0.035549 0.000000 0.000000 0.000000 0.035549 0.000000 0.000000 0.000000 0.018629 0.00000 0.00000 0.00000 Gao, Y.-G. Wang, A.H.-J. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 28.130 28.130 53.680 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 C26 H27 N O9 497.494 IDARUBICIN 4-DEMETHOXY-DAUNORUBICIN non-polymer C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking H2 O 18.015 WATER non-polymer Mg 2 24.305 MAGNESIUM ION 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 Y 112 N C N 113 N C N 114 N O Y 115 N C Y 116 N C N 117 N O Y 118 N C N 119 S C N 120 N O N 121 N C N 122 S C N 123 N O N 124 N C N 125 N O N 126 N C N 127 N C Y 128 N C Y 129 N C N 130 N O Y 131 N C N 132 N C N 133 N O Y 134 N C N 135 R C N 136 N C N 137 S C N 138 N N N 139 S C N 140 N O N 141 S C N 142 N O N 143 N C 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 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 O N 172 N P N 173 N O N 174 N O N 175 N O N 176 N C N 177 R C N 178 N O N 179 S C N 180 N O N 181 N C N 182 R C N 183 N N N 184 N C N 185 N O N 186 N N N 187 N C N 188 N O N 189 N C N 190 N C N 191 N C N 192 N H N 193 N H N 194 N H N 195 N H 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 O N 208 N H N 209 N H N 210 N MG 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 Y 120 N sing N 121 N sing N 122 N sing Y 123 N doub N 124 N doub N 125 N sing Y 126 N doub Y 127 N sing N 128 N sing Y 129 N sing N 130 N sing N 131 N sing Y 132 N doub 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 doub N 145 N sing N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing Y 152 N sing N 153 N sing Y 154 N doub N 155 N sing N 156 N sing N 157 N doub N 158 N sing 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 doub N 183 N sing N 184 N sing N 185 N sing N 186 N sing 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 doub 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 doub N 213 N sing N 214 N sing N 215 N sing N 216 N sing N 217 N sing N 218 N sing UK Anti-Cancer Drug Des. ACDDEA 0807 0266-9536 6 137 149 1872945 Influence of aglycone modifications on the binding of anthracycline drugs to DNA: the molecular structure of idarubicin and 4-O-demethyl-11-deoxydoxorubicin complexed to d(CGATCG). 