 39.174 A A 3 4 12.296 B B 20 19 4.282 8.186 0.276 0.299 AA_DG3DA4:DT19DC20_BB 3 1.416 -2.127 38.317 -0.849 -0.188 3.168 32.458 A A 4 5 2.375 B B 19 18 3.178 1.327 -0.082 -0.041 AA_DA4DC5:DG18DT19_BB 4 1.393 -2.494 32.402 -0.299 0.384 1.933 19.336 A A 6 7 -12.191 B B 17 16 2.906 -3.979 2.431 -0.577 AA_DA6DA7:DT16DT17_BB 5 -6.770 20.745 17.684 -0.183 -9.849 3.352 32.383 A A 7 8 5.787 B B 16 15 3.443 3.221 -0.186 -0.661 AA_DA7DG8:DC15DT16_BB 6 1.375 -2.470 32.198 -1.776 0.587 3.160 35.520 A A 8 9 4.260 B B 15 14 3.192 2.597 -0.139 -0.344 AA_DG8DA9:DT14DC15_BB 7 -0.103 0.169 35.428 -0.932 0.214 3.034 34.587 A A 9 10 12.241 B B 14 13 3.225 7.227 -0.217 -0.580 AA_DA9DA10:DT13DT14_BB 8 0.846 -1.433 33.836 -2.055 0.491 2.988 30.052 A A 10 11 0.376 B B 13 12 2.988 0.195 -0.081 -0.146 AA_DA10DG11:DC12DT13_BB 9 -0.496 0.956 30.048 -0.317 0.063 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list struct_conn struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 1999-12-16 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-16 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 1999-12-02 REL REL TBT 8,9,10,11-TETRAHYDRO-BENZO[A]ANTHRACENE-8,9,10-TRIOL Sequence Observed In human N-ras codon 61 sample This structure was determined using 2D homonuclear techniques back calculated data agree with experimental NOESY spectrum 1 1 2D NOESY 2D NOESY DQF-COSY TOCSY 0.1 M NaCl 7.0 1 atm 278 K 0.1 M NaCl 7.0 1 atm 293 K The structure is based on a total of 475 NOE derived distance constraints, 55 empirical sugar pucker restraints, 35 empirical backbone angle restraints, and 18 empirical planarity restraints. NOE-restrained molecular dynamics/simulated annealing 12 lowest energy 1.8 mM oligodeoxynucleotide; 10 mM phosphate buffer; 0.05 mM EDTA; 0.1 M NaCl 90% H2O/10% D2O 1.8 mM oligodeoxynucleotide; 10 mM phosphate buffer; 0.05 mM EDTA; 0.1 M NaCl 100% D2O Bruker collection XwinNMR 2.0 Brunger structure solution X-PLOR 3.851 Biosym Technologies processing Felix 97.0 Borgias, Thomas, Li, Kumar, Tonelli refinement CORMA 5.2 Borgias, Thomas, Li, Kumar, Tonelli iterative matrix relaxation MARDIGRAS 3.0 500 Bruker DMX 750 Bruker DMX ABA 6 3 TBT TBT 25 A C 1 n 1 DC 1 A G 2 n 2 DG 2 A G 3 n 3 DG 3 A A 4 n 4 DA 4 A C 5 n 5 DC 5 A ABA 6 n 6 DA 6 A A 7 n 7 DA 7 A G 8 n 8 DG 8 A A 9 n 9 DA 9 A A 10 n 10 DA 10 A G 11 n 11 DG 11 A C 12 n 1 DC 12 B T 13 n 2 DT 13 B T 14 n 3 DT 14 B C 15 n 4 DC 15 B