0.039849 0.000000 0.000000 -0.000000 0.024110 0.000000 0.000000 -0.000000 0.015223 0.00000 0.00000 0.00000 Szulik, M.W. Pallan, P. Egli, M. Stone, M.P. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 25.095 41.476 65.692 C10 H14 N3 O8 P 335.207 n 5-FORMYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE 2'-DEOXY-5-FORMYLCYTIDINE-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 N 1 N P N 2 N O N 3 N O N 4 N O N 5 N N N 6 N C N 7 N C N 8 N O N 9 N N N 10 N C N 11 N N N 12 N C N 13 N C N 14 N C N 15 R C N 16 N O N 17 R C N 18 S C N 19 N O N 20 N C N 21 N O 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 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 Y 49 N N Y 50 N C Y 51 N N Y 52 N C Y 53 N C N 54 N N Y 55 N N Y 56 N C Y 57 N N Y 58 N C 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 H N 73 N O N 74 N P N 75 N O N 76 N O N 77 N O N 78 N C N 79 R C N 80 N O N 81 S C N 82 N O N 83 N C N 84 R C N 85 N N N 86 N C N 87 N O N 88 N N N 89 N C N 90 N N N 91 N C N 92 N C N 93 N H 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 O N 108 N P N 109 N O N 110 N O N 111 N O N 112 N C N 113 R C N 114 N O N 115 S C N 116 N O N 117 N C N 118 R C Y 119 N N Y 120 N C Y 121 N N Y 122 N C N 123 N C N 124 N O N 125 N N N 126 N C N 127 N N N 128 N N Y 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 O N 145 N P N 146 N O N 147 N O N 148 N O N 149 N C N 150 R C N 151 N O N 152 S C N 153 N O N 154 N C N 155 R C N 156 N N N 157 N C N 158 N O N 159 N N N 160 N C N 161 N O N 162 N C N 163 N C N 164 N C N 165 N H 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 O N 181 N H N 182 N H N 1 N sing N 2 N doub N 3 N sing 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 doub N 11 N sing N 12 N doub N 13 N sing N 14 N doub 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 sing N 35 N doub N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N doub N 41 N sing 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 Y 61 N sing Y 62 N sing Y 63 N doub N 64 N sing Y 65 N sing Y 66 N sing Y 67 N doub N 68 N sing Y 69 N doub N 70 N sing N 71 N sing Y 72 N sing Y 73 N doub N 74 N sing Y 75 N sing N 76 N sing N 77 N sing N 78 N doub 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 N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N doub N 102 N sing N 103 N doub N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N doub N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N doub N 114 N sing 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 Y 134 N sing Y 135 N sing Y 136 N doub N 137 N sing Y 138 N sing N 139 N sing Y 140 N doub N 141 N doub N 142 N sing N 143 N sing N 144 N sing N 145 N sing N 146 N doub N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N doub N 153 N sing 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 doub N 176 N sing N 177 N sing N 178 N sing N 179 N doub N 180 N sing N 181 N sing N 182 N doub N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N sing US Biochemistry BICHAW 0033 0006-2960 54 1294 1305 10.1021/bi501534x 25632825 Differential stabilities and sequence-dependent base pair opening