1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Van Garderen, C.J. Van Houte, L.P.A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 Cl2 H6 N2 Pt 300.045 Cisplatin diammine(dichloro)platinum 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 N 1 N PT N 2 N N N 3 N N N 4 N H N 5 N H N 6 N H N 7 N H N 8 N CL N 9 N CL N 10 N H N 11 N H N 12 N O N 13 N P N 14 N O N 15 N O N 16 N O N 17 N C N 18 R C N 19 N O N 20 S C N 21 N O N 22 N C N 23 R C Y 24 N N Y 25 N C Y 26 N N Y 27 N C Y 28 N C N 29 N N Y 30 N N Y 31 N C Y 32 N N Y 33 N C 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 H N 41 N H N 42 N H N 43 N H N 44 N H N 45 N H N 46 N H N 47 N H N 48 N O N 49 N P N 50 N O N 51 N O N 52 N O N 53 N C N 54 R C N 55 N O N 56 S C N 57 N O N 58 N C N 59 R C N 60 N N N 61 N C N 62 N O N 63 N N N 64 N C N 65 N N N 66 N C N 67 N C 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 H N 77 N H N 78 N H N 79 N H N 80 N H N 81 N H N 82 N O N 83 N P N 84 N O N 85 N O N 86 N O N 87 N C N 88 R C N 89 N O N 90 S C N 91 N O N 92 N C N 93 R C Y 94 N N Y 95 N C Y 96 N N Y 97 N C N 98 N C N 99 N O N 100 N N N 101 N C N 102 N N N 103 N N Y 104 N C N 105 N H N 106 N H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N H N 112 N H N 113 N H N 114 N H N 115 N H N 116 N H N 117 N H N 118 N H N 119 N O N 120 N P N 121 N O N 122 N O N 123 N O N 124 N C N 125 R C N 126 N O N 127 S C N 128 N O N 129 N C N 130 R C N 131 N N N 132 N C N 133 N O N 134 N N N 135 N C N 136 N O N 137 N C N 138 N C N 139 N C 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 H N 148 N H N 149 N H N 150 N H N 151 N H N 152 N H N 153 N H N 154 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N doub N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N sing Y 34 N sing Y 35 N sing Y 36 N doub N 37 N sing Y 38 N sing Y 39 N sing Y 40 N doub N 41 N sing Y 42 N doub N 43 N sing N 44 N sing Y 45 N sing Y 46 N doub N 47 N sing Y 48 N sing N 49 N sing N 50 N sing N 51 N doub 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 N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N doub N 75 N sing N 76 N doub N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N doub N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N doub 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 Y 107 N sing Y 108 N sing Y 109 N doub N 110 N sing Y 111 N sing N 112 N sing Y 113 N doub 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 doub 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 N 