1991 US Proc.Natl.Acad.Sci.USA PNASA6 0040 0027-8424 88 4845 4849 Facile Formation of Crosslinked Adduct between DNA and the Daunorubicin Derivative MAR70 Mediated by Formaldehyde: Molecular Structure of the MAR70-d(CGTnACG) Covalent Adduct 1991 10.2210/pdb1d38/pdb pdb_00001d38 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 298.00 1 DIFFRACTOMETER RIGAKU AFC-5R x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU 1809.217 DNA (5'-D(*CP*GP*AP*TP*CP*G)-3') 1 syn polymer 497.494 IDARUBICIN 1 syn non-polymer 24.305 MAGNESIUM ION 1 syn non-polymer 18.015 water 60 nat water no no (DC)(DG)(DA)(DT)(DC)(DG) CGATCG A polydeoxyribonucleotide n n n n n n 2.93 58.09 VAPOR DIFFUSION 6.00 pH 6.00, VAPOR DIFFUSION, temperature 298.00K 298.00 WATER 1 MPD 1 BACL2 1 NA CACODYLATE 1 SPERMINE 1 WATER 2 MPD 2 13.601 1 19 A 1 A 6 0.089 A_DC1:DG6_A 1 4.354 0.228 -0.296 -0.263 -16.501 1 19 A 2 A 5 0.013 A_DG2:DC5_A 2 0.809 -0.110 -0.314 -0.161 -7.360 1 20 A 3 A 4 1.049 A_DA3:DT4_A 3 -2.238 -0.113 0.325 -0.221 7.360 1 20 A 4 A 3 1.049 A_DT4:DA3_A 4 -2.238 0.113 0.325 -0.221 16.501 1 19 A 5 A 2 0.013 A_DC5:DG2_A 5 0.809 0.110 -0.314 -0.161 -13.601 1 19 A 6 A 1 0.089 A_DG6:DC1_A 6 4.354 -0.228 -0.296 -0.263 7.181 33.942 A A 1 2 -1.249 A A 6 5 7.206 -0.729 1.309 1.085 AA_DC1DG2:DC5DG6_AA 1 -0.018 0.030 33.934 2.116 -2.248 3.475 32.489 A A 2 3 -0.510 A A 5 4 3.258 -0.283 -1.382 0.436 AA_DG2DA3:DT4DC5_AA 2 -7.123 12.831 31.718 0.832 1.170 3.146 31.976 A A 3 4 1.385 A A 4 3 3.164 0.763 0.000 -0.748 AA_DA3DT4:DA3DT4_AA 3 0.000 0.000 31.967 -1.492 0.000 3.475 32.489 A A 4 5 -0.510 A A 3 2 3.258 -0.283 1.382 0.436 AA_DT4DC5:DG2DA3_AA 4 7.123 -12.831 31.718 0.832 -1.170 7.181 33.942 A A 5 6 -1.249 A A 2 1 7.206 -0.729 -1.309 1.085 AA_DC5DG6:DC1DG2_AA 5 0.018 -0.030 33.934 2.116 2.248 chem_comp_atom chem_comp_bond database_2 pdbx_struct_conn_angle struct_conn struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 1992-04-15 1 1 2008-05-22 1 2 2011-07-13 1 3 2024-02-07 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _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_conn.ptnr2_symmetry _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id BNL Y NDB 1991-04-23 REL DM5 IDARUBICIN MG MAGNESIUM ION HOH water DM5 7 2 DM5 DM5 7 A MG 8 3 MG MG 8 A HOH 9 4 HOH HOH 9 A HOH 10 4 HOH HOH 10 A HOH 11 4 HOH HOH 11 A HOH 12 4 HOH HOH 12 A HOH 13 4 HOH HOH 13 A HOH 14 4 HOH HOH 14 A HOH 15 4 HOH HOH 15 A HOH 16 4 HOH HOH 16 A HOH 17 4 HOH HOH 17 A HOH 18 4 HOH HOH 18 A HOH 19 4 HOH HOH 19 A HOH 20 4 HOH HOH 20 A HOH 21 4 HOH HOH 21 A HOH 22 4 HOH HOH 22 A HOH 23 4 HOH HOH 23 A HOH 24 4 HOH HOH 24 A HOH 25 4 HOH HOH 25 A HOH 26 4 HOH HOH 26 A HOH 27 4 HOH HOH 27 A HOH 28 4 HOH HOH 28 A HOH 29 4 HOH HOH 29 A HOH 30 4 