0.038023 0.021952 0.000000 0.000000 0.043905 0.000000 0.000000 0.000000 0.009999 0.00000 0.00000 0.00000 Egli, M. Williams, L.D. Frederick, C.A. Rich, A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 12 90.00 90.00 120.00 26.300 26.300 100.010 C10 H16 N3 O7 P 321.224 n 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O6 P 331.222 y 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O7 P 347.221 y 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE DNA linking C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking H2 O 18.015 WATER non-polymer C39 H49 N O16 787.803 NOGALAMYCIN non-polymer N 1 N N N 2 N C N 3 N N N 4 N C N 5 N C N 6 N C N 7 N C N 8 N O N 9 N N N 10 R C N 11 N C N 12 S C N 13 R C N 14 N O N 15 N O N 16 N C N 17 N O N 18 N P N 19 N O N 20 N O N 21 N O 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 H N 36 N H N 37 N H N 38 N O N 39 N P N 40 N O N 41 N O N 42 N O N 43 N C N 44 R C N 45 N O N 46 S C N 47 N O N 48 N C N 49 R C Y 50 N N Y 51 N C Y 52 N N Y 53 N C Y 54 N C N 55 N N Y 56 N N Y 57 N C Y 58 N N Y 59 N C 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 N 72 N H N 73 N H N 74 N O N 75 N P N 76 N O N 77 N O N 78 N O N 79 N C N 80 R C N 81 N O N 82 S C N 83 N O N 84 N C N 85 R C Y 86 N N Y 87 N C Y 88 N N Y 89 N C N 90 N C N 91 N O N 92 N N N 93 N C N 94 N N N 95 N N Y 96 N C 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 N 108 N H N 109 N H N 110 N H N 111 N O N 112 N P N 113 N O N 114 N O N 115 N O N 116 N C N 117 R C N 118 N O N 119 S C N 120 N O N 121 N C N 122 R C N 123 N N N 124 N C N 125 N O N 126 N N N 127 N C N 128 N O N 129 N C N 130 N C N 131 N C 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 H N 140 N H N 141 N H N 142 N H N 143 N H N 144 N H N 145 N H N 146 N H N 147 N O N 148 N H N 149 N H Y 150 N C Y 151 N C Y 152 N C Y 153 N C N 154 N C Y 155 N C N 156 S C N 157 N C N 158 S C N 159 R C Y 160 N C N 161 N C N 162 N C N 163 N C N 164 N C Y 165 N C Y 166 N C Y 167 N C Y 168 N C Y 169 N C Y 170 N C N 171 N C N 172 N C N 173 N C N 174 N C N 175 N C N 176 N C N 177 N C N 178 N C N 179 S C N 180 S C N 181 R C N 182 R C N 183 R C N 184 R C N 185 R C N 186 R C N 187 S C N 188 S C N 189 N N N 190 N O N 191 N O N 192 N O N 193 N O N 194 N O N 195 N O N 196 N O N 197 N O N 198 N O N 199 N O N 200 N O N 201 N O N 202 N O N 203 N O N 204 N O N 205 N O N 206 N H N 207 N H N 208 N H N 209 N H N 210 N H N 211 N H N 212 N H N 213 N H N 214 N H N 215 N H N 216 N H N 217 N H N 218 N H N 219 N H N 220 N H N 221 N H N 222 N H N 223 N H N 224 N H N 225 N H N 226 N H N 227 N H N 228 N H N 229 N H N 230 N H N 231 N H N 232 N H N 233 N H N 234 N H 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 H N 250 N H N 251 N H N 252 N H N 253 N H N 254 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N doub N 6 N doub N 7 N sing N 8 N sing N 9 N sing N 10 N doub 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 sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N sing N 34 N doub N 35 N sing N 36 N sing N 37 N sing N 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 Y 62 N sing Y 63 N sing Y 64 N doub N 65 N sing Y 66 N sing Y 67 N sing Y 68 N doub N 69 N sing Y 70 N doub N 71 N sing N 72 N sing Y 73 N sing Y 74 N doub N 75 N sing Y 76 N sing N 77 N sing N 78 N sing N 79 N doub 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 N 97 N sing N 98 N sing N 99 N sing Y 100 N sing Y 101 N sing Y 102 N doub N 103 N sing Y 104 N sing N 105 N