0.040795 0.000000 0.000000 0.000000 0.024037 0.000000 0.000000 0.000000 0.015141 0.00000 0.00000 0.00000 Spingler, B. Renciuk, D. Vorlickova, M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 24.513 41.602 66.044 C10 H16 N3 O8 P 337.223 n 2'-deoxy-5-(hydroxymethyl)cytidine 5'-(dihydrogen phosphate) 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 N 1 N P N 2 N O N 3 N O N 4 N O N 5 N C N 6 R C N 7 N O N 8 S C N 9 N O N 10 N C N 11 R C N 12 N N N 13 N C N 14 N O N 15 N N N 16 N C N 17 N N N 18 N C N 19 N C N 20 N O N 21 N C N 22 N O 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 H N 39 N O N 40 N P N 41 N O N 42 N O N 43 N O N 44 N C N 45 R C N 46 N O N 47 S C N 48 N O N 49 N C N 50 R C Y 51 N N Y 52 N C Y 53 N N Y 54 N C Y 55 N C N 56 N N Y 57 N N Y 58 N C Y 59 N N Y 60 N C 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 H N 75 N O N 76 N P N 77 N O N 78 N O N 79 N O N 80 N C N 81 R C N 82 N O N 83 S C N 84 N O N 85 N C N 86 R C N 87 N N N 88 N C N 89 N O N 90 N N N 91 N C N 92 N N N 93 N C N 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 Y 121 N N Y 122 N C Y 123 N N Y 124 N C N 125 N C N 126 N O N 127 N N N 128 N C N 129 N N N 130 N N Y 131 N C 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 H N 146 N O N 147 N P N 148 N O N 149 N O N 150 N O N 151 N C N 152 R C N 153 N O N 154 S C N 155 N O N 156 N C N 157 R C N 158 N N N 159 N C N 160 N O N 161 N N N 162 N C N 163 N O N 164 N C N 165 N C N 166 N C 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 H N 182 N O N 183 N H N 184 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N doub 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 doub N 13 N sing N 14 N sing N 15 N doub N 16 N sing N 17 N doub 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 sing 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 sing N 42 N doub 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 Y 63 N sing Y 64 N sing Y 65 N doub N 66 N sing Y 67 N sing Y 68 N sing Y 69 N doub N 70 N sing Y 71 N doub N 72 N sing N 73 N sing Y 74 N sing Y 75 N doub N 76 N sing Y 77 N sing N 78 N sing N 79 N sing N 80 N doub 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 sing N 103 N doub N 104 N sing N 105 N doub N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N doub 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 Y 136 N sing Y 137 N sing Y 138 N doub N 139 N sing Y 140 N sing N 141 N sing Y 142 N doub N 143 N doub N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N doub N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N doub N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N doub 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 doub N 185 N sing N 186 N sing N 187 N sing N 188 N sing N 189 N sing N 190 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/pdb4glc/pdb pdb_00004glc 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 BARTELS MONOCHROMATOR