0.035651 0.000000 0.000000 0.000000 0.035651 0.000000 0.000000 0.000000 0.018811 0.00000 0.00000 0.00000 Shi, K. Pan, B. Sundaralingam, M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 28.05 28.05 53.16 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 C27 H29 N O10 527.520 DAUNOMYCIN DAUNORUBICIN non-polymer C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O8 P 363.221 y GUANOSINE-5'-MONOPHOSPHATE RNA linking H2 O 18.015 WATER non-polymer N 1 N O N 2 N P N 3 N O N 4 N O N 5 N O N 6 N C N 7 R C N 8 N O N 9 S C N 10 N O N 11 N C N 12 R C Y 13 N N Y 14 N C Y 15 N N Y 16 N C Y 17 N C N 18 N N Y 19 N N Y 20 N C Y 21 N N Y 22 N C N 23 N H N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N O N 38 N P N 39 N O N 40 N O N 41 N O N 42 N C N 43 R C N 44 N O N 45 S C N 46 N O N 47 N C N 48 R C N 49 N N N 50 N C N 51 N O N 52 N N N 53 N C N 54 N N N 55 N C N 56 N C N 57 N H 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 O N 72 N P N 73 N O N 74 N O N 75 N O N 76 N C N 77 R C N 78 N O N 79 S C N 80 N O N 81 N C N 82 R C Y 83 N N Y 84 N C Y 85 N N Y 86 N C N 87 N C N 88 N O N 89 N N N 90 N C N 91 N N N 92 N N Y 93 N C 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 Y 108 N C Y 109 N C Y 110 N C Y 111 N C N 112 N O Y 113 N C N 114 N C N 115 N O Y 116 N C Y 117 N C N 118 N O Y 119 N C N 120 S C N 121 N O N 122 N C N 123 S C N 124 N O N 125 N C N 126 N O N 127 N C N 128 N C Y 129 N C Y 130 N C N 131 N O Y 132 N C N 133 N C N 134 N O Y 135 N C N 136 N C N 137 R C N 138 N C N 139 S C N 140 N N N 141 S C N 142 N O N 143 S C N 144 N O N 145 N C 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 155 N H N 156 N H N 157 N H N 158 N H N 159 N H N 160 N H N 161 N H N 162 N H N 163 N H N 164 N H N 165 N H N 166 N H N 167 N H N 168 N H N 169 N H N 170 N H N 171 N H N 172 N H N 173 N H N 174 N H N 175 N O N 176 N P N 177 N O N 178 N O N 179 N O N 180 N C N 181 R C N 182 N O N 183 S C N 184 N O N 185 N C N 186 R C N 187 N N N 188 N C N 189 N O N 190 N N N 191 N C N 192 N O N 193 N C N 194 N C N 195 N C N 196 N H N 197 N H N 198 N H N 199 N H N 200 N H N 201 N H N 202 N H N 203 N H N 204 N H N 205 N H N 206 N H N 207 N H N 208 N H N 209 N H N 210 N H N 211 N O N 212 N P N 213 N O N 214 N O N 215 N O N 216 N C N 217 R C N 218 N O N 219 S C N 220 N O N 221 R C N 222 N O N 223 R C Y 224 N N Y 225 N C Y 226 N N Y 227 N C N 228 N C N 229 N O N 230 N N N 231 N C N 232 N N N 233 N N Y 234 N C N 235 N H N 236 N H N 237 N H N 238 N H N 239 N H N 240 N H N 241 N H 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 O N 250 N H N 251 N H N 1 N sing N 2 N sing N 3 N doub 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 sing 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 Y 24 N sing Y 25 N sing Y 26 N doub N 27 N sing Y 28 N sing Y 29 N sing Y 30 N doub N 31 N sing Y 32 N doub N 33 N sing N 34 N sing Y 35 N sing Y 36 N doub N 37 N sing Y 38 N sing N 39 N sing N 40 N sing N 41 N doub 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 N 64 N doub N 65 N sing N 66 N doub N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N doub N 72 N sing N 73 N sing N 74 N sing 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 sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing 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 Y 97 N sing Y 98 N sing Y 99 N doub N 100 N sing Y 101 N sing N 102 N sing Y 103 N doub N 104 N doub N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N doub N 