sing Y 106 N doub N 107 N doub N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N doub N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N doub N 119 N sing N 120 N sing 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 doub 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 doub N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing Y 155 N doub Y 156 N sing N 157 N sing Y 158 N sing N 159 N sing Y 160 N doub N 161 N sing Y 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N doub Y 167 N doub Y 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 Y 183 N sing Y 184 N doub N 185 N sing N 186 N sing N 187 N sing N 188 N doub N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N doub N 194 N sing N 195 N sing N 196 N sing N 197 N sing Y 198 N doub Y 199 N sing Y 200 N doub 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 sing N 210 N sing N 211 N sing N 212 N sing N 213 N sing N 214 N sing N 215 N sing N 216 N sing 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 sing 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 N 245 N sing N 246 N sing N 247 N sing N 248 N sing N 249 N sing N 250 N sing N 251 N sing N 252 N sing N 253 N sing N 254 N sing N 255 N sing N 256 N sing N 257 N sing N 258 N sing N 259 N sing N 260 N sing N 261 N sing N 262 N sing N 263 N sing N 264 N sing N 265 N sing US Biochemistry BICHAW 0033 0006-2960 30 1364 1372 10.1021/bi00219a029 1991116 DNA-nogalamycin interactions. 1991 US Proc.Natl.Acad.Sci.USA PNASA6 0040 0027-8424 87 2225 2229 Structure of Nogalamycin Bound to a DNA Hexamer 1990 10.2210/pdb1d17/pdb pdb_00001d17 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 300.00 1 DIFFRACTOMETER RIGAKU AFC-5 x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU 1837.271 DNA (5'-D(*(5CM)P*GP*TP*AP*(5CM)P*G)-3') 1 syn polymer 787.803 NOGALAMYCIN 1 syn non-polymer 18.015 water 39 nat water no yes (5CM)(DG)(DT)(DA)(5CM)(DG) CGTACG A polydeoxyribonucleotide n n n n n n 2.72 54.73 VAPOR DIFFUSION, SITTING DROP 6.00 pH 6.00, VAPOR DIFFUSION, SITTING DROP ROOM TEMPERATURE WATER 1 MPD 1 METHANOL 1 NA CACODYLATE 1 MGCL2 1 SPERMINE 1 WATER 2 MPD 2 12.620 1 19 A 1 A 6 -0.820 A_5CM1:DG6_A 1 -6.336 0.647 0.046 -0.449 -25.238 1 19 A 2 A 5 -2.501 A_DG2:5CM5_A 2 -0.324 -0.803 -0.580 -0.525 -11.447 1 20 A 3 A 4 1.196 A_DT3:DA4_A 3 -6.537 -0.317 0.279 -0.219 11.447 1 20 A 4 A 3 1.196 A_DA4:DT3_A 4 -6.537 0.317 0.279 -0.219 25.238 1 19 A 5 A 2 -2.501 A_5CM5:DG2_A 5 -0.324 0.803 -0.580 -0.525 -12.620 1 19 A 6 A 1 -0.820 A_DG6:5CM1_A 6 -6.336 -0.647 0.046 -0.449 7.313 27.366 A A 1 2 5.119 A A 6 5 7.377 2.402 0.392 0.454 AA_5CM1DG2:5CM5DG6_AA 1 5.671 -12.086 26.677 -0.395 2.370 3.150 28.865 A A 2 3 -4.657 A A 5 4 3.041 -2.296 -0.816 -0.148 AA_DG2DT3:DA45CM5_AA 2 -7.055 14.306 27.915 0.196 0.124 2.729 42.085 A A 3 4 0.453 A A 4 3 2.736 0.325 0.000 -0.894 AA_DT3DA4:DT3DA4_AA 3 0.000 0.000 42.084 -1.273 0.000 3.150 28.865 A A 4 5 -4.657 A A 3 2 3.041 -2.296 0.816 -0.148 AA_DA45CM5:DG2DT3_AA 4 7.055 -14.306 27.915 0.196 -0.124 7.313 27.366 A A 5 6 5.119 A A 2 1 7.377 2.402 -0.392 0.454 AA_5CM5DG6:5CM1DG2_AA 5 -5.671 12.086 26.677 -0.395 -2.370 chem_comp_atom chem_comp_bond database_2 struct_conn struct_site repository Initial release Version format compliance Version format compliance Atomic model Derived calculations Data collection Database references Derived calculations 1 0 1991-07-15 1 1 2008-05-22 1 2 2011-07-13 1 3 2011-08-24 1 4 2024-02-07 _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 1990-08-08 REL NGM NOGALAMYCIN HOH water NGM 7 2 NGM NGM 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 5CM 1 n 1 5CM 1 A DG 2 n 2 DG 2 A DT 3 n 3 DT 3 A DA 4 n 4 DA 4 A 5CM 5 n 5 5CM 5 A DG 6 n 6 DG 6 A author_defined_assembly 2 dimeric A 5CM 1 A 5CM 1 DC A 5CM 5 A 5CM 5 DC 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 11_655 -x+y+1,y,-z+1/2 crystal symmetry operation 26.3000000000 0.0000000000 50.0050000000 1 A DT 3 0.133 SIDE CHAIN 1 A DA 4 0.055 SIDE CHAIN 1 8.97 1.20 119.70 128.67 A A A C3' O3' P 5CM 5CM DG 1 1 2 Y 1 6.63 1.10 109.80 116.43 A A A C5' C4' O4' DG DG DG 2 2 2 N 1 -9.23 1.00 110.10 100.87 A A A C1' O4' C4' DG DG DG 2 2 2 N 1 -5.51 0.80 105.90 100.39 A A A O4' C1' C2' DG DG DG 2 2 2 N 1 7.08 0.30 108.30 115.38 A A A O4' C1' N9 DG DG DG 2 2 2 N 1 7.64 0.30 108.30 115.94 A A A O4' C1' N1 DT DT DT 3 3 3 N 1 -4.26 0.70 108.00 103.74 A A A O4' C1' N9 DA DA DA 4 4 4 N 1 -3.25 0.50 103.90 100.65 A A A C5 N7 C8 DA DA DA 4 4 4 N 1 3.80 0.50 113.80 117.60 A A A N7 C8 N9 DA DA DA 4 4 4 N 1 -2.49 0.40 105.80 103.31 A A A C8 N9 C4 DA DA DA 4 4 4 N 1 4.01 0.30 108.30 112.31 A A A O4' C1' N9 DG DG DG 6 6 6 N 1 -2.48 0.40 106.40 103.92 A A A C8 N9 C4 DG DG DG 6 6 6 N 1 2.60 0.40 105.40 108.00 A A A N9 C4 C5 DG DG DG 6 6 6 N 1 -4.34 0.60 119.90 115.56 A A A N1 C6 O6 DG DG DG 6 6 6 N 1 A A C5 C7 DT DT 3 3 0.054 0.006 1.496 1.550 N 1 A A N9 C4 DA DA 4 4 -0.037 0.006 1.374 1.337 N 0.206 0.206 2.000 809 1 2.000 TR isotropic TR isotropic 2.000 39 217 56 122 0 fix fix refinement X-PLOR DNA-NOGALAMYCIN INTERACTIONS 1 N N 2 N N 3 N N covale 1.656 both A 5CM 1 A O3' 5CM 1 1_555 A DG 2 A P DG 2 1_555 covale 1.620 both A DA 4 A O3' DA 4 1_555 A 5CM 5 A P 5CM 5 1_555 covale 1.643 both A 5CM 5 A O3' 5CM 5 1_555 A DG 6 A P DG 6 1_555 hydrog WATSON-CRICK A 5CM 1 A N3 5CM 1 1_555 A DG 6 A N1 DG 6 11_655 hydrog WATSON-CRICK A 5CM 1 A N4 5CM 1 1_555 A DG 6 A O6 DG 6 11_655 hydrog WATSON-CRICK A 5CM 1 A O2 5CM 1 1_555 A DG 6 A N2 DG 6 11_655 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 A 5CM 5 A N3 5CM 5 11_655 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 A 5CM 5 A O2 5CM 5 11_655 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 A 5CM 5 A N4 5CM 5 11_655 hydrog WATSON-CRICK A DT 3 A N3 DT 3 1_555 A DA 4 A N1 DA 4 11_655 hydrog WATSON-CRICK A DT 3 A O4 DT 3 1_555 A DA 4 A N6 DA 4 11_655 hydrog WATSON-CRICK A DA 4 A N1 DA 4 1_555 A DT 3 A N3 DT 3 11_655 hydrog WATSON-CRICK A DA 4 A N6 DA 4 1_555 A DT 3 A O4 DT 3 11_655 hydrog WATSON-CRICK A 5CM 5 A N3 5CM 5 1_555 A DG 2 A N1 DG 2 11_655 hydrog WATSON-CRICK A 5CM 5 A N4 5CM 5 1_555 A DG 2 A O6 DG 2 11_655 hydrog WATSON-CRICK A 5CM 5 A O2 5CM 5 1_555 A DG 2 A N2 DG 2 11_655 hydrog WATSON-CRICK A DG 6 A N1 DG 6 1_555 A 5CM 1 A N3 5CM 1 11_655 hydrog WATSON-CRICK A DG 6 A N2 DG 6 1_555 A 5CM 1 A O2 5CM 1 11_655 hydrog WATSON-CRICK A DG 6 A O6 DG 6 1_555 A 5CM 1 A N4 5CM 1 11_655 DNA RIGHT HANDED DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, MODIFIED, DNA 1D17 PDB 1 1D17 1 6 1D17 1 6 1D17 A 1 1 6 BINDING SITE FOR RESIDUE NGM A 7 A NGM 7 Software 14 A 5CM 1 A 5CM 1 14 1_555 A DG 2 A DG 2 14 1_555 A DG 2 A DG 2 14 9_655 A DT 3 A DT 3 14 1_555 A DT 3 A DT 3 14 5_564 A DA 4 A DA 4 14 1_555 A 5CM 5 A 5CM 5 14 11_655 A DG 6 A DG 6 14 11_655 A HOH 35 C HOH 14 1_555 A HOH 38 C HOH 14 5_564 A HOH 41 C HOH 14 1_555 A HOH 42 C HOH 14 1_555 A HOH 44 C HOH 14 1_555 A HOH 46 C HOH 14 1_555 178 P 61 2 2