0.041599 -0.010210 -0.001566 0.000000 0.041524 -0.010701 0.000000 0.000000 0.027653 0.00000 0.00000 0.00000 Song, H. Kaiser, J.T. Barton, J.K. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 2 74.67 84.42 76.21 24.039 24.797 37.521 Ba 2 137.327 BARIUM ION non-polymer 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 H2 O 18.015 WATER non-polymer C38 H26 N8 Ru 695.737 Delta-[Ru(bpy)2dppz]2+ non-polymer N 1 N BA N 2 N O N 3 N P N 4 N O N 5 N O N 6 N O N 7 N C N 8 R C N 9 N O N 10 S C N 11 N O N 12 N C N 13 R C Y 14 N N Y 15 N C Y 16 N N Y 17 N C Y 18 N C N 19 N N Y 20 N N Y 21 N C Y 22 N N Y 23 N C 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 N 50 N N N 51 N C N 52 N O N 53 N N N 54 N C N 55 N N N 56 N C N 57 N C 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 H N 72 N O N 73 N P N 74 N O N 75 N O N 76 N O N 77 N C N 78 R C N 79 N O N 80 S C N 81 N O N 82 N C N 83 R C Y 84 N N Y 85 N C Y 86 N N Y 87 N C N 88 N C N 89 N O N 90 N N N 91 N C N 92 N N N 93 N N Y 94 N C 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 H N 109 N O N 110 N P N 111 N O N 112 N O N 113 N O N 114 N C N 115 R C N 116 N O N 117 S C N 118 N O N 119 N C N 120 R C N 121 N N N 122 N C N 123 N O N 124 N N N 125 N C N 126 N O N 127 N C N 128 N C N 129 N C 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 H N 145 N O N 146 N H N 147 N H N 148 N RU Y 149 N N Y 150 N C Y 151 N C Y 152 N C Y 153 N C Y 154 N C Y 155 N C Y 156 N N Y 157 N C Y 158 N C Y 159 N C Y 160 N C Y 161 N N Y 162 N C Y 163 N C Y 164 N C Y 165 N C Y 166 N C Y 167 N C Y 168 N N Y 169 N C Y 170 N C Y 171 N C Y 172 N C Y 173 N C Y 174 N C Y 175 N N Y 176 N C Y 177 N C Y 178 N C Y 179 N C Y 180 N C Y 181 N N Y 182 N C Y 183 N C Y 184 N C Y 185 N C Y 186 N C Y 187 N C Y 188 N N Y 189 N C Y 190 N C Y 191 N C Y 192 N C Y 193 N C Y 194 N N 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 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 sing N 151 N sing Y 152 N doub Y 153 N sing Y 154 N sing Y 155 N doub Y 156 N sing Y 157 N sing Y 158 N doub N 159 N sing Y 160 N doub Y 161 N doub Y 162 N doub Y 163 N sing N 164 N sing Y 165 N sing N 166 N sing Y 167 N doub Y 168 N sing Y 169 N sing Y 170 N doub N 171 N sing Y 172 N doub N 173 N sing N 174 N sing N 175 N sing Y 176 N sing Y 177 N sing Y 178 N doub Y 179 N sing Y 180 N sing Y 181 N sing Y 182 N doub Y 183 N sing Y 184 N doub Y 185 N sing Y 186 N doub Y 187 N sing Y 188 N sing Y 189 N doub Y 190 N sing Y 191 N sing Y 192 N doub Y 193 N sing Y 194 N sing Y 195 N doub N 196 N sing Y 197 N doub Y 198 N sing Y 199 N doub Y 200 N sing Y 201 N doub Y 202 N doub Y 203 N doub Y 204 N sing Y 205 N doub Y 206 N sing Y 207 N sing Y 208 N doub Y 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 UK Nat Chem 1755-4349 4 615 620 10.1038/nchem.1375 22824892 Crystal structure of delta-[Ru(bpy)2dppz]2+ bound to mismatched DNA reveals side-by-side metalloinsertion and intercalation. 