0.039223 0.000000 0.000000 0.000000 0.024752 0.000000 0.000000 0.000000 0.015267 0.000000 0.000000 0.000000 Spingler, B. Renciuk, D. Vorlickova, M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 25.495 40.400 65.500 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 UK Nucleic Acids Res. NARHAD 0389 0305-1048 41 9891 9900 10.1093/nar/gkt738 23963698 Crystal structures of B-DNA dodecamer containing the epigenetic modifications 5-hydroxymethylcytosine or 5-methylcytosine. 2013 10.2210/pdb4gju/pdb pdb_00004gju 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 100 1 PIXEL 2012-06-09 DECTRIS PILATUS 2M-F BARTELS MONOCHROMATOR SINGLE WAVELENGTH M x-ray 1 1.00067 1.0 X06DA SLS 1.00067 1.00067 SYNCHROTRON SLS BEAMLINE X06DA 3677.419 5-Methylcytosine modified DNA oligomer 2 syn polymer 24.305 MAGNESIUM ION 1 syn non-polymer 18.015 water 127 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 1 2.29 46.36 VAPOR DIFFUSION, HANGING DROP 6.0 0.04M sodium cacodylate buffer, 0.08M NaCl, 0.02M MgCl2, 0.012M spermine tetra hydrochloride, 35% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K 298.0 1.824 1 19 A 1 B 12 -1.765 A_DC1:DG12_B 1 -13.698 0.228 0.245 -0.167 8.159 1 19 A 2 B 11 -2.717 A_DG2:DC11_B 2 -11.627 -0.199 0.564 -0.219 -4.155 1 19 A 3 B 10 -1.925 A_5CM3:DG10_B 3 -5.561 0.214 0.159 -0.200 13.808 1 19 A 4 B 9 -0.559 A_DG4:DC9_B 4 -5.754 -0.249 0.083 -0.149 5.846 1 20 A 5 B 8 3.232 A_DA5:DT8_B 5 -14.928 0.014 -0.090 -0.090 1.037 1 20 A 6 B 7 4.986 A_DA6:DT7_B 6 -17.577 0.056 0.066 -0.125 -2.397 1 20 A 7 B 6 4.151 A_DT7:DA6_B 7 -14.622 -0.107 0.132 -0.072 -0.801 1 20 A 8 B 5 3.387 A_DT8:DA5_B 8 -12.259 -0.067 -0.081 -0.107 -13.053 1 19 A 9 B 4 -1.703 A_DC9:DG4_B 9 -7.174 0.239 0.077 -0.085 6.158 1 19 A 10 B 3 2.941 A_DG10:5CM3_B 10 -7.471 -0.159 0.272 -0.074 4.620 1 19 A 11 B 2 -2.512 A_DC11:DG2_B 11 -16.929 0.144 0.180 -0.268 6.854 1 19 A 12 B 1 -1.895 A_DG12:DC1_B 12 -4.308 -0.230 0.265 -0.132 3.083 35.614 A A 1 2 8.565 B B 12 11 3.118 5.214 -0.106 -0.004 AA_DC1DG2:DC11DG12_BB 1 -3.227 5.301 35.099 -0.731 -0.275 3.518 43.508 A A 2 3 -10.607 B B 11 10 3.624 -7.812 0.567 0.520 AA_DG25CM3:DG10DC11_BB 2 4.201 -5.704 42.637 1.534 -0.317 2.946 26.181 A A 3 4 21.656 B B 10 9 2.964 9.589 -0.231 0.503 AA_5CM3DG4:DC9DG10_BB 3 -0.071 0.160 24.390 -1.324 0.493 3.416 38.206 A A 4 5 3.791 B B 9 8 3.434 2.480 -0.280 -0.080 AA_DG4DA5:DT8DC9_BB 4 0.846 -1.294 38.119 -0.449 0.539 3.241 37.266 A A 5 6 3.107 B B 8 7 3.267 1.984 0.093 -0.329 AA_DA5DA6:DT7DT8_BB 5 -1.211 