0.035907 0.000000 0.000000 0.000000 0.035907 0.000000 0.000000 0.000000 0.019109 0.00000 0.00000 0.00000 Lipscomb, L.A. Peek, M.E. Zhou, F.X. Bertrand, J.A. VanDerveer, D. Williams, L.D. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 27.850 27.850 52.330 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 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 H N 213 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 US Biochemistry BICHAW 0033 0006-2960 33 3649 3659 10.1021/bi00178a023 8142363 Water ring structure at DNA interfaces: hydration and dynamics of DNA-anthracycline complexes. 1994 10.2210/pdb152d/pdb pdb_0000152d 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 113.00 1 AREA DETECTOR SDMS x-ray 1 1.0 ROTATING ANODE RIGAKU RU200 1809.217 DNA (5'-D(*CP*GP*AP*TP*CP*G)-3') 1 syn polymer 527.520 DAUNOMYCIN 1 syn non-polymer 18.015 water 54 nat water no no (DC)(DG)(DA)(DT)(DC)(DG) CGATCG A polydeoxyribonucleotide n n n n n n 2.80 56.14 VAPOR DIFFUSION, SITTING DROP 6.50 pH 6.50, VAPOR DIFFUSION, SITTING DROP WATER 1 MPD 1 NA CACODYLATE 1 MGCL2 1 SPERMINE_HCL 1 WATER 2 MPD 2 9.586 1 19 A 1 A 6 -0.683 A_DC1:DG6_A 1 2.842 0.157 -0.202 -0.112 -21.595 1 19 A 2 A 5 0.808 A_DG2:DC5_A 2 -0.157 -0.130 -0.590 -0.058 -6.261 1 20 A 3 A 4 3.284 A_DA3:DT4_A 3 -1.449 0.012 0.184 -0.164 6.261 1 20 A 4 A 3 3.284 A_DT4:DA3_A 4 -1.449 -0.012 0.184 -0.164 21.595 1 19 A 5 A 2 0.808 A_DC5:DG2_A 5 -0.157 0.130 -0.590 -0.058 -9.586 1 19 A 6 A 1 -0.683 A_DG6:DC1_A 6 2.842 -0.157 -0.202 -0.112 7.175 35.940 A A 1 2 -2.988 A A 6 5 7.153 -1.840 1.381 1.269 AA_DC1DG2:DC5DG6_AA 1 3.281 -5.326 35.749 2.634 -1.210 3.136 31.170 A A 2 3 -2.437 A A 5 4 2.923 -1.294 -1.277 0.419 AA_DG2DA3:DT4DC5_AA 2 -8.373 15.771 30.024 1.013 0.869 3.027 33.133 A A 3 4 9.105 A A 4 3 3.194 5.172 0.000 -0.853 AA_DA3DT4:DA3DT4_AA 3 0.000 0.000 32.738 -2.328 0.000 3.136 31.170 A A 4 5 -2.437 A A 3 2 2.923 -1.294 1.277 0.419 AA_DT4DC5:DG2DA3_AA 4 8.373 -15.771 30.024 1.013 -0.869 7.175 35.940 A A 5 6 -2.988 A A 2 1 7.153 -1.840 -1.381 1.269 AA_DC5DG6:DC1DG2_AA 5 -3.280 5.326 35.749 2.634 1.210 chem_comp_atom chem_comp_bond database_2 struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 1994-05-04 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_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id BNL Y NDB 1993-12-13 REL DM1 DAUNOMYCIN HOH water DM1 7 2 DM1 DM1 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 HOH 45 3 HOH HOH 45 A HOH 46 3 HOH HOH 46 A HOH 47 3 HOH HOH 47 A HOH 48 3 HOH HOH 48 A HOH 49 3 HOH HOH 49 A HOH 50 3 HOH HOH 50 A HOH 51 3 HOH HOH 51 A HOH 52 3 HOH HOH 52 A HOH 53 3 HOH HOH 53 A HOH 54 3 HOH HOH 54 A HOH 55 3 HOH HOH 55 A HOH 56 3 HOH HOH 56 A HOH 57 3 HOH HOH 57 A HOH 58 3 HOH HOH 58 A HOH 59 3 HOH HOH 59 A HOH 60 3 HOH HOH 60 A HOH 61 3 HOH HOH 61 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 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 27.8500000000 27.8500000000 26.1650000000 1 5.75 0.50 119.90 125.65 A A A C2 N3 C4 DC DC DC 1 1 1 N 1 -5.73 0.40 121.90 116.17 A A A N3 C4 C5 DC DC DC 1 1 1 N 1 -5.67 0.80 109.40 103.73 A A A O5' C5' C4' DG DG DG 2 2 2 N 1 -6.49 0.80 102.40 95.91 A A A C3' C2' C1' DG DG DG 2 2 2 N 1 4.86 0.30 108.30 113.16 A A A