0.035411 0.020444 0.000000 0.000000 0.040889 0.000000 0.000000 0.000000 0.013747 0.00000 0.00000 0.00000 Williams, L.D. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 12 90.00 90.00 120.00 28.240 28.240 72.744 C49 H56 N6 O2 2 761.008 1,3-DI[[[10-METHOXY-7H-PYRIDO[4,3-C]CARBAZOL-2-IUMYL]-ETHYL]-PIPERIDIN-4-YL]-PROPANE BIS INTERCALATOR D232 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 Y 1 N C Y 2 N N Y 3 N C Y 4 N C Y 5 N C Y 6 N C Y 7 N N Y 8 N C Y 9 N C Y 10 N C Y 11 N C Y 12 N C Y 13 N C Y 14 N C Y 15 N C Y 16 N C N 17 N C Y 18 N C N 19 N O N 20 N C N 21 N C N 22 N N N 23 N C N 24 N C N 25 N C N 26 N C N 27 N C N 28 N C N 29 N C Y 30 N C Y 31 N N Y 32 N C Y 33 N C Y 34 N C Y 35 N C Y 36 N N Y 37 N C Y 38 N C Y 39 N C Y 40 N C Y 41 N C Y 42 N C Y 43 N C Y 44 N C Y 45 N C N 46 N C Y 47 N C N 48 N O N 49 N C N 50 N C N 51 N N N 52 N C N 53 N C N 54 N C N 55 N C N 56 N C N 57 N C N 58 N H N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N H 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 H N 83 N H N 84 N H N 85 N H N 86 N H N 87 N H N 88 N H N 89 N H N 90 N H N 91 N H N 92 N H N 93 N H N 94 N H N 95 N H N 96 N H N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H 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 O N 115 N P N 116 N O N 117 N O N 118 N O N 119 N C N 120 R C N 121 N O N 122 S C N 123 N O N 124 N C N 125 R C Y 126 N N Y 127 N C Y 128 N N Y 129 N C Y 130 N C N 131 N N Y 132 N N Y 133 N C Y 134 N N Y 135 N C N 136 N H N 137 N H N 138 N H N 139 N H 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 O N 151 N P N 152 N O N 153 N O N 154 N O N 155 N C N 156 R C N 157 N O N 158 S C N 159 N O N 160 N C N 161 R C N 162 N N N 163 N C N 164 N O N 165 N N N 166 N C N 167 N N N 168 N C N 169 N C N 170 N H N 171 N H N 172 N H N 173 N H N 174 N H N 175 N H N 176 N H N 177 N H N 178 N H N 179 N H N 180 N H N 181 N H N 182 N H N 183 N H N 184 N O N 185 N P N 186 N O N 187 N O N 188 N O N 189 N C N 190 R C N 191 N O N 192 S C N 193 N O N 194 N C N 195 R C Y 196 N N Y 197 N C Y 198 N N Y 199 N C N 200 N C N 201 N O N 202 N N N 203 N C N 204 N N N 205 N N Y 206 N C N 207 N H N 208 N H N 209 N H N 210 N H N 211 N H N 212 N H N 213 N H N 214 N H N 215 N H N 216 N H N 217 N H N 218 N H N 219 N H N 220 N H N 221 N O N 222 N P N 223 N O N 224 N O N 225 N O N 226 N C N 227 R C N 228 N O N 229 S C N 230 N O N 231 N C N 232 R C N 233 N N N 234 N C N 235 N O N 236 N N N 237 N C N 238 N O N 239 N C N 240 N C N 241 N C N 242 N H N 243 N H N 244 N H N 245 N H N 246 N H N 247 N H N 248 N H N 249 N H N 250 N H N 251 N H N 252 N H N 253 N H N 254 N H N 255 N H N 256 N H Y 1 N doub Y 2 N sing N 3 N sing Y 4 N sing N 5 N sing Y 6 N doub N 7 N sing Y 8 N sing N 9 N sing Y 10 N doub Y 11 N sing N 12 N sing Y 13 N sing N 14 N sing Y 15 N sing Y 16 N sing N 17 N sing Y 18 N doub Y 19 N sing N 20 N sing Y 21 N sing N 22 N sing Y 23 N sing Y 24 N doub N 25 N sing Y 26 N doub Y 27 N doub Y 28 N doub Y 29 N sing Y 30 N sing N 31 N sing N 32 N sing N 33 N sing N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing 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 Y 64 N doub Y 65 N sing N 66 N sing Y 67 N sing N 68 N sing Y 69 N doub N 70 N sing Y 71 N sing N 72 N sing Y 73 N doub Y 74 N sing N 75 N sing Y 76 N sing N 77 N sing Y 78 N sing Y 79 N sing N 80 N sing Y 81 N doub Y 82 N sing N 83 N sing Y 84 N sing N 85 N sing Y 86 N sing Y 87 N doub N 88 N sing Y 89 N doub Y 