2012 10.2210/pdb4e1u/pdb pdb_00004e1u 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100 1 PIXEL 2010-12-03 DECTRIS PILATUS 6M SINGLE WAVELENGTH M x-ray 1 .7749 1.0 BL12-2 SSRL .7749 SYNCHROTRON SSRL BEAMLINE BL12-2 3671.418 5'-D(*CP*GP*GP*AP*AP*AP*TP*TP*AP*CP*CP*G)-3' 2 syn polymer 695.737 Delta-[Ru(bpy)2dppz]2+ 5 syn non-polymer 137.327 BARIUM ION 2 syn non-polymer 18.015 water 197 nat water no no (DC)(DG)(DG)(DA)(DA)(DA)(DT)(DT)(DA)(DC)(DC)(DG) CGGAAATTACCG A,B polydeoxyribonucleotide n n n n n n n n n n n n 1 2.85 56.86 VAPOR DIFFUSION 7.0 20mM Cacodylate; 6mM Spermine*HCl; 40mM NaCl; 10mM BaCl2 5% 2-M-2,4PD, pH 7.0, VAPOR DIFFUSION, temperature 296K 296 0.604 1 19 A 1 B 12 -1.072 A_DC1:DG12_B 1 20.169 0.173 -0.368 -0.178 -8.060 1 19 A 2 B 11 -0.589 A_DG2:DC11_B 2 3.170 -0.239 -0.372 -0.155 14.888 1 19 A 3 B 10 -2.356 A_DG3:DC10_B 3 19.558 -0.187 -0.230 -0.199 -7.113 1 20 A 5 B 8 7.705 A_DA5:DT8_B 4 27.953 0.206 -0.658 -0.027 21.530 1 20 A 6 B 7 -2.231 A_DA6:DT7_B 5 10.392 0.048 -0.014 -0.027 -17.974 1 20 A 7 B 6 -0.674 A_DT7:DA6_B 6 9.147 -0.146 -0.017 -0.160 15.827 1 20 A 8 B 5 9.814 A_DT8:DA5_B 7 13.563 -0.049 -0.148 -0.114 -16.585 1 19 A 10 B 3 -1.540 A_DC10:DG3_B 8 23.716 0.295 0.053 -0.185 6.354 1 19 A 11 B 2 -0.311 A_DC11:DG2_B 9 10.028 0.233 -0.160 -0.117 5.628 22.674 A A 1 2 15.084 B B 12 11 6.285 5.535 0.122 2.161 AA_DC1DG2:DC11DG12_BB 1 12.499 -34.065 18.134 1.427 8.883 2.734 31.011 A A 2 3 -10.099 B B 11 10 2.919 -5.366 0.905 0.263 AA_DG2DG3:DC10DC11_BB 2 -2.978 5.605 30.412 1.394 -2.193 3.042 23.204 A A 5 6 -1.716 B B 8 7 3.016 -0.690 -0.776 -0.144 AA_DA5DA6:DT7DT8_BB 3 -0.733 1.822 23.183 -0.137 1.694 6.966 24.728 A A 6 7 18.053 B B 7 6 7.113 7.604 -0.182 0.635 AA_DA6DT7:DA6DT7_BB 4 -1.653 3.924 23.490 -3.628 -0.686 2.531 24.672 A A 7 8 15.639 B B 6 5 2.805 6.582 0.417 -0.346 AA_DT7DT8:DA5DA6_BB 5 -3.413 8.109 23.548 -2.490 -1.848 2.787 24.774 A A 10 11 -17.685 B B 3 2 2.999 -7.451 -0.995 -0.261 AA_DC10DC11:DG2DG3_BB 6 3.234 -7.677 23.425 1.446 3.211 chem_comp_atom chem_comp_bond database_2 pdbx_struct_conn_angle struct_conn struct_site repository Initial release Non-polymer description Database references Data collection Database references Derived calculations 1 0 2012-06-20 1 1 2013-02-20 1 2 2013-06-19 1 3 2024-02-28 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2012-03-07 REL REL R1Z Delta-[Ru(bpy)2dppz]2+ BA BARIUM ION HOH water Engineered mismatch sample R1Z 905 2 R1Z