1.896 37.196 -0.777 -0.305 3.324 31.571 A A 6 7 -4.154 B B 7 6 3.291 -2.258 0.021 -0.591 AA_DA6DT7:DA6DT7_BB 6 -0.323 0.594 31.490 -0.661 -0.099 3.149 34.904 A A 7 8 -2.516 B B 6 5 3.143 -1.508 -0.081 -0.435 AA_DT7DT8:DA5DA6_BB 7 2.042 -3.406 34.815 -0.505 0.432 3.507 43.274 A A 8 9 -3.032 B B 5 4 3.499 -2.235 -0.177 -0.223 AA_DT8DC9:DG4DA5_BB 8 -0.326 0.442 43.217 -0.069 0.206 2.913 25.243 A A 9 10 9.842 B B 4 3 2.970 4.270 0.680 0.552 AA_DC9DG10:5CM3DG4_BB 9 -3.186 7.344 24.683 0.130 -2.402 3.274 43.161 A A 10 11 -12.290 B B 3 2 3.352 -8.974 -1.283 0.441 AA_DG10DC11:DG25CM3_BB 10 -2.949 4.039 42.163 1.503 1.447 3.248 34.603 A A 11 12 6.862 B B 2 1 3.228 4.072 -0.028 0.362 AA_DC11DG12:DC1DG2_BB 11 -0.292 0.493 34.368 -0.015 0.002 chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model pdbx_struct_conn_angle struct_conn struct_site repository Initial release Database references Database references Data collection Database references Derived calculations Refinement description 1 0 2013-08-28 1 1 2013-09-04 1 2 2013-12-04 1 3 2023-09-13 _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 RCSB Y RCSB 2012-08-10 REL REL MG MAGNESIUM ION HOH water 32630 Synthetic DNA sample 1DPN PDB ENTRY 1DPN PDB experimental model MO6 51 2 MG MG 101 A MO6 51 3 HOH HOH 201 A MO6 51 3 HOH HOH 202 A HOH 101 3 HOH HOH 203 A HOH 102 3 HOH HOH 204 A HOH 104 3 HOH HOH 205 A HOH 106 3 HOH HOH 206 A HOH 107 3 HOH HOH 207 A HOH 108 3 HOH HOH 208 A HOH 109 3 HOH HOH 209 A HOH 110 3 HOH HOH 210 A HOH 111 3 HOH HOH 211 A HOH 112 3 HOH HOH 212 A HOH 115 3 HOH HOH 213 A HOH 116 3 HOH HOH 214 A HOH 118 3 HOH HOH 215 A HOH 119 3 HOH HOH 216 A HOH 121 3 HOH HOH 217 A HOH 122 3 HOH HOH 218 A HOH 128 3 HOH HOH 219 A HOH 129 3 HOH HOH 220 A HOH 132 3 HOH HOH 221 A HOH 134 3 HOH HOH 222 A HOH 136 3 HOH HOH 223 A HOH 140 3 HOH HOH 224 A HOH 144 3 HOH HOH 225 A HOH 145 3 HOH HOH 226 A HOH 148 3 HOH HOH 227 A HOH 151 3 HOH HOH 228 A HOH 152 3 HOH HOH 229 A HOH 156 3 HOH HOH 230 A HOH 161 3 HOH HOH 231 A HOH 162 3 HOH HOH 232 A HOH 163 3 HOH HOH 233 A HOH 164 3 HOH HOH 234 A HOH 166 3 HOH HOH 235 A HOH 168 3 HOH HOH 236 A HOH 170 3 HOH HOH 237 A HOH 174 3 HOH HOH 238 A HOH 176 3 HOH HOH 239 A HOH 177 3 HOH HOH 240 A HOH 178 3 HOH HOH 241 A HOH 179 3 HOH HOH 242 A HOH 180 3 HOH HOH 243 A HOH 181 3 HOH HOH 244 A HOH 182 3 HOH HOH 245 A HOH 183 3 HOH HOH 246 A HOH 184 3 HOH HOH 247 A HOH 185 3 HOH HOH 248 A HOH 186 3 HOH HOH 249 A HOH 187 3 HOH HOH 250 A HOH 189 3 HOH HOH 251 A HOH 192 3 HOH HOH 252 A