T 16 n 5 DT 16 B T 17 n 6 DT 17 B G 18 n 7 DG 18 B T 19 n 8 DT 19 B C 20 n 9 DC 20 B C 21 n 10 DC 21 B G 22 n 11 DG 22 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 3.33 0.30 108.30 111.63 A A A O4' C1' N1 DC DC DC 1 1 1 N 1 2.97 0.30 108.30 111.27 A A A O4' C1' N9 DG DG DG 2 2 2 N 1 4.49 0.50 113.10 117.59 A A A N7 C8 N9 DG DG DG 2 2 2 N 1 -2.77 0.40 106.40 103.63 A A A C8 N9 C4 DG DG DG 2 2 2 N 1 2.47 0.30 108.30 110.77 A A A O4' C1' N9 DG DG DG 3 3 3 N 1 4.59 0.50 113.10 117.69 A A A N7 C8 N9 DG DG DG 3 3 3 N 1 -2.64 0.40 106.40 103.76 A A A C8 N9 C4 DG DG DG 3 3 3 N 1 3.11 0.30 108.30 111.41 A A A O4' C1' N9 DA DA DA 4 4 4 N 1 3.70 0.50 113.80 117.50 A A A N7 C8 N9 DA DA DA 4 4 4 N 1 2.94 0.30 108.30 111.24 A A A O4' C1' N9 DA DA DA 6 6 6 N 1 3.82 0.50 113.80 117.62 A A A N7 C8 N9 DA DA DA 6 6 6 N 1 3.17 0.30 108.30 111.47 A A A O4' C1' N9 DA DA DA 7 7 7 N 1 3.88 0.50 113.80 117.68 A A A N7 C8 N9 DA DA DA 7 7 7 N 1 3.02 0.30 108.30 111.32 A A A O4' C1' N9 DG DG DG 8 8 8 N 1 4.57 0.50 113.10 117.67 A A A N7 C8 N9 DG DG DG 8 8 8 N 1 -2.66 0.40 106.40 103.74 A A A C8 N9 C4 DG DG DG 8 8 8 N 1 3.66 0.50 113.80 117.46 A A A N7 C8 N9 DA DA DA 9 9 9 N 1 2.48 0.30 108.30 110.78 A A A O4' C1' N9 DA DA DA 10 10 10 N 1 3.81 0.50 113.80 117.61 A A A N7 C8 N9 DA DA DA 10 10 10 N 1 2.77 0.30 108.30 111.07 A A A O4' C1' N9 DG DG DG 11 11 11 N 1 4.84 0.50 113.10 117.94 A A A N7 C8 N9 DG DG DG 11 11 11 N 1 -2.67 0.40 106.40 103.73 A A A C8 N9 C4 DG DG DG 11 11 11 N 1 3.21 0.30 108.30 111.51 B B B O4' C1' N1 DC DC DC 12 12 12 N 1 2.70 0.30 108.30 111.00 B B B O4' C1' N1 DT DT DT 13 13 13 N 1 3.03 0.30 108.30 111.33 B B B O4' C1' N1 DT DT DT 14 14 14 N 1 3.27 0.30 108.30 111.57 B B B O4' C1' N1 DC DC DC 15 15 15 N 1 3.13 0.30 108.30 111.43 B B B O4' C1' N1 DT DT DT 16 16 16 N 1 -3.65 0.60 122.90 119.25 B B B C6 C5 C7 DT DT DT 16 16 16 N 1 2.74 0.30 108.30 111.04 B B B O4' C1' N1 DT DT DT 17 17 17 N 1 2.29 0.30 108.30 110.59 B B B O4' C1' N9 DG DG DG 18 18 18 N 1 4.52 0.50 113.10 117.62 B B B N7 C8 N9 DG DG DG 18 18 18 N 1 -2.71 0.40 106.40 103.69 B B B C8 N9 C4 DG DG DG 18 18 18 N 1 2.35 0.30 108.30 110.65 B B B O4' C1' N1 DT DT DT 19 19 19 N 1 3.01 0.30 108.30 111.31 B B B O4' C1' N1 DC DC DC 20 20 20 N 1 3.27 0.30 108.30 111.57 B B B O4' C1' N9 DG DG DG 22 22 22 N 1 4.71 0.50 113.10 117.81 B B B N7 C8 N9 DG DG DG 22 22 22 N 1 -2.42 0.40 106.40 103.98 B B B C8 N9 C4 DG DG DG 22 22 