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/pdb1da5/pdb pdb_00001da5 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 4.592 1 19 A 1 B 26 -6.244 A_DC1:DG26_B 1 -17.021 -0.544 0.785 -0.091 3.103 1 20 A 2 B 25 -4.996 A_DT2:DA25_B 2 -24.003 0.516 0.334 -0.179 -8.082 1 19 A 3 B 24 -4.620 A_DC3:DG24_B 3 -19.637 0.975 0.662 -0.414 -6.767 1 20 A 4 B 23 -3.355 A_DT4:DA23_B 4 -14.905 0.614 0.637 -0.211 15.339 1 20 A 5 B 22 -4.142 A_DA5:DT22_B 5 -5.115 0.717 1.106 -0.136 -0.078 1 19 A 8 B 19 -2.160 A_DG8:DC19_B 6 2.956 0.431 0.827 -0.078 -2.039 1 19 A 9 B 18 -8.218 A_DC9:DG18_B 7 -21.130 0.573 1.278 -0.500 -8.268 1 20 A 10 B 17 -5.658 A_DT10:DA17_B 8 -22.976 0.639 1.023 -0.383 -8.855 1 19 A 11 B 16 -5.750 A_DC11:DG16_B 9 -19.881 1.048 0.842 -0.490 -4.303 1 20 A 12 B 15 -8.448 A_DA12:DT15_B 10 -19.301 -0.528 0.632 -0.256 -9.946 1 19 A 13 B 14 -3.972 A_DC13:DG14_B 11 -8.648 0.915 0.821 -0.285 3.106 39.801 A A 1 2 -1.499 B B 26 25 3.114 -1.020 -0.316 -0.793 AA_DC1DT2:DA25DG26_BB 1 2.616 -3.845 39.706 -1.052 0.753 3.232 39.151 A A 2 3 3.095 B B 25 24 3.289 2.072 0.163 -0.801 AA_DT2DC3:DG24DA25_BB 2 -1.974 2.948 39.051 -1.444 -0.479 2.953 32.510 A A 3 4 0.388 B B 24 23 2.954 0.217 0.203 -1.154 AA_DC3DT4:DA23DG24_BB 3 2.066 -3.692 32.445 -2.095 -0.036 2.456 34.239 A A 4 5 -9.426 B B 23 22 2.395 -5.516 0.460 -0.988 AA_DT4DA5:DT22DA23_BB 4 -3.816 6.522 33.595 -1.027 -1.232 3.630 46.163 A A 8 9 -25.316 B B 19 18 3.674 -19.301 -0.653 -0.646 AA_DG8DC9:DG18DC19_BB 5 -0.237 0.311 42.135 1.115 0.810 3.313 41.619 A A 9 10 -12.378 B B 18 17 3.201 -8.735 -0.502 -0.866 AA_DC9DT10:DA17DG18_BB 6 -0.332 0.471 40.730 -0.287 0.671 3.051 39.297 A A 10 11 -4.851 B B 17 16 3.011 -3.259 -0.139 -0.613 AA_DT10DC11:DG16DA17_BB 7 -0.438 0.652 39.165 -0.552 0.158 2.192 29.619 A A 11 12 18.988 B B 16 15 2.613 9.539 -0.355 -0.865 AA_DC11DA12:DT15DG16_BB 8 1.111 -2.212 28.052 -3.214 0.872 3.333 36.460 A A 12 13 0.064 B B 15 14 3.337 0.040 0.477 -1.060 AA_DA12DC13:DG14DT15_BB 9 -0.264 0.422 36.459 -1.700 -0.800 chem_comp_atom chem_comp_bond database_2 pdbx_database_status 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_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 88.3 A DG 6 A N7 DG 6 1_555 A CPT 14 C PT1 CPT 1_555 A CPT 14 C N2 CPT 1_555 180.0 A CPT 14 C N1 CPT 1_555 A CPT 14 C PT1 CPT 1_555 A CPT 14 C N2 CPT 1_555 91.7 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 91.7 A CPT 14 C N1 CPT 1_555 A CPT 14 C PT1 CPT 1_555 A DG 8 A N7 DG 8 1_555 180.0 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 88.3 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 DT 2 0.059 SIDE CHAIN 1 A DG 8 0.087 SIDE CHAIN 1 A DC 9 0.090 SIDE CHAIN 1 A DT 10 0.088 SIDE CHAIN 1 B DG 14 0.055 SIDE CHAIN 1 B DC 19 0.061 SIDE CHAIN 2 A DT 7 0.211 SIDE CHAIN 2 A DC 9 0.086 SIDE CHAIN 2 A DT 10 0.078 SIDE CHAIN 2 A DC 11 0.076 SIDE CHAIN 2 B DA 17 0.078 SIDE CHAIN 2 B DG 18 0.092 SIDE CHAIN 2 B DC 19 0.081 SIDE CHAIN 2 B DA 23 0.072 SIDE CHAIN 2 B DA 25 0.054 SIDE CHAIN 1 2.53 0.30 108.30 110.83 A A A O4' C1' N1 DC DC DC 1 1 1 N 1 2.51 0.30 108.30 110.81 A A A O4' C1' N1 DC DC DC 3 3 3 N 1 2.75 0.30 108.30 111.05 A A A O4' C1' N1 DT DT DT 4 4 4 N 1 4.25 0.30 108.30 112.55 