0.035112 0.000000 0.000000 0.000000 0.027693 0.000000 0.000000 0.000000 0.014368 0.00000 0.00000 0.00000 Gao, Y.-G. Sriram, M. Denny, W.A. Wang, A.H.-J. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 28.480 36.110 69.600 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 C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking C12 H18 N5 O7 P 375.274 n O6-ETHYL-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE DNA linking H2 O 18.015 WATER non-polymer C29 H27 N5 O 2 461.558 1-METHYL-4-[4-[4-(4-(1-METHYLQUINOLINIUM)AMINO)BENZAMIDO]ANILINO]PYRIDINIUM SN6999 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 N 108 N O N 109 N P N 110 N O N 111 N O N 112 N O N 113 N C N 114 R C N 115 N O N 116 S C N 117 N O N 118 N C N 119 R C N 120 N N N 121 N C N 122 N O N 123 N N N 124 N C N 125 N O N 126 N C N 127 N C N 128 N C 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 H N 140 N H N 141 N H N 142 N H N 143 N H N 144 N P N 145 N O N 146 N O N 147 N O N 148 N O N 149 N C N 150 R C N 151 N O N 152 S C N 153 N O N 154 N C N 155 N C N 156 R C Y 157 N N Y 158 N C Y 159 N N Y 160 N C Y 161 N C N 162 N O Y 163 N N Y 164 N C N 165 N N N 166 N C Y 167 N N Y 168 N C 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 H N 180 N H N 181 N H N 182 N H N 183 N H N 184 N H N 185 N H N 186 N H N 187 N O N 188 N H N 189 N H Y 190 N C Y 191 N C Y 192 N C Y 193 N C Y 194 N C Y 195 N C Y 196 N N Y 197 N C Y 198 N C Y 199 N C N 200 N N Y 201 N C Y 202 N C Y 203 N C Y 204 N C Y 205 N C Y 206 N C N 207 N C N 208 N O N 209 N N Y 210 N C Y 211 N C Y 212 N C Y 213 N C Y 214 N C Y 215 N C N 216 N N Y 217 N C Y 218 N C Y 219 N C Y 220 N N Y 221 N C Y 222 N C N 223 N C N 224 N C 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 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 N 113 N sing N 114 N sing N 115 N doub N 116 N sing N 117 N sing N 118 N sing 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 doub N 139 N sing N 140 N sing N 141 N sing N 142 N doub 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 doub 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 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 Y 177 N sing Y 178 N sing Y 179 N doub N 180 N sing Y 181 N sing Y 182 N doub Y 183 N sing N 184 N sing Y 185 N sing N 186 N sing Y 187 N doub N 188 N sing Y 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing Y 194 N doub N 195 N sing N 196 N sing Y 197 N doub Y 198 N sing N 199 N sing Y 200 N sing N 201 N sing Y 202 N doub Y 203 N sing Y 204 N sing Y 205 N sing Y 206 N doub N 207 N sing N 208 N sing Y 209 N doub N 210 N sing Y 211 N sing N 212 N sing Y 213 