1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Gao, X. Stassinopoulos, A. Ji, J. Kwon, Y. Bare, S. Goldberg, I.H. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 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 C35 H36 N O12 1 662.660 SPIRO[[7-METHOXY-5-METHYL-1,2-DIHYDRO-NAPHTHALENE]-3,1'-[5-HYDROXY-9-[2-METHYLAMINO-2,6-DIDEOXYGALACTOPYRANOSYL-OXY]-5-(2-OXO-[1,3]DIOXOLAN-4-YL)-3A,5,9,9A-TETRAHYDRO-3H-1-OXA-CYCLOPENTA[A]-S-INDACEN-2-ONE]] 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 Y 144 N C Y 145 N C Y 146 N C Y 147 N C Y 148 N C Y 149 N C N 150 N C N 151 N C N 152 R C N 153 N O N 154 R C N 155 R C N 156 R C N 157 R C N 158 N O N 159 N C N 160 N O N 161 N O N 162 N C N 163 N O N 164 N C N 165 N O N 166 S C N 167 N C N 168 N O N 169 N C N 170 N C Y 171 N C Y 172 N C Y 173 N C Y 174 N C N 175 N O Y 176 N C Y 177 N C N 178 N C N 179 N C N 180 N O N 181 R C N 182 R C N 183 N N N 184 N C N 185 R C N 186 N O N 187 R C N 188 N O N 189 R C N 190 N C N 191 N O N 192 N H N 193 N H N 194 N H 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 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 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 Y 150 N doub Y 151 N sing N 152 N sing Y 153 N sing N 154 N sing Y 155 N doub N 156 N sing Y 157 N sing N 158 N sing Y 159 N doub N 160 N sing N 161 N sing N 162 N doub 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 doub N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N doub N 188 N sing N 189 N sing N 190 N sing N 191 N doub N 192 N sing N 193 N doub N 194 N sing N 195 N sing N 196 N sing Y 197 N doub Y 198 N sing Y 199 N sing Y 200 N doub N 201 N sing N 202 N sing Y 203 N sing N 204 N sing Y 205 N doub 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 US Biochemistry BICHAW 0033 0006-2960 41 5131 5143 10.1021/bi012112o 11955061 Induced formation of a DNA bulge structure by a molecular wedge ligand-postactivated neocarzinostatin chromophore. 2002 10.2210/pdb1kvh/pdb pdb_00001kvh 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 SINGLE WAVELENGTH M 1 1.0 2387.581 5'-D(*CP*CP*CP*GP*AP*TP*GP*C)-3' 1 syn polymer 3085.029 5'-D(*GP*CP*AP*AP*TP*TP*CP*GP*GP*G)-3' 1 syn polymer 662.660 SPIRO[[7-METHOXY-5-METHYL-1,2-DIHYDRO-NAPHTHALENE]-3,1'-[5-HYDROXY-9-[2-METHYLAMINO-2,6-DIDEOXYGALACTOPYRANOSYL-OXY]-5-(2-OXO-[1,3]DIOXOLAN-4-YL)-3A,5,9,9A-TETRAHYDRO-3H-1-OXA-CYCLOPENTA[A]-S-INDACEN-2-ONE]] 1 syn non-polymer no no (DC)(DC)(DC)(DG)(DA)(DT)(DG)(DC) CCCGATGC A polydeoxyribonucleotide no no (DG)(DC)(DA)(DA)(DT)(DT)(DC)(DG)(DG)(DG) GCAATTCGGG B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n 4.829 1 19 A 1 B 18 -1.476 A_DC1:DG18_B 1 -0.424 0.733 0.038 -0.305 -28.410 1 19 A 2 B 17 -1.678 A_DC2:DG17_B 2 1.877 0.450 0.595 -0.127 -5.893 1 19 A 3 B 16 -1.669 A_DC3:DG16_B 3 -2.623 0.632 0.228 -0.265 19.792 1 19 A 4 B 15 -0.974 A_DG4:DC15_B 4 8.468 -0.639 0.371 -0.213 27.436 1 20 A 5 B 14 9.375 A_DA5:DT14_B 5 -13.468 0.081 -0.636 -0.361 -42.910 1 20 A 6 B 11 4.033 A_DT6:DA11_B 6 -10.776 0.516 0.520 -0.165 -36.705 1 19 A 7 B 10 -0.002 A_DG7:DC10_B 7 -15.975 -0.578 -0.697 -0.077 -24.298 1 19 A 8 B 9 -1.406 A_DC8:DG9_B 8 5.233 0.468 0.331 -0.140 4.906 51.910 A A 1 2 53.702 B B 18 17 5.178 41.255 0.630 2.192 AA_DC1DC2:DG17DG18_BB 1 -4.015 5.227 31.965 -2.966 -1.252 3.142 30.974 A A 2 3 3.461 B B 17 16 3.068 1.847 0.302 1.271 AA_DC2DC3:DG16DG17_BB 2 0.575 -1.077 30.915 2.042 -0.461 3.065 19.953 A A 3 4 21.416 B B 16 15 3.242 7.241 0.460 0.287 AA_DC3DG4:DC15DG16_BB 3 -2.001 5.917 18.498 -2.567 -2.267 3.665 37.702 A A 4 5 27.403 B B 15 14 3.600 16.761 -0.071 1.535 AA_DG4DA5:DT14DC15_BB 4 12.665 -20.707 31.485 -0.273 2.111 2.652 33.679 A A 6 7 28.794 B B 11 10 3.133 16.001 0.094 -0.236 AA_DT6DG7:DC10DA11_BB 5 4.054 -7.295 29.460 -2.877 0.463 3.440 34.205 A A 7 8 9.617 B B 10 9 3.299 5.603 -0.723 0.682 AA_DG7DC8:DG9DC10_BB 6 -6.102 10.472 33.216 0.234 0.222 database_2 pdbx_struct_assembly pdbx_struct_oper_list struct_site chem_comp_atom chem_comp_bond repository Initial release Version format compliance Version format compliance Database references Derived calculations Data collection 1 0 2002-06-19 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-23 1 4 2024-05-22 _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 RCSB Y RCSB 2002-01-26 REL NCS SPIRO[[7-METHOXY-5-METHYL-1,2-DIHYDRO-NAPHTHALENE]-3,1'-[5-HYDROXY-9-[2-METHYLAMINO-2,6-DIDEOXYGALACTOPYRANOSYL-OXY]-5-(2-OXO-[1,3]DIOXOLAN-4-YL)-3A,5,9,9A-TETRAHYDRO-3H-1-OXA-CYCLOPENTA[A]-S-INDACEN-2-ONE]] This structure was determined using 2D homonuclear and heteronuclear techniques all calculated structures submitted 7 7 2D NOESY 2D NOESY DQF-COSY PE-COSY TOCSY, H-P COSY 0.1M NACL, 10 mM SODIUM PHOSPHATE 6.4 270 K 0.1M NACL, 10 mM SODIUM PHOSPHATE 6.4 278 K A total of 681 NMR restraints is used to derive the final refined structures. The total restraints consist of 590 of NOE-derived distance restraints and 91 of dihedral angle restraints. Especially, 85 of intermolecular distance restraints are derived which represent the interaction between the drug and the bulge duplex. distance geometry (DG), restrained molecular dynamics (rMDS), and relaxation matrix refinement ca. 1 mM NCSi-gb-bulge-DNA complex; 0.1 M NaCl, 10 mM sodium phosphate, and 0.1 mM EDTA buffer (pH 6.4); 90% H2O, 10% D2O 90% H2O/10% D2O ca. 1 mM NCSi-gb-bulge-DNA complex; 0.1 M NaCl, 10 mM sodium phosphate, and 0.1 mM EDTA buffer (pH 6.4); 99.96% D2O 99.96% D2O Brunger refinement X-PLOR 3.01 600 Bruker AMX PEA 21 3 NCS NCS 21 B C 1 n 1 DC 1 A C 2 n 2 DC 2 A C 3 n 3 DC 3 A G 4 n 4 DG 4 A A 5 n 5 DA 5 A T 6 n 6 DT 6 A G 7 n 7 DG 7 A C 8 n 8 DC 8 A G 9 n 1 DG 9 B C 10 n 2 DC 10 B A 11 n 3 DA 11 B A 12 n 4 DA 12 B T 13 n 5 DT 13 B T 14 n 6 DT 14 B C 15 n 7 DC 15 B G 16 n 8 DG 16 