0.056402 0.000000 0.007937 0.000000 0.052274 0.000000 0.000000 0.000000 0.038310 0.00000 0.00000 0.00000 Williams, L.D. Egli, M. Ughetto, G. Van Der Marel, G.A. Van Boom, J.H. Quigley, G.J. Wang, A.H.-J. Rich, A. Frederick, C.A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 2 90.00 98.01 90.00 17.730 19.130 26.360 C10 H14 N5 O5 P S 347.287 n 2-DEOXY-ADENOSINE -5'-THIO-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 O9 511.520 6-DEOXYDAUNOMYCIN non-polymer C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking H2 O 18.015 WATER non-polymer N 1 N P N 2 N O N 3 N S 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 Y 131 N C N 132 N C N 133 N O Y 134 N C N 135 N C N 136 R C N 137 N C N 138 S C N 139 N N N 140 S C N 141 N O N 142 S C N 143 N O N 144 N C 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 H N 172 N H N 173 N H N 174 N O N 175 N P N 176 N O N 177 N O N 178 N O N 179 N C N 180 R C N 181 N O N 182 S C N 183 N O N 184 N C N 185 R C N 186 N N N 187 N C N 188 N O N 189 N N N 190 N C N 191 N O N 192 N C N 193 N C N 194 N C 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 H N 208 N H N 209 N H N 210 N O N 211 N H N 212 N H N 1 N sing N 2 N doub 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 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 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 sing N 183 N sing N 184 N sing N 185 N doub 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 sing N 206 N sing N 207 N sing N 208 N doub N 209 N sing N 210 N sing N 211 N sing N 212 N doub N 213 N sing N 214 N sing N 215 N doub N 216 N sing N 217 N sing N 218 N sing N 219 N sing N 220 N sing N 221 N sing UK J.Mol.Biol. JMOBAK 0070 0022-2836 215 313 320 10.1016/S0022-2836(05)80349-3 2152325 Structure of 11-deoxydaunomycin bound to DNA containing a phosphorothioate. 1990 10.2210/pdb1d14/pdb pdb_00001d14 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 283.00 1 DIFFRACTOMETER NICOLET P3 x-ray 1 1.0 1825.282 DNA (5'-D(*CP*GP*TP*(AS)P*CP*G)-3') 1 syn polymer 511.520 6-DEOXYDAUNOMYCIN 1 syn non-polymer 18.015 water 37 nat water no yes (DC)(DG)(DT)(AS)(DC)(DG) CGTACG A polydeoxyribonucleotide n n n n n n 2.43 49.28 VAPOR DIFFUSION 6.00 pH 6.00, VAPOR DIFFUSION ROOM TEMPERATURE WATER 1 MPD 1 NA CACODYLATE 1 SPERMINE 1 MGCL2 1 WATER 2 MPD 2 6.807 1 19 A 1 A 6 1.685 A_DC1:DG6_A 1 3.916 0.213 -0.127 -0.288 -15.981 1 19 A 2 A 5 2.481 A_DG2:DC5_A 2 -0.477 -0.394 -0.363 -0.212 -1.279 1 20 A 3 A 4 0.613 A_DT3:AS4_A 3 -7.390 -0.218 0.185 -0.152 1.279 1 20 A 4 A 3 0.613 A_AS4:DT3_A 4 -7.390 0.218 0.185 -0.152 15.981 1 19 A 5 A 2 2.481 A_DC5:DG2_A 5 -0.477 0.394 -0.363 -0.212 -6.807 1 19 A 6 A 1 1.685 A_DG6:DC1_A 6 3.916 -0.213 -0.127 -0.288 6.899 36.398 A A 1 2 -4.624 A A 6 5 7.027 -2.886 0.981 1.485 AA_DC1DG2:DC5DG6_AA 1 0.252 -0.404 36.287 3.233 -1.495 3.149 32.065 A A 2 3 -5.756 A A 5 4 3.042 -3.161 -0.939 -0.099 AA_DG2DT3:AS4DC5_AA 2 -5.302 9.656 31.480 0.364 0.788 3.187 42.381 A A 3 4 1.708 A A 4 3 3.205 1.235 0.000 -0.591 AA_DT3AS4:DT3AS4_AA 3 0.000 0.000 42.364 -0.940 0.000 3.149 32.065 A A 4 5 -5.756 A A 3 2 3.042 -3.161 0.939 -0.099 AA_AS4DC5:DG2DT3_AA 4 5.302 -9.656 31.480 0.364 -0.788 6.899 36.398 A A 5 6 -4.624 A A 2 1 7.027 -2.886 -0.981 1.485 AA_DC5DG6:DC1DG2_AA 5 -0.252 0.404 36.287 3.233 1.495 atom_site chem_comp_atom chem_comp_bond database_2 struct_conn struct_site repository Initial release Version format compliance Version format compliance Atomic model Data collection Database references Derived calculations 1 0 1990-10-15 1 1 2008-05-22 1 2 2011-07-13 2 0 2024-02-07 _atom_site.occupancy _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 BNL Y BNL 1989-10-20 REL DM3 6-DEOXYDAUNOMYCIN HOH water DM3 7 2 DM3 DM3 7 A HOH 8 3 HOH HOH 8 A HOH 9 3 HOH HOH 9 A HOH 10 3 HOH HOH 10 A HOH 11 3 HOH HOH 11 A HOH 12 3 HOH HOH 12 A HOH 13 3 HOH HOH 13 A HOH 14 3 HOH HOH 14 A HOH 15 3 HOH HOH 15 A HOH 16 3 HOH HOH 16 A HOH 17 3 HOH HOH 17 A HOH 18 3 HOH HOH 18 A HOH 19 3 HOH HOH 19 A HOH 20 3 HOH HOH 20 A HOH 21 3 HOH HOH 21 A HOH 22 3 HOH HOH 22 A HOH 23 3 HOH HOH 23 A HOH 24 3 HOH HOH 24 A HOH 25 3 HOH HOH 25 A HOH 26 3 HOH HOH 26 A HOH 27 3 HOH HOH 27 A HOH 28 3 HOH HOH 28 A HOH 29 3 HOH HOH 29 A HOH 30 3 HOH HOH 30 A HOH 31 3 HOH HOH 31 A HOH 32 3 HOH HOH 32 A HOH 33 3 HOH HOH 33 A HOH 34 3 HOH HOH 34 A HOH 35 3 HOH HOH 35 A HOH 36 3 HOH HOH 36 A HOH 37 3 HOH HOH 37 A HOH 38 3 HOH HOH 38 A HOH 39 3 HOH HOH 39 A HOH 40 3 HOH HOH 40 A HOH 41 3 HOH HOH 41 A HOH 42 3 HOH HOH 42 A HOH 43 3 HOH HOH 43 A HOH 44 3 HOH HOH 44 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 AS 4 A C 5 n 5 DC 5 A G 6 n 6 DG 6 A author_defined_assembly 2 dimeric A AS 4 A AS 4 DA 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 2_757 -x+2,y,-z+2 crystal symmetry operation 28.1136824005 0.0000000000 52.2056512049 1 A HOH 44 C HOH 1 -5.34 0.80 102.40 97.06 A A A C3' C2' C1' DC DC DC 1 1 1 N 1 -11.66 0.70 108.00 96.34 A A A O4' C1' N1 DC DC DC 1 1 1 N 1 4.34 0.50 119.90 124.24 A A A C2 N3 C4 DC DC DC 1 1 1 N 1 -5.22 0.40 121.90 116.68 A A A N3 C4 C5 DC DC DC 1 1 1 N 1 -8.18 1.20 119.70 111.52 A A