0.039401 0.000000 0.000000 0.000000 0.024830 0.000000 0.000000 0.000000 0.015289 0.00000 0.00000 0.00000 Yin, Y.W. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 25.380 40.274 65.405 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 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 Mg 2 24.305 MAGNESIUM ION 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 N 86 N N N 87 N C N 88 N O N 89 N N N 90 N C N 91 N N N 92 N C N 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 Y 120 N N Y 121 N C Y 122 N N Y 123 N C N 124 N C N 125 N O N 126 N N N 127 N C N 128 N N N 129 N N Y 130 N C 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 P N 147 N O N 148 N O N 149 N O N 150 N C N 151 R C N 152 N O N 153 S C N 154 N O N 155 N C N 156 R C N 157 N N N 158 N C N 159 N O N 160 N N N 161 N C N 162 N O N 163 N C N 164 N C N 165 N C 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 H N 176 N H N 177 N H N 178 N H N 179 N H N 180 N H N 181 N O N 182 N H N 183 N H N 184 N MG 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 N 100 N sing N 101 N sing N 102 N doub N 103 N sing 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 doub N 115 N sing 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 Y 135 N sing Y 136 N sing Y 137 N doub N 138 N sing Y 139 N sing N 140 N sing Y 141 N doub N 142 N doub N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N doub N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N doub 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 doub N 177 N sing N 178 N sing N 179 N sing N 180 N doub N 181 N sing N 182 N sing N 183 N doub N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N sing N 189 N sing US Biochemistry BICHAW 0033 0006-2960 52 8590 8598 10.1021/bi400980c 24147911 Comparison of the structural and dynamic effects of 5-methylcytosine and 5-chlorocytosine in a CpG dinucleotide sequence. 2013 10.2210/pdb4mkw/pdb pdb_00004mkw Chirality error at C3' of 5CM B 15 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 CCD ADSC QUANTUM 315r SINGLE WAVELENGTH M x-ray 1 1.0 19-ID APS SYNCHROTRON APS BEAMLINE 19-ID 3677.419 5methylC DNA dodecamer 2 syn polymer 24.305 MAGNESIUM ION 1 syn non-polymer 18.015 water 193 nat water no yes (DC)(DG)(5CM)(DG)(DA)(DA)(DT)(DT)(DC)(DG)(DC)(DG) CGCGAATTCGCG A,B polydeoxyribonucleotide n n n n n n n n n n n n 2.27 45.87 EVAPORATION 7 hanging drop, pH 7, EVAPORATION, temperature 290K 290 2.127 1 19 A 1 B 24 -0.863 A_DC1:DG24_B 1 -13.864 0.232 0.214 -0.178 8.194 1 19 A 2 B 23 -2.363 A_DG2:DC23_B 2 -12.514 -0.256 0.518 -0.199 -3.083 1 