dynamics of watson-crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine. 2015 10.2210/pdb4qc7/pdb pdb_00004qc7 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 IMAGE PLATE 2014-04-10 MAR scanner 300 mm plate Si(111) SINGLE WAVELENGTH M x-ray 1 1.000 1.0 21-ID-D APS 1.000 SYNCHROTRON APS BEAMLINE 21-ID-D 3691.402 short DNA strands 2 syn polymer 18.015 water 17 nat water no yes (DC)(DG)(DC)(DG)(DA)(DA)(DT)(DT)(5FC)(DG)(DC)(DG) CGCGAATTCGCG A,B polydeoxyribonucleotide n n n n n n n n n n n n 1 2.32 46.88 VAPOR DIFFUSION, HANGING DROP 6.0 5% MPD, 20 mM Na Cacodylate, 6 mM Spermine tetra-HCl, 6 mM NaCl, 40 mM KCl , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K 291 2.144 1 19 A 1 B 24 0.810 A_DC1:DG24_B 1 -4.019 0.338 0.026 -0.144 0.256 1 19 A 2 B 23 -4.213 A_DG2:DC23_B 2 -10.889 -0.144 0.416 -0.204 0.830 1 19 A 3 B 22 0.118 A_DC3:DG22_B 3 -4.831 0.237 -0.051 -0.152 10.648 1 19 A 4 B 21 2.220 A_DG4:5FC21_B 4 -9.423 -0.327 -0.040 -0.078 5.610 1 20 A 5 B 20 0.772 A_DA5:DT20_B 5 -15.046 0.047 -0.145 -0.040 2.004 1 20 A 6 B 19 3.924 A_DA6:DT19_B 6 -16.463 -0.170 0.118 -0.136 0.152 1 20 A 7 B 18 4.420 A_DT7:DA18_B 7 -17.844 0.039 0.103 -0.030 -3.608 1 20 A 8 B 17 4.886 A_DT8:DA17_B 8 -15.476 0.035 0.008 -0.142 -10.262 1 19 A 9 B 16 -1.552 A_5FC9:DG16_B 9 -7.640 0.335 0.044 -0.129 3.816 1 19 A 10 B 15 2.595 A_DG10:DC15_B 10 -2.026 -0.348 0.133 -0.168 1.657 1 19 A 11 B 14 -1.651 A_DC11:DG14_B 11 -14.458 0.085 0.325 -0.237 4.178 1 19 A 12 B 13 -2.409 A_DG12:DC13_B 12 -1.164 -0.210 -0.084 -0.260 3.508 36.502 A A 1 2 -4.821 B B 24 23 3.390 -3.003 -0.982 -0.188 AA_DC1DG2:DC23DG24_BB 1 -6.061 9.730 35.891 0.142 0.677 3.388 39.056 A A 2 3 -2.956 B B 23 22 3.354 -1.972 0.653 0.163 AA_DG2DC3:DG22DC23_BB 2 3.850 -5.770 38.825 0.489 -0.497 3.218 28.769 A A 3 4 18.194 B B 22 21 3.223 8.895 -0.360 0.541 AA_DC3DG4:5FC21DG22_BB 3 1.160 -2.374 27.363 -0.925 0.988 3.395 34.069 A A 4 5 2.386 B B 21 20 3.410 1.397 -0.148 -0.234 AA_DG4DA5:DT205FC21_BB 4 0.603 -1.030 34.036 -0.630 0.352 3.240 37.786 A A 5 6 0.940 B B 20 19 3.249 0.608 -0.064 -0.289 AA_DA5DA6:DT19DT20_BB 5 -2.917 4.509 37.673 -0.525 -0.274 3.254 35.106 A A 6 7 -4.051 B B 19 18 3.229 -2.442 -0.053 -0.487 AA_DA6DT7:DA18DT19_BB 6 0.147 -0.244 35.023 -0.445 0.109 3.279 36.910 A A 7 8 -3.342 B B 18 17 3.278 -2.114 -0.068 -0.218 AA_DT7DT8:DA17DA18_BB 7 1.581 -2.499 36.819 -0.058 0.322 3.387 40.279 A A 8 9 -0.971 B B 17 16 3.384 -0.669 -0.012 -0.308 AA_DT85FC9:DG16DA17_BB 8 1.003 -1.457 40.262 -0.369 0.135 3.090 26.427 A A 9 10 6.754 B B 16 15 3.087 3.078 0.635 0.669 AA_5FC9DG10:DC15DG16_BB 9 -1.916 4.203 26.181 0.687 -1.873 3.385 43.400 A A 10 11 -8.978 B B 15 14 3.389 -6.607 -1.429 0.550 AA_DG10DC11:DG14DC15_BB 10 -3.964 5.386 42.743 1.413 1.531 3.444 35.897 A A 11 12 -2.906 B B 14 13 3.392 -1.785 0.977 0.805 AA_DC11DG12:DC13DG14_BB 11 4.634 -7.542 35.563 1.574 -0.889 chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model struct_conn repository Initial release Database references Data collection Database references Derived calculations Refinement description 1 0 2015-02-11 1 1 2015-02-25 1 2 2023-09-20 