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 C11 H16 N5 O6 P 345.248 n N6-METHYL-DEOXY-ADENOSINE-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 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/pdb1oq2/pdb pdb_00001oq2 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 3637.394 5'-D(*CP*GP*CP*AP*GP*(6MA)P*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 yes (DC)(DG)(DC)(DA)(DG)(6MA)(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 8.500 1 19 A 1 B 24 -1.872 A_DG1:DC24_B 1 -6.180 -0.205 0.678 -0.346 -18.082 1 19 A 2 B 23 1.667 A_DC2:DG23_B 2 11.737 1.054 0.052 -0.390 -6.300 1 19 A 3 B 22 8.818 A_DG3:DC22_B 3 14.307 -0.183 1.020 -0.539 0.528 1 20 A 4 B 21 0.241 A_DA4:DT21_B 4 15.422 0.154 0.513 -0.277 5.627 1 19 A 5 B 20 -1.221 A_DG5:DC20_B 5 5.343 -0.161 0.312 -0.250 7.286 1 20 A 6 B 19 -15.518 A_DA6:DT19_B 6 1.656 0.213 0.161 0.139 -7.394 1 19 A 8 B 17 0.075 A_DC8:DG17_B 7 -6.755 -0.209 0.273 -0.176 -7.348 1 20 A 9 B 16 6.118 A_DT9:DA16_B 8 17.871 0.250 0.025 -0.260 0.596 1 19 A 10 B 15 0.096 A_DG10:DC15_B 9 32.381 0.272 -0.058 -0.224 -0.275 1 19 A 11 B 14 -4.557 A_DC11:DG14_B 10 16.719 0.073 -0.617 -0.373 16.712 1 19 A 12 B 13 -7.377 A_DG12:DC13_B 11 12.459 0.291 -0.377 -0.124 4.514 48.283 A A 1 2 26.389 B B 24 23 4.777 20.946 0.663 0.379 AA_DG1DC2:DG23DC24_BB 1 0.444 -0.559 43.747 -1.989 -0.759 3.384 46.622 A A 2 3 -52.998 B B 23 22 4.065 -36.458 -0.167 -1.151 AA_DC2DG3:DC22DG23_BB 2 -10.038 14.591 27.786 3.035 -1.025 3.191 35.586 A A 3 4 -1.600 B B 22 21 3.280 -0.973 -0.477 -1.645 AA_DG3DA4:DT21DC22_BB 3 6.318 -10.391 35.025 -2.550 1.698 3.447 30.775 A A 4 5 18.002 B B 21 20 3.580 9.404 -0.821 -0.008 AA_DA4DG5:DC20DT21_BB 4 -1.396 2.672 29.303 -2.041 1.245 2.851 37.971 A A 5 6 20.384 B B 20 19 3.395 13.007 -1.351 -0.832 AA_DG5DA6:DT19DC20_BB 5 2.080 -3.260 35.692 -2.917 2.338 7.069 69.035 A A 6 8 -0.765 B B 19 17 7.085 -0.867 0.673 -0.008 AA_DA6DC8:DG17DT19_BB 6 -1.607 1.418 69.013 0.062 -0.721 4.024 40.969 A A 8 9 -30.029 B B 17 16 4.225 -20.132 0.151 -0.734 AA_DC8DT9:DA16DG17_BB 7 -4.402 6.567 35.603 1.942 -0.870 2.773 35.067 A A 9 10 18.306 B B 16 15 3.204 10.859 -0.507 -0.951 AA_DT9DG10:DC15DA16_BB 8 -0.271 0.457 33.392 -3.106 0.803 3.690 32.799 A A 10 11 15.867 B B 15 14 3.982 8.839 -0.567 -0.281 AA_DG10DC11:DG14DC15_BB 9 3.404 -6.110 31.438 -2.319 1.706 3.089 28.437 A A 11 12 12.199 B B 14 13 3.123 5.950 -0.261 0.135 AA_DC11DG12:DC13DG14_BB 10 -0.491 1.007 27.816 -1.035 0.424 database_2 pdbx_struct_assembly pdbx_struct_oper_list struct_conn 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 _struct_conn.pdbx_leaving_atom_flag NMR structure of unmethylated GATC site NMR structure of hemimethylated GATC site, N6-methyl in trans(respect to N1) configuration RCSB Y PDBJ 2003-03-07 REL REL Chemical Synthesis sample Chemical Synthesis sample structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy 100 17 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 6MA 18 n 6 6MA 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 B 6MA 18 B 6MA 6 A 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 3 A B H21 O2 DG DC 1 24 1.54 4 A B H21 O2 DG DC 1 24 1.59 7 A B H21 O2 DG DC 1 24 1.56 9 A B H21 O2 DG DC 1 24 1.59 10 A B H21 O2 DG DC 1 24 1.60 11 A B H21 O2 DG DC 1 24 1.59 12 A B H21 O2 DG DC 1 24 1.55 14 A B H21 O2 DG DC 1 24 1.55 minimized average NMR structure of hemimethylated GATC site 1 N N 2 N N covale 1.608 both B DG 17 B O3' DG 5 1_555 B 6MA 18 B P 6MA 6 1_555 covale 1.611 both B 6MA 18 B O3' 6MA 6 1_555 B DT 19 B P DT 7 1_555 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 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, hemimethylation, SeqA, MutH, N6-methyl, Dam (DNA adenine methyltransferase), DNA 1OQ2 PDB 1 1OQ2 1OQ2 PDB 2 1OQ2 1 12 1OQ2 1 12 1OQ2 A 1 1 12 13 24 1OQ2 13 24 1OQ2 B 2 1 12 1 P 1