19 A 3 B 22 0.386 A_5CM3:DG22_B 3 -8.050 0.205 0.178 -0.117 12.999 1 19 A 4 B 21 -0.045 A_DG4:DC21_B 4 -8.258 -0.268 0.020 -0.178 5.752 1 20 A 5 B 20 2.757 A_DA5:DT20_B 5 -14.732 0.028 -0.055 -0.119 1.255 1 20 A 6 B 19 3.665 A_DA6:DT19_B 6 -16.824 0.023 0.131 -0.137 -1.010 1 20 A 7 B 18 3.244 A_DT7:DA18_B 7 -16.286 -0.039 0.087 -0.123 -1.560 1 20 A 8 B 17 3.587 A_DT8:DA17_B 8 -12.457 -0.074 -0.006 -0.174 -12.540 1 19 A 9 B 16 -2.210 A_DC9:DG16_B 9 -8.036 0.203 0.078 -0.150 4.984 1 19 A 10 B 15 2.741 A_DG10:5CM15_B 10 -6.693 -0.160 0.186 -0.102 1.967 1 19 A 11 B 14 -2.687 A_DC11:DG14_B 11 -16.061 0.117 0.155 -0.240 8.907 1 19 A 12 B 13 -9.793 A_DG12:DC13_B 12 25.520 -0.139 -0.554 -0.484 3.074 35.104 A A 1 2 9.369 B B 24 23 3.100 5.621 -0.155 0.061 AA_DC1DG2:DC23DG24_BB 1 -3.013 5.022 34.538 -0.699 -0.172 3.516 43.699 A A 2 3 -11.648 B B 23 22 3.646 -8.608 0.665 0.576 AA_DG25CM3:DG22DC23_BB 2 3.898 -5.274 42.714 1.687 -0.479 2.966 26.734 A A 3 4 24.206 B B 22 21 3.001 10.876 -0.270 0.567 AA_5CM3DG4:DC21DG22_BB 3 0.905 -2.014 24.442 -1.472 0.809 3.379 38.523 A A 4 5 4.719 B B 21 20 3.389 3.110 -0.268 -0.054 AA_DG4DA5:DT20DC21_BB 4 -0.616 0.934 38.397 -0.481 0.327 3.236 36.716 A A 5 6 2.130 B B 20 19 3.257 1.341 0.064 -0.356 AA_DA5DA6:DT19DT20_BB 5 -1.643 2.610 36.657 -0.746 -0.325 3.279 32.457 A A 6 7 -3.799 B B 19 18 3.247 -2.122 0.037 -0.607 AA_DA6DT7:DA18DT19_BB 6 0.653 -1.170 32.383 -0.714 0.048 3.211 34.676 A A 7 8 -3.104 B B 18 17 3.199 -1.849 -0.071 -0.396 AA_DT7DT8:DA17DA18_BB 7 1.177 -1.977 34.609 -0.387 0.296 3.497 42.557 A A 8 9 -3.034 B B 17 16 3.491 -2.201 -0.192 -0.259 AA_DT8DC9:DG16DA17_BB 8 0.484 -0.667 42.500 -0.120 0.316 2.993 25.329 A A 9 10 7.924 B B 16 15 3.001 3.460 0.693 0.627 AA_DC9DG10:5CM15DG16_BB 9 -2.055 4.707 25.013 0.505 -2.130 3.333 43.670 A A 10 11 -10.984 B B 15 14 3.406 -8.122 -1.221 0.503 AA_DG10DC11:DG145CM15_BB 10 -2.882 3.898 42.852 1.487 1.354 3.361 38.570 A A 11 12 -16.723 B B 14 13 3.639 -10.902 0.334 0.555 AA_DC11DG12:DC13DG14_BB 11 1.904 -2.920 37.006 2.315 -0.249 chem_comp_atom chem_comp_bond database_2 pdbx_struct_conn_angle struct_conn struct_site repository Initial release Database references Data collection Database references Derived calculations 1 0 2013-11-06 1 1 2013-12-11 1 2 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_seq_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Different modification of the same DNA. RCSB Y RCSB 2013-09-05 REL REL MG MAGNESIUM ION HOH water synthetic DNA oligos sample MG 25 2 MG MG 101 A HOH 1 3 HOH HOH 201 A HOH 3 3 HOH HOH 202 