22 N THE SOLUTION STRUCTURE OF A NON-BAY REGION 11R-BENZ[A]ANTHRACENE OXIDE ADDUCT AT THE N6 POSITION OF ADENINE OF AN OLIGODEOXYNUCLEOTIDE CONTAINING THE HUMAN N-RAS CODON 61 SEQUENCE 1 N N 2 N N 3 N N covale 1.343 none A DA 6 A N6 DA 6 1_555 A TBT 25 C C4C TBT 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 22 B N1 DG 11 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 22 B O6 DG 11 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 22 B N2 DG 11 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 B DC 21 B N3 DC 10 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B DC 21 B O2 DC 10 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B DC 21 B N4 DC 10 1_555 hydrog WATSON-CRICK A DG 3 A N1 DG 3 1_555 B DC 20 B N3 DC 9 1_555 hydrog WATSON-CRICK A DG 3 A N2 DG 3 1_555 B DC 20 B O2 DC 9 1_555 hydrog WATSON-CRICK A DG 3 A O6 DG 3 1_555 B DC 20 B N4 DC 9 1_555 hydrog WATSON-CRICK A DA 4 A N1 DA 4 1_555 B DT 19 B N3 DT 8 1_555 hydrog WATSON-CRICK A DA 4 A N6 DA 4 1_555 B DT 19 B O4 DT 8 1_555 hydrog WATSON-CRICK A DC 5 A N3 DC 5 1_555 B DG 18 B N1 DG 7 1_555 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 B DG 18 B O6 DG 7 1_555 hydrog WATSON-CRICK A DC 5 A O2 DC 5 1_555 B DG 18 B N2 DG 7 1_555 hydrog DA-DT PAIR A DA 6 A N6 DA 6 1_555 B DT 17 B O4 DT 6 1_555 hydrog WATSON-CRICK A DA 7 A N1 DA 7 1_555 B DT 16 B N3 DT 5 1_555 hydrog WATSON-CRICK A DA 7 A N6 DA 7 1_555 B DT 16 B O4 DT 5 1_555 hydrog WATSON-CRICK A DG 8 A N1 DG 8 1_555 B DC 15 B N3 DC 4 1_555 hydrog WATSON-CRICK A DG 8 A N2 DG 8 1_555 B DC 15 B O2 DC 4 1_555 hydrog WATSON-CRICK A DG 8 A O6 DG 8 1_555 B DC 15 B N4 DC 4 1_555 hydrog WATSON-CRICK A DA 9 A N1 DA 9 1_555 B DT 14 B N3 DT 3 1_555 hydrog WATSON-CRICK A DA 9 A N6 DA 9 1_555 B DT 14 B O4 DT 3 1_555 hydrog WATSON-CRICK A DA 10 A N1 DA 10 1_555 B DT 13 B N3 DT 2 1_555 hydrog WATSON-CRICK A DA 10 A N6 DA 10 1_555 B DT 13 B O4 DT 2 1_555 hydrog WATSON-CRICK A DG 11 A N1 DG 11 1_555 B DC 12 B N3 DC 1 1_555 hydrog WATSON-CRICK A DG 11 A N2 DG 11 1_555 B DC 12 B O2 DC 1 1_555 hydrog WATSON-CRICK A DG 11 A O6 DG 11 1_555 B DC 12 B N4 DC 1 1_555 DNA BENZ[A]ANTHRACENE-DNA DUPLEX, DNA 1DJD PDB 1 1DJD 1DJD PDB 2 1DJD 1 11 1DJD 1 11 1DJD A 1 1 11 12 22 1DJD 12 22 1DJD B 2 1 11 BINDING SITE FOR RESIDUE TBT A 25 A TBT 25 Software 5 A DA 6 A DA 6 5 1_555 A DA 7 A DA 7 5 1_555 B DT 16 B DT 5 5 1_555 B DT 17 B DT 6 5 1_555 B DG 18 B DG 7 5 1_555 1 P 1