N doub N 214 N sing N 215 N sing N 216 N sing N 217 N sing Y 218 N doub Y 219 N sing Y 220 N sing N 221 N sing Y 222 N doub N 223 N sing Y 224 N sing N 225 N sing Y 226 N doub N 227 N sing N 228 N sing N 229 N doub N 230 N sing N 231 N sing N 232 N sing Y 233 N doub Y 234 N sing Y 235 N sing N 236 N sing Y 237 N doub N 238 N sing Y 239 N sing N 240 N sing Y 241 N doub N 242 N sing N 243 N sing N 244 N sing N 245 N sing Y 246 N doub Y 247 N sing Y 248 N sing N 249 N sing Y 250 N doub N 251 N sing Y 252 N sing N 253 N sing Y 254 N doub 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 US Biochemistry BICHAW 0033 0006-2960 32 9639 9648 10.1021/bi00088a016 8373768 Minor groove binding of SN6999 to an alkylated DNA: molecular structure of d(CGC[e6G]AATTCGCG)-SN6999 complex. 1993 10.2210/pdb144d/pdb pdb_0000144d 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 ROOM TEMPERATURE 1 DIFFRACTOMETER RIGAKU AFC-5R x-ray 1 1.0 ROTATING ANODE 3691.445 DNA (5'-D(*CP*GP*CP*(G36)P*AP*AP*TP*TP*CP*GP*CP*G)-3') 2 syn polymer 461.558 1-METHYL-4-[4-[4-(4-(1-METHYLQUINOLINIUM)AMINO)BENZAMIDO]ANILINO]PYRIDINIUM 1 syn non-polymer 18.015 water 65 nat water no yes (DC)(DG)(DC)(G36)(DA)(DA)(DT)(DT)(DC)(DG)(DC)(DG) CGCGAATTCGCG A,B polydeoxyribonucleotide n n n n n n n n n n n n 2.42 49.25 VAPOR DIFFUSION 7.00 pH 7.00, VAPOR DIFFUSION ROOM TEMPERATURE WATER 1 MPD 1 NA CACODYLATE 1 MGCL2 1 SPERMINE 1 NH4 ACETATE 1 WATER 2 MPD 2 -8.605 1 19 A 1 B 24 -2.868 A_DC1:DG24_B 1 -3.201 0.078 0.231 -0.056 4.582 1 19 A 2 B 23 -7.193 A_DG2:DC23_B 2 -17.716 0.290 0.167 -0.211 -7.193 1 19 A 3 B 22 -4.923 A_DC3:DG22_B 3 -6.780 0.001 0.469 -0.327 9.802 1 19 A 4 B 21 -7.061 A_G364:DC21_B 4 -6.525 -0.973 -0.019 -0.717 -1.022 1 20 A 5 B 20 3.633 A_DA5:DT20_B 5 -11.806 -0.528 0.015 -0.248 0.209 1 20 A 6 B 19 -4.025 A_DA6:DT19_B 6 -10.025 -0.189 -0.073 -0.098 8.900 1 20 A 7 B 18 1.174 A_DT7:DA18_B 7 -17.758 0.308 -0.219 -0.328 -11.682 1 20 A 8 B 17 2.909 A_DT8:DA17_B 8 -3.878 0.107 0.277 -0.167 -1.559 1 19 A 9 B 16 -4.312 A_DC9:G3616_B 9 -13.443 -1.093 0.106 -0.429 -4.128 1 19 A 10 B 15 1.808 A_DG10:DC15_B 10 -3.989 -0.629 0.099 -0.289 -5.013 1 19 A 11 B 14 -3.042 A_DC11:DG14_B 11 -13.543 0.108 0.498 -0.251 16.267 1 19 A 12 B 13 -4.538 A_DG12:DC13_B 12 -11.589 0.263 1.105 -0.220 3.334 31.987 A A 1 2 -2.248 B B 24 23 3.139 -1.226 -1.174 -0.193 AA_DC1DG2:DC23DG24_BB 1 -7.822 14.336 31.017 -0.128 0.708 3.697 41.252 A A 2 3 -5.249 B B 23 22 3.749 -3.694 1.023 0.650 AA_DG2DC3:DG22DC23_BB 2 0.744 -1.057 41.087 1.376 -1.361 3.028 23.661 A A 3 4 8.983 B B 22 21 3.238 3.646 -0.587 0.021 AA_DC3G364:DC21DG22_BB 3 4.640 -11.433 22.924 -1.129 2.933 3.505 40.565 A A 4 5 -1.924 B B 21 20 3.479 -1.334 1.063 0.269 AA_G364DA5:DT20DC21_BB 4 1.526 -2.203 40.516 0.547 -1.352 3.372 37.164 A A 5 6 1.848 B B 20 19 3.371 1.178 -0.217 0.142 AA_DA5DA6:DT19DT20_BB 5 0.313 -0.491 37.144 0.060 0.383 3.062 36.328 A A 6 7 -0.203 B B 19 18 3.023 -0.127 0.503 -0.694 AA_DA6DT7:DA18DT19_BB 6 4.193 -6.740 36.093 -1.097 -0.260 3.889 33.389 A A 7 8 2.979 B B 18 17 3.907 1.707 0.095 0.505 AA_DT7DT8:DA17DA18_BB 7 -4.038 7.048 33.108 0.541 -0.967 3.093 34.191 A A 8 9 -3.979 B B 17 16 3.032 -2.335 -1.201 0.396 AA_DT8DC9:G3616DA17_BB 8 -3.090 5.267 33.978 1.020 1.584 3.659 31.874 A A 9 10 -1.064 B B 16 15 3.736 -0.584 0.404 2.058 AA_DC9DG10:DC15G3616_BB 9 -2.411 4.395 31.780 3.867 -1.232 3.653 40.316 A A 10 11 -5.692 B B 15 14 3.671 -3.909 -0.804 0.734 AA_DG10DC11:DG14DC15_BB 10 -4.656 6.779 39.873 1.562 0.574 2.769 34.338 A A 11 12 -9.333 B B 14 13 2.810 -5.488 1.248 0.107 AA_DC11DG12:DC13DG14_BB 11 0.267 -0.454 33.908 0.919 -2.078 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 1995-05-30 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_leaving_atom_flag _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id BNL Y NDB 1993-10-26 REL SN6 1-METHYL-4-[4-[4-(4-(1-METHYLQUINOLINIUM)AMINO)BENZAMIDO]ANILINO]PYRIDINIUM HOH water SN6 25 2 SN6 SN6 25 B HOH 26 3 HOH HOH 26 A HOH 27 3 HOH HOH 27 A HOH 30 3 HOH HOH 30 A HOH 31 3 HOH HOH 31 A HOH 33 3 HOH HOH 33 A HOH 37 3 HOH HOH 37 A HOH 38 3 HOH HOH 38 A HOH 39 3 HOH HOH 39 A HOH 43 3 HOH HOH 43 A HOH 46 3 HOH HOH 46 A HOH 48 3 HOH HOH 48 A HOH 49 3 HOH HOH 49 A HOH 52 3 HOH HOH 52 A HOH 53 3 HOH HOH 53 A HOH 54 3 HOH HOH 54 A HOH 61 3 HOH HOH 61 A HOH 64 3 HOH HOH 64 A HOH 66 3 HOH HOH 66 A HOH 67 3 HOH HOH 67 A HOH 70 3 HOH HOH 70 A HOH 72 3 HOH HOH 72 A HOH 73 3 HOH HOH 73 A HOH 74 3 HOH HOH 74 A HOH 75 3 HOH HOH 75 A HOH 77 3 HOH HOH 77 A HOH 80 3 HOH HOH 80 A HOH 81 3 HOH HOH 81 A HOH 82 3 HOH HOH 82 A HOH 83 3 HOH HOH 83 A HOH 84 3 HOH HOH 84 A HOH 85 3 HOH HOH 85 A HOH 86 3 HOH HOH 86 A HOH 87 3 HOH HOH 87 A HOH 89 3 HOH HOH 89 A HOH 90 3 HOH HOH 90 A HOH 28 3 HOH HOH 28 B HOH 29 3 HOH HOH 29 B HOH 32 3 HOH HOH 32 B HOH 34 3 HOH HOH 34 B HOH 35 3 HOH HOH 35 B HOH 36 3 HOH HOH 36 B HOH 40 3 HOH HOH 40 B HOH 41 3 HOH HOH 41 B HOH 42 3 HOH HOH 42 B HOH 44 3 HOH HOH 44 B HOH 45 3 HOH HOH 45 B HOH 47 3 HOH HOH 47 B HOH 50 3 HOH HOH 50 B HOH 51 3 HOH HOH 51 B HOH 55 3 HOH HOH 55 B HOH 56 3 HOH HOH 56 B HOH 57 3 HOH HOH 57 B HOH 58 3 HOH HOH 58 B HOH 59 3 HOH HOH 59 B HOH 60 3 HOH HOH 60 B HOH 62 3 HOH HOH 62 B HOH 63 3 HOH HOH 63 B HOH 65 3 HOH HOH 65 B HOH 68 3 HOH HOH 68 B HOH 69 3 