B G 17 n 9 DG 17 B G 18 n 10 DG 18 B 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 1 B DT 14 0.072 SIDE CHAIN 2 B DT 14 0.075 SIDE CHAIN 3 B DT 14 0.074 SIDE CHAIN 4 B DT 14 0.070 SIDE CHAIN 5 B DT 14 0.074 SIDE CHAIN 6 B DT 14 0.074 SIDE CHAIN 7 A DA 5 0.084 SIDE CHAIN 7 B DT 14 0.111 SIDE CHAIN 1 2.85 0.30 108.30 111.15 A A A O4' C1' N1 DC DC DC 1 1 1 N 1 1.80 0.30 108.30 110.10 A A A O4' C1' N1 DC DC DC 2 2 2 N 1 2.00 0.30 108.30 110.30 A A A O4' C1' N1 DC DC DC 3 3 3 N 1 2.58 0.30 108.30 110.88 A A A O4' C1' N9 DG DG DG 4 4 4 N 1 3.49 0.50 113.10 116.59 A A A N7 C8 N9 DG DG DG 4 4 4 N 1 -3.06 0.40 106.40 103.34 A A A C8 N9 C4 DG DG DG 4 4 4 N 1 3.21 0.50 113.80 117.01 A A A N7 C8 N9 DA DA DA 5 5 5 N 1 -2.71 0.40 105.80 103.09 A A A C8 N9 C4 DA DA DA 5 5 5 N 1 3.59 0.30 108.30 111.89 A A A O4' C1' N1 DT DT DT 6 6 6 N 1 3.80 0.30 108.30 112.10 A A A O4' C1' N9 DG DG DG 7 7 7 N 1 3.49 0.50 113.10 116.59 A A A N7 C8 N9 DG DG DG 7 7 7 N 1 -3.13 0.40 106.40 103.27 A A A C8 N9 C4 DG DG DG 7 7 7 N 1 2.24 0.30 108.30 110.54 A A A O4' C1' N1 DC DC DC 8 8 8 N 1 2.74 0.30 108.30 111.04 B B B O4' C1' N9 DG DG DG 9 9 9 N 1 3.61 0.50 113.10 116.71 B B B N7 C8 N9 DG DG DG 9 9 9 N 1 -3.08 0.40 106.40 103.32 B B B C8 N9 C4 DG DG DG 9 9 9 N 1 2.94 0.30 108.30 111.24 B B B O4' C1' N1 DC DC DC 10 10 10 N 1 2.75 0.30 108.30 111.05 B B B O4' C1' N9 DA DA DA 11 11 11 N 1 3.17 0.50 113.80 116.97 B B B N7 C8 N9 DA DA DA 11 11 11 N 1 -2.59 0.40 105.80 103.21 B B B C8 N9 C4 DA DA DA 11 11 11 N 1 3.34 0.30 108.30 111.64 B B B O4' C1' N9 DA DA DA 12 12 12 N 1 3.30 0.50 113.80 117.10 B B B N7 C8 N9 DA DA DA 12 12 12 N 1 -2.77 0.40 105.80 103.03 B B B C8 N9 C4 DA DA DA 12 12 12 N 1 3.83 0.30 108.30 112.13 B B B O4' C1' N1 DT DT DT 13 13 13 N 1 2.19 0.30 108.30 110.49 B B B O4' C1' N1 DC DC DC 15 15 15 N 1 2.76 0.30 108.30 111.06 B B B O4' C1' N9 DG DG DG 16 16 16 N 1 3.58 0.50 113.10 116.68 B B B N7 C8 N9 DG DG DG 16 16 16 N 1 -3.09 0.40 106.40 103.31 B B B C8 N9 C4 DG DG DG 16 16 16 N 1 1.88 0.30 108.30 110.18 B B B O4' C1' N9 DG DG DG 17 17 17 N 1 3.62 0.50 113.10 116.72 B B B N7 C8 N9 DG DG DG 17 17 17 N 1 -3.07 0.40 106.40 103.33 B B B C8 N9 C4 DG DG DG 17 17 17 N 1 2.06 0.30 108.30 110.36 B B B O4' C1' N9 DG DG DG 18 18 18 N 1 3.64 0.50 113.10 116.74 B B B N7 C8 N9 DG DG DG 18 18 18 N 1 -3.04 0.40 106.40 103.36 B B B C8 N9 C4 DG DG DG 18 18 18 N 2 2.73 0.30 108.30 111.03 A A A O4' C1' N1 DC DC DC 1 1 1 N 2 1.84 0.30 108.30 110.14 A A A O4' C1' N1 DC DC DC 2 2 2 N 2 1.94 0.30 108.30 110.24 A A A O4' C1' N1 DC DC DC 3 3 3 N 2 2.60 0.30 108.30 110.90 A A A O4' C1' N9 DG DG DG 4 4 4 N 2 3.63 0.50 113.10 116.73 A A A N7 C8 N9 DG DG DG 4 4 4 N 2 -3.13 0.40 106.40 103.27 A A A C8 N9 C4 DG DG DG 4 4 4 N 2 3.29 0.50 113.80 117.09 A A A N7 C8 N9 DA DA DA 5 5 5 N 2 -2.74 0.40 105.80 103.06 A A A C8 N9 C4 DA DA DA 5 5 5 N 2 3.82 0.30 108.30 112.12 A A A