HOH HOH 30 A HOH 31 4 HOH HOH 31 A HOH 32 4 HOH HOH 32 A HOH 33 4 HOH HOH 33 A HOH 34 4 HOH HOH 34 A HOH 35 4 HOH HOH 35 A HOH 36 4 HOH HOH 36 A HOH 37 4 HOH HOH 37 A HOH 38 4 HOH HOH 38 A HOH 39 4 HOH HOH 39 A HOH 40 4 HOH HOH 40 A HOH 41 4 HOH HOH 41 A HOH 42 4 HOH HOH 42 A HOH 43 4 HOH HOH 43 A HOH 44 4 HOH HOH 44 A HOH 45 4 HOH HOH 45 A HOH 46 4 HOH HOH 46 A HOH 47 4 HOH HOH 47 A HOH 48 4 HOH HOH 48 A HOH 49 4 HOH HOH 49 A HOH 50 4 HOH HOH 50 A HOH 51 4 HOH HOH 51 A HOH 52 4 HOH HOH 52 A HOH 53 4 HOH HOH 53 A HOH 54 4 HOH HOH 54 A HOH 55 4 HOH HOH 55 A HOH 56 4 HOH HOH 56 A HOH 57 4 HOH HOH 57 A HOH 58 4 HOH HOH 58 A HOH 59 4 HOH HOH 59 A HOH 60 4 HOH HOH 60 A HOH 61 4 HOH HOH 61 A HOH 62 4 HOH HOH 62 A HOH 63 4 HOH HOH 63 A HOH 64 4 HOH HOH 64 A HOH 65 4 HOH HOH 65 A HOH 66 4 HOH HOH 66 A HOH 67 4 HOH HOH 67 A HOH 68 4 HOH HOH 68 A C 1 n 1 DC 1 A G 2 n 2 DG 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 A DG 6 A N7 DG 6 1_555 A MG 8 C MG MG 1_555 A HOH 9 D O HOH 1_555 98.8 A DG 6 A N7 DG 6 1_555 A MG 8 C MG MG 1_555 A HOH 10 D O HOH 7_555 134.8 A HOH 9 D O HOH 1_555 A MG 8 C MG MG 1_555 A HOH 10 D O HOH 7_555 104.2 A DG 6 A N7 DG 6 1_555 A MG 8 C MG MG 1_555 A HOH 11 D O HOH 1_555 142.2 A HOH 9 D O HOH 1_555 A MG 8 C MG MG 1_555 A HOH 11 D O HOH 1_555 99.2 A HOH 10 D O HOH 7_555 A MG 8 C MG MG 1_555 A HOH 11 D O HOH 1_555 71.0 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 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 28.1300000000 28.1300000000 26.8400000000 1 A A O O HOH HOH 31 62 1.57 1 3.60 0.50 119.90 123.50 A A A C2 N3 C4 DC DC DC 1 1 1 N 1 5.19 0.70 121.90 127.09 A A A N3 C2 O2 DC DC DC 1 1 1 N 1 7.94 1.20 119.70 127.64 A A A C3' O3' P DC DC DG 1 1 2 Y 1 9.67 1.10 110.50 120.17 A A A O3' P OP2 DC DG DG 1 2 2 Y 1 9.32 1.20 110.70 120.02 A A A O5' P OP1 DG DG DG 2 2 2 N 1 -8.99 0.90 105.70 96.71 A A A O5' P OP2 DG DG DG 2 2 2 N 1 -7.11 0.80 109.40 102.29 A A A O5' C5' C4' DG DG DG 2 2 2 N 1 -13.62 1.60 120.90 107.28 A A A P O5' C5' DG DG DG 2 2 2 N 1 -6.82 0.80 102.40 95.58 A A A C3' C2' C1' DG DG DG 2 2 2 N 1 5.64 0.30 108.30 113.94 A A A O4' C1' N9 DG DG DG 2 2 2 N 1 -4.56 0.60 125.10 120.54 A A A C6 N1 C2 DG DG DG 2 2 2 N 1 3.48 0.50 111.50 114.98 A A A C5 C6 N1 DG DG DG 2 2 2 N 1 -3.82 0.60 119.90 116.08 A A A N1 C6 O6 DG DG DG 2 2 2 N 1 10.84 1.50 119.60 130.44 A A A OP1 P OP2 DA DA DA 3 3 3 N 1 -8.28 0.80 109.40 101.12 A A A O5' C5' C4' DA DA DA 3 3 3 N 1 2.02 0.30 108.30 110.32 A A A O4' C1' N9 DA DA DA 3 3 3 N 1 