R1Z 101 A R1Z 904 2 R1Z R1Z 102 A R1Z 903 2 R1Z R1Z 103 A R1Z 902 2 R1Z R1Z 104 A R1Z 901 2 R1Z R1Z 105 A BA 2 3 BA BA 106 A BA 1 3 BA BA 101 B HOH 2 4 HOH HOH 201 A HOH 3 4 HOH HOH 202 A HOH 5 4 HOH HOH 203 A HOH 6 4 HOH HOH 204 A HOH 9 4 HOH HOH 205 A HOH 12 4 HOH HOH 206 A HOH 17 4 HOH HOH 207 A HOH 19 4 HOH HOH 208 A HOH 20 4 HOH HOH 209 A HOH 21 4 HOH HOH 210 A HOH 22 4 HOH HOH 211 A HOH 24 4 HOH HOH 212 A HOH 25 4 HOH HOH 213 A HOH 26 4 HOH HOH 214 A HOH 27 4 HOH HOH 215 A HOH 34 4 HOH HOH 216 A HOH 35 4 HOH HOH 217 A HOH 36 4 HOH HOH 218 A HOH 37 4 HOH HOH 219 A HOH 38 4 HOH HOH 220 A HOH 40 4 HOH HOH 221 A HOH 41 4 HOH HOH 222 A HOH 45 4 HOH HOH 223 A HOH 48 4 HOH HOH 224 A HOH 50 4 HOH HOH 225 A HOH 52 4 HOH HOH 226 A HOH 53 4 HOH HOH 227 A HOH 54 4 HOH HOH 228 A HOH 56 4 HOH HOH 229 A HOH 60 4 HOH HOH 230 A HOH 61 4 HOH HOH 231 A HOH 62 4 HOH HOH 232 A HOH 63 4 HOH HOH 233 A HOH 65 4 HOH HOH 234 A HOH 66 4 HOH HOH 235 A HOH 68 4 HOH HOH 236 A HOH 69 4 HOH HOH 237 A HOH 70 4 HOH HOH 238 A HOH 72 4 HOH HOH 239 A HOH 73 4 HOH HOH 240 A HOH 75 4 HOH HOH 241 A HOH 76 4 HOH HOH 242 A HOH 77 4 HOH HOH 243 A HOH 89 4 HOH HOH 244 A HOH 91 4 HOH HOH 245 A HOH 93 4 HOH HOH 246 A HOH 96 4 HOH HOH 247 A HOH 97 4 HOH HOH 248 A HOH 98 4 HOH HOH 249 A HOH 99 4 HOH HOH 250 A HOH 100 4 HOH HOH 251 A HOH 103 4 HOH HOH 252 A HOH 105 4 HOH HOH 253 A HOH 110 4 HOH HOH 254 A HOH 111 4 HOH HOH 255 A HOH 112 4 HOH HOH 256 A HOH 115 4 HOH HOH 257 A HOH 117 4 HOH HOH 258 A HOH 122 4 HOH HOH 259 A HOH 124 4 HOH HOH 260 A HOH 127 4 HOH HOH 261 A HOH 133 4 HOH HOH 262 A HOH 134 4 HOH HOH 263 A HOH 135 4 HOH HOH 264 A HOH 136 4 HOH HOH 265 A HOH 137 4 HOH HOH 266 A HOH 143 4 HOH HOH 267 A HOH 144 4 HOH HOH 268 A HOH 148 4 HOH HOH 269 A HOH 149 4 HOH HOH 270 A HOH 153 4 HOH HOH 271 A HOH 159 4 HOH HOH 272 A HOH 163 4 HOH HOH 273 A HOH 167 4 HOH HOH 274 A HOH 168 4 HOH HOH 275 A HOH 169 4 HOH HOH 276 A HOH 173 4 HOH HOH 277 A HOH 176 4 HOH HOH 278 A HOH 178 4 HOH HOH 279 A HOH 180 4 HOH HOH 280 A HOH 183 4 HOH HOH 281 A HOH 184 4 HOH HOH 282 A HOH 189 4 HOH HOH 283 A HOH 192 4 HOH HOH 284 A HOH 194 4 HOH HOH 285 A HOH 196 4 HOH HOH 286 A HOH 1 4 HOH HOH 1001 B HOH 4 4 HOH HOH 1002 B HOH 7 4 HOH HOH 1003 B HOH 8 4 HOH HOH 1004 B HOH 10 4 HOH HOH 1005 B HOH 11 4 HOH HOH 1006 B HOH 13 4 HOH HOH 1007 B HOH 14 4 HOH HOH 1008 B HOH 15 4 HOH HOH 1009 B HOH 16 4 HOH HOH 1010 B HOH 18 4 HOH HOH 1011 B HOH 23 4 HOH HOH 1012 B HOH 28 4 HOH HOH 1013 B HOH 29 4 HOH HOH 1014 B HOH 30 4 HOH HOH 1015 B HOH 31 4 HOH HOH 1016 B HOH 32 4 HOH HOH 1017 B HOH 33 4 HOH HOH 1018 B HOH 39 4 HOH HOH 1019 B HOH 42 4 HOH HOH 1020 B HOH 43 4 HOH HOH 1021 B HOH 44 4 HOH HOH 1022 B HOH 46 4 HOH