O4' C1' N1 DT DT DT 6 6 6 N 2 3.67 0.30 108.30 111.97 A A A O4' C1' N9 DG DG DG 7 7 7 N 2 3.55 0.50 113.10 116.65 A A A N7 C8 N9 DG DG DG 7 7 7 N 2 -3.11 0.40 106.40 103.29 A A A C8 N9 C4 DG DG DG 7 7 7 N 2 2.03 0.30 108.30 110.33 A A A O4' C1' N1 DC DC DC 8 8 8 N 2 2.64 0.30 108.30 110.94 B B B O4' C1' N9 DG DG DG 9 9 9 N 2 3.68 0.50 113.10 116.78 B B B N7 C8 N9 DG DG DG 9 9 9 N 2 -3.12 0.40 106.40 103.28 B B B C8 N9 C4 DG DG DG 9 9 9 N 2 3.06 0.30 108.30 111.36 B B B O4' C1' N1 DC DC DC 10 10 10 N 2 2.77 0.30 108.30 111.07 B B B O4' C1' N9 DA DA DA 11 11 11 N 2 3.03 0.50 113.80 116.83 B B B N7 C8 N9 DA DA DA 11 11 11 N 2 -2.56 0.40 105.80 103.24 B B B C8 N9 C4 DA DA DA 11 11 11 N 2 3.23 0.30 108.30 111.53 B B B O4' C1' N9 DA DA DA 12 12 12 N 2 3.25 0.50 113.80 117.05 B B B N7 C8 N9 DA DA DA 12 12 12 N 2 -2.76 0.40 105.80 103.04 B B B C8 N9 C4 DA DA DA 12 12 12 N 2 3.55 0.30 108.30 111.85 B B B O4' C1' N1 DT DT DT 13 13 13 N 2 -3.79 0.60 122.90 119.11 B B B C6 C5 C7 DT DT DT 13 13 13 N 2 2.10 0.30 108.30 110.40 B B B O4' C1' N1 DC DC DC 15 15 15 N 2 2.69 0.30 108.30 110.99 B B B O4' C1' N9 DG DG DG 16 16 16 N 2 3.56 0.50 113.10 116.66 B B B N7 C8 N9 DG DG DG 16 16 16 N 2 -3.04 0.40 106.40 103.36 B B B C8 N9 C4 DG DG DG 16 16 16 N 2 1.83 0.30 108.30 110.13 B B B O4' C1' N9 DG DG DG 17 17 17 N 2 3.59 0.50 113.10 116.69 B B B N7 C8 N9 DG DG DG 17 17 17 N 2 -3.06 0.40 106.40 103.34 B B B C8 N9 C4 DG DG DG 17 17 17 N 2 2.08 0.30 108.30 110.38 B B B O4' C1' N9 DG DG DG 18 18 18 N 2 3.57 0.50 113.10 116.67 B B B N7 C8 N9 DG DG DG 18 18 18 N 2 -3.10 0.40 106.40 103.30 B B B C8 N9 C4 DG DG DG 18 18 18 N 3 3.13 0.30 108.30 111.43 A A A O4' C1' N1 DC DC DC 1 1 1 N 3 2.04 0.30 108.30 110.34 A A A O4' C1' N1 DC DC DC 2 2 2 N 3 2.09 0.30 108.30 110.39 A A A O4' C1' N1 DC DC DC 3 3 3 N 3 2.73 0.30 108.30 111.03 A A A O4' C1' N9 DG DG DG 4 4 4 N 3 3.50 0.50 113.10 116.60 A A A N7 C8 N9 DG DG DG 4 4 4 N 3 -3.02 0.40 106.40 103.38 A A A C8 N9 C4 DG DG DG 4 4 4 N 3 3.27 0.50 113.80 117.07 A A A N7 C8 N9 DA DA DA 5 5 5 N 3 -2.69 0.40 105.80 103.11 A A A C8 N9 C4 DA DA DA 5 5 5 N 3 3.59 0.30 108.30 111.89 A A A O4' C1' N1 DT DT DT 6 6 6 N 3 3.60 0.30 108.30 111.90 A A A O4' C1' N9 DG DG DG 7 7 7 N 3 3.57 0.50 113.10 116.67 A A A N7 C8 N9 DG DG DG 7 7 7 N 3 -3.10 0.40 106.40 103.30 A A A C8 N9 C4 DG DG DG 7 7 7 N 3 2.24 0.30 108.30 110.54 A A A O4' C1' N1 DC DC DC 8 8 8 N 3 2.88 0.30 108.30 111.18 B B B O4' C1' N9 DG DG DG 9 9 9 N 3 3.62 0.50 113.10 116.72 B B B N7 C8 N9 DG DG DG 9 9 9 N 3 -3.07 0.40 106.40 103.33 B B B C8 N9 C4 DG DG DG 9 9 9 N 3 2.81 0.30 108.30 111.11 B B B O4' C1' N1 DC DC DC 10 10 10 N 3 2.60 0.30 108.30 110.90 B B B O4' C1' N9 DA DA DA 11 11 11 N 3 3.04 0.50 113.80 116.84 B B B N7 C8 N9 DA DA DA 11 11 11 N 3 -2.54 0.40 105.80 103.26 B B B C8 N9 C4 DA DA DA 11 11 11 N 3 3.50 0.30 108.30 111.80 B B B O4' C1' N9 DA DA DA 12 12 12 N 3 