90 N doub Y 91 N doub Y 92 N sing Y 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 N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing 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 Y 146 N sing Y 147 N sing Y 148 N doub N 149 N sing Y 150 N sing Y 151 N sing Y 152 N doub N 153 N sing Y 154 N doub N 155 N sing N 156 N sing Y 157 N sing Y 158 N doub N 159 N sing Y 160 N sing N 161 N sing N 162 N sing N 163 N doub N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N doub N 187 N sing N 188 N doub N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N doub N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N doub N 199 N sing N 200 N sing N 201 N sing N 202 N sing N 203 N sing N 204 N sing N 205 N sing N 206 N sing N 207 N sing N 208 N sing N 209 N sing N 210 N sing N 211 N sing N 212 N sing N 213 N sing N 214 N sing N 215 N sing N 216 N sing N 217 N sing N 218 N sing Y 219 N sing Y 220 N sing Y 221 N doub N 222 N sing Y 223 N sing N 224 N sing Y 225 N doub N 226 N doub N 227 N sing N 228 N sing N 229 N sing N 230 N sing N 231 N doub N 232 N sing N 233 N sing N 234 N sing N 235 N sing N 236 N sing N 237 N doub N 238 N sing N 239 N sing N 240 N sing N 241 N sing N 242 N sing N 243 N sing N 244 N sing N 245 N sing N 246 N sing N 247 N sing N 248 N sing N 249 N sing N 250 N sing N 251 N sing N 252 N sing N 253 N sing N 254 N sing N 255 N sing N 256 N sing N 257 N sing N 258 N sing N 259 N sing N 260 N doub N 261 N sing N 262 N sing N 263 N sing N 264 N doub N 265 N sing N 266 N sing N 267 N doub N 268 N sing N 269 N sing N 270 N sing N 271 N sing NE Curr.Med.Chem. 0929-8673 7 59 71 10637357 Effects of cationic charge on three-dimensional structures of intercalative complexes: structure of a bis-intercalated DNA complex solved by MAD phasing. 2000 10.2210/pdb1c9z/pdb pdb_00001c9z 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 300 1 AREA DETECTOR 1995-09-09 UCSD MARK II SINGLE WAVELENGTH M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU RU200 COMPLEXED WITH BIS-INTERCALATOR D232 1809.217 5'-D(*CP*GP*TP*AP*CP*G)-3' 1 syn polymer 761.008 1,3-DI[[[10-METHOXY-7H-PYRIDO[4,3-C]CARBAZOL-2-IUMYL]-ETHYL]-PIPERIDIN-4-YL]-PROPANE 1 syn non-polymer no no (DC)(DG)(DT)(DA)(DC)(DG) CGTACG A polydeoxyribonucleotide n n n n n n 1 2.22 44.50 VAPOR DIFFUSION, SITTING DROP 6.0 MPD, SPERMINE, MAGNESIUM CHLORIDE, SODIUM CACODYLATE, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 300K 300 SPERMINE 1 MGCL2 1 SODIUM CACODYLATE 1 MPD 1 MPD 2 -6.552 1 19 A 1 A 6 0.943 A_DC1:DG6_A 1 -6.046 0.589 0.685 -0.378 -6.426 1 19 A 2 A 5 -4.641 A_DG2:DC5_A 2 -2.145 -0.252 0.131 -0.473 4.780 1 20 A 3 A 4 -9.422 A_DT3:DA4_A 3 -10.356 0.246 -0.145 -0.121 -4.780 1 20 A 4 A 3 -9.422 A_DA4:DT3_A 4 -10.356 -0.246 -0.145 -0.121 6.426 1 19 A 5 A 2 -4.641 A_DC5:DG2_A 5 -2.145 0.252 0.131 -0.473 6.553 1 19 A 6 A 1 0.943 A_DG6:DC1_A 6 -6.046 -0.589 0.685 -0.378 6.390 14.413 A A 1 2 2.991 A A 6 5 6.815 0.734 0.078 -0.098 AA_DC1DG2:DC5DG6_AA 1 5.112 -20.833 13.460 -1.768 9.295 3.129 34.907 A A 2 3 -0.555 A A 5 4 3.156 -0.333 -0.633 -0.218 AA_DG2DT3:DA4DC5_AA 2 1.495 -2.493 34.875 -0.315 1.273 3.671 38.509 A A 3 4 14.770 A A 4 3 3.597 9.645 0.000 0.747 AA_DT3DA4:DT3DA4_AA 3 0.000 0.000 37.326 -0.218 0.000 3.129 34.907 A A 4 5 -0.555 A A 3 2 3.156 -0.333 0.633 -0.218 AA_DA4DC5:DG2DT3_AA 4 -1.495 2.493 34.875 -0.315 -1.273 6.390 14.413 A A 5 6 2.991 A A 2 1 6.815 0.734 -0.078 -0.098 AA_DC5DG6:DC1DG2_AA 