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 C18 H16 O3 280.318 1R,2S,3R,4S-TETRAHYDRO-BENZO[A]ANTHRACENE-2,3,4-TRIOL 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 US Biochemistry BICHAW 0033 0006-2960 38 16045 16057 10.1021/bi9903650 10587427 Intercalation of the (1S,2R,3S,4R)-N6-[1-(1,2,3,4-tetrahydro-2,3, 4-trihydroxybenz[a]anthracenyl)]-2'-deoxyadenosyl adduct in an oligodeoxynucleotide containing the human N-ras codon 61 sequence. 1999 10.2210/pdb1dl4/pdb pdb_00001dl4 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 BENZ[A]ANTHRACENE-MODIFIED ADENINE-6 3416.263 DNA (5'-D(*CP*GP*GP*AP*CP*(BZA)AP*AP*GP*AP*AP*G)-3') 1 syn polymer 3291.145 DNA (5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3') 1 syn polymer 280.318 1R,2S,3R,4S-TETRAHYDRO-BENZO[A]ANTHRACENE-2,3,4-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 -8.158 1 19 A 1 B 22 -3.851 A_DC1:DG22_B 1 1.279 0.545 0.253 -0.314 -0.833 1 19 A 2 B 21 -3.087 A_DG2:DC21_B 2 -5.306 0.189 -0.084 -0.053 -0.979 1 19 A 3 B 20 -2.071 A_DG3:DC20_B 3 -3.857 -0.687 -0.030 -0.299 9.806 1 20 A 4 B 19 -7.108 A_DA4:DT19_B 4 1.774 0.358 0.204 -0.025 23.823 1 19 A 5 B 18 5.633 A_DC5:DG18_B 5 9.594 1.350 -0.127 -0.399 -28.810 1 20 A 7 B 16 -7.891 A_DA7:DT16_B 6 -5.666 1.418 -0.873 -0.240 -3.598 1 19 A 8 B 15 -5.336 A_DG8:DC15_B 7 2.328 -0.111 -0.111 -0.091 9.028 1 20 A 9 B 14 1.173 A_DA9:DT14_B 8 -2.321 0.466 -0.080 -0.094 21.548 1 20 A 10 B 13 -1.394 A_DA10:DT13_B 9 -9.349 0.196 0.095 0.025 9.620 1 19 A 11 B 12 -4.999 A_DG11:DC12_B 10 -1.487 -0.783 -0.052 -0.339 2.725 33.752 A A 1 2 9.194 B B 22 21 2.772 5.287 0.626 -0.535 AA_DC1DG2:DC21DG22_BB 1 6.330 -11.008 32.757 -1.653 -0.202 2.968 34.636 A A 2 3 6.594 B B 21 20 3.079 3.917 -0.112 -0.868 AA_DG2DG3:DC20DC21_BB 2 -1.522 2.562 34.388 -2.016 -0.029 2.977 39.422 A A 3 4 0.315 B B 20 19 2.969 0.213 -0.383 -0.291 AA_DG3DA4:DT19DC20_BB 3 -1.095 1.624 39.406 -0.454 0.451 3.021 35.372 A A 4 5 -2.293 B B 19 18 3.055 -1.391 0.687 -0.753 AA_DA4DC5:DG18DT19_BB 4 -2.768 4.561 35.240 -1.049 -1.510 2.380 26.844 A A 7 8 7.499 B B 16 15 2.444 3.453 0.188 0.231 AA_DA7DG8:DC15DT16_BB 5 -4.906 10.655 26.177 -0.167 -1.349 2.917 35.404 A A 8 9 5.499 B B 15 14 2.969 3.339 0.320 -0.324 AA_DG8DA9:DT14DC15_BB 6 -1.069 1.761 35.235 -0.976 -0.668 2.926 37.085 A A 9 10 -1.793 B B 14 13 2.893 -1.139 -0.660 0.033 AA_DA9DA10:DT13DT14_BB 