A HOH 4 3 HOH HOH 203 A HOH 7 3 HOH HOH 204 A HOH 8 3 HOH HOH 205 A HOH 9 3 HOH HOH 206 A HOH 11 3 HOH HOH 207 A HOH 12 3 HOH HOH 208 A HOH 13 3 HOH HOH 209 A HOH 14 3 HOH HOH 210 A HOH 18 3 HOH HOH 211 A HOH 21 3 HOH HOH 212 A HOH 22 3 HOH HOH 213 A HOH 23 3 HOH HOH 214 A HOH 25 3 HOH HOH 215 A HOH 26 3 HOH HOH 216 A HOH 27 3 HOH HOH 217 A HOH 28 3 HOH HOH 218 A HOH 30 3 HOH HOH 219 A HOH 31 3 HOH HOH 220 A HOH 32 3 HOH HOH 221 A HOH 36 3 HOH HOH 222 A HOH 38 3 HOH HOH 223 A HOH 40 3 HOH HOH 224 A HOH 41 3 HOH HOH 225 A HOH 42 3 HOH HOH 226 A HOH 43 3 HOH HOH 227 A HOH 45 3 HOH HOH 228 A HOH 47 3 HOH HOH 229 A HOH 48 3 HOH HOH 230 A HOH 49 3 HOH HOH 231 A HOH 53 3 HOH HOH 232 A HOH 54 3 HOH HOH 233 A HOH 57 3 HOH HOH 234 A HOH 58 3 HOH HOH 235 A HOH 61 3 HOH HOH 236 A HOH 62 3 HOH HOH 237 A HOH 64 3 HOH HOH 238 A HOH 65 3 HOH HOH 239 A HOH 70 3 HOH HOH 240 A HOH 71 3 HOH HOH 241 A HOH 73 3 HOH HOH 242 A HOH 75 3 HOH HOH 243 A HOH 77 3 HOH HOH 244 A HOH 78 3 HOH HOH 245 A HOH 79 3 HOH HOH 246 A HOH 80 3 HOH HOH 247 A HOH 82 3 HOH HOH 248 A HOH 83 3 HOH HOH 249 A HOH 85 3 HOH HOH 250 A HOH 86 3 HOH HOH 251 A HOH 89 3 HOH HOH 252 A HOH 91 3 HOH HOH 253 A HOH 93 3 HOH HOH 254 A HOH 94 3 HOH HOH 255 A HOH 95 3 HOH HOH 256 A HOH 99 3 HOH HOH 257 A HOH 101 3 HOH HOH 258 A HOH 107 3 HOH HOH 259 A HOH 108 3 HOH HOH 260 A HOH 110 3 HOH HOH 261 A HOH 111 3 HOH HOH 262 A HOH 112 3 HOH HOH 263 A HOH 115 3 HOH HOH 264 A HOH 116 3 HOH HOH 265 A HOH 117 3 HOH HOH 266 A HOH 118 3 HOH HOH 267 A HOH 120 3 HOH HOH 268 A HOH 121 3 HOH HOH 269 A HOH 122 3 HOH HOH 270 A HOH 123 3 HOH HOH 271 A HOH 124 3 HOH HOH 272 A HOH 126 3 HOH HOH 273 A HOH 127 3 HOH HOH 274 A HOH 128 3 HOH HOH 275 A HOH 129 3 HOH HOH 276 A HOH 131 3 HOH HOH 277 A HOH 134 3 HOH HOH 278 A HOH 135 3 HOH HOH 279 A HOH 136 3 HOH HOH 280 A HOH 138 3 HOH HOH 281 A HOH 139 3 HOH HOH 282 A HOH 141 3 HOH HOH 283 A HOH 142 3 HOH HOH 284 A HOH 143 3 HOH HOH 285 A HOH 145 3 HOH HOH 286 A HOH 147 3 HOH HOH 287 A HOH 148 3 HOH HOH 288 A HOH 149 3 HOH HOH 289 A HOH 153 3 HOH HOH 290 A HOH 157 3 HOH HOH 291 A HOH 158 3 HOH HOH 292 A HOH 162 3 HOH HOH 293 A HOH 163 3 HOH HOH 294 A HOH 168 3 HOH HOH 295 A HOH 169 3 HOH HOH 296 A HOH 170 3 HOH HOH 297 A HOH 171 3 HOH HOH 298 A HOH 172 3 HOH HOH 299 A HOH 175 3 HOH HOH 300 A HOH 178 3 HOH HOH 301 A HOH 179 3 HOH HOH 302 A HOH 181 3 HOH HOH 303 A HOH 182 3 HOH HOH 304 A HOH 186 3 HOH HOH 305 A HOH 188 3 HOH HOH 306 A HOH 189 3 HOH HOH 307 A HOH 191 3 HOH HOH 308 A HOH 192 3 HOH HOH 309 A HOH 193 3 HOH HOH 310 A HOH 2 3 HOH HOH 101 B HOH 5 3 