HOH 193 3 HOH HOH 253 A HOH 194 3 HOH HOH 254 A HOH 195 3 HOH HOH 255 A HOH 196 3 HOH HOH 256 A HOH 197 3 HOH HOH 257 A HOH 200 3 HOH HOH 258 A HOH 201 3 HOH HOH 259 A HOH 205 3 HOH HOH 260 A HOH 206 3 HOH HOH 261 A HOH 210 3 HOH HOH 262 A HOH 212 3 HOH HOH 263 A HOH 213 3 HOH HOH 264 A HOH 214 3 HOH HOH 265 A HOH 215 3 HOH HOH 266 A HOH 216 3 HOH HOH 267 A HOH 220 3 HOH HOH 268 A HOH 221 3 HOH HOH 269 A MO6 51 3 HOH HOH 101 B MO6 51 3 HOH HOH 102 B MO6 51 3 HOH HOH 103 B MO6 51 3 HOH HOH 104 B HOH 103 3 HOH HOH 105 B HOH 105 3 HOH HOH 106 B HOH 113 3 HOH HOH 107 B HOH 114 3 HOH HOH 108 B HOH 117 3 HOH HOH 109 B HOH 120 3 HOH HOH 110 B HOH 123 3 HOH HOH 111 B HOH 124 3 HOH HOH 112 B HOH 125 3 HOH HOH 113 B HOH 126 3 HOH HOH 114 B HOH 127 3 HOH HOH 115 B HOH 130 3 HOH HOH 116 B HOH 131 3 HOH HOH 117 B HOH 133 3 HOH HOH 118 B HOH 135 3 HOH HOH 119 B HOH 137 3 HOH HOH 120 B HOH 138 3 HOH HOH 121 B HOH 139 3 HOH HOH 122 B HOH 141 3 HOH HOH 123 B HOH 142 3 HOH HOH 124 B HOH 143 3 HOH HOH 125 B HOH 146 3 HOH HOH 126 B HOH 147 3 HOH HOH 127 B HOH 149 3 HOH HOH 128 B HOH 150 3 HOH HOH 129 B HOH 153 3 HOH HOH 130 B HOH 154 3 HOH HOH 131 B HOH 155 3 HOH HOH 132 B HOH 157 3 HOH HOH 133 B HOH 158 3 HOH HOH 134 B HOH 159 3 HOH HOH 135 B HOH 160 3 HOH HOH 136 B HOH 165 3 HOH HOH 137 B HOH 167 3 HOH HOH 138 B HOH 169 3 HOH HOH 139 B HOH 171 3 HOH HOH 140 B HOH 172 3 HOH HOH 141 B HOH 173 3 HOH HOH 142 B HOH 175 3 HOH HOH 143 B HOH 188 3 HOH HOH 144 B HOH 190 3 HOH HOH 145 B HOH 191 3 HOH HOH 146 B HOH 198 3 HOH HOH 147 B HOH 199 3 HOH HOH 148 B HOH 202 3 HOH HOH 149 B HOH 203 3 HOH HOH 150 B HOH 204 3 HOH HOH 151 B HOH 207 3 HOH HOH 152 B HOH 208 3 HOH HOH 153 B HOH 209 3 HOH HOH 154 B HOH 211 3 HOH HOH 155 B HOH 217 3 HOH HOH 156 B HOH 218 3 HOH HOH 157 B HOH 219 3 HOH HOH 158 B C 1 n 1 DC 1 A G 2 n 2 DG 2 A 5CM 3 n 3 5CM 3 A G 4 n 4 DG 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 1 n 1 DC 1 B G 2 n 2 DG 2 B 5CM 3 n 3 5CM 3 B G 4 n 4 DG 4 B A 5 n 5 DA 5 B A 6 n 6 DA 6 B T 7 n 7 DT 7 B T 8 n 8 DT 8 B C 9 n 9 DC 9 B G 10 n 10 DG 10 B C 11 n 11 DC 11 B G 12 n 12 DG 12 B 0.176 0.178 0.174 0.177 0.210 0.215 1145 1235 5.010 5.013 22852 author_and_software_defined_assembly PISA 2 dimeric 2380 3 4330 A HOH 201 D O HOH 1_555 A MG 101 C MG MG 1_555 A HOH 202 D O HOH 1_555 90.3 A HOH 201 D O HOH 1_555 A MG 101 C MG MG 1_555 B HOH 101 E O HOH 1_555 92.1 A HOH 202 D O HOH 1_555 A MG 101 C MG MG 1_555 B HOH 101 E O HOH 1_555 94.4 A HOH 201 D O HOH 1_555 A MG 101 C MG MG 1_555 B HOH 