0.035787 0.000000 0.000000 0.000000 0.035787 0.000000 0.000000 0.000000 0.019141 0.00000 0.00000 0.00000 Wang, A.H.-J. Gao, Y.-G. Liaw, Y.-C. Li, Y.-K. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 27.943 27.943 52.243 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 C11 H16 N5 O7 P 361.248 n N2-METHYL-2'-DEOXY-GUANOSINE-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 N 13 N N N 14 N C N 15 N O N 16 N N N 17 N C N 18 N N N 19 N C N 20 N C N 21 N H N 22 N H 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 O N 36 N P N 37 N O N 38 N O N 39 N O N 40 N C N 41 R C N 42 N O N 43 S C N 44 N O N 45 N C N 46 R C Y 47 N N Y 48 N C Y 49 N N Y 50 N C N 51 N C N 52 N O N 53 N N N 54 N C N 55 N N N 56 N N Y 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 Y 72 N C Y 73 N C Y 74 N C Y 75 N C N 76 N O Y 77 N C N 78 N C N 79 N O Y 80 N C Y 81 N C N 82 N O Y 83 N C N 84 S C N 85 N O N 86 N C N 87 S C N 88 N O N 89 N C N 90 N O N 91 N C N 92 N C Y 93 N C Y 94 N C N 95 N O Y 96 N C N 97 N C N 98 N O Y 99 N C N 100 N C N 101 R C N 102 N C N 103 S C N 104 N N N 105 S C N 106 N O N 107 S C N 108 N O N 109 N C 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 H N 120 N H N 121 N H N 122 N H N 123 N H N 124 N H N 125 N H N 126 N H N 127 N H N 128 N H N 129 N H N 130 N H N 131 N H N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 139 N P N 140 N O N 141 N O N 142 N O N 143 N O N 144 N C N 145 R C N 146 N O N 147 S C N 148 N O N 149 N C N 150 R C Y 151 N N Y 152 N C Y 153 N N Y 154 N C N 155 N C N 156 N O N 157 N N N 158 N C N 159 N N N 160 N C N 161 N N Y 162 N C 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 H N 176 N H N 177 N H N 178 N H N 179 N O N 180 N H N 181 N H N 182 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 N 24 N sing N 25 N sing N 26 N doub N 27 N sing N 28 N doub N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N doub N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N doub 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 Y 59 N sing Y 60 N sing Y 61 N doub N 62 N sing Y 63 N sing N 64 N sing Y 65 N doub 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 Y 75 N doub Y 76 N sing N 77 N sing Y 78 N sing N 79 N sing Y 80 N doub N 81 N sing N 82 N sing Y 83 N sing N 84 N sing N 85 N sing Y 86 N doub N 87 N doub N 88 N sing Y 89 N doub Y 90 N sing N 91 N sing Y 92 N sing N 93 N sing N 94 N sing Y 95 N doub 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 doub 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 Y 115 N sing N 116 N sing Y 117 N doub N 118 N sing N 119 N sing N 120 N doub N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing 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 doub N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing 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 Y 169 N sing Y 170 N sing Y 171 N doub N 172 N sing Y 173 N sing N 174 N sing Y 175 N doub N 176 N doub N 177 N sing N 178 N sing N 179 N sing N 180 N sing N 181 N doub N 182 N sing 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 US Biochemistry BICHAW 0033 0006-2960 30 3812 3815 10.1021/bi00230a002 2018756 Formaldehyde cross-links daunorubicin and DNA efficiently: HPLC and X-ray diffraction studies. 1991 10.2210/pdb1d33/pdb pdb_00001d33 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 1824.232 5'-D(*CP*GP*CP*(G49)P*CP*G)-3' 1 syn polymer 527.520 DAUNOMYCIN 1 syn non-polymer 24.305 MAGNESIUM ION 1 syn non-polymer 18.015 water 65 nat water no yes (DC)(DG)(DC)(G49)(DC)(DG) CGCGCG A polydeoxyribonucleotide n n n n n n 2.80 55.99 VAPOR DIFFUSION 6.00 pH 6.00, VAPOR DIFFUSION ROOM TEMPERATURE WATER 1 MPD 1 HCHO 1 BACL2 1 NA CACODYLATE 1 SPERMINE 1 WATER 2 HCHO 2 MPD 2 6.442 1 19 A 1 A 6 -2.380 A_DC1:DG6_A 1 1.246 0.228 -0.023 -0.166 -15.149 1 19 A 2 A 5 0.770 A_DG2:DC5_A 2 0.972 -0.082 -0.365 -0.187 -3.218 1 19 A 3 A 4 2.077 A_DC3:G494_A 3 -7.137 0.262 0.109 -0.254 3.218 1 19 A 4 A 3 2.077 A_G494:DC3_A 4 -7.137 -0.262 0.109 -0.254 15.149 1 19 A 5 A 2 0.770 A_DC5:DG2_A 5 0.972 0.082 -0.365 -0.187 -6.442 1 19 A 6 A 1 -2.380 A_DG6:DC1_A 6 1.246 -0.228 -0.023 -0.166 6.937 34.269 A A 1 2 -4.210 A A 6 5 6.982 -2.478 1.234 1.127 AA_DC1DG2:DC5DG6_AA 1 1.725 -2.931 34.140 2.742 -1.516 3.140 30.742 A A 2 3 -6.549 A A 5 4 3.040 -3.456 -1.169 0.026 AA_DG2DC3:G494DC5_AA 2 -3.898 7.387 30.308 0.693 1.479 3.116 36.970 A A 3 4 12.274 A A 4 3 3.189 7.730 0.000 -0.037 AA_DC3G494:DC3G494_AA 3 0.000 0.000 36.180 -1.073 0.000 3.140 30.742 A A 4 5 -6.549 A A 3 2 3.040 -3.456 1.169 0.026 AA_G494DC5:DG2DC3_AA 4 3.898 -7.387 30.308 0.693 -1.479 6.937 34.269 A A 5 6 -4.210 A A 2 1 6.982 -2.478 -1.234 1.127 AA_DC5DG6:DC1DG2_AA 5 -1.725 2.931 34.140 2.742 1.516 chem_comp_atom chem_comp_bond database_2 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 _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _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 BNL Y NDB 1991-02-27 REL DM1 DAUNOMYCIN MG MAGNESIUM ION HOH water A METHYLENE GROUP LINKS THE N3* ATOM OF DAUNOMYCIN AND N2 G A 4. DM1 4 2 DM1 DM1 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 HOH 69 4 HOH HOH 69 A HOH 70 4 HOH HOH 70 A HOH 71 4 HOH HOH 71 A HOH 72 4 HOH HOH 72 A HOH 73 4 HOH HOH 73 A C 1 n 1 DC 1 A G 2 n 2 DG 2 A C 3 n 3 DC 3 A +G 4 n 4 G49 4 A C 5 n 5 DC 5 A G 6 n 6 DG 6 A author_and_software_defined_assembly PISA 2 dimeric 4290 -1.1 1690 A G49 4 A G49 4 DG 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 27.9430000000 27.9430000000 26.1215000000 1 A A O O HOH HOH 71 73 1.45 1 A A O O HOH HOH 71 72 1.46 1 A A O O HOH HOH 23 67 1.96 1 11.29 1.20 119.70 130.99 A A A C3' O3' P DC DC DG 1 1 2 Y 1 -5.68 0.80 102.40 96.72 A A A C3' C2' C1' DG DG DG 2 2 2 N 1 6.52 0.30 108.30 114.82 A A A O4' C1' N9 DG DG DG 2 2 2 N 1 12.30 1.20 119.70 132.00 A A A C3' O3' P DG DG DC 2 2 3 Y 1 3.59 0.50 119.90 123.49 A A A C2 N3 C4 DC DC DC 3 3 3 N 1 -3.17 0.40 121.90 118.73 A A A N3 C4 C5 DC DC DC 3 3 3 N 1 -5.71 0.80 102.40 96.69 A A A C3' C2' C1' DC DC DC 5 5 5 N 1 9.88 0.30 108.30 118.18 A A A O4' C1' N1 DC DC DC 5 5 5 N 1 7.65 1.10 110.50 118.15 A A A O3' P OP1 DC DG DG 5 6 6 Y 1 -3.66 0.60 125.10 121.44 A A A C6 N1 C2 DG DG DG 6 6 6 N 1 4.62 0.50 111.50 116.12 A A A C5 C6 N1 DG DG DG 6 6 6 N 1 -4.16 0.60 128.60 124.44 A A A C5 C6 O6 DG DG DG 6 6 6 N 1 A A P O5' DC DC 5 5 0.091 0.010 1.593 1.684 N 1 A A N3 C4 DC DC 5 5 0.044 0.007 1.335 1.379 N 1 A A O O HOH HOH 42 56 2.01 1_555 4_454 0.185 1.500 2229 1 3.000 TR isotropic TR isotropic 1.500 65 225 40 120 0 0.016 fix fix 1.500 1D33 3.000 1 refinement NUCLSQ Formaldehyde cross-links daunorubicin and DNA efficiently: HPLC and X-RAY diffraction studies 1 N N 2 N N 3 N N 4 N N covale 1.611 both A DC 3 A O3' DC 3 1_555 A G49 4 A P G49 4 1_555 covale 1.633 one A G49 4 A O3' G49 4 1_555 A DC 5 A P DC 5 1_555 covale 1.532 none A G49 4 A CM2 G49 4 1_555 A DM1 7 B N3' DM1 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 DC 3 A N3 DC 3 1_555 A G49 4 A N1 G49 4 8_665 hydrog WATSON-CRICK A DC 3 A N4 DC 3 1_555 A G49 4 A O6 G49 4 8_665 hydrog WATSON-CRICK A DC 3 A O2 DC 3 1_555 A G49 4 A N2 G49 4 8_665 hydrog WATSON-CRICK A G49 4 A N1 G49 4 1_555 A DC 3 A N3 DC 3 8_665 hydrog WATSON-CRICK A G49 4 A N2 G49 4 1_555 A DC 3 A O2 DC 3 8_665 hydrog WATSON-CRICK A G49 4 A O6 G49 4 1_555 A DC 3 A N4 DC 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, MODIFIED, DNA 1D33 PDB 1 1D33 1 6 1D33 1 6 1D33 A 1 1 6 BINDING SITE FOR RESIDUE DM1 A 7 A DM1 7 Software 12 BINDING SITE FOR RESIDUE MG A 8 A MG 8 Software 5 A DC 1 A DC 1 12 8_665 A DG 2 A DG 2 12 8_665 A DC 3 A DC 3 12 8_665 A G49 4 A G49 4 12 1_555 A DC 5 A DC 5 12 1_555 A DG 6 A DG 6 12 1_555 A MG 8 C MG 12 1_555 A HOH 29 D HOH 12 1_555 A HOH 34 D HOH 12 1_555 A HOH 36 D HOH 12 1_555 A HOH 60 D HOH 12 1_555 A HOH 71 D HOH 12 1_555 A DG 6 A DG 6 5 1_555 A DM1 7 B DM1 5 1_555 A HOH 9 D HOH 5 1_555 A HOH 10 D HOH 5 1_555 A HOH 11 D HOH 5 1_555 92 tetragonal P 41 21 2