SINGLE WAVELENGTH M x-ray 1 1.00067 1.0 X06DA SLS 1.00067 SYNCHROTRON SLS BEAMLINE X06DA 3693.418 DNA (5'-D(*CP*GP*(5HC)P*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') 2 syn polymer 18.015 water 40 nat water no yes (DC)(DG)(5HC)(DG)(DA)(DA)(DT)(DT)(DC)(DG)(DC)(DG) CGXGAATTCGCG A,B polydeoxyribonucleotide n n n n n n n n n n n n 1 1.98 46.04 7.0 0.04M sodium cacodylate buffer, 0.08M sodium chloride, 0.012M spermine tetra hydrochloride, 30% MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K 293 5.148 1 19 A 1 B 12 -0.440 A_DC1:DG12_B 1 12.788 0.153 -0.660 -0.239 -12.471 1 19 A 2 B 11 -5.540 A_DG2:DC11_B 2 -16.269 -0.320 0.413 -0.233 7.422 1 19 A 4 B 9 0.225 A_DG4:DC9_B 3 -6.877 -0.192 0.030 -0.140 5.553 1 20 A 5 B 8 0.997 A_DA5:DT8_B 4 -16.534 0.013 0.002 -0.141 4.367 1 20 A 6 B 7 4.571 A_DA6:DT7_B 5 -17.190 0.299 0.163 -0.098 0.287 1 20 A 7 B 6 2.958 A_DT7:DA6_B 6 -15.979 0.061 0.032 -0.088 0.636 1 20 A 8 B 5 4.124 A_DT8:DA5_B 7 -17.388 0.098 -0.160 -0.144 -13.463 1 19 A 9 B 4 -0.283 A_DC9:DG4_B 8 -9.727 0.297 -0.077 -0.145 4.279 1 19 A 11 B 2 -2.869 A_DC11:DG2_B 9 -18.864 0.285 0.333 -0.162 20.815 1 19 A 12 B 1 0.318 A_DG12:DC1_B 10 -4.207 -0.423 0.552 -0.201 3.974 39.707 A A 1 2 -26.358 B B 12 11 4.078 -17.191 -1.367 -0.195 AA_DC1DG2:DC11DG12_BB 1 -9.014 13.820 34.808 2.357 0.626 6.314 69.093 A A 2 4 10.453 B B 11 9 6.393 11.809 -0.120 -0.017 AA_DG2DG4:DC9DC11_BB 2 1.842 -1.631 68.179 -0.862 0.238 3.369 35.622 A A 4 5 -2.645 B B 9 8 3.368 -1.618 0.026 -0.099 AA_DG4DA5:DT8DC9_BB 3 1.010 -1.652 35.572 0.080 0.109 3.195 40.349 A A 5 6 -1.734 B B 8 7 3.199 -1.195 0.172 -0.293 AA_DA5DA6:DT7DT8_BB 4 -1.877 2.723 40.290 -0.294 -0.456 3.380 32.163 A A 6 7 -5.178 B B 7 6 3.346 -2.865 0.030 -0.554 AA_DA6DT7:DA6DT7_BB 5 1.231 -2.226 32.016 -0.472 0.172 3.133 35.906 A A 7 8 -0.518 B B 6 5 3.135 -0.319 0.066 -0.297 AA_DT7DT8:DA5DA6_BB 6 2.808 -4.560 35.798 -0.438 0.278 3.533 41.737 A A 8 9 -0.738 B B 5 4 3.532 -0.526 -0.078 -0.156 AA_DT8DC9:DG4DA5_BB 7 0.258 -0.362 41.733 -0.159 0.139 6.238 70.398 A A 9 11 -3.524 B B 4 2 6.265 -4.060 -0.295 0.512 AA_DC9DC11:DG2DG4_BB 8 -3.168 2.750 70.234 0.717 0.043 3.003 31.357 A A 11 12 -2.430 B B 2 1 3.088 -1.312 1.302 0.506 AA_DC11DG12:DC1DG2_BB 9 -1.464 2.711 31.297 1.167 -2.665 chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model struct_conn 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 _struct_conn.pdbx_leaving_atom_flag RCSB Y RCSB 2012-08-14 REL REL HOH water 32630 Synthetic construct sample 1DPN PDB ENTRY 1DPN PDB experimental model HOH 102 2 HOH HOH 101 A HOH 103 2 HOH HOH 102 A HOH 104 2 HOH HOH 103 A HOH 106 2 HOH HOH 104 A HOH 111 2 HOH HOH 105 A HOH 114 2 HOH HOH 106 A HOH 115 2 HOH HOH 107 A HOH 117 2 HOH HOH 108 A HOH 121 2 HOH HOH 109 A HOH 124 2 HOH HOH 110 A HOH 126 2 HOH HOH 111 A HOH 128 2 HOH HOH 112 A HOH 130 2 HOH HOH 113 A HOH 134 2 HOH HOH 114 A HOH 137 2 HOH HOH 115 