102 E O HOH 1_555 176.4 A HOH 202 D O HOH 1_555 A MG 101 C MG MG 1_555 B HOH 102 E O HOH 1_555 88.2 B HOH 101 E O HOH 1_555 A MG 101 C MG MG 1_555 B HOH 102 E O HOH 1_555 84.8 A HOH 201 D O HOH 1_555 A MG 101 C MG MG 1_555 B HOH 103 E O HOH 1_555 91.1 A HOH 202 D O HOH 1_555 A MG 101 C MG MG 1_555 B HOH 103 E O HOH 1_555 84.3 B HOH 101 E O HOH 1_555 A MG 101 C MG MG 1_555 B HOH 103 E O HOH 1_555 176.5 B HOH 102 E O HOH 1_555 A MG 101 C MG MG 1_555 B HOH 103 E O HOH 1_555 92.0 A HOH 201 D O HOH 1_555 A MG 101 C MG MG 1_555 B HOH 104 E O HOH 1_555 92.0 A HOH 202 D O HOH 1_555 A MG 101 C MG MG 1_555 B HOH 104 E O HOH 1_555 171.6 B HOH 101 E O HOH 1_555 A MG 101 C MG MG 1_555 B HOH 104 E O HOH 1_555 93.7 B HOH 102 E O HOH 1_555 A MG 101 C MG MG 1_555 B HOH 104 E O HOH 1_555 90.0 B HOH 103 E O HOH 1_555 A MG 101 C MG MG 1_555 B HOH 104 E O HOH 1_555 87.5 A 5CM 3 A 5CM 3 DC B 5CM 3 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 -4.77 0.70 108.00 103.23 A A A O4' C1' N1 DC DC DC 1 1 1 N 1 -5.40 0.70 108.00 102.60 A A A O4' C1' N9 DG DG DG 2 2 2 N 1 8.76 1.20 119.70 128.46 A A A C3' O3' P DG DG DA 4 4 5 Y 1 -5.86 0.70 108.00 102.14 A A A O4' C1' N9 DA DA DA 5 5 5 N 1 4.21 0.60 118.60 122.81 A A A C6 N1 C2 DA DA DA 5 5 5 N 1 -3.89 0.50 117.70 113.81 A A A C5 C6 N1 DA DA DA 5 5 5 N 1 8.26 1.20 119.70 127.96 A A A C3' O3' P DA DA DA 5 5 6 Y 1 -5.69 0.70 108.00 102.31 A A A O4' C1' N9 DA DA DA 6 6 6 N 1 3.32 0.50 117.00 120.32 A A A C4 C5 C6 DA DA DA 6 6 6 N 1 -4.61 0.70 108.00 103.39 A A A O4' C1' N1 DT DT DT 7 7 7 N 1 -6.34 0.70 108.00 101.66 A A A O4' C1' N1 DT DT DT 8 8 8 N 1 -3.83 0.60 122.30 118.47 A A A N3 C2 O2 DT DT DT 8 8 8 N 1 9.29 1.40 114.30 123.59 A A A N1 C1' C2' DC DC DC 9 9 9 N 1 -10.13 0.70 108.00 97.87 A A A O4' C1' N1 DC DC DC 9 9 9 N 1 -3.59 0.40 121.90 118.31 A A A N3 C4 C5 DC DC DC 9 9 9 N 1 3.04 0.50 117.40 120.44 A A A C4 C5 C6 DC DC DC 9 9 9 N 1 -6.46 0.80 102.40 95.94 A A A C3' C2' C1' DG DG DG 10 10 10 N 1 2.21 0.30 108.30 110.51 A A A O4' C1' N9 DG DG DG 10 10 10 N 1 -4.04 0.60 125.10 121.06 A A A C6 N1 C2 DG DG DG 10 10 10 N 1 9.60 1.40 114.30 123.90 A A A N1 C1' C2' DC DC DC 11 11 11 N 1 -8.45 0.70 108.00 99.55 A A A O4' C1' N1 DC DC DC 11 11 11 N 1 -2.43 0.40 120.30 117.87 A A A C6 N1 C2 DC DC DC 11 11 11 N 1 -3.97 0.50 119.90 115.93 A A A C2 N3 C4 DC DC DC 11 11 11 N 1 4.79 0.70 110.30 115.09 A A A C1' O4' C4' DG DG DG 12 12 12 N 1 -5.68 0.70 108.00 102.32 A A A O4' C1' N9 DG DG DG 12 12 12 N 1 3.52 0.40 121.90 125.42 B B B N3 C4 C5 DC