1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Subramaniam, G. Paz, M.M. Kumar, G.S. Das, A. Palom, Y. Clement, C.C. Patel, D.J. Tomasz, M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 C10 H14 N5 O6 P 331.222 y 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE DNA linking C13 H16 N3 O2 1 246.285 DECARBAMOYL-2,7-DIAMINOMITOSENE non-polymer 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 10473 10484 10.1021/bi010965a 11523988 Solution structure of a guanine-N7-linked complex of the mitomycin C metabolite 2,7-diaminomitosene and DNA. Basis of sequence selectivity. 2001 10.2210/pdb1jo1/pdb pdb_00001jo1 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 SINGLE WAVELENGTH M 1 1.0 3662.404 5'-D(*GP*TP*GP*(DAJ)GP*TP*AP*TP*AP*CP*CP*AP*C)-3' 2 syn polymer 246.285 DECARBAMOYL-2,7-DIAMINOMITOSENE 2 syn non-polymer no no (DG)(DT)(DG)(DG)(DT)(DA)(DT)(DA)(DC)(DC)(DA)(DC) GTGGTATACCAC A,B polydeoxyribonucleotide n n n n n n n n n n n n 16.720 1 19 A 1 B 12 2.902 A_DG1:DC12_B 1 0.748 -1.162 0.561 -0.319 1.397 1 20 A 2 B 11 -0.418 A_DT2:DA11_B 2 -11.578 -0.244 0.224 -0.247 16.186 1 19 A 3 B 10 -0.207 A_DG3:DC10_B 3 2.519 -0.644 0.936 -0.408 -28.666 1 19 A 4 B 9 -1.918 A_DG4:DC9_B 4 -20.654 -0.234 -0.138 -0.129 -11.445 1 20 A 5 B 8 7.407 A_DT5:DA8_B 5 4.696 -0.017 0.226 -0.093 -6.187 1 20 A 6 B 7 5.702 A_DA6:DT7_B 6 -5.988 0.174 -1.021 -0.505 6.159 1 20 A 7 B 6 5.708 A_DT7:DA6_B 7 -5.977 -0.175 -1.021 -0.504 11.440 1 20 A 8 B 5 7.400 A_DA8:DT5_B 8 4.719 0.018 0.225 -0.091 28.677 1 19 A 9 B 4 -1.895 A_DC9:DG4_B 9 -20.594 0.236 -0.139 -0.127 -16.164 1 19 A 10 B 3 -0.205 A_DC10:DG3_B 10 2.533 0.649 0.937 -0.410 -1.358 1 20 A 11 B 2 -0.418 A_DA11:DT2_B 11 -11.575 0.249 0.225 -0.252 -16.703 1 19 A 12 B 1 2.897 A_DC12:DG1_B 12 0.731 1.161 0.559 -0.326 3.623 38.501 A A 1 2 -3.136 B B 12 11 3.589 -2.066 -0.303 -1.140 AA_DG1DT2:DA11DC12_BB 1 2.065 -3.134 38.394 -1.446 0.742 2.623 33.272 A A 2 3 -10.209 B B 11 10 2.779 -5.768 0.880 -0.892 AA_DT2DG3:DC10DA11_BB 2 -7.622 13.492 31.906 -0.745 -2.611 4.738 40.423 A A 3 4 -4.093 B B 10 9 4.733 -2.759 0.581 -2.077 AA_DG3DG4:DC9DC10_BB 3 15.501 -22.995 37.349 -2.538 1.790 2.675 31.783 A A 4 5 8.468 B B 9 8 2.711 4.618 -0.203 -0.114 AA_DG4DT5:DA8DC9_BB 4 -2.193 4.022 31.379 -0.908 0.038 3.211 42.792 A A 5 6 11.532 B B 8 7 3.020 8.255 0.635 1.011 AA_DT5DA6:DT7DA8_BB 5 12.299 -17.181 40.260 0.573 0.340 2.410 33.332 A A 6 7 10.637 B B 7 6 2.566 6.069 0.000 -0.650 AA_DA6DT7:DA6DT7_BB 