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. Tamura, P.J. Wilkinson, A.S. 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 40 6743 6755 10.1021/bi002785r 11389588 Intercalation of the (1R,2S,3R,4S)-N6-[1-(1,2,3,4-tetrahydro-2,3,4-trihydroxybenz[a]anthracenyl)]-2'-deoxyadenosyl adduct in the N-ras codon 61 sequence: DNA sequence effects 2001 10.2210/pdb1i7v/pdb pdb_00001i7v 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 5'-D(*CP*GP*GP*AP*CP*AP*(BZA)AP*GP*AP*AP*G)-3' 1 syn polymer 3291.145 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 -12.141 1 19 A 1 B 22 -1.770 A_DC1:DG22_B 1 -0.330 0.552 0.336 -0.262 8.065 1 19 A 2 B 21 -2.638 A_DG2:DC21_B 2 0.107 -0.420 0.270 -0.260 0.585 1 19 A 3 B 20 -3.377 A_DG3:DC20_B 3 -4.694 -0.455 -0.052 -0.185 1.325 1 20 A 4 B 19 -0.671 A_DA4:DT19_B 4 -3.268 0.362 -0.078 -0.073 5.538 1 19 A 5 B 18 -0.282 A_DC5:DG18_B 5 -1.748 0.828 -0.195 -0.323 41.889 A 6 B 17 -8.055 A_DA6:DT17_B 6 7.133 0.635 0.863 0.744 -39.092 1 20 A 7 B 16 -18.416 A_DA7:DT16_B 7 23.670 -0.032 0.082 0.344 -2.224 1 19 A 8 B 15 0.283 A_DG8:DC15_B 8 4.233 -0.562 0.125 -0.163 10.331 1 20 A 9 B 14 -4.507 A_DA9:DT14_B 9 -8.415 0.369 0.021 -0.047 5.403 1 20 A 10 B 13 -3.112 A_DA10:DT13_B 10 -7.138 0.074 -0.006 -0.103 7.148 1 19 A 11 B 12 -1.471 A_DG11:DC12_B 11 -6.273 -0.529 0.062 -0.273 2.412 30.451 A A 1 2 5.949 B B 22 21 2.477 3.116 0.142 -0.560 AA_DC1DG2:DC21DG22_BB 1 2.513 -4.798 30.193 -1.533 0.106 2.685 35.640 A A 2 3 25.298 B B 21 20 3.371 15.025 -0.017 -0.940 AA_DG2DG3:DC20DC21_BB 2 1.392 -2.344 32.383 -3.659 0.225 3.240 38.449 A A 3 4 5.690 B B 20 19 3.306 3.742 0.398 -0.476 AA_DG3DA4:DT19DC20_BB 3 -0.683 1.039 38.268 -1.189 -0.690 3.315 37.707 A A 4 5 -5.833 B B 19 18 3.299 -3.763 -0.185 -0.396 AA_DA4DC5:DG18DT19_BB 4 1.085 -1.681 37.510 -0.118 0.429 2.930 35.558 A A 5 6 -18.080 B B 18 17 3.260 -10.875 -0.898 0.557 AA_DC5DA6:DT17DG18_BB 5 0.725 -1.206 33.898 2.452 1.574 2.378 26.145 A A 7 8 11.592 B B 16 15 2.609 5.206 1.268 -0.471 AA_DA7DG8:DC15DT16_BB 6 -1.736 3.865 25.573 -2.133 -3.166 2.964 36.773 A A 8 9 4.831 B B 15 14 3.015 3.044 -0.507 -0.293 AA_DG8DA9:DT14DC15_BB 7 1.247 -1.980 36.631 -0.843 0.960 3.231 35.916 A A 9 10 11.904 B B 14 13 3.402 7.293 -0.056 -0.535 AA_DA9DA10:DT13DT14_BB 8 -0.329 0.536 35.190 -1.935 0.042 3.118 33.293 A A 10 11 5.100 B B 13 12 3.175 2.918 0.008 -0.524 AA_DA10DG11:DC12DT13_BB 9 -0.570 0.996 33.164 -1.383 -0.105 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 2001-03-28 1 1 2007-10-16 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _struct_conn.pdbx_leaving_atom_flag _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2001-03-10 REL REL BZA 1R,2S,3R,4S-TETRAHYDRO-BENZO[A]ANTHRACENE-2,3,4-TRIOL 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 288 K The structure was based on a total of 485 NOE derived distance constraints. NOE-restrained molecular dynamics/simulated annealing 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 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 