3.29 0.50 113.80 117.09 B B B N7 C8 N9 DA DA DA 12 12 12 N 3 -2.78 0.40 105.80 103.02 B B B C8 N9 C4 DA DA DA 12 12 12 N 3 3.77 0.30 108.30 112.07 B B B O4' C1' N1 DT DT DT 13 13 13 N 3 -3.80 0.60 122.90 119.10 B B B C6 C5 C7 DT DT DT 13 13 13 N 3 -3.60 0.60 122.90 119.30 B B B C6 C5 C7 DT DT DT 14 14 14 N 3 2.39 0.30 108.30 110.69 B B B O4' C1' N1 DC DC DC 15 15 15 N 3 2.86 0.30 108.30 111.16 B B B O4' C1' N9 DG DG DG 16 16 16 N 3 3.67 0.50 113.10 116.77 B B B N7 C8 N9 DG DG DG 16 16 16 N 3 -3.08 0.40 106.40 103.32 B B B C8 N9 C4 DG DG DG 16 16 16 N 3 1.92 0.30 108.30 110.22 B B B O4' C1' N9 DG DG DG 17 17 17 N 3 3.56 0.50 113.10 116.66 B B B N7 C8 N9 DG DG DG 17 17 17 N 3 -3.04 0.40 106.40 103.36 B B B C8 N9 C4 DG DG DG 17 17 17 N 3 1.89 0.30 108.30 110.19 B B B O4' C1' N9 DG DG DG 18 18 18 N 3 3.62 0.50 113.10 116.72 B B B N7 C8 N9 DG DG DG 18 18 18 N 3 -3.07 0.40 106.40 103.33 B B B C8 N9 C4 DG DG DG 18 18 18 N 4 3.33 0.30 108.30 111.63 A A A O4' C1' N1 DC DC DC 1 1 1 N 4 2.00 0.30 108.30 110.30 A A A O4' C1' N1 DC DC DC 3 3 3 N 4 2.49 0.30 108.30 110.79 A A A O4' C1' N9 DG DG DG 4 4 4 N 4 3.59 0.50 113.10 116.69 A A A N7 C8 N9 DG DG DG 4 4 4 N 4 -3.01 0.40 106.40 103.39 A A A C8 N9 C4 DG DG DG 4 4 4 N 4 3.30 0.50 113.80 117.10 A A A N7 C8 N9 DA DA DA 5 5 5 N 4 -2.78 0.40 105.80 103.02 A A A C8 N9 C4 DA DA DA 5 5 5 N 4 3.28 0.30 108.30 111.58 A A A O4' C1' N1 DT DT DT 6 6 6 N 4 4.00 0.30 108.30 112.30 A A A O4' C1' N9 DG DG DG 7 7 7 N 4 3.54 0.50 113.10 116.64 A A A N7 C8 N9 DG DG DG 7 7 7 N 4 -3.14 0.40 106.40 103.26 A A A C8 N9 C4 DG DG DG 7 7 7 N 4 2.30 0.30 108.30 110.60 A A A O4' C1' N1 DC DC DC 8 8 8 N 4 2.84 0.30 108.30 111.14 B B B O4' C1' N9 DG DG DG 9 9 9 N 4 3.67 0.50 113.10 116.77 B B B N7 C8 N9 DG DG DG 9 9 9 N 4 -3.12 0.40 106.40 103.28 B B B C8 N9 C4 DG DG DG 9 9 9 N 4 2.76 0.30 108.30 111.06 B B B O4' C1' N1 DC DC DC 10 10 10 N 4 2.34 0.30 108.30 110.64 B B B O4' C1' N9 DA DA DA 11 11 11 N 4 3.11 0.50 113.80 116.91 B B B N7 C8 N9 DA DA DA 11 11 11 N 4 -2.60 0.40 105.80 103.20 B B B C8 N9 C4 DA DA DA 11 11 11 N 4 3.21 0.30 108.30 111.51 B B B O4' C1' N9 DA DA DA 12 12 12 N 4 3.32 0.50 113.80 117.12 B B B N7 C8 N9 DA DA DA 12 12 12 N 4 -2.72 0.40 105.80 103.08 B B B C8 N9 C4 DA DA DA 12 12 12 N 4 3.91 0.30 108.30 112.21 B B B O4' C1' N1 DT DT DT 13 13 13 N 4 -3.68 0.60 122.90 119.22 B B B C6 C5 C7 DT DT DT 14 14 14 N 4 2.15 0.30 108.30 110.45 B B B O4' C1' N1 DC DC DC 15 15 15 N 4 2.85 0.30 108.30 111.15 B B B O4' C1' N9 DG DG DG 16 16 16 N 4 3.54 0.50 113.10 116.64 B B B N7 C8 N9 DG DG DG 16 16 16 N 4 -3.04 0.40 106.40 103.36 B B B C8 N9 C4 DG DG DG 16 16 16 N 4 2.15 0.30 108.30 110.45 B B B O4' C1' N9 DG DG DG 17 17 17 N 4 3.57 0.50 113.10 116.67 B B B N7 C8 N9 DG DG DG 17 17 17 N 4 -3.05 0.40 106.40 103.35 B B B C8 N9 C4 DG DG DG 17 17 17 N 4 1.98 0.30 108.30 110.28 B B B O4' C1' N9 DG DG DG 18 18 18 N 4 3.63 