7 -2.359 3.712 36.995 0.187 0.757 3.357 33.129 A A 10 11 3.086 B B 13 12 3.371 1.758 -0.711 -0.918 AA_DA10DG11:DC12DT13_BB 8 -2.187 3.840 33.013 -1.916 0.867 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 2000-01-12 1 1 2007-10-16 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 1999-12-08 REL REL BZA 1R,2S,3R,4S-TETRAHYDRO-BENZO[A]ANTHRACENE-2,3,4-TRIOL THIS SEQUENCE WAS SYNTHESIZED BY CHEMICAL METHOD sample THIS SEQUENCE WAS SYNTHESIZED BY CHEMICAL METHOD sample THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES structures with the lowest energy 7 1 2D NOESY 2D NOESY 2D NOESY 2D ROESY DQF-COSY 0.1 M NACL 7.0 1 atm 278 K 0.1 M NACL 7.0 1 atm 283 K 0.1 M NACL 7.0 1 atm 298 K THE STRUCTURE IS BASED ON A TOTAL OF 477 NOE-DERIVED DISTANCE CONSTRAINTS, 80 EMPIRICAL SUGAR PUCKER RESTRAINTS, 32 BACKBONE ANGLE DIHEDRAL RESTRAINTS, AND 18 EMPIRICAL PLANARITY RESTRAINTS. NOE-RESTRAINTED MOLECULAR DYNAMICS /SIMULATED ANNEALING 1 lowest energy 1.7 MM OLIGODEOXYNUCLEOTIDE; 10 MM PHOSPHATE BUFFER; 0.05 MM EDTA; 0.1 M NACL 1.7 MM OLIGODEOXYNUCLEOTIDE; 10 MM PHOSPHATE BUFFER; 0.05 MM EDTA; 0.1 M NACL BRUKER collection XwinNMR 2.0 A.BRUNGER structure solution X-PLOR 3.851 BIOSYM TECHNOLOGIES processing Felix 97.0 BORGIAS, B.A., THOMAS, P.D., LI, H., KUMAR, A., AND TONELLI, M. refinement CORMA 5.2 BORGIAS, B.A., THOMAS, P.D., LI, H., KUMAR, A., AND TONELLI, M. iterative matrix relaxation MARDIGRAS 3.0 750 Bruker DRX 500 Bruker DRX ABA 6 3 BZA BZA 12 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 A C9C BZA 12 WRONG HAND 1 A C3B BZA 12 WRONG HAND 1 A DA 6 0.061 SIDE CHAIN 1 2.11 0.30 108.30 110.41 A A A O4' C1' N1 DC DC DC 1 1 1 N 1 4.13 0.30 108.30 112.43 A A A O4' C1' N9 DG DG DG 2 2 2 N 1 4.35 0.50 113.10 117.45 A A A N7 C8 N9 DG DG DG 2 2 2 N 1 -2.57 0.40 106.40 103.83 A A A C8 N9 C4 DG DG DG 2 2 2 N 1 2.40 0.30 108.30 110.70 A A A O4' C1' N9 DG DG DG 3 3 3 N 1 4.62 0.50 113.10 117.72 A A A N7 C8 N9 DG DG DG 3 3 3 N 1 -2.48 0.40 106.40 103.92 A A A C8 N9 C4 DG DG DG 3 3 3 N 1 2.68 0.30 108.30 110.98 A A A O4' C1' N9 DA DA DA 4 4 4 N 1 3.89 0.50 113.80 117.69 A A A N7 C8 N9 DA DA DA 4 4 4 N 1 2.63 0.30 108.30 110.93 A A A O4' C1' N1 DC DC DC 5 5 5 N 1 3.40 0.50 113.80 117.20 A A A N7 C8 N9 DA DA DA 6 6 6 N 1 3.01 0.30 108.30 111.31 A A A O4' C1' N9 DA DA DA 7 7 7 N 1 3.62 0.50 113.80 117.42 A A A