HOH HOH 102 B HOH 6 3 HOH HOH 103 B HOH 10 3 HOH HOH 104 B HOH 15 3 HOH HOH 105 B HOH 16 3 HOH HOH 106 B HOH 17 3 HOH HOH 107 B HOH 19 3 HOH HOH 108 B HOH 20 3 HOH HOH 109 B HOH 24 3 HOH HOH 110 B HOH 29 3 HOH HOH 111 B HOH 33 3 HOH HOH 112 B HOH 34 3 HOH HOH 113 B HOH 35 3 HOH HOH 114 B HOH 37 3 HOH HOH 115 B HOH 39 3 HOH HOH 116 B HOH 44 3 HOH HOH 117 B HOH 46 3 HOH HOH 118 B HOH 50 3 HOH HOH 119 B HOH 51 3 HOH HOH 120 B HOH 52 3 HOH HOH 121 B HOH 55 3 HOH HOH 122 B HOH 56 3 HOH HOH 123 B HOH 59 3 HOH HOH 124 B HOH 60 3 HOH HOH 125 B HOH 63 3 HOH HOH 126 B HOH 66 3 HOH HOH 127 B HOH 67 3 HOH HOH 128 B HOH 68 3 HOH HOH 129 B HOH 69 3 HOH HOH 130 B HOH 72 3 HOH HOH 131 B HOH 74 3 HOH HOH 132 B HOH 76 3 HOH HOH 133 B HOH 81 3 HOH HOH 134 B HOH 84 3 HOH HOH 135 B HOH 87 3 HOH HOH 136 B HOH 88 3 HOH HOH 137 B HOH 90 3 HOH HOH 138 B HOH 92 3 HOH HOH 139 B HOH 96 3 HOH HOH 140 B HOH 97 3 HOH HOH 141 B HOH 98 3 HOH HOH 142 B HOH 100 3 HOH HOH 143 B HOH 102 3 HOH HOH 144 B HOH 103 3 HOH HOH 145 B HOH 104 3 HOH HOH 146 B HOH 105 3 HOH HOH 147 B HOH 106 3 HOH HOH 148 B HOH 109 3 HOH HOH 149 B HOH 113 3 HOH HOH 150 B HOH 114 3 HOH HOH 151 B HOH 119 3 HOH HOH 152 B HOH 125 3 HOH HOH 153 B HOH 130 3 HOH HOH 154 B HOH 132 3 HOH HOH 155 B HOH 133 3 HOH HOH 156 B HOH 137 3 HOH HOH 157 B HOH 140 3 HOH HOH 158 B HOH 144 3 HOH HOH 159 B HOH 146 3 HOH HOH 160 B HOH 150 3 HOH HOH 161 B HOH 151 3 HOH HOH 162 B HOH 152 3 HOH HOH 163 B HOH 154 3 HOH HOH 164 B HOH 155 3 HOH HOH 165 B HOH 156 3 HOH HOH 166 B HOH 159 3 HOH HOH 167 B HOH 160 3 HOH HOH 168 B HOH 161 3 HOH HOH 169 B HOH 164 3 HOH HOH 170 B HOH 165 3 HOH HOH 171 B HOH 166 3 HOH HOH 172 B HOH 167 3 HOH HOH 173 B HOH 173 3 HOH HOH 174 B HOH 174 3 HOH HOH 175 B HOH 176 3 HOH HOH 176 B HOH 177 3 HOH HOH 177 B HOH 180 3 HOH HOH 178 B HOH 183 3 HOH HOH 179 B HOH 184 3 HOH HOH 180 B HOH 185 3 HOH HOH 181 B HOH 187 3 HOH HOH 182 B HOH 190 3 HOH HOH 183 B DC 1 n 1 DC 1 A DG 2 n 2 DG 2 A 5CM 3 n 3 5CM 3 A DG 4 n 4 DG 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 DC 9 n 9 DC 9 A DG 10 n 10 DG 10 A DC 11 n 11 DC 11 A DG 12 n 12 DG 12 A DC 13 n 1 DC 13 B DG 14 n 2 DG 14 B 5CM 15 n 3 5CM 15 B DG 16 n 4 DG 16 B DA 17 n 5 DA 17 B DA 18 n 6 DA 18 B DT 19 n 7 DT 19 B DT 20 n 8 DT 20 B DC 21 n 9 DC 21 B DG 22 n 10 DG 22 B DC 23 n 11 DC 23 B DG 24 n 12 DG 24 B 0.1275 0.1388 0.5881 0.6043 -0.9972 1.5483 0.0896 0.0407 -0.0097 0.0763 0.0944 0.1500 -0.0977 -0.0297 -0.0970 0.1691 0.0145 0.0056 0.1760 0.0075 0.1810 refined 10.4426 0.8733 24.0836 X-RAY DIFFRACTION X-RAY DIFFRACTION 1 all