0.50 113.10 116.73 B B B N7 C8 N9 DG DG DG 18 18 18 N 4 -3.09 0.40 106.40 103.31 B B B C8 N9 C4 DG DG DG 18 18 18 N 5 3.07 0.30 108.30 111.37 A A A O4' C1' N1 DC DC DC 1 1 1 N 5 1.83 0.30 108.30 110.13 A A A O4' C1' N1 DC DC DC 2 2 2 N 5 1.94 0.30 108.30 110.24 A A A O4' C1' N1 DC DC DC 3 3 3 N 5 2.65 0.30 108.30 110.95 A A A O4' C1' N9 DG DG DG 4 4 4 N 5 3.56 0.50 113.10 116.66 A A A N7 C8 N9 DG DG DG 4 4 4 N 5 -3.07 0.40 106.40 103.33 A A A C8 N9 C4 DG DG DG 4 4 4 N 5 3.25 0.50 113.80 117.05 A A A N7 C8 N9 DA DA DA 5 5 5 N 5 -2.73 0.40 105.80 103.07 A A A C8 N9 C4 DA DA DA 5 5 5 N 5 3.63 0.30 108.30 111.93 A A A O4' C1' N1 DT DT DT 6 6 6 N 5 3.62 0.30 108.30 111.92 A A A O4' C1' N9 DG DG DG 7 7 7 N 5 3.53 0.50 113.10 116.63 A A A N7 C8 N9 DG DG DG 7 7 7 N 5 -3.15 0.40 106.40 103.25 A A A C8 N9 C4 DG DG DG 7 7 7 N 5 2.29 0.30 108.30 110.59 A A A O4' C1' N1 DC DC DC 8 8 8 N 5 2.78 0.30 108.30 111.08 B B B O4' C1' N9 DG DG DG 9 9 9 N 5 3.66 0.50 113.10 116.76 B B B N7 C8 N9 DG DG DG 9 9 9 N 5 -3.11 0.40 106.40 103.29 B B B C8 N9 C4 DG DG DG 9 9 9 N 5 2.92 0.30 108.30 111.22 B B B O4' C1' N1 DC DC DC 10 10 10 N 5 2.69 0.30 108.30 110.99 B B B O4' C1' N9 DA DA DA 11 11 11 N 5 3.10 0.50 113.80 116.90 B B B N7 C8 N9 DA DA DA 11 11 11 N 5 -2.62 0.40 105.80 103.18 B B B C8 N9 C4 DA DA DA 11 11 11 N 5 3.40 0.30 108.30 111.70 B B B O4' C1' N9 DA DA DA 12 12 12 N 5 3.34 0.50 113.80 117.14 B B B N7 C8 N9 DA DA DA 12 12 12 N 5 -2.79 0.40 105.80 103.01 B B B C8 N9 C4 DA DA DA 12 12 12 N 5 3.73 0.30 108.30 112.03 B B B O4' C1' N1 DT DT DT 13 13 13 N 5 2.02 0.30 108.30 110.32 B B B O4' C1' N1 DC DC DC 15 15 15 N 5 2.89 0.30 108.30 111.19 B B B O4' C1' N9 DG DG DG 16 16 16 N 5 3.66 0.50 113.10 116.76 B B B N7 C8 N9 DG DG DG 16 16 16 N 5 -3.08 0.40 106.40 103.32 B B B C8 N9 C4 DG DG DG 16 16 16 N 5 1.96 0.30 108.30 110.26 B B B O4' C1' N9 DG DG DG 17 17 17 N 5 3.61 0.50 113.10 116.71 B B B N7 C8 N9 DG DG DG 17 17 17 N 5 -3.01 0.40 106.40 103.39 B B B C8 N9 C4 DG DG DG 17 17 17 N 5 2.12 0.30 108.30 110.42 B B B O4' C1' N9 DG DG DG 18 18 18 N 5 3.60 0.50 113.10 116.70 B B B N7 C8 N9 DG DG DG 18 18 18 N 5 -3.03 0.40 106.40 103.37 B B B C8 N9 C4 DG DG DG 18 18 18 N 6 3.05 0.30 108.30 111.35 A A A O4' C1' N1 DC DC DC 1 1 1 N 6 1.83 0.30 108.30 110.13 A A A O4' C1' N1 DC DC DC 2 2 2 N 6 2.00 0.30 108.30 110.30 A A A O4' C1' N1 DC DC DC 3 3 3 N 6 2.59 0.30 108.30 110.89 A A A O4' C1' N9 DG DG DG 4 4 4 N 6 3.56 0.50 113.10 116.66 A A A N7 C8 N9 DG DG DG 4 4 4 N 6 -3.09 0.40 106.40 103.31 A A A C8 N9 C4 DG DG DG 4 4 4 N 6 3.30 0.50 113.80 117.10 A A A N7 C8 N9 DA DA DA 5 5 5 N 6 -2.71 0.40 105.80 103.09 A A A C8 N9 C4 DA DA DA 5 5 5 N 6 3.67 0.30 108.30 111.97 A A A O4' C1' N1 DT DT DT 6 6 6 N 6 3.69 0.30 108.30 111.99 A A A O4' C1' N9 DG DG DG 7 7 7 N 6 3.55 0.50 113.10 116.65 A A A N7 C8 N9 DG DG DG 7 7 7 N 6 -3.14 0.40 106.40 103.26 A A A C8 N9 C4 DG