4.33 0.60 118.60 122.93 A A A C6 N1 C2 DA DA DA 3 3 3 N 1 -3.79 0.50 129.30 125.51 A A A N1 C2 N3 DA DA DA 3 3 3 N 1 -4.08 0.50 117.70 113.62 A A A C5 C6 N1 DA DA DA 3 3 3 N 1 4.18 0.60 114.60 118.78 A A A N1 C2 N3 DT DT DT 4 4 4 N 1 -4.11 0.60 127.20 123.09 A A A C2 N3 C4 DT DT DT 4 4 4 N 1 7.70 1.20 119.70 127.40 A A A C3' O3' P DT DT DC 4 4 5 Y 1 -5.41 0.80 109.40 103.99 A A A O5' C5' C4' DC DC DC 5 5 5 N 1 -5.63 0.80 102.40 96.77 A A A C3' C2' C1' DC DC DC 5 5 5 N 1 7.76 0.30 108.30 116.06 A A A O4' C1' N1 DC DC DC 5 5 5 N 1 -6.37 0.70 108.00 101.63 A A A O4' C1' N9 DG DG DG 6 6 6 N 1 -3.72 0.60 128.60 124.88 A A A C5 C6 O6 DG DG DG 6 6 6 N 1 A A P O5' DG DG 2 2 0.065 0.010 1.593 1.658 N 1 A A P O5' DT DT 4 4 0.066 0.010 1.593 1.659 N 1 A A O4' C4' DT DT 4 4 -0.061 0.010 1.446 1.385 N 1 A A C6 N1 DG DG 6 6 -0.044 0.007 1.391 1.347 N 1 A A O O HOH HOH 48 67 2.17 1_555 7_555 0.1880000 1.700 1724 1 2.000 TR isotropic TR isotropic 1.700 60 217 37 120 0 fix fix 1.700 1D38 1724 2.000 1 refinement NUCLSQ INFLUENCE OF AGLYCONE MODIFICATIONS ON THE BINDING OF ANTHRACYCLINE DRUGS TO DNA: THE MOLECULAR STRUCTURE OF IDARUBICIN AND 4-O-DEMETHYL-11-DEOXYDOXORUBICIN COMPLEXED TO D(CGATCG) 1 N N 2 N N 3 N N 4 N N metalc 2.625 A DG 6 A N7 DG 6 1_555 A MG 8 C MG MG 1_555 metalc 2.787 A MG 8 C MG MG 1_555 A HOH 9 D O HOH 1_555 metalc 2.845 A MG 8 C MG MG 1_555 A HOH 10 D O HOH 7_555 metalc 2.788 A MG 8 C MG MG 1_555 A HOH 11 D O HOH 1_555 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 DG 2 A N1 DG 2 1_555 A DC 5 A N3 DC 5 8_665 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 A DC 5 A O2 DC 5 8_665 hydrog WATSON-CRICK A DG 2 A O6 DG 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 DG 2 A N1 DG 2 8_665 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 A DG 2 A O6 DG 2 8_665 hydrog WATSON-CRICK A DC 5 A O2 DC 5 1_555 A DG 2 A N2 DG 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 RIGHT HANDED DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, DNA 1D38 PDB 1 1D38 1 6 1D38 1 6 1D38 A 1 1 6 BINDING SITE FOR RESIDUE DM5 A 7 A DM5 7 Software 10 BINDING SITE FOR RESIDUE MG A 8 A MG 8 Software 5 A DC 1 A DC 1 10 8_665 A DG 2 A DG 2 10 8_665 A DA 3 A DA 3 10 8_665 A DT 4 A DT 4 10 1_555 A DC 5 A DC 5 10 1_555 A DG 6 A DG 6 10 1_555 A MG 8 C MG 10 1_555 A HOH 29 D HOH 10 1_555 A HOH 33 D HOH 10 1_555 A HOH 64 D HOH 10 1_555 A DG 6 A DG 6 5 1_555 A DM5 7 B DM5 5 1_555 A HOH 9 D HOH 5 1_555 A HOH 10 D HOH 5 7_555 A HOH 11 D HOH 5 1_555 92 P 41 21 2