6 0.002 -0.003 32.790 -1.908 0.000 3.210 42.787 A A 7 8 11.535 B B 6 5 3.019 8.256 -0.636 1.011 AA_DT7DA8:DT5DA6_BB 7 -12.298 17.182 40.254 0.574 -0.339 2.675 31.774 A A 8 9 8.476 B B 5 4 2.711 4.621 0.204 -0.113 AA_DA8DC9:DG4DT5_BB 8 2.189 -4.015 31.370 -0.908 -0.040 4.739 40.436 A A 9 10 -4.097 B B 4 3 4.734 -2.763 -0.581 -2.077 AA_DC9DC10:DG3DG4_BB 9 -15.509 22.999 37.360 -2.536 -1.790 2.623 33.274 A A 10 11 -10.206 B B 3 2 2.779 -5.766 -0.880 -0.892 AA_DC10DA11:DT2DG3_BB 10 7.613 -13.474 31.911 -0.745 2.609 3.624 38.483 A A 11 12 -3.144 B B 2 1 3.590 -2.070 0.302 -1.141 AA_DA11DC12:DG1DT2_BB 11 -2.049 3.111 38.377 -1.447 -0.740 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 2001-09-12 1 1 2008-04-27 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_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 2001-07-26 REL REL DAJ DECARBAMOYL-2,7-DIAMINOMITOSENE synthesized using ABI-380B synthesizer sample This structure was determined using standard 2d-NOE buildup studies in H2O and D2O buffers. lowest number of NOE violations 12 1 2D NOESY 2D NOESY P-COSY HOHAHA P-COSY 2D NOESY 0.1 M NaCl 6.8 ambient 278 K 0.1 M NaCl 6.8 ambient 303 K The structure is based on 126 intramolecular DNA constraints, 30 H-bonding constraints, 48 intermolecular drug-DNA constraints, and 48 dihedral constraints distance geometry and molecular dynamics 1.2 mM d(GTG(+G)TATACCAC) duplex in 0.01 M sodium phosphate, 0.1 M NaCl, 0.001M EDTA 90% H2O/10% D2O 1.2 mM d(GTG(+G)TATACCAC) duplex in 0.01 M sodium phosphate, 0.1 M NaCl, 0.001M EDTA 100% D2O Varian Instruments collection VNMR 6.1 MSI data analysis Felix 3.0 A. Brunger structure solution X-PLOR 3.01 A. Brunger refinement X-PLOR 3.01 500 Varian UNITYPLUS 600 Varian UNITYPLUS DAM 13 2 DAJ DAJ 13 A DAM 13 2 DAJ DAJ 13 B G 1 n 1 DG 1 A T 2 n 2 DT 2 A G 3 n 3 DG 3 A +G 4 n 4 DG 4 A T 5 n 5 DT 5 A A 6 n 6 DA 6 A T 7 n 7 DT 7 A A 8 n 8 DA 8 A C 9 n 9 DC 9 A C 10 n 10 DC 10 A A 11 n 11 DA 11 A C 12 n 12 DC 12 A G 1 n 1 DG 1 B T 2 n 2 DT 2 B G 3 n 3 DG 3 B +G 4 n 4 DG 4 B T 5 n 5 DT 5 B A 6 n 6 DA 6 B T 7 n 7 DT 7 B A 8 n 8 DA 8 B C 9 n 9 DC 9 B C 10 n 10 DC 10 B A 11 n 11 DA 11 B C 12 n 12 DC 12 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 B A O4 HN1 DT DAJ 7 13 1.48 1 A B O4 HN1 DT DAJ 7 13 1.48 1 3.99 0.30 108.30 112.29 A A A O4' C1' N9 DG DG DG 1 1 1 N 1 3.81 0.50 113.10 116.91 A A A N7 C8 N9 DG DG DG 1 1 1 N 1 3.35 0.30 108.30 111.65 A A A O4' C1' N1 DT DT DT 2 2 2 N 1 7.29 0.30 