A A A O4' C1' N9 DA DA DA 5 5 5 N 1 2.00 0.30 108.30 110.30 A A A O4' C1' N9 DG DG DG 6 6 6 N 1 -2.82 0.40 110.80 107.98 A A A C4 C5 N7 DG DG DG 6 6 6 N 1 3.01 0.50 104.30 107.31 A A A C5 N7 C8 DG DG DG 6 6 6 N 1 5.10 0.30 108.30 113.40 A A A O4' C1' N1 DT DT DT 7 7 7 N 1 -3.68 0.60 122.90 119.22 A A A C6 C5 C7 DT DT DT 7 7 7 N 1 8.02 0.30 108.30 116.32 A A A O4' C1' N9 DG DG DG 8 8 8 N 1 -2.86 0.40 110.80 107.94 A A A C4 C5 N7 DG DG DG 8 8 8 N 1 3.22 0.50 104.30 107.52 A A A C5 N7 C8 DG DG DG 8 8 8 N 1 3.29 0.30 108.30 111.59 A A A O4' C1' N1 DC DC DC 9 9 9 N 1 2.08 0.30 108.30 110.38 A A A O4' C1' N1 DC DC DC 11 11 11 N 1 2.86 0.30 108.30 111.16 A A A O4' C1' N9 DA DA DA 12 12 12 N 1 3.43 0.30 108.30 111.73 A A A O4' C1' N1 DC DC DC 13 13 13 N 1 2.34 0.30 108.30 110.64 B B B O4' C1' N1 DT DT DT 15 15 15 N 1 3.07 0.30 108.30 111.37 B B B O4' C1' N9 DG DG DG 16 16 16 N 1 2.19 0.30 108.30 110.49 B B B O4' C1' N9 DA DA DA 17 17 17 N 1 2.75 0.30 108.30 111.05 B B B O4' C1' N9 DG DG DG 18 18 18 N 1 2.60 0.30 108.30 110.90 B B B O4' C1' N9 DA DA DA 20 20 20 N 1 3.79 0.30 108.30 112.09 B B B O4' C1' N1 DC DC DC 21 21 21 N 1 3.10 0.30 108.30 111.40 B B B O4' C1' N1 DT DT DT 22 22 22 N 1 2.56 0.30 108.30 110.86 B B B O4' C1' N9 DG DG DG 24 24 24 N 1 2.04 0.30 108.30 110.34 B B B O4' C1' N9 DA DA DA 25 25 25 N 1 3.36 0.30 108.30 111.66 B B B O4' C1' N9 DG DG DG 26 26 26 N 2 2.31 0.30 108.30 110.61 A A A O4' C1' N1 DC DC DC 1 1 1 N 2 3.40 0.30 108.30 111.70 A A A O4' C1' N1 DT DT DT 2 2 2 N 2 2.57 0.30 108.30 110.87 A A A O4' C1' N1 DC DC DC 3 3 3 N 2 3.58 0.30 108.30 111.88 A A A O4' C1' N1 DT DT DT 4 4 4 N 2 2.30 0.30 108.30 110.60 A A A O4' C1' N9 DA DA DA 5 5 5 N 2 5.71 0.30 108.30 114.01 A A A O4' C1' N9 DG DG DG 6 6 6 N 2 -3.94 0.40 110.80 106.86 A A A C4 C5 N7 DG DG DG 6 6 6 N 2 3.33 0.50 104.30 107.63 A A A C5 N7 C8 DG DG DG 6 6 6 N 2 6.29 0.30 108.30 114.59 A A A O4' C1' N9 DG DG DG 8 8 8 N 2 -3.62 0.40 110.80 107.18 A A A C4 C5 N7 DG DG DG 8 8 8 N 2 3.32 0.50 104.30 107.62 A A A C5 N7 C8 DG DG DG 8 8 8 N 2 2.34 0.30 108.30 110.64 A A A O4' C1' N1 DT DT DT 10 10 10 N 2 4.39 0.30 108.30 112.69 A A A O4' C1' N1 DC DC DC 11 11 11 N 2 3.29 0.30 108.30 111.59 A A A O4' C1' N1 DC DC DC 13 13 13 N 2 4.15 0.30 108.30 112.45 B B B O4' C1' N1 DT DT DT 15 15 15 N 2 1.86 0.30 108.30 110.16 B B B O4' C1' N9 DG DG DG 16 16 16 N 2 2.13 0.30 108.30 110.43 B B B O4' C1' N9 DG DG DG 18 18 18 N 2 2.53 0.30 108.30 110.83 B B B O4' C1' N9 DA DA DA 20 20 20 N 2 5.42 0.30 108.30 113.72 B B B O4' C1' N1 DC DC DC 21 21 21 N 2 2.34 0.30 108.30 110.64 B B B O4' C1' N9 DG DG DG 24 24 24 N 2 3.19 0.30 108.30 111.49 B B B O4' C1' N9 DG DG DG 26 26 26 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 2.008 A DG 6 A N7 DG 6 1_555 A CPT 14 C PT1 CPT 1_555 metalc 2.010 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 DG-DG MISPAIR A DG 8 A N1 DG 8 1_555 B DG 18 B O6 DG 5 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 DC-DT MISPAIR A DC 11 A N4 DC 11 1_555 B DT 15 B O4 DT 2 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 1DA5 PDB 1 1DA5 1DA5 PDB 2 1DA5 1 13 1DA5 1 13 1DA5 A 1 1 13 14 26 1DA5 14 26 1DA5 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