HOH 1023 B HOH 47 4 HOH HOH 1024 B HOH 49 4 HOH HOH 1025 B HOH 51 4 HOH HOH 1026 B HOH 55 4 HOH HOH 1027 B HOH 57 4 HOH HOH 1028 B HOH 58 4 HOH HOH 1029 B HOH 59 4 HOH HOH 1030 B HOH 64 4 HOH HOH 1031 B HOH 67 4 HOH HOH 1032 B HOH 71 4 HOH HOH 1033 B HOH 74 4 HOH HOH 1034 B HOH 78 4 HOH HOH 1035 B HOH 79 4 HOH HOH 1036 B HOH 80 4 HOH HOH 1037 B HOH 81 4 HOH HOH 1038 B HOH 82 4 HOH HOH 1039 B HOH 83 4 HOH HOH 1040 B HOH 84 4 HOH HOH 1041 B HOH 85 4 HOH HOH 1042 B HOH 86 4 HOH HOH 1043 B HOH 87 4 HOH HOH 1044 B HOH 88 4 HOH HOH 1045 B HOH 90 4 HOH HOH 1046 B HOH 92 4 HOH HOH 1047 B HOH 94 4 HOH HOH 1048 B HOH 95 4 HOH HOH 1049 B HOH 101 4 HOH HOH 1050 B HOH 102 4 HOH HOH 1051 B HOH 104 4 HOH HOH 1052 B HOH 106 4 HOH HOH 1053 B HOH 107 4 HOH HOH 1054 B HOH 108 4 HOH HOH 1055 B HOH 109 4 HOH HOH 1056 B HOH 113 4 HOH HOH 1057 B HOH 114 4 HOH HOH 1058 B HOH 116 4 HOH HOH 1059 B HOH 118 4 HOH HOH 1060 B HOH 119 4 HOH HOH 1061 B HOH 120 4 HOH HOH 1062 B HOH 121 4 HOH HOH 1063 B HOH 123 4 HOH HOH 1064 B HOH 125 4 HOH HOH 1065 B HOH 126 4 HOH HOH 1066 B HOH 128 4 HOH HOH 1067 B HOH 129 4 HOH HOH 1068 B HOH 130 4 HOH HOH 1069 B HOH 131 4 HOH HOH 1070 B HOH 132 4 HOH HOH 1071 B HOH 138 4 HOH HOH 1072 B HOH 139 4 HOH HOH 1073 B HOH 140 4 HOH HOH 1074 B HOH 141 4 HOH HOH 1075 B HOH 142 4 HOH HOH 1076 B HOH 145 4 HOH HOH 1077 B HOH 146 4 HOH HOH 1078 B HOH 147 4 HOH HOH 1079 B HOH 150 4 HOH HOH 1080 B HOH 151 4 HOH HOH 1081 B HOH 152 4 HOH HOH 1082 B HOH 154 4 HOH HOH 1083 B HOH 155 4 HOH HOH 1084 B HOH 156 4 HOH HOH 1085 B HOH 157 4 HOH HOH 1086 B HOH 158 4 HOH HOH 1087 B HOH 160 4 HOH HOH 1088 B HOH 161 4 HOH HOH 1089 B HOH 162 4 HOH HOH 1090 B HOH 164 4 HOH HOH 1091 B HOH 165 4 HOH HOH 1092 B HOH 166 4 HOH HOH 1093 B HOH 170 4 HOH HOH 1094 B HOH 171 4 HOH HOH 1095 B HOH 172 4 HOH HOH 1096 B HOH 174 4 HOH HOH 1097 B HOH 175 4 HOH HOH 1098 B HOH 177 4 HOH HOH 1099 B HOH 179 4 HOH HOH 1100 B HOH 181 4 HOH HOH 1101 B HOH 182 4 HOH HOH 1102 B HOH 185 4 HOH HOH 1103 B HOH 186 4 HOH HOH 1104 B HOH 187 4 HOH HOH 1105 B HOH 188 4 HOH HOH 1106 B HOH 190 4 HOH HOH 1107 B HOH 191 4 HOH HOH 1108 B HOH 193 4 HOH HOH 1109 B HOH 195 4 HOH HOH 1110 B HOH 197 4 HOH HOH 1111 B DC 1 n 1 DC 1 A DG 2 n 2 DG 2 A DG 3 n 3 DG 3 A DA 4 n 4 DA 4 A DA 5 n 5 DA 5 A DA 6 n 6 DA 6 A DT 7 n 7 DT 7 A DT 8 n 8 DT 8 A DA 9 n 9 DA 9 A DC 10 n 10 DC 10 A DC 11 n 11 DC 11 A DG 12 n 12 DG 12 A DC 1 n 1 DC 1 B DG 2 n 2 DG 2 B DG 3 n 3 DG 3 B DA 4 n 4 DA 4 B DA 5 n 5 DA 5 B DA 6 n 6 DA 6 B DT 7 n 7 DT 7 B DT 8 n 8 DT 8 B DA 9 n 9 DA 9 B DC 10 n 10 DC 10 B DC 11 n 11 DC 11 B DG 12 n 12 DG 12 B author_and_software_defined_assembly PISA 2 dimeric 1070 -5 5510 A DG 2 A O6 DG 2 1_555 A BA 106 H BA BA 