author_and_software_defined_assembly PISA 2 dimeric 2360 2 4350 A HOH 211 D O HOH 1_555 A MG 101 C MG MG 1_555 A HOH 263 D O HOH 1_555 91.3 A HOH 211 D O HOH 1_555 A MG 101 C MG MG 1_555 B HOH 108 E O HOH 1_555 91.6 A HOH 263 D O HOH 1_555 A MG 101 C MG MG 1_555 B HOH 108 E O HOH 1_555 91.6 A HOH 211 D O HOH 1_555 A MG 101 C MG MG 1_555 B HOH 109 E O HOH 1_555 176.6 A HOH 263 D O HOH 1_555 A MG 101 C MG MG 1_555 B HOH 109 E O HOH 1_555 87.0 B HOH 108 E O HOH 1_555 A MG 101 C MG MG 1_555 B HOH 109 E O HOH 1_555 85.5 A HOH 211 D O HOH 1_555 A MG 101 C MG MG 1_555 B HOH 150 E O HOH 1_555 91.6 A HOH 263 D O HOH 1_555 A MG 101 C MG MG 1_555 B HOH 150 E O HOH 1_555 86.6 B HOH 108 E O HOH 1_555 A MG 101 C MG MG 1_555 B HOH 150 E O HOH 1_555 176.4 B HOH 109 E O HOH 1_555 A MG 101 C MG MG 1_555 B HOH 150 E O HOH 1_555 91.3 A HOH 211 D O HOH 1_555 A MG 101 C MG MG 1_555 B HOH 152 E O HOH 1_555 89.0 A HOH 263 D O HOH 1_555 A MG 101 C MG MG 1_555 B HOH 152 E O HOH 1_555 177.1 B HOH 108 E O HOH 1_555 A MG 101 C MG MG 1_555 B HOH 152 E O HOH 1_555 91.2 B HOH 109 E O HOH 1_555 A MG 101 C MG MG 1_555 B HOH 152 E O HOH 1_555 92.9 B HOH 150 E O HOH 1_555 A MG 101 C MG MG 1_555 B HOH 152 E O HOH 1_555 90.5 A 5CM 3 A 5CM 3 DC B 5CM 15 B 5CM 3 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 B C3' 5CM 15 PLANAR 1 A B O O HOH HOH 268 171 1.85 1 A A OP1 O DC HOH 11 265 1.86 1 B B O O HOH HOH 131 139 1.92 1 A A O O HOH HOH 241 296 2.04 1 B B O O HOH HOH 174 176 2.05 1 A A O O HOH HOH 213 297 2.06 1 B B O O HOH HOH 153 176 2.07 1 B B O O HOH HOH 117 171 2.08 1 A A OP1 O DG HOH 10 296 2.09 1 A A OP1 O DG HOH 12 246 2.09 1 B B OP2 O DG HOH 14 140 2.15 1 A A O O HOH HOH 249 297 2.16 1 A A O O HOH HOH 295 304 2.16 1 A A O O HOH HOH 256 258 2.16 1 B B OP2 O DT HOH 20 165 2.16 1 B B O5' O DG HOH 22 162 2.17 1 -4.99 0.70 108.00 103.01 A A A O4' C1' N1 DC DC DC 9 9 9 N 1 -5.13 0.80 102.40 97.27 A A A C3' C2' C1' DG DG DG 10 10 10 N 1 2.53 0.30 108.30 110.83 A A A O4' C1' N9 DG DG DG 10 10 10 N 1 -5.51 0.70 108.00 102.49 A A A O4' C1' N1 DC DC DC 11 11 11 N 1 -5.13 0.70 108.00 102.87 A A A O4' C1' N9 DG DG DG 12 12 12 N 1 3.41 0.30 108.30 111.71 B B B O4' C1' N9 DG DG DG 16 16 16 N 1 -4.95 0.70 108.00 103.05 B B B O4' C1' N9 DA DA DA 17 17 17 N 1 -5.45 0.70 108.00 102.55 B B B O4' C1' N1 DT DT DT 20 20 20 N 1 A B O O HOH HOH 300 183 1.81 1_555 3_645 1 A A O O HOH HOH 294 295 2.09 1_555 3_555 0.2400 0.2101 0.2132 1.219 9.586 1736 17417 17380 9.99 84.24 0.14 10% random 1 1.36 MOLECULAR REPLACEMENT 26.64 0.90 1.11 ML FLAT BULK SOLVENT MODEL 1.219 9.586 193 682 1 