108.30 115.59 A A A O4' C1' N9 DG DG DG 3 3 3 N 1 -4.73 0.70 102.20 97.47 A A A C4' C3' C2' DG DG DG 4 4 4 N 1 5.22 0.30 108.30 113.52 A A A O4' C1' N9 DG DG DG 4 4 4 N 1 2.81 0.40 105.40 108.21 A A A N9 C4 C5 DG DG DG 4 4 4 N 1 5.51 0.60 119.00 124.51 A A A C4 C5 C7 DT DT DT 5 5 5 N 1 -6.81 0.60 122.90 116.09 A A A C6 C5 C7 DT DT DT 5 5 5 N 1 2.65 0.30 108.30 110.95 A A A O4' C1' N9 DA DA DA 6 6 6 N 1 -6.76 0.80 105.90 99.14 A A A O4' C1' C2' DC DC DC 9 9 9 N 1 6.43 0.30 108.30 114.73 A A A O4' C1' N1 DC DC DC 9 9 9 N 1 3.80 0.60 118.90 122.70 A A A N1 C2 O2 DC DC DC 9 9 9 N 1 2.07 0.30 108.30 110.37 A A A O4' C1' N1 DC DC DC 10 10 10 N 1 3.60 0.60 118.90 122.50 A A A N1 C2 O2 DC DC DC 10 10 10 N 1 3.37 0.30 108.30 111.67 A A A O4' C1' N1 DC DC DC 12 12 12 N 1 4.02 0.30 108.30 112.32 B B B O4' C1' N9 DG DG DG 1 1 1 N 1 3.80 0.50 113.10 116.90 B B B N7 C8 N9 DG DG DG 1 1 1 N 1 3.30 0.30 108.30 111.60 B B B O4' C1' N1 DT DT DT 2 2 2 N 1 7.27 0.30 108.30 115.57 B B B O4' C1' N9 DG DG DG 3 3 3 N 1 -4.75 0.70 102.20 97.45 B B B C4' C3' C2' DG DG DG 4 4 4 N 1 5.28 0.30 108.30 113.58 B B B O4' C1' N9 DG DG DG 4 4 4 N 1 2.87 0.40 105.40 108.27 B B B N9 C4 C5 DG DG DG 4 4 4 N 1 5.57 0.60 119.00 124.57 B B B C4 C5 C7 DT DT DT 5 5 5 N 1 -6.84 0.60 122.90 116.06 B B B C6 C5 C7 DT DT DT 5 5 5 N 1 2.69 0.30 108.30 110.99 B B B O4' C1' N9 DA DA DA 6 6 6 N 1 -3.63 0.60 122.30 118.67 B B B N3 C2 O2 DT DT DT 7 7 7 N 1 -6.73 0.80 105.90 99.17 B B B O4' C1' C2' DC DC DC 9 9 9 N 1 6.37 0.30 108.30 114.67 B B B O4' C1' N1 DC DC DC 9 9 9 N 1 3.78 0.60 118.90 122.68 B B B N1 C2 O2 DC DC DC 9 9 9 N 1 2.07 0.30 108.30 110.37 B B B O4' C1' N1 DC DC DC 10 10 10 N 1 3.60 0.60 118.90 122.50 B B B N1 C2 O2 DC DC DC 10 10 10 N 1 3.43 0.30 108.30 111.73 B B B O4' C1' N1 DC DC DC 12 12 12 N 1 A A C5 C7 DT DT 2 2 0.041 0.006 1.496 1.537 N 1 A A N7 C8 DG DG 4 4 0.068 0.006 1.305 1.373 N 1 A A C5 C7 DT DT 5 5 0.051 0.006 1.496 1.547 N 1 A A C5 C7 DT DT 7 7 0.038 0.006 1.496 1.534 N 1 B B C5 C7 DT DT 2 2 0.041 0.006 1.496 1.537 N 1 B B N7 C8 DG DG 4 4 0.068 0.006 1.305 1.373 N 1 B B C5 C7 DT DT 5 5 0.051 0.006 1.496 1.547 N 1 B B C5 C7 DT DT 7 7 0.037 0.006 1.496 1.533 N N7-Guanine Adduct of 2,7-diaminomitosene with DNA 1 N N 1 N N 2 N N 2 N N covale 1.503 none A DG 4 A N7 DG 4 1_555 A DAJ 13 C C10 DAJ 1_555 covale 1.504 none B DG 4 B N7 DG 4 1_555 B DAJ 13 D C10 DAJ 1_555 hydrog WATSON-CRICK A DG 1 A N1 DG 1 1_555 B DC 12 B N3 DC 12 1_555 hydrog WATSON-CRICK