HOH HOH 69 B HOH 71 3 HOH HOH 71 B HOH 76 3 HOH HOH 76 B HOH 78 3 HOH HOH 78 B HOH 79 3 HOH HOH 79 B HOH 88 3 HOH HOH 88 B 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 G36 4 A A 5 n 5 DA 5 A A 6 n 6 DA 6 A T 7 n 7 DT 7 A T 8 n 8 DT 8 A C 9 n 9 DC 9 A G 10 n 10 DG 10 A C 11 n 11 DC 11 A G 12 n 12 DG 12 A C 13 n 1 DC 13 B G 14 n 2 DG 14 B C 15 n 3 DC 15 B +G 16 n 4 G36 16 B A 17 n 5 DA 17 B A 18 n 6 DA 18 B T 19 n 7 DT 19 B T 20 n 8 DT 20 B C 21 n 9 DC 21 B G 22 n 10 DG 22 B C 23 n 11 DC 23 B G 24 n 12 DG 24 B author_defined_assembly 2 dimeric A G36 4 A G36 4 DG B G36 16 B G36 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 1 -6.56 0.40 104.50 97.94 A A A O4' C4' C3' DC DC DC 1 1 1 N 1 -6.72 0.80 102.40 95.68 A A A C3' C2' C1' DC DC DC 1 1 1 N 1 8.46 1.20 110.70 119.16 A A A O5' P OP2 DG DG DG 2 2 2 N 1 3.61 0.30 108.30 111.91 A A A O4' C1' N9 DG DG DG 2 2 2 N 1 -8.98 0.80 109.40 100.42 A A A O5' C5' C4' DC DC DC 3 3 3 N 1 -6.84 0.80 102.40 95.56 A A A C3' C2' C1' DC DC DC 3 3 3 N 1 10.78 0.30 108.30 119.08 A A A O4' C1' N1 DC DC DC 3 3 3 N 1 3.48 0.50 121.00 124.48 A A A C5 C6 N1 DC DC DC 3 3 3 N 1 5.09 0.70 121.90 126.99 A A A N3 C2 O2 DC DC DC 3 3 3 N 1 6.00 0.70 118.00 124.00 A A A N3 C4 N4 DC DC DC 3 3 3 N 1 -5.28 0.70 120.20 114.92 A A A C5 C4 N4 DC DC DC 3 3 3 N 1 20.79 1.20 119.70 140.49 A A A C3' O3' P G36 G36 DA 4 4 5 Y 1 5.04 0.30 108.30 113.34 A A A O4' C1' N9 DA DA DA 5 5 5 N 1 -3.99 0.50 129.30 125.31 A A A N1 C2 N3 DA DA DA 5 5 5 N 1 10.65 1.20 119.70 130.35 A A A C3' O3' P DA DA DA 5 5 6 Y 1 -4.95 0.80 105.90 100.95 A A A O4' C1' C2' DA DA DA 6 6 6 N 1 4.51 0.60 118.60 123.11 A A A N1 C6 N6 DA DA DA 6 6 6 N 1 8.02 1.20 110.70 118.72 A A A O5' P OP2 DT DT DT 7 7 7 N 1 -3.38 0.50 121.30 117.92 A A A C6 N1 C2 DT DT DT 7 7 7 N 1 9.11 1.50 120.40 129.51 A A A C6 N1 C1' DT DT DT 7 7 7 N 1 -10.22 1.60 120.90 110.68 A A A P O5' C5' DT DT DT 8 8 8 N 1 -5.10 0.70 102.20 97.10 A A A C4' C3' C2' DT DT DT 8 8 8 N 1 -5.02 0.80 102.40 97.38 A A A C3' C2' C1' DT DT DT 8 8 8 N 1 12.16 0.30 108.30 120.46 A A A O4' C1' N1 DT DT DT 8 8 8 N 1 3.76 0.60 119.00 122.76 A A A C4 C5 C7 DT DT DT 8 8 8 N 1 -9.50 1.50 119.60 110.10 A A A OP1 P OP2 DC DC DC 9 9 9 N 1 7.67 1.20 110.70 118.37 A A A O5' P OP2 DC DC DC 9 9 9 N 1 -4.98 0.70 102.20 97.22 A A A C4' C3' C2' DC DC DC 9 9 9 N 1 6.21 0.30 108.30 114.51 A A A O4' C1' N1 DC DC DC 9 9 9 N 1 3.67 0.50 121.00 124.67 A A A C5 C6 N1 DC DC DC 9 9 9 N 1 10.02 1.20 119.70 129.72 A A A C3' O3' P DC DC DG 9 9 10 Y 1 7.61 1.20 110.70 118.31 A A A O5' P OP2 DG DG DG 10 10 10 N 1 -14.51 1.60 120.90 106.39 A A A P O5' C5' DG DG DG 10 10 10 N 