110 N sing N 111 N sing N 112 N sing Y 113 N doub Y 114 N sing N 115 N sing Y 116 N sing N 117 N sing Y 118 N doub N 119 N sing N 120 N sing Y 121 N sing N 122 N sing N 123 N sing Y 124 N doub N 125 N doub N 126 N sing Y 127 N doub Y 128 N sing N 129 N sing Y 130 N sing N 131 N sing N 132 N sing Y 133 N doub 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 doub N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing Y 153 N sing N 154 N sing Y 155 N doub N 156 N sing N 157 N sing N 158 N doub N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing 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 sing N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N sing 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 doub N 210 N sing N 211 N sing N 212 N sing N 213 N doub N 214 N sing N 215 N sing N 216 N doub N 217 N sing N 218 N sing N 219 N sing N 220 N sing N 221 N sing N 222 N sing N 223 N doub N 224 N sing N 225 N sing N 226 N sing N 227 N sing N 228 N sing N 229 N sing N 230 N sing N 231 N sing N 232 N sing N 233 N sing N 234 N sing N 235 N sing N 236 N sing N 237 N sing 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 Y 245 N sing Y 246 N sing Y 247 N doub N 248 N sing Y 249 N sing N 250 N sing Y 251 N doub N 252 N doub N 253 N sing N 254 N sing N 255 N sing N 256 N sing N 257 N doub N 258 N sing N 259 N sing N 260 N sing N 261 N sing N 262 N sing DK Acta Crystallogr.,Sect.D ABCRE6 0766 0907-4449 59 1377 1383 10.1107/S0907444903011788 12876339 Structure of a B-form DNA/RNA chimera (dC)(rG)d(ATCG) complexed with daunomycin at 1.5 A resolution. 2003 10.2210/pdb1jo2/pdb pdb_00001jo2 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 293.0 1 MIRRORS IMAGE PLATE 1996-06-24 RIGAKU RAXIS IIC GRAPHITE SINGLE WAVELENGTH M x-ray 1 1.54 1.0 1.54 1.54 ROTATING ANODE RIGAKU 1825.217 5'-D(*C)-R(P*G)-D(P*AP*TP*CP*G)-3' 1 syn polymer 527.520 DAUNOMYCIN 1 syn non-polymer 18.015 water 40 nat water no no (DC)G(DA)(DT)(DC)(DG) CGATCG A polydeoxyribonucleotide/polyribonucleotide hybrid n n n n n n 1 2.77 55.55 EVAPORATION 7.00 magnesium chloride, cacodylate, MPD, pH 7.00, EVAPORATION, temperature 293K 293 MgCl2 1 cacodylate 1 MPD 1 8.887 1 19 A 1 A 6 -0.597 A_DC1:DG6_A 1 1.882 0.211 -0.021 -0.123 -20.355 1 19 A 2 A 5 2.014 A_G2:DC5_A 2 4.981 -0.201 -0.430 0.013 -9.746 1 20 A 3 A 4 1.760 A_DA3:DT4_A 3 -1.771 0.012 0.029 -0.130 9.746 1 20 A 4 A 3 1.760 A_DT4:DA3_A 4 -1.771 -0.012 0.029 -0.130 20.355 1 19 A 5 A 2 2.014 A_DC5:G2_A 5 4.981 0.201 -0.430 0.013 -8.887 1 19 A 6 A 1 -0.597 A_DG6:DC1_A 6 1.882 -0.211 -0.021 -0.123 7.048 33.904 A A 1 2 -7.608 A A 6 5 7.200 -4.423 1.366 1.166 AA_DC1G2:DC5DG6_AA 1 1.577 -2.713 33.587 3.555 -1.788 3.333 32.236 A A 2 3 0.691 A A 5 4 3.180 0.382 -1.363 0.369 AA_G2DA3:DT4DC5_AA 2 -4.255 7.686 31.959 0.597 1.697 2.880 32.537 A A 3 4 7.230 A A 4 3 2.974 4.041 0.000 -0.595 AA_DA3DT4:DA3DT4_AA 3 0.000 0.000 32.292 -1.697 0.000 3.333 32.236 A A 4 5 0.690 A A 3 2 3.180 0.382 1.363 0.369 AA_DT4DC5:G2DA3_AA 4 4.256 -7.686 31.959 0.597 -1.697 7.048 33.904 A A 5 6 -7.608 A A 2 1 7.200 -4.423 -1.366 1.166 AA_DC5DG6:DC1G2_AA 5 -1.577 2.713 33.587 3.555 1.788 software chem_comp_atom chem_comp_bond database_2 struct_site repository Initial release Version format compliance Version format compliance Refinement description Data collection Database references Derived calculations 1 0 2003-07-29 1 1 2008-04-01 1 2 2011-07-13 1 3 2017-10-04 1 4 2024-02-07 _database_2.pdbx_DOI _database_2.pdbx_database_accession _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 DM1 DAUNOMYCIN HOH water DM1 7 2 DM1 DM1 7 A WAT 101 3 HOH HOH 101 A WAT 102 3 HOH HOH 102 A WAT 103 3 HOH HOH 103 A WAT 104 3 HOH HOH 104 A WAT 105 3 HOH HOH 105 A WAT 106 3 HOH HOH 106 A WAT 107 3 HOH HOH 107 A WAT 108 3 HOH HOH 108 A WAT 109 3 HOH HOH 109 A WAT 110 3 HOH HOH 110 A WAT 111 3 HOH HOH 111 A WAT 112 3 HOH HOH 112 A WAT 113 3 HOH HOH 113 A WAT 114 3 HOH HOH 114 A WAT 115 3 HOH HOH 115 A WAT 116 3 HOH HOH 116 A WAT 117 3 HOH HOH 117 A WAT 118 3 HOH HOH 118 A WAT 119 3 HOH HOH 119 A WAT 120 3 HOH HOH 120 A WAT 121 3 HOH HOH 121 A WAT 122 3 HOH HOH 122 A WAT 123 3 HOH HOH 123 A WAT 124 3 HOH HOH 124 A WAT 125 3 HOH HOH 125 A WAT 127 3 HOH HOH 127 A WAT 128 3 HOH HOH 128 A WAT 129 3 HOH HOH 129 A WAT 130 3 HOH HOH 130 A WAT 131 3 HOH HOH 131 A WAT 132 3 HOH HOH 132 A WAT 133 3 HOH HOH 133 A WAT 134 3 HOH HOH 134 A WAT 135 3 HOH HOH 135 A WAT 136 3 HOH HOH 136 A WAT 137 3 HOH HOH 137 A WAT 138 3 HOH HOH 138 A WAT 139 3 HOH HOH 139 A WAT 140 3 HOH HOH 140 A WAT 141 3 HOH HOH 141 A C 1 n 1 DC 1 A G 2 n 2 G 2 A A 3 n 3 DA 3 A T 4 n 4 DT 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 0.0000000000 -1.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 8_665 -y+1,-x+1,-z+1/2 crystal symmetry operation 28.0500000000 28.0500000000 26.5800000000 1 A DC 5 0.090 SIDE CHAIN 22.1 0.12 0.00 0.00 0.12 0.00 -0.24 0.233 0.015 0.198 1.50 10.00 256 2778 2699 10.00 74.3 RANDOM 2.00 2.00 1 THROUGHOUT 2.000 0.21 0.19 5.00 0.14 0.16 1.50 10.00 40 199 38 121 0 0.014 1.5 17.5 1.94 0.40 1.50 0.69 2.00 0.00 2.00 0.00 2.50 0.258 0.072 0.286 1.59 13 112 6 10.4 21.2 14.6 1.500 10.000 1JO2 2.0 1 data scaling SCALEPACK refinement CNS Crystal Structure of the B-DNA Hexamer (CgATCG).Daunomycin Complex Containing a Ribose at the Intercalation Site 1 N N 2 N N 3 N N hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 A DG 6 A N1 DG 6 8_665 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 A DG 6 A O6 DG 6 8_665 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 A DG 6 A N2 DG 6 8_665 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 A DC 5 A N3 DC 5 8_665 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 A DC 5 A O2 DC 5 8_665 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 A DC 5 A N4 DC 5 8_665 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 A DT 4 A N3 DT 4 8_665 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 A DT 4 A O4 DT 4 8_665 hydrog WATSON-CRICK A DT 4 A N3 DT 4 1_555 A DA 3 A N1 DA 3 8_665 hydrog WATSON-CRICK A DT 4 A O4 DT 4 1_555 A DA 3 A N6 DA 3 8_665 hydrog WATSON-CRICK A DC 5 A N3 DC 5 1_555 A G 2 A N1 G 2 8_665 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 A G 2 A O6 G 2 8_665 hydrog WATSON-CRICK A DC 5 A O2 DC 5 1_555 A G 2 A N2 G 2 8_665 hydrog WATSON-CRICK A DG 6 A N1 DG 6 1_555 A DC 1 A N3 DC 1 8_665 hydrog WATSON-CRICK A DG 6 A N2 DG 6 1_555 A DC 1 A O2 DC 1 8_665 hydrog WATSON-CRICK A DG 6 A O6 DG 6 1_555 A DC 1 A N4 DC 1 8_665 DNA, RNA intercalation, DNA/RNA chimer, DNA, RNA 1JO2 PDB 1 1JO2 1 6 1JO2 1 6 1JO2 A 1 1 6 BINDING SITE FOR RESIDUE DM1 A 7 A DM1 7 Software 12 A DC 1 A DC 1 12 1_555 A G 2 A G 2 12 1_555 A DA 3 A DA 3 12 1_555 A DT 4 A DT 4 12 8_665 A DC 5 A DC 5 12 8_665 A DG 6 A DG 6 12 8_665 A HOH 102 C HOH 12 1_555 A HOH 110 C HOH 12 1_555 A HOH 111 C HOH 12 1_555 A HOH 113 C HOH 12 1_555 A HOH 123 C HOH 12 1_555 A HOH 135 C HOH 12 1_555 92 P 41 21 2