A HOH 138 2 HOH HOH 116 A HOH 101 2 HOH HOH 101 B HOH 105 2 HOH HOH 102 B HOH 107 2 HOH HOH 103 B HOH 108 2 HOH HOH 104 B HOH 109 2 HOH HOH 105 B HOH 110 2 HOH HOH 106 B HOH 112 2 HOH HOH 107 B HOH 113 2 HOH HOH 108 B HOH 116 2 HOH HOH 109 B HOH 118 2 HOH HOH 110 B HOH 119 2 HOH HOH 111 B HOH 120 2 HOH HOH 112 B HOH 122 2 HOH HOH 113 B HOH 123 2 HOH HOH 114 B HOH 125 2 HOH HOH 115 B HOH 127 2 HOH HOH 116 B HOH 129 2 HOH HOH 117 B HOH 131 2 HOH HOH 118 B HOH 132 2 HOH HOH 119 B HOH 133 2 HOH HOH 120 B HOH 135 2 HOH HOH 121 B HOH 136 2 HOH HOH 122 B HOH 139 2 HOH HOH 123 B HOH 140 2 HOH HOH 124 B DC 1 n 1 DC 1 A DG 2 n 2 DG 2 A 5HC 3 n 3 5HC 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 1 n 1 DC 1 B DG 2 n 2 DG 2 B 5HC 3 n 3 5HC 3 B DG 4 n 4 DG 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 DC 9 n 9 DC 9 B DG 10 n 10 DG 10 B DC 11 n 11 DC 11 B DG 12 n 12 DG 12 B 0.244 0.251 0.225 0.233 0.298 0.306 400 435 7.052 7.015 5672 author_and_software_defined_assembly PISA 2 dimeric 1170 -5 4550 A 5HC 3 A 5HC 3 DC B 5HC 3 B 5HC 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 -5.17 0.70 108.00 102.83 A A A O4' C1' N9 DG DG DG 2 2 2 N 1 -5.10 0.70 108.00 102.90 A A A O4' C1' N9 DA DA DA 6 6 6 N 1 -5.62 0.70 108.00 102.38 A A A O4' C1' N1 DT DT DT 8 8 8 N 1 -7.53 0.70 108.00 100.47 A A A O4' C1' N1 DC DC DC 9 9 9 N 1 -7.16 0.80 102.40 95.24 A A A C3' C2' C1' DG DG DG 10 10 10 N 1 -5.26 0.70 108.00 102.74 A A A O4' C1' N1 DC DC DC 11 11 11 N 1 -3.87 0.60 118.90 115.03 B B B N1 C2 O2 DC DC DC 1 1 1 N 1 -5.80 0.70 108.00 102.20 B B B O4' C1' N9 DA DA DA 6 6 6 N 1 -6.74 0.70 108.00 101.26 B B B O4' C1' N1 DT DT DT 8 8 8 N 1 8.54 1.40 114.30 122.84 B B B N1 C1' C2' DC DC DC 9 9 9 N 1 -7.29 0.70 108.00 100.71 B B B O4' C1' N1 DC DC DC 9 9 9 N 1 -5.74 0.80 102.40 96.66 B B B C3' C2' C1' DG DG DG 10 10 10 N 0.306 0.233 0.251 0.233 1.831 35.2 2123 435 6201 6119 2406 7.015 97.5 RANDOM 1 FREE R 0.0 MOLECULAR REPLACEMENT PDB ENTRY 1DPN ENGH AND HUBER 0 0.00 528.60 1.831 35.2 40 530 0 490 0 0.007 0.028 0.000 0.012 0.000 0.006 0.008 0.000 0.070 0.000 1.831 41.60 4GLC 6201 0.034 0.021 1 24.06 3.68 97.5 0.216 1.831 1.94 6.65 1 3.62 96.6 data collection RemDAq phasing PHASER refinement SHELXL-97 data reduction XDS data scaling XDS DNA dodecamer containing 5-hydroxymethyl-cytosine 1 N N 1 N N 2 N N 2 N N covale 1.609 both A DG 2 A O3' DG 2 1_555 A 5HC 3 A P 5HC 3 1_555 covale 1.613 both A 5HC 3 A O3' 5HC 3 1_555 A DG 4 A P DG 4 1_555 covale 1.615 both B DG 2 B O3' DG 2 1_555 B 5HC 3 B P 5HC 3 1_555 covale 1.603 both B 5HC 3 B O3' 5HC 3 1_555 B DG 4 B P DG 4 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 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 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 B-DNA dodecamer, epigenetics, 5-hydroxymethyl cytosine, DNA 4GLC PDB 1 4GLC 1 12 4GLC 1 12 4GLC A 1 1 12 1 12 4GLC 1 12 4GLC B 1 1 12 19 P 21 21 21