1_555 A DG 3 A A O6 DG 3 1_555 69.2 A DG 2 A O6 DG 2 1_555 A BA 106 H BA BA 1_555 A DG 3 B A O6 DG 3 1_555 71.1 A DG 3 A A O6 DG 3 1_555 A BA 106 H BA BA 1_555 A DG 3 B A O6 DG 3 1_555 3.8 A DG 2 A O6 DG 2 1_555 A BA 106 H BA BA 1_555 A HOH 209 J O HOH 1_555 120.6 A DG 3 A A O6 DG 3 1_555 A BA 106 H BA BA 1_555 A HOH 209 J O HOH 1_555 74.5 A DG 3 B A O6 DG 3 1_555 A BA 106 H BA BA 1_555 A HOH 209 J O HOH 1_555 75.7 A DG 2 A O6 DG 2 1_555 A BA 106 H BA BA 1_555 A HOH 244 J O HOH 1_555 72.9 A DG 3 A A O6 DG 3 1_555 A BA 106 H BA BA 1_555 A HOH 244 J O HOH 1_555 101.5 A DG 3 B A O6 DG 3 1_555 A BA 106 H BA BA 1_555 A HOH 244 J O HOH 1_555 99.2 A HOH 209 J O HOH 1_555 A BA 106 H BA BA 1_555 A HOH 244 J O HOH 1_555 161.5 A DG 2 A O6 DG 2 1_555 A BA 106 H BA BA 1_555 B HOH 1085 K O HOH 1_555 146.9 A DG 3 A A O6 DG 3 1_555 A BA 106 H BA BA 1_555 B HOH 1085 K O HOH 1_555 133.1 A DG 3 B A O6 DG 3 1_555 A BA 106 H BA BA 1_555 B HOH 1085 K O HOH 1_555 129.9 A HOH 209 J O HOH 1_555 A BA 106 H BA BA 1_555 B HOH 1085 K O HOH 1_555 91.5 A HOH 244 J O HOH 1_555 A BA 106 H BA BA 1_555 B HOH 1085 K O HOH 1_555 78.0 A DG 2 A O6 DG 2 1_555 A BA 106 H BA BA 1_555 B HOH 1102 K O HOH 1_555 119.0 A DG 3 A A O6 DG 3 1_555 A BA 106 H BA BA 1_555 B HOH 1102 K O HOH 1_555 69.0 A DG 3 B A O6 DG 3 1_555 A BA 106 H BA BA 1_555 B HOH 1102 K O HOH 1_555 65.3 A HOH 209 J O HOH 1_555 A BA 106 H BA BA 1_555 B HOH 1102 K O HOH 1_555 87.6 A HOH 244 J O HOH 1_555 A BA 106 H BA BA 1_555 B HOH 1102 K O HOH 1_555 74.2 B HOH 1085 K O HOH 1_555 A BA 106 H BA BA 1_555 B HOH 1102 K O HOH 1_555 65.9 B DG 2 B B O6 DG 2 1_555 B BA 101 I BA BA 1_555 B DG 2 A B O6 DG 2 1_555 8.1 B DG 2 B B O6 DG 2 1_555 B BA 101 I BA BA 1_555 B HOH 1004 K O HOH 1_555 61.5 B DG 2 A B O6 DG 2 1_555 B BA 101 I BA BA 1_555 B HOH 1004 K O HOH 1_555 69.2 B DG 2 B B O6 DG 2 1_555 B BA 101 I BA BA 1_555 B HOH 1024 K O HOH 1_555 75.6 B DG 2 A B O6 DG 2 1_555 B BA 101 I BA BA 1_555 B HOH 1024 K O HOH 1_555 79.1 B HOH 1004 K O HOH 1_555 B BA 101 I BA BA 1_555 B HOH 1024 K O HOH 1_555 79.1 B DG 2 B B O6 DG 2 1_555 B BA 101 I BA BA 1_555 B HOH 1033 K O HOH 1_555 117.1 B DG 2 A B O6 DG 2 1_555 B BA 101 I BA BA 1_555 B HOH 1033 K O HOH 1_555 119.0 B HOH 1004 K O HOH 1_555 B BA 101 I BA BA 1_555 B HOH 1033 K O HOH 1_555 76.7 B HOH 1024 K O HOH 1_555 B BA 101 I BA BA 1_555 B HOH 1033 K O HOH 1_555 141.0 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 A B O O HOH HOH 267 1103 1.84 1 B B O O HOH HOH 1083 1084 1.88 1 B B O O HOH HOH 1077 1079 1.89 1 B B O O HOH HOH 1071 1108 1.91 1 A A O O HOH HOH 240 274 1.94 1 A A OP2 O DG HOH 12 271 1.94 B 1 B B O O HOH HOH 1022 1111 1.95 1 A A O O HOH HOH 247 264 1.96 1 A B O O HOH HOH 