140 N sing N 141 N sing N 142 N sing N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N doub 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 doub N 156 N sing N 157 N sing N 158 N sing N 159 N sing IX Eur.J.Biochem. EJBCAI 0262 0014-2956 225 1169 1179 10.1111/j.1432-1033.1994.1169b.x 7957208 The solution structure of a DNA duplex containing the cis-Pt(NH3)2[d(-GTG-)-N7(G),N7(G)] adduct, as determined with high-field NMR and molecular mechanics/dynamics. 1994 10.2210/pdb1da4/pdb pdb_00001da4 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 3902.548 DNA (5'-D(P*CP*TP*CP*TP*AP*GP*TP*GP*CP*TP*CP*AP*C)-3') 1 syn polymer 4040.647 DNA (5'-D(P*GP*TP*GP*AP*GP*CP*AP*CP*TP*AP*GP*AP*G)-3') 1 syn polymer 300.045 Cisplatin 1 syn non-polymer no no (DC)(DT)(DC)(DT)(DA)(DG)(DT)(DG)(DC)(DT)(DC)(DA)(DC) CTCTAGTGCTCAC A polydeoxyribonucleotide no no (DG)(DT)(DG)(DA)(DG)(DC)(DA)(DC)(DT)(DA)(DG)(DA)(DG) GTGAGCACTAGAG B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n n n n n n n 0.126 1 19 A 1 B 26 -6.355 A_DC1:DG26_B 1 -18.913 -0.427 0.837 -0.115 -3.997 1 20 A 2 B 25 -5.730 A_DT2:DA25_B 2 -22.579 0.541 0.721 -0.250 -9.713 1 19 A 3 B 24 -6.369 A_DC3:DG24_B 3 -18.835 0.875 0.879 -0.433 -6.630 1 20 A 4 B 23 -5.892 A_DT4:DA23_B 4 -15.299 0.537 0.900 -0.301 7.805 1 20 A 5 B 22 -1.407 A_DA5:DT22_B 5 -15.482 0.966 0.840 -0.113 12.167 1 19 A 8 B 19 -0.126 A_DG8:DC19_B 6 8.588 -0.759 0.398 -0.122 12.264 1 19 A 9 B 18 -11.113 A_DC9:DG18_B 7 -27.157 0.476 1.154 -0.542 -2.555 1 20 A 10 B 17 -6.748 A_DT10:DA17_B 8 -22.134 0.583 0.829 -0.329 -6.418 1 19 A 11 B 16 -5.727 A_DC11:DG16_B 9 -18.783 0.890 0.748 -0.419 -0.010 1 20 A 12 B 15 -7.535 A_DA12:DT15_B 10 -14.592 -0.173 0.675 -0.134 -4.598 1 19 A 13 B 14 -4.634 A_DC13:DG14_B 11 -10.106 1.019 0.826 -0.398 3.247 39.269 A A 1 2 -2.860 B B 26 25 3.210 -1.921 -0.213 -0.990 AA_DC1DT2:DA25DG26_BB 1 0.992 -1.477 39.211 -1.247 0.434 3.215 38.567 A A 2 3 -3.073 B B 25 24 3.169 -2.029 0.021 -1.019 AA_DT2DC3:DG24DA25_BB 2 -0.750 1.136 38.509 -1.298 -0.123 3.094 33.202 A A 3 4 -6.356 B B 24 23 2.980 -3.625 -0.118 -1.256 AA_DC3DT4:DA23DG24_BB 3 0.505 -0.886 33.005 -1.632 0.285 2.754 39.447 A A 4 5 -11.437 B B 23 22 2.695 -7.672 0.387 -0.495 AA_DT4DA5:DT22DA23_BB 4 1.730 -2.579 38.686 0.028 -0.402 3.642 48.775 A A 8 9 -24.375 B B 19 18 3.732 -19.614 -1.072 -0.370 AA_DG8DC9:DG18DC19_BB 5 -2.712 3.371 44.802 1.323 1.053 3.672 43.470 A A 9 10 -15.685 B B 18 17 3.591 -11.492 0.149 -0.779 AA_DC9DT10:DA17DG18_BB 6 -0.011 0.015 41.995 