1 5.07 0.30 108.30 113.37 A A A O4' C1' N9 DG DG DG 10 10 10 N 1 3.24 0.50 111.50 114.74 A A A C5 C6 N1 DG DG DG 10 10 10 N 1 -4.24 0.60 128.60 124.36 A A A C5 C6 O6 DG DG DG 10 10 10 N 1 13.56 0.30 108.30 121.86 A A A O4' C1' N1 DC DC DC 11 11 11 N 1 -2.43 0.40 121.90 119.47 A A A N3 C4 C5 DC DC DC 11 11 11 N 1 4.41 0.60 106.00 110.41 A A A O4' C4' C3' DG DG DG 12 12 12 N 1 -6.51 0.80 109.40 102.89 B B B O5' C5' C4' DC DC DC 13 13 13 N 1 -8.99 1.20 119.70 110.71 B B B C3' O3' P DC DC DG 13 13 14 Y 1 -9.33 1.50 119.60 110.27 B B B OP1 P OP2 DG DG DG 14 14 14 N 1 -9.51 0.80 109.40 99.89 B B B O5' C5' C4' DG DG DG 14 14 14 N 1 -8.33 0.70 108.00 99.67 B B B O4' C1' N1 DC DC DC 15 15 15 N 1 36.69 1.20 119.70 156.39 B B B C3' O3' P G36 G36 DA 16 16 17 Y 1 13.53 1.90 104.00 117.53 B B B O3' P O5' G36 DA DA 16 17 17 Y 1 -18.18 1.50 119.60 101.42 B B B OP1 P OP2 DA DA DA 17 17 17 N 1 6.16 0.30 108.30 114.46 B B B O4' C1' N9 DA DA DA 17 17 17 N 1 3.70 0.60 118.60 122.30 B B B C6 N1 C2 DA DA DA 17 17 17 N 1 -3.87 0.50 129.30 125.43 B B B N1 C2 N3 DA DA DA 17 17 17 N 1 -3.61 0.50 117.70 114.09 B B B C5 C6 N1 DA DA DA 17 17 17 N 1 24.94 1.20 119.70 144.64 B B B C3' O3' P DA DA DA 17 17 18 Y 1 -14.15 1.50 119.60 105.45 B B B OP1 P OP2 DA DA DA 18 18 18 N 1 -16.49 1.60 120.90 104.41 B B B P O5' C5' DA DA DA 18 18 18 N 1 -2.84 0.40 104.50 101.66 B B B O4' C4' C3' DA DA DA 18 18 18 N 1 -8.05 0.80 102.40 94.35 B B B C3' C2' C1' DA DA DA 18 18 18 N 1 -7.08 0.80 105.90 98.82 B B B O4' C1' C2' DA DA DA 18 18 18 N 1 5.64 0.30 108.30 113.94 B B B O4' C1' N9 DA DA DA 18 18 18 N 1 5.26 0.60 118.60 123.86 B B B C6 N1 C2 DA DA DA 18 18 18 N 1 -5.17 0.50 129.30 124.13 B B B N1 C2 N3 DA DA DA 18 18 18 N 1 7.25 0.60 118.60 125.85 B B B N1 C6 N6 DA DA DA 18 18 18 N 1 -9.72 0.80 109.40 99.68 B B B O5' C5' C4' DT DT DT 19 19 19 N 1 -10.08 1.60 120.90 110.82 B B B P O5' C5' DT DT DT 19 19 19 N 1 6.65 0.70 110.30 116.95 B B B C1' O4' C4' DT DT DT 19 19 19 N 1 -7.60 0.80 105.90 98.30 B B B O4' C1' C2' DT DT DT 19 19 19 N 1 4.88 0.60 114.60 119.48 B B B N1 C2 N3 DT DT DT 19 19 19 N 1 -6.28 0.60 127.20 120.92 B B B C2 N3 C4 DT DT DT 19 19 19 N 1 -5.70 0.60 122.30 116.60 B B B N3 C2 O2 DT DT DT 19 19 19 N 1 -3.90 0.60 119.90 116.00 B B B N3 C4 O4 DT DT DT 19 19 19 N 1 -7.21 1.20 119.70 112.49 B B B C3' O3' P DT DT DT 19 19 20 Y 1 12.71 1.10 110.50 123.21 B B B O3' P OP1 DT DT DT 19 20 20 Y 1 -15.33 1.60 120.90 105.57 B B B P O5' C5' DT DT DT 20 20 20 N 1 7.60 1.20 115.70 123.30 B B B C5' C4' C3' DT DT DT 20 20 20 N 1 -2.84 0.40 104.50 101.66 B B B O4' C4' C3' DC DC DC 21 21 21 N 1 -6.04 0.80 102.40 96.36 B B B