249 1009 1.99 1 B B O O HOH HOH 1104 1110 1.99 1 A A O O HOH HOH 238 241 2.10 1 B B O O HOH HOH 1066 1069 2.10 1 B B O O HOH HOH 1087 1096 2.11 1 A A O O HOH HOH 217 246 2.12 1 B B O O HOH HOH 1067 1071 2.12 1 B B O O HOH HOH 1029 1092 2.14 1 B B O O HOH HOH 1038 1066 2.14 1 A A OP1 O DT HOH 7 242 2.16 B 1 A B O O HOH HOH 236 1046 2.17 1 A A OP2 O DG HOH 12 271 2.19 A 1 B B O O HOH HOH 1068 1098 2.19 1 A A O3' P DC DG 11 12 1.78 A 1 A A O3' P DC DG 11 12 1.79 B 1 2.15 0.30 108.30 110.45 A A A O4' C1' N1 DC DC DC 1 1 1 N 1 2.05 0.30 108.30 110.35 A A A O4' C1' N9 DG DG DG 2 2 2 N 1 4.59 0.30 108.30 112.89 A A A O4' C1' N9 DG DG DG 3 3 3 A A A N 1 8.42 0.30 108.30 116.72 A A A O4' C1' N9 DA DA DA 5 5 5 B B B N 1 2.26 0.30 108.30 110.56 A A A O4' C1' N9 DA DA DA 6 6 6 A A A N 1 -5.02 0.80 102.40 97.38 A A A C3' C2' C1' DC DC DC 10 10 10 N 1 2.15 0.30 108.30 110.45 A A A O4' C1' N9 DG DG DG 12 12 12 A A A N 1 1.94 0.30 108.30 110.24 A A A O4' C1' N9 DG DG DG 12 12 12 B B B N 1 8.17 0.30 108.30 116.47 B B B O4' C1' N9 DG DG DG 3 3 3 A A A N 1 2.81 0.30 108.30 111.11 B B B O4' C1' N9 DG DG DG 3 3 3 B B B N 1 -4.46 0.70 108.00 103.54 B B B O4' C1' N9 DA DA DA 4 4 4 N 1 3.41 0.30 108.30 111.71 B B B O4' C1' N9 DA DA DA 6 6 6 N 1 3.03 0.30 108.30 111.33 B B B O4' C1' N1 DC DC DC 10 10 10 N 1 A A O3' P DC DG 11 12 0.169 0.012 1.607 1.776 A Y 1 A A O3' P DC DG 11 12 0.181 0.012 1.607 1.788 B Y 1 A B O O HOH HOH 270 1078 1.07 1_555 1_655 1 A B O O HOH HOH 254 1055 1.30 1_555 1_545 1 A B O O HOH HOH 268 1079 1.79 1_555 1_664 1 A B O O HOH HOH 249 1111 1.94 1_555 1_545 -0.2315 -1.9032 0.7312 1.5877 0.3666 -1.3562 0.1490 0.1397 0.1401 0.920 23.330 4695 46920 5.10 81.74 0.10 1 1.98 SAD 15.14 0.47 0.80 ML FLAT BULK SOLVENT MODEL 42.295 0.439 0.920 23.330 197 922 237 488 0 0.011 1050 1.620 1572 34.206 338 0.074 134 0.017 59 0.3264 0.2866 0.9305 88 1572 45.00 0.2910 0.2697 0.9414 116 2133 60.00 0.2969 0.2642 0.9529 143 2743 75.00 0.2756 0.2504 0.9650 149 2817 80.00 0.2312 0.2157 0.9777 142 2890 81.00 0.2629 0.2046 0.9911 157 2956 82.00 0.2218 0.1955 1.0052 146 2834 80.00 0.2175 0.1824 1.0202 156 2788 81.00 0.1964 0.1802 1.0362 131 2910 78.00 0.1948 0.1664 1.0532 156 2721 79.00 0.1820 0.1530 1.0713 156 3082 85.00 0.1612 0.1470 1.0908 156 3040 85.00 0.1522 0.1409 1.1118 173 3029 87.00 0.1746 0.1354 1.1345 165 3079 85.00 0.1443 0.1297 1.1592 192 2952 84.00 0.1507 0.1253 1.1861 174 2895 82.00 0.1398 0.1234 1.2158 150 2681 76.00 0.1276 0.1196 1.2487 170 3184 88.00 0.1467 0.1141 1.2854 157 3076 87.00 0.1195 0.1062 1.3269 204 3108 88.00 0.1321 0.1073 1.3743 167 3142 88.00 0.1351 0.1073 1.4293 153 3130 87.00 0.1324 0.1042 1.4944 190 2856 81.00 0.1286 0.1150 1.5731 145 