1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Bae, S.-H. Cheong, H.-K. Kang, S. Hwang, D.S. Cheong, C. Choi, B.-S. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 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 US J.Biol.Chem. JBCHA3 0071 0021-9258 278 45987 45993 10.1074/jbc.M306038200 12944412 Structure and dynamics of hemimethylated GATC sites: implications for DNA-SeqA recognition 2003 10.2210/pdb1opq/pdb pdb_00001opq 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 SINGLE WAVELENGTH M 1 1.0 3703.416 5'-D(*GP*CP*GP*AP*GP*AP*TP*CP*TP*GP*CP*G)-3' 1 syn polymer 3623.368 5'-D(*CP*GP*CP*AP*GP*AP*TP*CP*TP*CP*GP*C)-3' 1 syn polymer no no (DG)(DC)(DG)(DA)(DG)(DA)(DT)(DC)(DT)(DG)(DC)(DG) GCGAGATCTGCG A polydeoxyribonucleotide no no (DC)(DG)(DC)(DA)(DG)(DA)(DT)(DC)(DT)(DC)(DG)(DC) CGCAGATCTCGC B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n n n n n -8.465 1 19 A 1 B 24 -0.449 A_DG1:DC24_B 1 0.372 -0.432 0.057 -0.267 -2.162 1 19 A 2 B 23 -4.226 A_DC2:DG23_B 2 -4.605 -0.015 0.552 -0.174 1.083 1 19 A 3 B 22 -3.697 A_DG3:DC22_B 3 -1.851 0.411 0.850 -0.299 -13.280 1 20 A 4 B 21 3.177 A_DA4:DT21_B 4 -2.017 -0.419 -0.470 -0.249 -13.858 1 19 A 5 B 20 -0.378 A_DG5:DC20_B 5 -0.249 -0.225 -0.656 -0.295 -5.286 1 20 A 6 B 19 -8.691 A_DA6:DT19_B 6 11.038 -0.216 -0.588 -0.368 13.285 1 20 A 7 B 18 -9.711 A_DT7:DA18_B 7 10.959 0.094 -0.756 -0.289 17.110 1 19 A 8 B 17 -3.247 A_DC8:DG17_B 8 -1.492 -0.300 -1.313 -0.419 -9.292 1 20 A 9 B 16 0.621 A_DT9:DA16_B 9 -2.804 0.124 0.143 -0.284 4.427 1 19 A 10 B 15 -1.066 A_DG10:DC15_B 10 3.800 0.215 0.361 -0.190 -14.927 1 19 A 11 B 14 3.502 A_DC11:DG14_B 11 21.766 0.378 0.602 -0.324 7.648 1 19 A 12 B 13 0.447 A_DG12:DC13_B 12 10.574 -0.175 -0.182 -0.168 3.329 37.992 A A 1 2 -1.576 B B 24 23 3.314 -1.025 -0.730 1.137 AA_DG1DC2:DG23DC24_BB 1 -3.014 4.635 37.863 1.880 0.730 3.329 37.646 A A 2 3 19.540 B B 23 22 3.344 12.387 0.394 0.556 AA_DC2DG3:DC22DG23_BB 2 -1.529 2.412 35.588 -0.829 -0.819 3.976 37.025 A A 3 4 13.135 B B 22 21 4.044 8.249 1.069 -0.370 AA_DG3DA4:DT21DC22_BB 3 5.238 -8.340 35.756 -1.966 -0.804 3.327 32.919 A A 4 5 3.371 B B 21 20 3.354 1.909 -0.732 -0.159 AA_DA4DG5:DC20DT21_BB 4 0.567 -1.002 32.860 -0.613 1.390 2.957 38.058 A A 5 6 2.425 B B 20 19 2.970 1.580 -0.314 -0.545 AA_DG5DA6:DT19DC20_BB 5 -1.718 2.637 37.989 -1.018 0.284 3.101 37.739 A A 6 7 -19.440 B B 19 18 3.210 -12.345 0.194 -0.163 AA_DA6DT7:DA18DT19_BB 6 3.089 -4.864 35.602 1.335 0.097 3.089 32.616 A A 7 8 2.528 B B 18 17 3.075 1.412 0.574 -0.857 AA_DT7DC8:DG17DA18_BB 7 5.836 -10.448 32.074 -1.760 -0.059 3.920 39.032 A A 8 9 15.971 B B 17 16 4.331 10.523 0.360 -0.724 AA_DC8DT9:DA16DG17_BB 8 -4.787 7.266 37.344 -2.724 -1.284 3.305 29.596 A A 9 10 6.007 B B 16 15 3.274 3.059 0.197 0.437 AA_DT9DG10:DC15DA16_BB 9 2.880 -5.656 29.303 0.202 0.231 4.463 38.522 A A 10 11 12.818 B B 15 14 4.658 8.376 0.628 0.031 AA_DG10DC11:DG14DC15_BB 10 -4.409 6.747 37.384 -1.424 -1.725 3.133 31.414 A A 11 12 -12.215 B B 14 13 3.045 -6.493 0.150 -1.067 AA_DC11DG12:DC13DG14_BB 11 8.194 -15.415 29.664 -0.785 1.218 database_2 pdbx_struct_assembly pdbx_struct_oper_list repository Initial release Version format compliance Version format compliance Database references Derived calculations 1 0 2004-04-27 1 1 2008-04-29 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession NMR structure of hemimethylated GATC site, N6-methyl in cis(respect to N1) configuration NMR structure of hemimethylated GATC site, N6-methyl in trans(respect to N1) configuration RCSB Y PDBJ 2003-03-06 REL REL chemical synthesis (phosphoramidite method) sample chemical synthesis (phosphoramidite method) sample structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy 100 19 1 minimized average structure G 1 n 1 DG 1 A C 2 n 2 DC 2 A G 3 n 3 DG 3 A A 4 n 4 DA 4 A G 5 n 5 DG 5 A A 6 n 6 DA 6 A T 7 n 7 DT 7 A C 8 n 8 DC 8 A T 9 n 9 DT 9 A G 10 n 10 DG 10 A C 11 n 11 DC 11 A G 12 n 12 DG 12 A C 13 n 1 DC 13 B G 14 n 2 DG 14 B C 15 n 3 DC 15 B A 16 n 4 DA 16 B G 17 n 5 DG 17 B A 18 n 6 DA 18 B T 19 n 7 DT 19 B C 20 n 8 DC 20 B T 21 n 9 DT 21 B C 22 n 10 DC 22 B G 23 n 11 DG 23 B C 24 n 12 DC 24 B author_defined_assembly 2 dimeric 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 minimized average NMR structure of unmethylated GATC site 1 N N 2 N N hydrog WATSON-CRICK A DG 1 A N1 DG 1 1_555 B DC 24 B N3 DC 12 1_555 hydrog WATSON-CRICK A DG 1 A N2 DG 1 1_555 B DC 24 B O2 DC 12 1_555 hydrog WATSON-CRICK A DG 1 A O6 DG 1 1_555 B DC 24 B N4 DC 12 1_555 hydrog WATSON-CRICK A DC 2 A N3 DC 2 1_555 B DG 23 B N1 DG 11 1_555 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 B DG 23 B O6 DG 11 1_555 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 B DG 23 B N2 DG 11 1_555 hydrog WATSON-CRICK A DG 3 A N1 DG 3 1_555 B DC 22 B N3 DC 10 1_555 hydrog WATSON-CRICK A DG 3 A N2 DG 3 1_555 B DC 22 B O2 DC 10 1_555 hydrog WATSON-CRICK A DG 3 A O6 DG 3 1_555 B DC 22 B N4 DC 10 1_555 hydrog WATSON-CRICK A DA 4 A N1 DA 4 1_555 B DT 21 B N3 DT 9 1_555 hydrog WATSON-CRICK A DA 4 A N6 DA 4 1_555 B DT 21 B O4 DT 9 1_555 hydrog WATSON-CRICK A DG 5 A N1 DG 5 1_555 B DC 20 B N3 DC 8 1_555 hydrog WATSON-CRICK A DG 5 A N2 DG 5 1_555 B DC 20 B O2 DC 8 1_555 hydrog WATSON-CRICK A DG 5 A O6 DG 5 1_555 B DC 20 B N4 DC 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 DC 8 A N3 DC 8 1_555 B DG 17 B N1 DG 5 1_555 hydrog WATSON-CRICK A DC 8 A N4 DC 8 1_555 B DG 17 B O6 DG 5 1_555 hydrog WATSON-CRICK A DC 8 A O2 DC 8 1_555 B DG 17 B N2 DG 5 1_555 hydrog WATSON-CRICK A DT 9 A N3 DT 9 1_555 B DA 16 B N1 DA 4 1_555 hydrog WATSON-CRICK A DT 9 A O4 DT 9 1_555 B DA 16 B N6 DA 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 GATC, AGATCT, oriC, Dam (DNA adenine methyltransferase), SeqA, MutH, hemimethylation, DNA 1OPQ PDB 1 1OPQ 1OPQ PDB 2 1OPQ 1 12 1OPQ 1 12 1OPQ A 1 1 12 13 24 1OPQ 13 24 1OPQ B 2 1 12 1 P 1