A DG 1 A N2 DG 1 1_555 B DC 12 B O2 DC 12 1_555 hydrog WATSON-CRICK A DG 1 A O6 DG 1 1_555 B DC 12 B N4 DC 12 1_555 hydrog WATSON-CRICK A DT 2 A N3 DT 2 1_555 B DA 11 B N1 DA 11 1_555 hydrog WATSON-CRICK A DT 2 A O4 DT 2 1_555 B DA 11 B N6 DA 11 1_555 hydrog WATSON-CRICK A DG 3 A N1 DG 3 1_555 B DC 10 B N3 DC 10 1_555 hydrog WATSON-CRICK A DG 3 A N2 DG 3 1_555 B DC 10 B O2 DC 10 1_555 hydrog WATSON-CRICK A DG 3 A O6 DG 3 1_555 B DC 10 B N4 DC 10 1_555 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 B DC 9 B N3 DC 9 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B DC 9 B O2 DC 9 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 B DC 9 B N4 DC 9 1_555 hydrog WATSON-CRICK A DT 5 A N3 DT 5 1_555 B DA 8 B N1 DA 8 1_555 hydrog WATSON-CRICK A DT 5 A O4 DT 5 1_555 B DA 8 B N6 DA 8 1_555 hydrog WATSON-CRICK A DA 6 A N1 DA 6 1_555 B DT 7 B N3 DT 7 1_555 hydrog WATSON-CRICK A DA 6 A N6 DA 6 1_555 B DT 7 B O4 DT 7 1_555 hydrog WATSON-CRICK A DT 7 A N3 DT 7 1_555 B DA 6 B N1 DA 6 1_555 hydrog WATSON-CRICK A DT 7 A O4 DT 7 1_555 B DA 6 B N6 DA 6 1_555 hydrog WATSON-CRICK A DA 8 A N1 DA 8 1_555 B DT 5 B N3 DT 5 1_555 hydrog WATSON-CRICK A DA 8 A N6 DA 8 1_555 B DT 5 B O4 DT 5 1_555 hydrog WATSON-CRICK A DC 9 A N3 DC 9 1_555 B DG 4 B N1 DG 4 1_555 hydrog WATSON-CRICK A DC 9 A N4 DC 9 1_555 B DG 4 B O6 DG 4 1_555 hydrog WATSON-CRICK A DC 9 A O2 DC 9 1_555 B DG 4 B N2 DG 4 1_555 hydrog WATSON-CRICK A DC 10 A N3 DC 10 1_555 B DG 3 B N1 DG 3 1_555 hydrog WATSON-CRICK A DC 10 A N4 DC 10 1_555 B DG 3 B O6 DG 3 1_555 hydrog WATSON-CRICK A DC 10 A O2 DC 10 1_555 B DG 3 B N2 DG 3 1_555 hydrog WATSON-CRICK A DA 11 A N1 DA 11 1_555 B DT 2 B N3 DT 2 1_555 hydrog WATSON-CRICK A DA 11 A N6 DA 11 1_555 B DT 2 B O4 DT 2 1_555 hydrog WATSON-CRICK A DC 12 A N3 DC 12 1_555 B DG 1 B N1 DG 1 1_555 hydrog WATSON-CRICK A DC 12 A N4 DC 12 1_555 B DG 1 B O6 DG 1 1_555 hydrog WATSON-CRICK A DC 12 A O2 DC 12 1_555 B DG 1 B N2 DG 1 1_555 DNA double helix, major groove binding drug, guanine-N7-alkylator, DNA 1JO1 PDB 1 1JO1 1 12 1JO1 1 12 1JO1 A 1 1 12 1 12 1JO1 1 12 1JO1 B 1 1 12 BINDING SITE FOR RESIDUE DAJ A 13 A DAJ 13 Software 6 BINDING SITE FOR RESIDUE DAJ B 13 B DAJ 13 Software 6 A DG 3 A DG 3 6 1_555 A DG 4 A DG 4 6 1_555 A DT 5 A DT 5 6 1_555 A DA 6 A DA 6 6 1_555 B DA 6 B DA 6 6 1_555 B DT 7 B DT 7 6 1_555 A DA 6 A DA 6 6 1_555 A DT 7 A DT 7 6 1_555 B DG 3 B DG 3 6 1_555 B DG 4 B DG 4 6 1_555 B DT 5 B DT 5 6 1_555 B DA 6 B DA 6 6 1_555