3.0 500 Bruker DMX 750 Bruker DMX ABA 7 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 A 6 n 6 DA 6 A ABA 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 2.79 0.30 108.30 111.09 A A A O4' C1' N1 DC DC DC 1 1 1 N 1 3.19 0.30 108.30 111.49 A A A O4' C1' N9 DG DG DG 2 2 2 N 1 4.56 0.50 113.10 117.66 A A A N7 C8 N9 DG DG DG 2 2 2 N 1 -2.65 0.40 106.40 103.75 A A A C8 N9 C4 DG DG DG 2 2 2 N 1 3.33 0.30 108.30 111.63 A A A O4' C1' N9 DG DG DG 3 3 3 N 1 4.54 0.50 113.10 117.64 A A A N7 C8 N9 DG DG DG 3 3 3 N 1 -2.67 0.40 106.40 103.73 A A A C8 N9 C4 DG DG DG 3 3 3 N 1 3.17 0.30 108.30 111.47 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 2.59 0.30 108.30 110.89 A A A O4' C1' N1 DC DC DC 5 5 5 N 1 3.64 0.50 113.80 117.44 A A A N7 C8 N9 DA DA DA 6 6 6 N 1 -2.49 0.40 105.80 103.31 A A A C8 N9 C4 DA DA DA 6 6 6 N 1 3.00 0.30 108.30 111.30 A A A O4' C1' N9 DA DA DA 7 7 7 N 1 3.76 0.50 113.80 117.56 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 4.45 0.50 113.10 117.55 A A A N7 C8 N9 DG DG DG 8 8 8 N 1 -2.69 0.40 106.40 103.71 A A A C8 N9 C4 DG DG DG 8 8 8 N 1 2.72 0.30 108.30 111.02 A A A O4' C1' N9 DA DA DA 9 9 9 N 1 3.76 0.50 113.80 117.56 A A A N7 C8 N9 DA DA DA 9 9 9 N 1 2.60 0.30 108.30 110.90 A A A O4' C1' N9 DA DA DA 10 10 10 N 1 3.80 0.50 113.80 117.60 A A A N7 C8 N9 DA DA DA 10 10 10 N 1 2.70 0.30 108.30 111.00 A A A O4' C1' N9 DG DG DG 11 11 11 N 1 4.50 0.50 113.10 117.60 A A A N7 C8 N9 DG DG DG 11 11 11 N 1 -2.71 0.40 106.40 103.69 A A A C8 N9 C4 DG DG DG 11 11 11 N 1 3.03 0.30 108.30 111.33 B B B O4' C1' N1 DC DC DC 12 12 12 N 1 3.06 0.30 108.30 111.36 B B B O4' C1' N1 DT DT DT 13 13 13 N 1 2.80 0.30 108.30 111.10 B B B O4' C1' N1 DT DT DT 14 14 14 N 1 2.27 0.30 108.30 110.57 B B B O4' C1' N1 DC DC DC 15 15 15 N 1 1.90 0.30 108.30 110.20 B B B O4' C1' N1 DT DT DT 16 16 16 N 1 -4.03 0.60 122.90 118.87 B B B C6 C5 C7 DT DT DT 16 16 16 N 1 2.81 0.30 108.30 111.11 B B B O4' C1' N1 DT DT DT 17 17 17 N 1 3.50 0.30 108.30 111.80 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 -2.71 0.40 106.40 103.69 B B B C8 N9 C4 DG DG DG 18 18 18 N 1 2.80 0.30 108.30 111.10 B B B O4' C1' N1 DT DT DT 19 19 19 N 1 3.18 0.30 108.30 111.48 B B B O4' C1' N1 DC DC DC 20 20 20 N 1 2.76 0.30 108.30 111.06 B B B O4' C1' N1 DC DC DC 21 21 21 N 1 2.81 0.30 108.30 111.11 B B B O4' C1' N9 DG DG DG 22 22 22 N 1 4.52 0.50 113.10 117.62 B B B N7 C8 N9 DG DG DG 22 22 22 N 1 -2.64 0.40 106.40 103.76 B B B C8 N9 C4 DG DG DG 22 22 22 N THE SOLUTION STRUCTURE OF A BAY REGION 1R-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 1.344 none A DA 7 A N6 DA 7 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 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 1I7V PDB 1 1I7V 1I7V PDB 2 1I7V 1 11 1I7V 1 11 1I7V A 1 1 11 12 22 1I7V 12 22 1I7V B 2 1 11 BINDING SITE FOR RESIDUE BZA A 12 A BZA 12 Software 6 A DA 6 A DA 6 6 1_555 A DA 7 A DA 7 6 1_555 A DG 8 A DG 8 6 1_555 B DC 15 B DC 4 6 1_555 B DT 16 B DT 5 6 1_555 B DT 17 B DT 6 6 1_555 1 P 1