C3' C2' C1' DC DC DC 21 21 21 N 1 7.36 0.70 118.00 125.36 B B B N3 C4 N4 DC DC DC 21 21 21 N 1 -5.64 0.70 120.20 114.56 B B B C5 C4 N4 DC DC DC 21 21 21 N 1 -11.30 1.50 119.60 108.30 B B B OP1 P OP2 DG DG DG 22 22 22 N 1 10.39 1.60 120.90 131.29 B B B P O5' C5' DG DG DG 22 22 22 N 1 -6.19 0.80 105.90 99.71 B B B O4' C1' C2' DG DG DG 22 22 22 N 1 12.41 0.30 108.30 120.71 B B B O4' C1' N9 DG DG DG 22 22 22 N 1 4.52 0.50 111.50 116.02 B B B C5 C6 N1 DG DG DG 22 22 22 N 1 -3.91 0.60 119.90 115.99 B B B N1 C6 O6 DG DG DG 22 22 22 N 1 -4.50 0.70 102.20 97.70 B B B C4' C3' C2' DC DC DC 23 23 23 N 1 3.55 0.50 119.90 123.45 B B B C2 N3 C4 DC DC DC 23 23 23 N 1 -2.73 0.40 121.90 119.17 B B B N3 C4 C5 DC DC DC 23 23 23 N 1 3.47 0.50 121.00 124.47 B B B C5 C6 N1 DC DC DC 23 23 23 N 1 4.31 0.60 118.90 123.21 B B B N1 C2 O2 DC DC DC 23 23 23 N 1 4.32 0.70 118.00 122.32 B B B N3 C4 N4 DC DC DC 23 23 23 N 1 -8.70 0.80 109.40 100.70 B B B O5' C5' C4' DG DG DG 24 24 24 N 1 3.50 0.30 108.30 111.80 B B B O4' C1' N9 DG DG DG 24 24 24 N 1 -4.06 0.60 125.10 121.04 B B B C6 N1 C2 DG DG DG 24 24 24 N 1 3.22 0.50 111.50 114.72 B B B C5 C6 N1 DG DG DG 24 24 24 N 1 A A C2' C1' DC DC 3 3 0.065 0.010 1.519 1.584 N 1 A A O4' C1' DT DT 7 7 0.077 0.011 1.420 1.497 N 1 A A P O5' DT DT 8 8 0.074 0.010 1.593 1.667 N 1 A A C4' C3' DT DT 8 8 0.073 0.010 1.529 1.602 N 1 A A P O5' DC DC 11 11 0.076 0.010 1.593 1.669 N 1 A A C2' C1' DC DC 11 11 0.065 0.010 1.519 1.584 N 1 B B O4' C4' DC DC 13 13 -0.072 0.010 1.446 1.374 N 1 B B O5' C5' DG DG 14 14 0.110 0.016 1.440 1.550 N 1 B B N3 C4 DC DC 15 15 0.042 0.007 1.335 1.377 N 1 B B O3' P G36 DA 16 17 -0.157 0.012 1.607 1.450 Y 1 B B O3' P DA DA 17 18 -0.095 0.012 1.607 1.512 Y 1 B B P O5' DA DA 18 18 0.064 0.010 1.593 1.657 N 1 B B O4' C4' DT DT 19 19 -0.072 0.010 1.446 1.374 N 1 B B P O5' DT DT 20 20 0.099 0.010 1.593 1.692 N 1 B B OP1 O DT HOH 20 88 2.18 1_555 1_455 0.17 2.250 10.000 1618 1 2.000 TR isotropic TR isotropic 2.250 10.000 65 590 39 486 0 fix fix 2.250 144D 1618 2.000 1 refinement NUCLSQ MINOR GROOVE BINDING OF SN6999 TO AN ALKYLATED DNA: MOLECULAR STRUCTURE OF D(CGC[E6G]AATTCGCG)-SN6999 COMPLEX 1 N N 1 N N 2 N N 3 N N 3 N N covale 1.622 both A DC 3 A O3' DC 3 1_555 A G36 4 A P G36 4 1_555 covale 1.567 one A G36 4 A O3' G36 4 1_555 A DA 5 A P DA 5 1_555 covale 1.607 both B DC 15 B O3' DC 3 1_555 B G36 16 B P G36 4 1_555 covale 1.450 one B G36 16 B O3' G36 4 1_555 B DA 17 B P DA 5 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 24 B N1 DG 12 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 24 B O6 DG 12 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 