488 0 0.009 546 2.070 840 31.262 230 0.282 92 0.022 26 0.3594 0.3406 1.2549 63 571 38.00 0.3261 0.3223 1.2953 95 844 56.00 0.3112 0.3065 1.3415 129 1173 76.00 0.2724 0.2756 1.3951 162 1451 95.00 0.2715 0.2480 1.4584 166 1499 99.00 0.2512 0.2373 1.5350 171 1530 99.00 0.2272 0.2141 1.6307 165 1513 99.00 0.1970 0.1864 1.7559 169 1523 99.00 0.2193 0.1900 1.9313 173 1557 100.00 0.2021 0.1836 2.2078 171 1546 100.00 0.2394 0.1969 2.7704 174 1555 98.00 0.2859 0.2307 9.5866 98 882 53.00 1.219 10 4MKW 17417 17380 2.0 2.0 1 99 refinement PHENIX (phenix.refine: 1.8.2_1309) Comparison of the structural and dynamic effects of 5-methylcytosine and 5-chlorocytosine in a CpG dinucleotide sequence 1 N N 1 N N 2 N N 3 N N 3 N N covale 1.607 both A DG 2 A O3' DG 2 1_555 A 5CM 3 A P 5CM 3 1_555 covale 1.603 both A 5CM 3 A O3' 5CM 3 1_555 A DG 4 A P DG 4 1_555 covale 1.601 both B DG 14 B O3' DG 2 1_555 B 5CM 15 B P 5CM 3 1_555 covale 1.602 both B 5CM 15 B O3' 5CM 3 1_555 B DG 16 B P DG 4 1_555 metalc 2.156 A MG 101 C MG MG 1_555 A HOH 211 D O HOH 1_555 metalc 2.034 A MG 101 C MG MG 1_555 A HOH 263 D O HOH 1_555 metalc 2.076 A MG 101 C MG MG 1_555 B HOH 108 E O HOH 1_555 metalc 2.130 A MG 101 C MG MG 1_555 B HOH 109 E O HOH 1_555 metalc 2.051 A MG 101 C MG MG 1_555 B HOH 150 E O HOH 1_555 metalc 2.120 A MG 101 C MG MG 1_555 B HOH 152 E O HOH 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 5CM 3 A N3 5CM 3 1_555 B DG 22 B N1 DG 10 1_555 hydrog WATSON-CRICK A 5CM 3 A N4 5CM 3 1_555 B DG 22 B O6 DG 10 1_555 hydrog WATSON-CRICK A 5CM 3 A O2 5CM 3 1_555 B DG 22 B N2 DG 10 1_555 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 B DC 21 B N3 DC 9 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B DC 21 B O2 DC 9 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 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 DG 16 B N1 DG 4 1_555 hydrog WATSON-CRICK A DC 9 A N4 DC 9 1_555 B DG 16 B O6 DG 4 1_555 hydrog WATSON-CRICK A DC 9 A O2 DC 9 1_555 B DG 16 B N2 DG 4 1_555 hydrog WATSON-CRICK A DG 10 A N1 DG 10 1_555 B 5CM 15 B N3 5CM 3 1_555 hydrog WATSON-CRICK A DG 10 A N2 DG 10 1_555 B 5CM 15 B O2 5CM 3 1_555 hydrog WATSON-CRICK A DG 10 A O6 DG 10 1_555 B 5CM 15 B N4 5CM 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 Modified DNA dodecamer, DNA 4MKW PDB 1 4MKW 1 12 4MKW 1 12 4MKW A 1 1 12 13 24 4MKW 13 24 4MKW B 1 1 12 BINDING SITE FOR RESIDUE MG A 101 A MG 101 Software 6 A HOH 211 D HOH 6 1_555 A HOH 263 D HOH 6 1_555 B HOH 108 E HOH 6 1_555 B HOH 109 E HOH 6 1_555 B HOH 150 E HOH 6 1_555 B HOH 152 E HOH 6 1_555 19 P 21 21 21