A C3' O3' P DC DC DG 1 1 2 Y 1 -12.26 1.60 120.90 108.64 A A A P O5' C5' DG DG DG 2 2 2 N 1 -2.44 0.40 104.50 102.06 A A A O4' C4' C3' DG DG DG 2 2 2 N 1 -7.85 0.80 102.40 94.55 A A A C3' C2' C1' DG DG DG 2 2 2 N 1 3.26 0.30 108.30 111.57 A A A O4' C1' N9 DG DG DG 2 2 2 N 1 -4.57 0.60 118.80 114.23 A A A C4 C5 C6 DG DG DG 2 2 2 N 1 7.32 0.50 111.50 118.82 A A A C5 C6 N1 DG DG DG 2 2 2 N 1 -4.50 0.50 113.10 108.60 A A A N7 C8 N9 DG DG DG 2 2 2 N 1 5.13 0.40 106.40 111.53 A A A C8 N9 C4 DG DG DG 2 2 2 N 1 -2.91 0.40 105.40 102.49 A A A N9 C4 C5 DG DG DG 2 2 2 N 1 4.99 0.60 126.00 130.99 A A A N3 C4 N9 DG DG DG 2 2 2 N 1 3.80 0.60 130.40 134.20 A A A C6 C5 N7 DG DG DG 2 2 2 N 1 7.60 0.90 116.20 123.80 A A A N1 C2 N2 DG DG DG 2 2 2 N 1 -7.30 0.70 119.90 112.60 A A A N3 C2 N2 DG DG DG 2 2 2 N 1 -7.78 0.60 128.60 120.82 A A A C5 C6 O6 DG DG DG 2 2 2 N 1 8.94 1.20 119.70 128.64 A A A C3' O3' P DG DG DT 2 2 3 Y 1 8.95 1.20 110.70 119.65 A A A O5' P OP2 DT DT DT 3 3 3 N 1 -14.06 1.60 120.90 106.84 A A A P O5' C5' DT DT DT 3 3 3 N 1 4.39 0.60 106.00 110.39 A A A O4' C4' C3' DT DT DT 3 3 3 N 1 -9.68 0.70 108.00 98.32 A A A O4' C1' N1 DT DT DT 3 3 3 N 1 -2.89 0.40 104.50 101.61 A A A O4' C4' C3' DC DC DC 5 5 5 N 1 5.17 0.70 110.30 115.47 A A A C1' O4' C4' DC DC DC 5 5 5 N 1 12.05 0.30 108.30 120.35 A A A O4' C1' N1 DC DC DC 5 5 5 N 1 3.35 0.50 119.90 123.25 A A A C2 N3 C4 DC DC DC 5 5 5 N 1 -4.79 0.40 121.90 117.11 A A A N3 C4 C5 DC DC DC 5 5 5 N 1 3.17 0.50 117.40 120.57 A A A C4 C5 C6 DC DC DC 5 5 5 N 1 8.75 0.70 120.20 128.95 A A A C5 C4 N4 DC DC DC 5 5 5 N 1 7.25 1.20 119.70 126.95 A A A C3' O3' P DC DC DG 5 5 6 Y 1 -16.85 0.90 105.70 88.85 A A A O5' P OP1 DG DG DG 6 6 6 N 1 4.89 0.60 123.90 128.79 A A A N1 C2 N3 DG DG DG 6 6 6 N 1 -4.13 0.50 111.90 107.77 A A A C2 N3 C4 DG DG DG 6 6 6 N 1 3.24 0.50 111.50 114.74 A A A C5 C6 N1 DG DG DG 6 6 6 N 1 6.97 0.90 116.20 123.17 A A A N1 C2 N2 DG DG DG 6 6 6 N 1 -11.86 0.70 119.90 108.04 A A A N3 C2 N2 DG DG DG 6 6 6 N 1 A A C2' C1' DC DC 1 1 0.109 0.010 1.519 1.628 N 1 A A N1 C2 DC DC 1 1 -0.080 0.010 1.397 1.317 N 1 A A N3 C4 DC DC 1 1 0.066 0.007 1.335 1.401 N 1 A A P O5' DG DG 2 2 0.065 0.010 1.593 1.658 N 1 A A O3' C3' DG DG 2 2 -0.036 0.006 1.419 1.383 N 1 A A C6 N1 DG DG 2 2 -0.078 0.007 1.391 1.313 N 1 A A C8 N9 DG DG 2 2 -0.045 0.007 1.374 1.329 N 1 A A C2 N2 DG DG 2 2 -0.141 0.010 1.341 1.200 N 1 A A O4' C1' DT DT 3 3 0.089 0.011 1.420 1.509 N 1 A A O3' C3' DT DT 3 3 -0.052 0.006 1.419 1.367 N 1 A A P OP1 DC DC 5 5 -0.125 0.017 1.485 1.360 N 1 A A P O5' DC DC 5 5 