DC DC 1 1 1 N 1 -3.10 0.50 117.40 114.30 B B B C4 C5 C6 DC DC DC 1 1 1 N 1 11.33 1.50 119.60 130.93 B B B OP1 P OP2 DG DG DG 2 2 2 N 1 -10.99 1.60 120.90 109.91 B B B P O5' C5' DG DG DG 2 2 2 N 1 2.92 0.30 108.30 111.22 B B B O4' C1' N9 DG DG DG 4 4 4 N 1 10.63 1.20 119.70 130.33 B B B C3' O3' P DG DG DA 4 4 5 Y 1 -9.66 0.70 108.00 98.34 B B B O4' C1' N9 DA DA DA 5 5 5 N 1 -6.35 0.70 108.00 101.65 B B B O4' C1' N9 DA DA DA 6 6 6 N 1 7.45 1.20 119.70 127.15 B B B C3' O3' P DA DA DT 6 6 7 Y 1 -5.93 0.70 108.00 102.07 B B B O4' C1' N1 DT DT DT 7 7 7 N 1 -5.22 0.80 105.90 100.68 B B B O4' C1' C2' DT DT DT 8 8 8 N 1 11.27 1.40 114.30 125.57 B B B N1 C1' C2' DT DT DT 8 8 8 N 1 -10.86 0.70 108.00 97.14 B B B O4' C1' N1 DT DT DT 8 8 8 N 1 -9.60 1.60 120.90 111.30 B B B P O5' C5' DC DC DC 9 9 9 N 1 -6.59 0.70 108.00 101.41 B B B O4' C1' N1 DC DC DC 9 9 9 N 1 -3.58 0.40 120.30 116.72 B B B C6 N1 C2 DC DC DC 9 9 9 N 1 4.12 0.50 119.90 124.02 B B B C2 N3 C4 DC DC DC 9 9 9 N 1 -4.62 0.40 121.90 117.28 B B B N3 C4 C5 DC DC DC 9 9 9 N 1 3.27 0.50 121.00 124.27 B B B C5 C6 N1 DC DC DC 9 9 9 N 1 -6.60 0.80 102.40 95.80 B B B C3' C2' C1' DG DG DG 10 10 10 N 1 -2.88 0.40 105.40 102.52 B B B N9 C4 C5 DG DG DG 10 10 10 N 1 -3.54 0.40 104.50 100.96 B B B O4' C4' C3' DC DC DC 11 11 11 N 1 -8.56 0.70 108.00 99.44 B B B O4' C1' N1 DC DC DC 11 11 11 N 1 -6.94 0.70 108.00 101.06 B B B O4' C1' N9 DG DG DG 12 12 12 N 1 A A O4' C1' DC DC 9 9 0.087 0.011 1.420 1.507 N 1 A A O4' C1' DC DC 11 11 0.075 0.011 1.420 1.495 N 1 B B O4' C1' DT DT 8 8 0.073 0.011 1.420 1.493 N 1 B B O4' C1' DG DG 12 12 0.067 0.011 1.420 1.487 N 0.215 0.177 0.178 0.177 1.412 40.4 4907 1235 24635 22852 10677 5.013 92.8 RANDOM 1 FREE R 4 2 MOLECULAR REPLACEMENT PDB ENTRY 1DPN KLOSTERMAN & SINES 0 0. 611.0 1.412 40.4 127 616 1 488 0 0.0183 0.0388 0.0000 0.0636 0.0000 0.0156 0.0141 0.0120 0.0262 0.0000 1.412 40.40 4GJU 24635 22852 4 2 1 30.59 3.61 92.8 1.412 1.50 8.12 3958 1 3.72 97.1 data collection RemDAq phasing PHASER refinement SHELXL-97 data reduction XDS data scaling XDS 5-Methylcytosine modified DNA oligomer 1 N N 1 N N 2 N N 3 N N 3 N N covale 1.571 both A DG 2 A O3' DG 2 1_555 A 5CM 3 A P 5CM 3 1_555 covale 1.562 both A 5CM 3 A O3' 5CM 3 1_555 A DG 4 A P DG 4 1_555 covale 1.628 both B DG 2 B O3' DG 2 1_555 B 5CM 3 B P 5CM 3 1_555 covale 1.577 both B 5CM 3 B O3' 5CM 3 1_555 B DG 4 B P DG 4 1_555 metalc 2.075 A MG 101 C MG MG 1_555 A HOH 201 D O HOH 1_555 metalc 2.058 A MG 101 C MG MG 1_555 A HOH 202 D O HOH 1_555 