0.206 -0.203 3.197 41.052 A A 10 11 -6.984 B B 17 16 3.132 -4.887 0.140 -0.768 AA_DT10DC11:DG16DA17_BB 7 -0.498 0.711 40.769 -0.579 -0.253 2.329 29.276 A A 11 12 13.518 B B 16 15 2.644 6.773 -0.536 -1.118 AA_DC11DA12:DT15DG16_BB 8 -0.427 0.852 28.495 -3.342 0.989 3.318 36.587 A A 12 13 -0.995 B B 15 14 3.308 -0.624 0.097 -1.089 AA_DA12DC13:DG14DT15_BB 9 -1.578 2.515 36.549 -1.647 -0.375 chem_comp_atom chem_comp_bond database_2 pdbx_database_status struct_conn struct_site repository Initial release Version format compliance Non-polymer description Version format compliance Data collection Database references Derived calculations Other 1 0 1994-01-31 1 1 2008-03-24 1 2 2011-07-13 1 3 2024-04-10 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.process_site _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 Y BNL 1993-01-13 REL CPT Cisplatin 2 CPT 1 3 CPT CPT 14 A C 1 n 1 DC 1 A T 2 n 2 DT 2 A C 3 n 3 DC 3 A T 4 n 4 DT 4 A A 5 n 5 DA 5 A G 6 n 6 DG 6 A T 7 n 7 DT 7 A G 8 n 8 DG 8 A C 9 n 9 DC 9 A T 10 n 10 DT 10 A C 11 n 11 DC 11 A A 12 n 12 DA 12 A C 13 n 13 DC 13 A G 14 n 1 DG 14 B T 15 n 2 DT 15 B G 16 n 3 DG 16 B A 17 n 4 DA 17 B G 18 n 5 DG 18 B C 19 n 6 DC 19 B A 20 n 7 DA 20 B C 21 n 8 DC 21 B T 22 n 9 DT 22 B A 23 n 10 DA 23 B G 24 n 11 DG 24 B A 25 n 12 DA 25 B G 26 n 13 DG 26 B author_defined_assembly 2 dimeric A DG 6 A N7 DG 6 1_555 A CPT 14 C PT1 CPT 1_555 A CPT 14 C N1 CPT 1_555 180.0 A DG 6 A N7 DG 6 1_555 A CPT 14 C PT1 CPT 1_555 A CPT 14 C N2 CPT 1_555 94.8 A CPT 14 C N1 CPT 1_555 A CPT 14 C PT1 CPT 1_555 A CPT 14 C N2 CPT 1_555 85.1 A DG 6 A N7 DG 6 1_555 A CPT 14 C PT1 CPT 1_555 A DG 8 A N7 DG 8 1_555 85.2 A CPT 14 C N1 CPT 1_555 A CPT 14 C PT1 CPT 1_555 A DG 8 A N7 DG 8 1_555 94.8 A CPT 14 C N2 CPT 1_555 A CPT 14 C PT1 CPT 1_555 A DG 8 A N7 DG 8 1_555 180.0 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 DG 6 0.128 SIDE CHAIN 1 A DC 9 0.102 SIDE CHAIN 2 A DG 6 0.129 SIDE CHAIN 2 A DT 7 0.065 SIDE CHAIN 2 A DG 8 0.059 SIDE CHAIN 2 A DC 9 0.101 SIDE CHAIN 2 A DC 11 0.065 SIDE CHAIN 2 B DC 19 0.073 SIDE CHAIN 1 2.98 0.30 108.30 111.28 A A A O4' C1' N1 DC DC DC 1 1 1 N 1 1.95 0.30 108.30 110.25 A A A O4' C1' N1 DT DT DT 2 2 2 N 1 2.52 0.30 108.30 110.82 A A A O4' C1' N1 DC DC DC 3 3 3 N 1 2.37 0.30 108.30 110.67 A A A O4' C1' N1 DT DT DT 4 4 4 N 1 1.80 0.30 108.30 110.10 A A A O4' C1' N9 DA DA DA 5 5 5 N 1 4.02 0.30 108.30 112.32 A A A O4' C1' N9 DG DG DG 6 6 6 N 1 -3.49 0.40 110.80 107.31 A A A C4 C5 N7 DG DG DG 6 6 6 N 