0.105 0.010 1.593 1.698 N 1 A A C5' C4' DC DC 5 5 0.051 0.007 1.512 1.563 N 1 A A O4' C1' DC DC 5 5 -0.086 0.012 1.418 1.332 N 1 A A O4' C4' DC DC 5 5 -0.080 0.010 1.446 1.366 N 1 A A N1 C6 DC DC 5 5 0.039 0.006 1.367 1.406 N 1 A A N3 C4 DC DC 5 5 0.070 0.007 1.335 1.405 N 1 A A P O5' DG DG 6 6 0.066 0.010 1.593 1.659 N 1 A A C4' C3' DG DG 6 6 0.093 0.010 1.529 1.622 N 1 A A O4' C1' DG DG 6 6 0.090 0.011 1.420 1.510 N 1 A A N1 C2 DG DG 6 6 -0.061 0.008 1.373 1.312 N 1 A A C6 N1 DG DG 6 6 -0.059 0.007 1.391 1.332 N 1 A A C2 N2 DG DG 6 6 -0.116 0.010 1.341 1.225 N 1 A A O O HOH HOH 43 43 1.95 1_555 2_857 0.224 1.500 2129 1 2.000 TR isotropic TR isotropic 1.500 37 194 38 119 0 fix fix 1.500 1D14 2129 2.000 1 refinement NUCLSQ STRUCTURE OF 11-DEOXYDAUNOMYCIN BOUND TO DNA CONTAINING A PHOSPHOROTHIOATE 1 N N 2 N N 3 N N covale 1.557 both A DT 3 A O3' DT 3 1_555 A AS 4 A P AS 4 1_555 covale 1.575 both A AS 4 A O3' AS 4 1_555 A DC 5 A P DC 5 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 A DG 6 A N1 DG 6 2_757 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 A DG 6 A O6 DG 6 2_757 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 A DG 6 A N2 DG 6 2_757 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 A DC 5 A N3 DC 5 2_757 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 A DC 5 A O2 DC 5 2_757 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 A DC 5 A N4 DC 5 2_757 hydrog WATSON-CRICK A DT 3 A N3 DT 3 1_555 A AS 4 A N1 AS 4 2_757 hydrog WATSON-CRICK A DT 3 A O4 DT 3 1_555 A AS 4 A N6 AS 4 2_757 hydrog WATSON-CRICK A AS 4 A N1 AS 4 1_555 A DT 3 A N3 DT 3 2_757 hydrog WATSON-CRICK A AS 4 A N6 AS 4 1_555 A DT 3 A O4 DT 3 2_757 hydrog WATSON-CRICK A DC 5 A N3 DC 5 1_555 A DG 2 A N1 DG 2 2_757 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 A DG 2 A O6 DG 2 2_757 hydrog WATSON-CRICK A DC 5 A O2 DC 5 1_555 A DG 2 A N2 DG 2 2_757 hydrog WATSON-CRICK A DG 6 A N1 DG 6 1_555 A DC 1 A N3 DC 1 2_757 hydrog WATSON-CRICK A DG 6 A N2 DG 6 1_555 A DC 1 A O2 DC 1 2_757 hydrog WATSON-CRICK A DG 6 A O6 DG 6 1_555 A DC 1 A N4 DC 1 2_757 DNA RIGHT HANDED DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, MODIFIED, DNA 1D14 PDB 1 1D14 1 6 1D14 1 6 1D14 A 1 1 6 BINDING SITE FOR RESIDUE DM3 A 7 A DM3 7 Software 12 A DC 1 A DC 1 12 1_555 A DG 2 A DG 2 12 1_555 A DT 3 A DT 3 12 1_455 A DT 3 A DT 3 12 1_555 A AS 4 A AS 4 12 1_555 A HOH 12 C HOH 12 1_555 A HOH 13 C HOH 12 1_555 A HOH 15 C HOH 12 1_555 A HOH 17 C HOH 12 1_555 A HOH 26 C HOH 12 1_555 A HOH 29 C HOH 12 1_555 A HOH 39 C HOH 12 1_655 3 P 1 2 1