N7 C8 N9 DA DA DA 7 7 7 N 1 3.21 0.30 108.30 111.51 A A A O4' C1' N9 DG DG DG 8 8 8 N 1 4.41 0.50 113.10 117.51 A A A N7 C8 N9 DG DG DG 8 8 8 N 1 -2.65 0.40 106.40 103.75 A A A C8 N9 C4 DG DG DG 8 8 8 N 1 2.97 0.30 108.30 111.27 A A A O4' C1' N9 DA DA DA 9 9 9 N 1 3.81 0.50 113.80 117.61 A A A N7 C8 N9 DA DA DA 9 9 9 N 1 2.10 0.30 108.30 110.40 A A A O4' C1' N9 DA DA DA 10 10 10 N 1 3.92 0.50 113.80 117.72 A A A N7 C8 N9 DA DA DA 10 10 10 N 1 2.31 0.30 108.30 110.61 A A A O4' C1' N9 DG DG DG 11 11 11 N 1 4.66 0.50 113.10 117.76 A A A N7 C8 N9 DG DG DG 11 11 11 N 1 -2.51 0.40 106.40 103.89 A A A C8 N9 C4 DG DG DG 11 11 11 N 1 1.93 0.30 108.30 110.23 B B B O4' C1' N1 DC DC DC 12 12 12 N 1 2.98 0.30 108.30 111.28 B B B O4' C1' N1 DT DT DT 13 13 13 N 1 3.38 0.30 108.30 111.68 B B B O4' C1' N1 DT DT DT 14 14 14 N 1 2.86 0.30 108.30 111.16 B B B O4' C1' N1 DC DC DC 15 15 15 N 1 3.59 0.30 108.30 111.89 B B B O4' C1' N1 DT DT DT 16 16 16 N 1 -3.86 0.60 122.90 119.04 B B B C6 C5 C7 DT DT DT 16 16 16 N 1 3.20 0.30 108.30 111.50 B B B O4' C1' N1 DT DT DT 17 17 17 N 1 5.09 0.30 108.30 113.39 B B B O4' C1' N9 DG DG DG 18 18 18 N 1 4.59 0.50 113.10 117.69 B B B N7 C8 N9 DG DG DG 18 18 18 N 1 -3.03 0.40 106.40 103.37 B B B C8 N9 C4 DG DG DG 18 18 18 N 1 2.94 0.30 108.30 111.24 B B B O4' C1' N1 DT DT DT 19 19 19 N 1 2.87 0.30 108.30 111.17 B B B O4' C1' N1 DC DC DC 20 20 20 N 1 2.98 0.30 108.30 111.28 B B B O4' C1' N1 DC DC DC 21 21 21 N 1 1.87 0.30 108.30 110.17 B B B O4' C1' N9 DG DG DG 22 22 22 N 1 4.72 0.50 113.10 117.82 B B B N7 C8 N9 DG DG DG 22 22 22 N 1 -2.43 0.40 106.40 103.97 B B B C8 N9 C4 DG DG DG 22 22 22 N THE SOLUTION STRUCTURE OF A BAY-REGION 1S-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 BZA 12 C C4C BZA 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 DC-DA MISPAIR A DC 5 A N3 DC 5 1_555 A DA 6 A N6 DA 6 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 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 DG-DT MISPAIR A DG 8 A N2 DG 8 1_555 B DT 16 B O2 DT 5 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 1DL4 PDB 1 1DL4 1DL4 PDB 2 1DL4 1 11 1DL4 1 11 1DL4 A 1 1 11 12 22 1DL4 12 22 1DL4 B 2 1 11 BINDING SITE FOR RESIDUE BZA A 12 A BZA 12 Software 6 A DC 5 A DC 5 6 1_555 A DA 6 A DA 6 6 1_555 A DA 7 A DA 7 6 1_555 B DT 16 B DT 5 6 1_555 B DT 17 B DT 6 6 1_555 B DG 18 B DG 7 6 1_555 1 P 1