1 3.87 0.50 104.30 108.17 A A A C5 N7 C8 DG DG DG 6 6 6 N 1 2.94 0.40 105.40 108.34 A A A N9 C4 C5 DG DG DG 6 6 6 N 1 -4.86 0.80 105.90 101.04 A A A O4' C1' C2' DT DT DT 7 7 7 N 1 7.16 0.30 108.30 115.46 A A A O4' C1' N1 DT DT DT 7 7 7 N 1 8.22 0.30 108.30 116.52 A A A O4' C1' N9 DG DG DG 8 8 8 N 1 3.12 0.40 105.40 108.52 A A A N9 C4 C5 DG DG DG 8 8 8 N 1 1.90 0.30 108.30 110.20 A A A O4' C1' N1 DC DC DC 9 9 9 N 1 2.27 0.30 108.30 110.57 A A A O4' C1' N9 DA DA DA 12 12 12 N 1 2.83 0.30 108.30 111.13 A A A O4' C1' N1 DC DC DC 13 13 13 N 1 2.49 0.30 108.30 110.79 B B B O4' C1' N1 DT DT DT 15 15 15 N 1 4.27 0.30 108.30 112.57 B B B O4' C1' N9 DG DG DG 16 16 16 N 1 2.02 0.30 108.30 110.32 B B B O4' C1' N9 DG DG DG 18 18 18 N 1 3.90 0.30 108.30 112.20 B B B O4' C1' N9 DA DA DA 20 20 20 N 1 5.88 0.30 108.30 114.18 B B B O4' C1' N1 DC DC DC 21 21 21 N 1 2.38 0.30 108.30 110.68 B B B O4' C1' N1 DT DT DT 22 22 22 N 1 2.64 0.30 108.30 110.94 B B B O4' C1' N9 DG DG DG 24 24 24 N 1 3.19 0.30 108.30 111.49 B B B O4' C1' N9 DG DG DG 26 26 26 N 2 1.96 0.30 108.30 110.26 A A A O4' C1' N1 DC DC DC 1 1 1 N 2 3.31 0.30 108.30 111.61 A A A O4' C1' N1 DT DT DT 2 2 2 N 2 2.20 0.30 108.30 110.50 A A A O4' C1' N1 DC DC DC 3 3 3 N 2 3.78 0.30 108.30 112.08 A A A O4' C1' N1 DT DT DT 4 4 4 N 2 2.03 0.30 108.30 110.33 A A A O4' C1' N9 DA DA DA 5 5 5 N 2 5.21 0.30 108.30 113.51 A A A O4' C1' N9 DG DG DG 6 6 6 N 2 -3.50 0.40 110.80 107.30 A A A C4 C5 N7 DG DG DG 6 6 6 N 2 3.65 0.60 130.40 134.05 A A A C6 C5 N7 DG DG DG 6 6 6 N 2 -5.19 0.80 105.90 100.71 A A A O4' C1' C2' DT DT DT 7 7 7 N 2 8.06 0.30 108.30 116.36 A A A O4' C1' N1 DT DT DT 7 7 7 N 2 -4.06 0.60 122.90 118.84 A A A C6 C5 C7 DT DT DT 7 7 7 N 2 5.84 0.30 108.30 114.14 A A A O4' C1' N9 DG DG DG 8 8 8 N 2 -3.92 0.40 110.80 106.88 A A A C4 C5 N7 DG DG DG 8 8 8 N 2 4.35 0.60 130.40 134.75 A A A C6 C5 N7 DG DG DG 8 8 8 N 2 2.06 0.30 108.30 110.36 A A A O4' C1' N1 DT DT DT 10 10 10 N 2 4.13 0.30 108.30 112.43 A A A O4' C1' N1 DC DC DC 11 11 11 N 2 3.02 0.30 108.30 111.32 A A A O4' C1' N1 DC DC DC 13 13 13 N 2 4.21 0.30 108.30 112.51 B B B O4' C1' N1 DT DT DT 15 15 15 N 2 2.68 0.30 108.30 110.98 B B B O4' C1' N9 DG DG DG 18 18 18 N 2 5.70 0.30 108.30 114.00 B B B O4' C1' N9 DA DA DA 20 20 20 N 2 6.21 0.30 108.30 114.51 B B B O4' C1' N1 DC DC DC 21 21 21 N 2 2.13 0.30 108.30 110.43 B B B O4' C1' N9 DG DG DG 24 24 24 N 2 2.90 0.30 108.30 111.20 B B B O4' C1' N9 DG DG DG 26 26 26 N 1 A A C5 N7 DG DG 6 6 -0.038 0.006 1.388 1.350 