5 -5.112 20.833 13.460 -1.768 -9.294 chem_comp_atom chem_comp_bond database_2 pdbx_unobs_or_zero_occ_atoms struct_conn struct_site pdbx_database_status repository Initial release Version format compliance Version format compliance Database references Advisory Data collection Database references Derived calculations Other 1 0 2000-04-02 1 1 2008-04-27 1 2 2011-07-13 1 3 2011-12-07 1 4 2024-02-07 1 5 2024-04-17 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _pdbx_database_status.status_code_sf DITERCALINIUM-CGCG RCSB Y RCSB 1999-08-03 REL REL 232 1,3-DI[[[10-METHOXY-7H-PYRIDO[4,3-C]CARBAZOL-2-IUMYL]-ETHYL]-PIPERIDIN-4-YL]-PROPANE SYNTHETIC sample 232 7 2 232 232 7 A C 1 n 1 DC 1 A G 2 n 2 DG 2 A T 3 n 3 DT 3 A A 4 n 4 DA 4 A C 5 n 5 DC 5 A G 6 n 6 DG 6 A 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 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 11_556 -x+y,y,-z+3/2 crystal symmetry operation 0.0000000000 0.0000000000 109.1160000000 1 A 232 7 B 232 1 -7.98 0.80 109.40 101.42 A A A O5' C5' C4' DG DG DG 2 2 2 N 1 4.38 0.60 106.00 110.38 A A A O4' C4' C3' DG DG DG 2 2 2 N 1 -5.31 0.80 105.90 100.59 A A A O4' C1' C2' DT DT DT 3 3 3 N 1 -4.73 0.60 122.30 117.57 A A A N3 C2 O2 DT DT DT 3 3 3 N 1 -5.93 0.70 108.00 102.07 A A A O4' C1' N9 DA DA DA 4 4 4 N 1 3.59 0.50 129.30 132.89 A A A N1 C2 N3 DA DA DA 4 4 4 N 1 -4.69 0.50 110.60 105.91 A A A C2 N3 C4 DA DA DA 4 4 4 N 1 A A C5' C4' DC DC 1 1 0.043 0.007 1.512 1.555 N 1 A A C4' C3' DG DG 2 2 -0.064 0.010 1.521 1.457 N 1 A A C6 N1 DA DA 4 4 -0.045 0.007 1.351 1.306 N 1 A A N9 C4 DA DA 4 4 -0.044 0.006 1.374 1.330 N 0.1961000 0.1961000 0.1961000 2.4 10 99 5220 4682 90 RANDOM 1 4. 2. PARKINSON ET AL. 2.4 10 0 149 29 120 0 21 2.4 10.0 1C9Z 5220 4698 2.0 4.0 0.0510000 1 9.2 3.2 91 0.0600000 2.4 2.51 1 4.2 84 phasing MADSYS refinement X-PLOR 3.851 data reduction SDMS data scaling SDMS D232-CGTACG 1 N N 2 N N covale 1.533 none A 232 7 B C27 232 1_555 A 232 7 B C28 232 11_556 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 A DG 6 A N1 DG 6 11_556 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 A DG 6 A O6 DG 6 11_556 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 A DG 6 A N2 DG 6 11_556 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 A DC 5 A N3 DC 5 11_556 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 A DC 5 A O2 DC 5 11_556 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 A DC 5 A N4 DC 5 11_556 hydrog WATSON-CRICK A DT 3 A N3 DT 3 1_555 A DA 4 A N1 DA 4 11_556 hydrog WATSON-CRICK A DT 3 A O4 DT 3 1_555 A DA 4 A N6 DA 4 11_556 hydrog WATSON-CRICK A DA 4 A N1 DA 4 1_555 A DT 3 A N3 DT 3 11_556 hydrog WATSON-CRICK A DA 4 A N6 DA 4 1_555 A DT 3 A O4 DT 3 11_556 hydrog WATSON-CRICK A DC 5 A N3 DC 5 1_555 A DG 2 A N1 DG 2 11_556 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 A DG 2 A O6 DG 2 11_556 hydrog WATSON-CRICK A DC 5 A O2 DC 5 1_555 A DG 2 A N2 DG 2 11_556 hydrog WATSON-CRICK A DG 6 A N1 DG 6 1_555 A DC 1 A N3 DC 1 11_556 hydrog WATSON-CRICK A DG 6 A N2 DG 6 1_555 A DC 1 A O2 DC 1 11_556 hydrog WATSON-CRICK A DG 6 A O6 DG 6 1_555 A DC 1 A N4 DC 1 11_556 DNA DNA, INTERCALATOR, INTERCALATION, DRUG, MAJOR GROOVE 1C9Z PDB 1 1C9Z 1 6 1C9Z 1 6 1C9Z A 1 1 6 BINDING SITE FOR RESIDUE 232 A 7 A 232 7 Software 7 A DC 1 A DC 1 7 1_555 A DG 2 A DG 2 7 1_555 A DT 3 A DT 3 7 1_555 A DA 4 A DA 4 7 5_565 A DC 5 A DC 5 7 11_556 A DG 6 A DG 6 7 11_556 A DG 6 A DG 6 7 5_555 179 hexagonal P 65 2 2