metalc 2.036 A MG 101 C MG MG 1_555 B HOH 101 E O HOH 1_555 metalc 2.055 A MG 101 C MG MG 1_555 B HOH 102 E O HOH 1_555 metalc 2.069 A MG 101 C MG MG 1_555 B HOH 103 E O HOH 1_555 metalc 2.022 A MG 101 C MG MG 1_555 B HOH 104 E 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 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 WATSON-CRICK A 5CM 3 A N3 5CM 3 1_555 B DG 10 B N1 DG 10 1_555 hydrog WATSON-CRICK A 5CM 3 A N4 5CM 3 1_555 B DG 10 B O6 DG 10 1_555 hydrog WATSON-CRICK A 5CM 3 A O2 5CM 3 1_555 B DG 10 B N2 DG 10 1_555 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 B DC 9 B N3 DC 9 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B DC 9 B O2 DC 9 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 B DC 9 B N4 DC 9 1_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 B DT 8 B N3 DT 8 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 B DT 8 B O4 DT 8 1_555 hydrog WATSON-CRICK A DA 6 A N1 DA 6 1_555 B DT 7 B N3 DT 7 1_555 hydrog WATSON-CRICK A DA 6 A N6 DA 6 1_555 B DT 7 B O4 DT 7 1_555 hydrog WATSON-CRICK A DT 7 A N3 DT 7 1_555 B DA 6 B N1 DA 6 1_555 hydrog WATSON-CRICK A DT 7 A O4 DT 7 1_555 B DA 6 B N6 DA 6 1_555 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 B DA 5 B N1 DA 5 1_555 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 B DA 5 B N6 DA 5 1_555 hydrog WATSON-CRICK A DC 9 A N3 DC 9 1_555 B DG 4 B N1 DG 4 1_555 hydrog WATSON-CRICK A DC 9 A N4 DC 9 1_555 B DG 4 B O6 DG 4 1_555 hydrog WATSON-CRICK A DC 9 A O2 DC 9 1_555 B DG 4 B N2 DG 4 1_555 hydrog WATSON-CRICK A DG 10 A N1 DG 10 1_555 B 5CM 3 B N3 5CM 3 1_555 hydrog WATSON-CRICK A DG 10 A N2 DG 10 1_555 B 5CM 3 B O2 5CM 3 1_555 hydrog WATSON-CRICK A DG 10 A O6 DG 10 1_555 B 5CM 3 B N4 5CM 3 1_555 hydrog WATSON-CRICK A DC 11 A N3 DC 11 1_555 B DG 2 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 11 A N4 DC 11 1_555 B DG 2 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 11 A O2 DC 11 1_555 B DG 2 B N2 DG 2 1_555 hydrog WATSON-CRICK A DG 12 A N1 DG 12 1_555 B DC 1 B N3 DC 1 1_555 hydrog WATSON-CRICK A DG 12 A N2 DG 12 1_555 B DC 1 B O2 DC 1 1_555 hydrog WATSON-CRICK A DG 12 A O6 DG 12 1_555 B DC 1 B N4 DC 1 1_555 DNA double-stranded B-DNA, 5-Methylcytosine, epigenetics, DNA 4GJU PDB 1 4GJU 1 12 4GJU 1 12 4GJU A 1 1 12 1 12 4GJU 1 12 4GJU B 1 1 12 BINDING SITE FOR RESIDUE MG A 101 A MG 101 Software 6 A HOH 201 D HOH 6 1_555 A HOH 202 D HOH 6 1_555 B HOH 101 E HOH 6 1_555 B HOH 102 E HOH 6 1_555 B HOH 103 E HOH 6 1_555 B HOH 104 E HOH 6 1_555 19 P 21 21 21