3048 85.00 0.1122 0.1197 1.6717 172 3226 90.00 0.1357 0.1237 1.8007 171 3103 88.00 0.1502 0.1319 1.9818 122 3153 87.00 0.1521 0.1390 2.2684 142 2904 81.00 0.1553 0.1604 2.8571 197 3157 90.00 0.1494 0.1524 23.3378 155 3110 86.00 0.92 36 4E1U 46920 -1 -1 0.030 0.030 1 20.0 3.9 82.7 data collection Blu-Ice phasing SHELXD refinement PHENIX (phenix.refine: 1.7.3_928) data reduction XDS data scaling SCALA [Ru(bpy)2 dppz]2+ bound to DNA 1 N N 1 N N 2 N N 2 N N 2 N N 2 N N 2 N N 3 N N 3 N N 4 N N 4 N N metalc 2.934 A DG 2 A O6 DG 2 1_555 A BA 106 H BA BA 1_555 metalc 2.780 A A DG 3 A O6 DG 3 1_555 A BA 106 H BA BA 1_555 metalc 3.203 B A DG 3 A O6 DG 3 1_555 A BA 106 H BA BA 1_555 metalc 3.118 A BA 106 H BA BA 1_555 A HOH 209 J O HOH 1_555 metalc 2.669 A BA 106 H BA BA 1_555 A HOH 244 J O HOH 1_555 metalc 3.020 A BA 106 H BA BA 1_555 B HOH 1085 K O HOH 1_555 metalc 2.811 A BA 106 H BA BA 1_555 B HOH 1102 K O HOH 1_555 metalc 2.976 B B DG 2 B O6 DG 2 1_555 B BA 101 I BA BA 1_555 metalc 3.123 A B DG 2 B O6 DG 2 1_555 B BA 101 I BA BA 1_555 metalc 2.904 B BA 101 I BA BA 1_555 B HOH 1004 K O HOH 1_555 metalc 2.542 B BA 101 I BA BA 1_555 B HOH 1024 K O HOH 1_555 metalc 3.129 B BA 101 I BA BA 1_555 B HOH 1033 K O HOH 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 12 B N1 DG 12 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 12 B O6 DG 12 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 12 B N2 DG 12 1_555 hydrog DG-DA MISPAIR A A DG 2 A N2 DG 2 1_555 A DA 4 A N1 DA 4 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 B DC 11 B N3 DC 11 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B DC 11 B O2 DC 11 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B DC 11 B N4 DC 11 1_555 hydrog DG-DA MISPAIR A A A DG 3 A N2 DG 3 1_555 A DA 4 A N1 DA 4 1_555 hydrog WATSON-CRICK A A DG 3 A N1 DG 3 1_555 B DC 10 B N3 DC 10 1_555 hydrog WATSON-CRICK A A DG 3 A N2 DG 3 1_555 B DC 10 B O2 DC 10 1_555 hydrog WATSON-CRICK A A DG 3 A O6 DG 3 1_555 B DC 10 B N4 DC 10 1_555 hydrog DA-DC MISPAIR A A DA 4 A N6 DA 4 1_555 B DC 11 B O2 DC 11 1_555 hydrog WATSON-CRICK A A DA 5 A N1 DA 5 1_555 B DT 8 B N3 DT 8 1_555 hydrog WATSON-CRICK A A DA 5 A N6 DA 5 1_555 B DT 8 B O4 DT 8 1_555 hydrog WATSON-CRICK A A A DA 6 A N1 DA 6 1_555 B DT 7 B N3 DT 7 1_555 hydrog WATSON-CRICK A A A DA 6 A N6 DA 6 1_555 B DT 7 B O4 DT 7 1_555 hydrog DA-DA MISPAIR A A DA 6 A N3 DA 6 1_555 B DA 9 B N6 DA 9 1_555 hydrog WATSON-CRICK A A DT 7 A N3 DT 7 1_555 B DA 6 B N1 DA 6 1_555 hydrog WATSON-CRICK A A DT 7 A O4 DT 7 1_555 B DA 6 B N6 DA 6 1_555 hydrog WATSON-CRICK A A DT 8 A N3 DT 8 1_555 B DA 5 B N1 DA 5 1_555 hydrog WATSON-CRICK A A DT 8 A O4 DT 8 1_555 B DA 5 B N6 DA 5 1_555 