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag RCSB Y RCSB 2014-05-09 REL REL HOH water Chemically synthesized nucleic acid. sample 436D PDB ID 436D PDB experimental model HOH 1 2 HOH HOH 101 A HOH 3 2 HOH HOH 102 A HOH 4 2 HOH HOH 103 A HOH 5 2 HOH HOH 104 A HOH 8 2 HOH HOH 105 A HOH 23 2 HOH HOH 106 A HOH 24 2 HOH HOH 107 A HOH 2 2 HOH HOH 101 B HOH 6 2 HOH HOH 102 B HOH 7 2 HOH HOH 103 B HOH 9 2 HOH HOH 104 B HOH 15 2 HOH HOH 105 B HOH 20 2 HOH HOH 106 B HOH 21 2 HOH HOH 107 B HOH 22 2 HOH HOH 108 B HOH 27 2 HOH HOH 109 B HOH 28 2 HOH HOH 110 B DC 1 n 1 DC 1 A DG 2 n 2 DG 2 A DC 3 n 3 DC 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 5FC 9 n 9 5FC 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 DC 15 n 3 DC 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 5FC 21 n 9 5FC 21 B DG 22 n 10 DG 22 B DC 23 n 11 DC 23 B DG 24 n 12 DG 24 B author_and_software_defined_assembly PISA 2 dimeric 2410 3 4260 A 5FC 9 A 5FC 9 DC B 5FC 21 B 5FC 9 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 0.970 0.967 0.24529 0.22637 0.22767 1.90 35.07 413 5842 5362 7.2 99.35 4.094 0.117 RANDOM 1 THROUGHOUT 5 MOLECULAR REPLACEMENT 0.172 0.147 0.80 0.80 1.20 PDB ID 436D MAXIMUM LIKELIHOOD MASK 1.90 35.07 17 507 0 490 0 0.011 0.011 548 0.002 0.020 268 1.333 1.295 842 1.467 3.000 634 0.080 0.200 72 0.026 0.020 292 0.003 0.020 118 5.987 4.947 548 5.991 4.948 547 7.896 7.424 843 7.725 46.792 786 7.721 46.813 780 0.337 0.314 1.947 33 380 380 20 99.04 1.9 50 4QC7 5842 5801 0.064 1 60 10.2 99.3 0.738 1.90 1.93 3.25 1 6.7 100 data collection MD2 diffractometer software from EMBL (with LS-CAT developed extensions) phasing MOLREP refinement REFMAC 5.8.0069 data reduction HKL-2000 data scaling HKL-2000 Dodecamer structure of 5-formylcytosine containing DNA 1 N N 1 N N 2 N N 2 N N covale 1.588 both A DT 8 A O3' DT 8 1_555 A 5FC 9 A P 5FC 9 1_555 covale 1.589 both A 5FC 9 A O3' 5FC 9 1_555 A DG 10 A P DG 10 1_555 covale 1.588 both B DT 20 B O3' DT 8 1_555 B 5FC 21 B P 5FC 9 1_555 covale 1.607 both B 5FC 21 B O3' 5FC 9 1_555 B DG 22 B P DG 10 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 DC 3 A N3 DC 3 1_555 B DG 22 B N1 DG 10 1_555 hydrog WATSON-CRICK A DC 3 A N4 DC 3 1_555 B DG 22 B O6 DG 10 1_555 hydrog WATSON-CRICK A DC 3 A O2 DC 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 5FC 21 B N3 5FC 9 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B 5FC 21 B O2 5FC 9 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 B 5FC 21 B N4 5FC 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 5FC 9 A N3 5FC 9 1_555 B DG 16 B N1 DG 4 1_555 hydrog WATSON-CRICK A 5FC 9 A N4 5FC 9 1_555 B DG 16 B O6 DG 4 1_555 hydrog WATSON-CRICK A 5FC 9 A O2 5FC 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 DC 15 B N3 DC 3 1_555 hydrog WATSON-CRICK A DG 10 A N2 DG 10 1_555 B DC 15 B O2 DC 3 1_555 hydrog WATSON-CRICK A DG 10 A O6 DG 10 1_555 B DC 15 B N4 DC 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 double helix, B-form DNA, 5-formylcytosine, DNA 4QC7 PDB 1 4QC7 CGCGAATTCGCG 1 12 4QC7 1 12 4QC7 A 1 1 12 13 24 4QC7 13 24 4QC7 B 1 1 12 19 P 21 21 21