24 B N2 DG 12 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 B DC 23 B N3 DC 11 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B DC 23 B O2 DC 11 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B DC 23 B N4 DC 11 1_555 hydrog WATSON-CRICK A DC 3 A N3 DC 3 1_555 B DG 22 B N1 DG 10 1_555 hydrog WATSON-CRICK A DC 3 A N4 DC 3 1_555 B DG 22 B O6 DG 10 1_555 hydrog WATSON-CRICK A DC 3 A O2 DC 3 1_555 B DG 22 B N2 DG 10 1_555 hydrog WATSON-CRICK A G36 4 A N1 G36 4 1_555 B DC 21 B N3 DC 9 1_555 hydrog WATSON-CRICK A G36 4 A N2 G36 4 1_555 B DC 21 B O2 DC 9 1_555 hydrog WATSON-CRICK A G36 4 A O6 G36 4 1_555 B DC 21 B N4 DC 9 1_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 B DT 20 B N3 DT 8 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 B DT 20 B O4 DT 8 1_555 hydrog WATSON-CRICK A DA 6 A N1 DA 6 1_555 B DT 19 B N3 DT 7 1_555 hydrog WATSON-CRICK A DA 6 A N6 DA 6 1_555 B DT 19 B O4 DT 7 1_555 hydrog WATSON-CRICK A DT 7 A N3 DT 7 1_555 B DA 18 B N1 DA 6 1_555 hydrog WATSON-CRICK A DT 7 A O4 DT 7 1_555 B DA 18 B N6 DA 6 1_555 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 B DA 17 B N1 DA 5 1_555 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 B DA 17 B N6 DA 5 1_555 hydrog WATSON-CRICK A DC 9 A N3 DC 9 1_555 B G36 16 B N1 G36 4 1_555 hydrog WATSON-CRICK A DC 9 A N4 DC 9 1_555 B G36 16 B O6 G36 4 1_555 hydrog WATSON-CRICK A DC 9 A O2 DC 9 1_555 B G36 16 B N2 G36 4 1_555 hydrog WATSON-CRICK A DG 10 A N1 DG 10 1_555 B DC 15 B N3 DC 3 1_555 hydrog WATSON-CRICK A DG 10 A N2 DG 10 1_555 B DC 15 B O2 DC 3 1_555 hydrog WATSON-CRICK A DG 10 A O6 DG 10 1_555 B DC 15 B N4 DC 3 1_555 hydrog WATSON-CRICK A DC 11 A N3 DC 11 1_555 B DG 14 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 11 A N4 DC 11 1_555 B DG 14 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 11 A O2 DC 11 1_555 B DG 14 B N2 DG 2 1_555 hydrog WATSON-CRICK A DG 12 A N1 DG 12 1_555 B DC 13 B N3 DC 1 1_555 hydrog WATSON-CRICK A DG 12 A N2 DG 12 1_555 B DC 13 B O2 DC 1 1_555 hydrog WATSON-CRICK A DG 12 A O6 DG 12 1_555 B DC 13 B N4 DC 1 1_555 DNA B-DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, MODIFIED, DNA 144D PDB 1 144D 1 12 144D 1 12 144D A 1 1 12 13 24 144D 13 24 144D B 1 1 12 BINDING SITE FOR RESIDUE SN6 B 25 B SN6 25 Software 14 A G36 4 A G36 4 14 1_555 A DA 5 A DA 5 14 1_555 A DA 6 A DA 6 14 1_555 A DT 7 A DT 7 14 1_555 A DT 8 A DT 8 14 1_555 A DC 9 A DC 9 14 1_555 A DG 12 A DG 12 14 2_565 A HOH 90 D HOH 14 1_555 B DA 18 B DA 6 14 1_555 B DT 19 B DT 7 14 1_555 B DT 20 B DT 8 14 1_555 B DC 21 B DC 9 14 1_555 B DG 22 B DG 10 14 1_555 B DC 23 B DC 11 14 1_555 19 P 21 21 21