hydrog DA-DA MISPAIR A DA 9 A N6 DA 9 1_555 B DA 6 B N3 DA 6 1_555 hydrog WATSON-CRICK A A DC 10 A N3 DC 10 1_555 B DG 3 B N1 DG 3 1_555 hydrog WATSON-CRICK A A DC 10 A N4 DC 10 1_555 B DG 3 B O6 DG 3 1_555 hydrog WATSON-CRICK A A DC 10 A O2 DC 10 1_555 B DG 3 B N2 DG 3 1_555 hydrog WATSON-CRICK A A DC 11 A N3 DC 11 1_555 B DG 2 B N1 DG 2 1_555 hydrog WATSON-CRICK A A DC 11 A N4 DC 11 1_555 B DG 2 B O6 DG 2 1_555 hydrog WATSON-CRICK A A DC 11 A O2 DC 11 1_555 B DG 2 B N2 DG 2 1_555 hydrog DC-DA MISPAIR A DC 11 A O2 DC 11 1_555 B DA 4 B N6 DA 4 1_555 hydrog DG-DA MISPAIR A B DG 2 B N2 DG 2 1_555 B DA 4 B N1 DA 4 1_555 hydrog DG-DA MISPAIR A B DG 3 B N2 DG 3 1_555 B DA 4 B N1 DA 4 1_555 DNA Mismatch, Small molecule, DNA 4E1U PDB 1 4E1U CGGAAATTACCG 1 12 4E1U 1 12 4E1U A 1 1 12 1 12 4E1U 1 12 4E1U B 1 1 12 BINDING SITE FOR RESIDUE R1Z A 103 A R1Z 103 Software 9 BINDING SITE FOR RESIDUE R1Z A 102 A R1Z 102 Software 10 BINDING SITE FOR RESIDUE R1Z A 101 A R1Z 101 Software 13 BINDING SITE FOR RESIDUE BA A 106 A BA 106 Software 6 BINDING SITE FOR RESIDUE R1Z A 105 A R1Z 105 Software 10 BINDING SITE FOR RESIDUE R1Z A 104 A R1Z 104 Software 9 BINDING SITE FOR RESIDUE BA B 101 B BA 101 Software 6 A DA 6 A DA 6 9 1_555 A DT 7 A DT 7 9 1_555 A DT 8 A DT 8 9 1_555 A DA 9 A DA 9 9 1_555 B DG 3 B DG 3 9 1_545 B DA 6 B DA 6 9 1_555 B DT 7 B DT 7 9 1_555 B DT 8 B DT 8 9 1_555 B DA 9 B DA 9 9 1_555 A DC 1 A DC 1 10 1_655 A DG 3 A DG 3 10 1_555 A DA 4 A DA 4 10 1_555 A DA 5 A DA 5 10 1_555 A DA 6 A DA 6 10 1_555 A DG 12 A DG 12 10 1_546 B DT 8 B DT 8 10 1_555 B DA 9 B DA 9 10 1_555 B DC 10 B DC 10 10 1_555 B DC 11 B DC 11 10 1_555 A DC 1 A DC 1 13 1_555 A DG 2 A DG 2 13 1_555 A DG 3 A DG 3 13 1_555 A DA 4 A DA 4 13 1_555 A DC 10 A DC 10 13 1_456 A DG 12 A DG 12 13 1_446 A R1Z 105 G R1Z 13 1_446 A HOH 217 J HOH 13 1_456 A HOH 224 J HOH 13 1_555 A HOH 246 J HOH 13 1_456 B DC 1 B DC 1 13 1_446 B DC 11 B DC 11 13 1_555 B DG 12 B DG 12 13 1_555 A DG 2 A DG 2 6 1_555 A DG 3 A DG 3 6 1_555 A DG 12 A DG 12 6 1_446 A HOH 244 J HOH 6 1_555 B HOH 1085 K HOH 6 1_555 B HOH 1102 K HOH 6 1_555 A DC 1 A DC 1 10 1_664 A DA 9 A DA 9 10 1_565 A DC 10 A DC 10 10 1_565 A DC 11 A DC 11 10 1_555 A R1Z 101 C R1Z 10 1_664 B DG 2 B DG 2 10 1_555 B DG 3 B DG 3 10 1_555 B DA 4 B DA 4 10 1_555 B DG 12 B DG 12 10 1_664 B HOH 1004 K HOH 10 1_555 A DT 8 A DT 8 9 1_555 A DA 9 A DA 9 9 1_555 A DC 10 A DC 10 9 1_555 A DC 11 A DC 11 9 1_555 B DG 3 B DG 3 9 1_555 B DA 4 B DA 4 9 1_555 B DA 5 B DA 5 9 1_555 B DA 6 B DA 6 9 1_555 B DG 12 B DG 12 9 1_564 B DG 2 B DG 2 6 1_555 B HOH 1004 K HOH 6 1_555 B HOH 1007 K HOH 6 1_655 B HOH 1024 K HOH 6 1_555 B HOH 1054 K HOH 6 1_555 B HOH 1083 K HOH 6 1_655 1 P 1