N 1 A A N7 C8 DG DG 8 8 0.051 0.006 1.305 1.356 N refinement AMBER Solution structure of a DNA duplex containing the CIS-PT(NH3)2[D(-GTG-)-N7-(G)-N7(G)N7(G)]Adduct as determined with high field NMR and molecular mechanics/dynamics 1 N N 2 N N 3 N N metalc 1.966 A DG 6 A N7 DG 6 1_555 A CPT 14 C PT1 CPT 1_555 metalc 2.171 A DG 8 A N7 DG 8 1_555 A CPT 14 C PT1 CPT 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 26 B N1 DG 13 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 26 B O6 DG 13 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 26 B N2 DG 13 1_555 hydrog WATSON-CRICK A DT 2 A N3 DT 2 1_555 B DA 25 B N1 DA 12 1_555 hydrog WATSON-CRICK A DT 2 A O4 DT 2 1_555 B DA 25 B N6 DA 12 1_555 hydrog WATSON-CRICK A DC 3 A N3 DC 3 1_555 B DG 24 B N1 DG 11 1_555 hydrog WATSON-CRICK A DC 3 A N4 DC 3 1_555 B DG 24 B O6 DG 11 1_555 hydrog WATSON-CRICK A DC 3 A O2 DC 3 1_555 B DG 24 B N2 DG 11 1_555 hydrog WATSON-CRICK A DT 4 A N3 DT 4 1_555 B DA 23 B N1 DA 10 1_555 hydrog WATSON-CRICK A DT 4 A O4 DT 4 1_555 B DA 23 B N6 DA 10 1_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 B DT 22 B N3 DT 9 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 B DT 22 B O4 DT 9 1_555 hydrog WATSON-CRICK A DG 8 A N1 DG 8 1_555 B DC 19 B N3 DC 6 1_555 hydrog WATSON-CRICK A DG 8 A N2 DG 8 1_555 B DC 19 B O2 DC 6 1_555 hydrog WATSON-CRICK A DG 8 A O6 DG 8 1_555 B DC 19 B N4 DC 6 1_555 hydrog WATSON-CRICK A DC 9 A N3 DC 9 1_555 B DG 18 B N1 DG 5 1_555 hydrog WATSON-CRICK A DC 9 A N4 DC 9 1_555 B DG 18 B O6 DG 5 1_555 hydrog WATSON-CRICK A DC 9 A O2 DC 9 1_555 B DG 18 B N2 DG 5 1_555 hydrog WATSON-CRICK A DT 10 A N3 DT 10 1_555 B DA 17 B N1 DA 4 1_555 hydrog WATSON-CRICK A DT 10 A O4 DT 10 1_555 B DA 17 B N6 DA 4 1_555 hydrog WATSON-CRICK A DC 11 A N3 DC 11 1_555 B DG 16 B N1 DG 3 1_555 hydrog WATSON-CRICK A DC 11 A N4 DC 11 1_555 B DG 16 B O6 DG 3 1_555 hydrog WATSON-CRICK A DC 11 A O2 DC 11 1_555 B DG 16 B N2 DG 3 1_555 hydrog WATSON-CRICK A DA 12 A N1 DA 12 1_555 B DT 15 B N3 DT 2 1_555 hydrog WATSON-CRICK A DA 12 A N6 DA 12 1_555 B DT 15 B O4 DT 2 1_555 hydrog WATSON-CRICK A DC 13 A N3 DC 13 1_555 B DG 14 B N1 DG 1 1_555 hydrog WATSON-CRICK A DC 13 A N4 DC 13 1_555 B DG 14 B O6 DG 1 1_555 hydrog WATSON-CRICK A DC 13 A O2 DC 13 1_555 B DG 14 B N2 DG 1 1_555 DNA DNA 1DA4 PDB 1 1DA4 1DA4 PDB 2 1DA4 1 13 1DA4 1 13 1DA4 A 1 1 13 14 26 1DA4 14 26 1DA4 B 2 1 13 BINDING SITE FOR RESIDUE CPT A 14 A CPT 14 Software 2 A DG 6 A DG 6 2 1_555 A DG 8 A DG 8 2 1_555 1 P 1