DG DG 7 7 7 N 6 2.16 0.30 108.30 110.46 A A A O4' C1' N1 DC DC DC 8 8 8 N 6 2.75 0.30 108.30 111.05 B B B O4' C1' N9 DG DG DG 9 9 9 N 6 3.66 0.50 113.10 116.76 B B B N7 C8 N9 DG DG DG 9 9 9 N 6 -3.14 0.40 106.40 103.26 B B B C8 N9 C4 DG DG DG 9 9 9 N 6 2.93 0.30 108.30 111.23 B B B O4' C1' N1 DC DC DC 10 10 10 N 6 2.49 0.30 108.30 110.79 B B B O4' C1' N9 DA DA DA 11 11 11 N 6 3.05 0.50 113.80 116.85 B B B N7 C8 N9 DA DA DA 11 11 11 N 6 -2.57 0.40 105.80 103.23 B B B C8 N9 C4 DA DA DA 11 11 11 N 6 3.44 0.30 108.30 111.74 B B B O4' C1' N9 DA DA DA 12 12 12 N 6 3.31 0.50 113.80 117.11 B B B N7 C8 N9 DA DA DA 12 12 12 N 6 -2.76 0.40 105.80 103.04 B B B C8 N9 C4 DA DA DA 12 12 12 N 6 3.67 0.30 108.30 111.97 B B B O4' C1' N1 DT DT DT 13 13 13 N 6 2.07 0.30 108.30 110.37 B B B O4' C1' N1 DC DC DC 15 15 15 N 6 2.83 0.30 108.30 111.13 B B B O4' C1' N9 DG DG DG 16 16 16 N 6 3.63 0.50 113.10 116.73 B B B N7 C8 N9 DG DG DG 16 16 16 N 6 -3.05 0.40 106.40 103.35 B B B C8 N9 C4 DG DG DG 16 16 16 N 6 2.02 0.30 108.30 110.32 B B B O4' C1' N9 DG DG DG 17 17 17 N 6 3.56 0.50 113.10 116.66 B B B N7 C8 N9 DG DG DG 17 17 17 N 6 -3.05 0.40 106.40 103.35 B B B C8 N9 C4 DG DG DG 17 17 17 N 6 1.94 0.30 108.30 110.24 B B B O4' C1' N9 DG DG DG 18 18 18 N 6 3.56 0.50 113.10 116.66 B B B N7 C8 N9 DG DG DG 18 18 18 N 6 -3.03 0.40 106.40 103.37 B B B C8 N9 C4 DG DG DG 18 18 18 N 7 3.19 0.30 108.30 111.49 A A A O4' C1' N1 DC DC DC 1 1 1 N 7 1.87 0.30 108.30 110.17 A A A O4' C1' N1 DC DC DC 2 2 2 N 7 2.09 0.30 108.30 110.39 A A A O4' C1' N1 DC DC DC 3 3 3 N 7 2.89 0.30 108.30 111.19 A A A O4' C1' N9 DG DG DG 4 4 4 N 7 3.55 0.50 113.10 116.65 A A A N7 C8 N9 DG DG DG 4 4 4 N 7 -2.98 0.40 106.40 103.42 A A A C8 N9 C4 DG DG DG 4 4 4 N 7 3.37 0.50 113.80 117.17 A A A N7 C8 N9 DA DA DA 5 5 5 N 7 -3.26 0.40 105.80 102.54 A A A C8 N9 C4 DA DA DA 5 5 5 N 7 -4.43 0.60 118.60 114.17 A A A N1 C6 N6 DA DA DA 5 5 5 N 7 3.66 0.30 108.30 111.96 A A A O4' C1' N1 DT DT DT 6 6 6 N 7 3.78 0.30 108.30 112.08 A A A O4' C1' N9 DG DG DG 7 7 7 N 7 3.49 0.50 113.10 116.59 A A A N7 C8 N9 DG DG DG 7 7 7 N 7 -3.05 0.40 106.40 103.35 A A A C8 N9 C4 DG DG DG 7 7 7 N 7 2.06 0.30 108.30 110.36 A A A O4' C1' N1 DC DC DC 8 8 8 N 7 2.65 0.30 108.30 110.95 B B B O4' C1' N9 DG DG DG 9 9 9 N 7 3.61 0.50 113.10 116.71 B B B N7 C8 N9 DG DG DG 9 9 9 N 7 -3.09 0.40 106.40 103.31 B B B C8 N9 C4 DG DG DG 9 9 9 N 7 2.95 0.30 108.30 111.25 B B B O4' C1' N1 DC DC DC 10 10 10 N 7 2.44 0.30 108.30 110.74 B B B O4' C1' N9 DA DA DA 11 11 11 N 7 3.02 0.50 113.80 116.82 B B B N7 C8 N9 DA DA DA 11 11 11 N 7 -2.56 0.40 105.80 103.24 B B B C8 N9 C4 DA DA DA 11 11 11 N 7 2.85 0.30 108.30 111.15 B B B O4' C1' N9 DA DA DA 12 12 12 N 7 3.47 0.50 113.80 117.27 B B B N7 C8 N9 DA DA DA 12 12 12 N 7 -2.82 0.40 105.80 102.98 B B B C8 N9 C4 DA DA DA 12 12 12 N 7 4.38 0.30 108.30 112.68 B B B O4' C1' N1 DT DT DT 13 13 13 N 7 -3.82 