O4' C1' N9 DG DG DG 2 2 2 N 1 -5.28 0.60 125.10 119.82 A A A C6 N1 C2 DG DG DG 2 2 2 N 1 4.72 0.60 123.90 128.62 A A A N1 C2 N3 DG DG DG 2 2 2 N 1 -3.08 0.50 111.90 108.82 A A A C2 N3 C4 DG DG DG 2 2 2 N 1 6.39 0.50 111.50 117.89 A A A C5 C6 N1 DG DG DG 2 2 2 N 1 -8.41 0.70 119.90 111.49 A A A N3 C2 N2 DG DG DG 2 2 2 N 1 -3.81 0.60 119.90 116.09 A A A N1 C6 O6 DG DG DG 2 2 2 N 1 -5.42 0.90 105.70 100.28 A A A O5' P OP1 DA DA DA 3 3 3 N 1 -8.86 0.80 109.40 100.54 A A A O5' C5' C4' DA DA DA 3 3 3 N 1 11.09 1.20 119.70 130.79 A A A C3' O3' P DA DA DT 3 3 4 Y 1 -5.41 0.70 108.00 102.59 A A A O4' C1' N1 DT DT DT 4 4 4 N 1 4.28 0.60 119.00 123.28 A A A C4 C5 C7 DT DT DT 4 4 4 N 1 9.62 1.50 119.60 129.22 A A A OP1 P OP2 DC DC DC 5 5 5 N 1 -7.36 0.90 105.70 98.34 A A A O5' P OP1 DC DC DC 5 5 5 N 1 -5.17 0.80 109.40 104.23 A A A O5' C5' C4' DC DC DC 5 5 5 N 1 -7.12 0.80 102.40 95.28 A A A C3' C2' C1' DC DC DC 5 5 5 N 1 3.05 0.50 106.80 109.85 A A A O4' C1' C2' DC DC DC 5 5 5 N 1 10.32 0.30 108.30 118.62 A A A O4' C1' N1 DC DC DC 5 5 5 N 1 5.67 0.50 119.90 125.57 A A A C2 N3 C4 DC DC DC 5 5 5 N 1 -4.18 0.40 121.90 117.72 A A A N3 C4 C5 DC DC DC 5 5 5 N 1 6.69 0.60 118.90 125.59 A A A N1 C2 O2 DC DC DC 5 5 5 N 1 5.75 0.70 120.20 125.95 A A A C5 C4 N4 DC DC DC 5 5 5 N 1 5.07 0.70 110.30 115.37 A A A C1' O4' C4' DG DG DG 6 6 6 N 1 -4.62 0.60 125.10 120.48 A A A C6 N1 C2 DG DG DG 6 6 6 N 1 5.06 0.60 123.90 128.96 A A A N1 C2 N3 DG DG DG 6 6 6 N 1 5.30 0.50 111.50 116.80 A A A C5 C6 N1 DG DG DG 6 6 6 N 1 -9.33 0.70 119.90 110.57 A A A N3 C2 N2 DG DG DG 6 6 6 N 1 -3.98 0.60 128.60 124.62 A A A C5 C6 O6 DG DG DG 6 6 6 N 1 A A C2' C1' DC DC 1 1 0.072 0.010 1.519 1.591 N 1 A A O3' C3' DC DC 1 1 -0.038 0.006 1.419 1.381 N 1 A A C2' C1' DG DG 2 2 0.104 0.010 1.519 1.623 N 1 A A C6 N1 DG DG 2 2 -0.056 0.007 1.391 1.335 N 1 A A N7 C8 DG DG 2 2 0.046 0.006 1.305 1.351 N 1 A A C2 N2 DG DG 2 2 -0.094 0.010 1.341 1.247 N 1 A A C2' C1' DA DA 3 3 0.095 0.010 1.519 1.614 N 1 A A O3' C3' DA DA 3 3 -0.087 0.006 1.419 1.332 N 1 A A P O5' DT DT 4 4 0.063 0.010 1.593 1.656 N 1 A A O3' C3' DT DT 4 4 -0.069 0.006 1.419 1.350 N 1 A A P O5' DC DC 5 5 0.086 0.010 1.593 1.679 N 1 A A C5' C4' DC DC 5 5 0.056 0.007 1.512 1.568 N 1 A A C2' C1' DC DC 5 5 0.082 0.010 1.519 1.601 N 1 A A N1 C2 DG DG 6 6 -0.055 0.008 1.373 1.318 N 1 A A C6 N1 DG DG 6 6 -0.057 0.007 1.391 1.334 N 1 A A N9 C4 DG DG 6 6 0.051 0.008 1.375 1.426 N 1 A A C2 N2 DG DG 6 6 -0.081 0.010 1.341 1.260 N 0.2260000 1.400 3817 1 1.000 TR isotropic TR isotropic 1.400 54 212 38 120 0 0.027 fix fix 1.400 152D 54233 3817 1.000 1 refinement NUCLSQ DIVERSITY OF WATER RING SIZE AT DNA INTERFACES: HYDRATION AND DYNAMICS OF DNA-ANTHRACYCLINE COMPLEXES 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 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 152D PDB 1 152D 1 6 152D 1 6 152D A 1 1 6 BINDING SITE FOR RESIDUE DM1 A 7 A DM1 7 Software 13 A DC 1 A DC 1 13 8_665 A DG 2 A DG 2 13 8_665 A DA 3 A DA 3 13 8_665 A DT 4 A DT 4 13 1_555 A DC 5 A DC 5 13 1_555 A DG 6 A DG 6 13 1_555 A HOH 8 C HOH 13 8_665 A HOH 11 C HOH 13 1_555 A HOH 12 C HOH 13 8_665 A HOH 19 C HOH 13 1_555 A HOH 22 C HOH 13 1_555 A HOH 23 C HOH 13 1_555 A HOH 27 C HOH 13 1_555 92 P 41 21 2