0.60 122.90 119.08 B B B C6 C5 C7 DT DT DT 13 13 13 N 7 8.43 1.20 119.70 128.13 B B B C3' O3' P DT DT DT 13 13 14 Y 7 3.66 0.60 118.00 121.66 B B B C4 C5 C6 DT DT DT 14 14 14 N 7 -4.05 0.60 122.90 118.85 B B B C6 C5 C7 DT DT DT 14 14 14 N 7 2.76 0.30 108.30 111.06 B B B O4' C1' N1 DC DC DC 15 15 15 N 7 2.77 0.30 108.30 111.07 B B B O4' C1' N9 DG DG DG 16 16 16 N 7 3.57 0.50 113.10 116.67 B B B N7 C8 N9 DG DG DG 16 16 16 N 7 -3.06 0.40 106.40 103.34 B B B C8 N9 C4 DG DG DG 16 16 16 N 7 2.14 0.30 108.30 110.44 B B B O4' C1' N9 DG DG DG 17 17 17 N 7 3.60 0.50 113.10 116.70 B B B N7 C8 N9 DG DG DG 17 17 17 N 7 -3.07 0.40 106.40 103.33 B B B C8 N9 C4 DG DG DG 17 17 17 N 7 2.06 0.30 108.30 110.36 B B B O4' C1' N9 DG DG DG 18 18 18 N 7 3.55 0.50 113.10 116.65 B B B N7 C8 N9 DG DG DG 18 18 18 N 7 -3.06 0.40 106.40 103.34 B B B C8 N9 C4 DG DG DG 18 18 18 N NCSi-gb-bulge-DNA complex induced formation of a DNA bulge structure by a molecular wedge ligand-post-activated neocarzinostatin chromophore 1 N N 2 N N 3 N N hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 18 B N1 DG 10 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 18 B O6 DG 10 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 18 B N2 DG 10 1_555 hydrog WATSON-CRICK A DC 2 A N3 DC 2 1_555 B DG 17 B N1 DG 9 1_555 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 B DG 17 B O6 DG 9 1_555 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 B DG 17 B N2 DG 9 1_555 hydrog WATSON-CRICK A DC 3 A N3 DC 3 1_555 B DG 16 B N1 DG 8 1_555 hydrog WATSON-CRICK A DC 3 A N4 DC 3 1_555 B DG 16 B O6 DG 8 1_555 hydrog WATSON-CRICK A DC 3 A O2 DC 3 1_555 B DG 16 B N2 DG 8 1_555 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 B DC 15 B N3 DC 7 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B DC 15 B O2 DC 7 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 B DC 15 B N4 DC 7 1_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 B DT 14 B N3 DT 6 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 B DT 14 B O4 DT 6 1_555 hydrog WATSON-CRICK A DT 6 A N3 DT 6 1_555 B DA 11 B N1 DA 3 1_555 hydrog WATSON-CRICK A DT 6 A O4 DT 6 1_555 B DA 11 B N6 DA 3 1_555 hydrog WATSON-CRICK A DG 7 A N1 DG 7 1_555 B DC 10 B N3 DC 2 1_555 hydrog WATSON-CRICK A DG 7 A N2 DG 7 1_555 B DC 10 B O2 DC 2 1_555 hydrog WATSON-CRICK A DG 7 A O6 DG 7 1_555 B DC 10 B N4 DC 2 1_555 hydrog WATSON-CRICK A DC 8 A N3 DC 8 1_555 B DG 9 B N1 DG 1 1_555 hydrog WATSON-CRICK A DC 8 A N4 DC 8 1_555 B DG 9 B O6 DG 1 1_555 hydrog WATSON-CRICK A DC 8 A O2 DC 8 1_555 B DG 9 B N2 DG 1 1_555 DNA DNA 1KVH PDB 1 1KVH 1KVH PDB 2 1KVH 1 8 1KVH 1 8 1KVH A 1 1 8 9 18 1KVH 9 18 1KVH B 2 1 10 BINDING SITE FOR RESIDUE NCS B 21 B NCS 21 Software 8 A DC 3 A DC 3 8 1_555 A DG 4 A DG 4 8 1_555 A DA 5 A DA 5 8 1_555 A DT 6 A DT 6 8 1_555 B DA 11 B DA 3 8 1_555 B DA 12 B DA 4 8 1_555 B DT 13 B DT 5 8 1_555 B DT 14 B DT 6 8 1_555