1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Denisov, A. Bekiroglu, S. Maltseva, T. Sandstrom, A. Altmann, K.-H. Egli, M. Chattopadhyaya, J. 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 C12 H19 N2 O7 P 334.262 n 6'-ALPHA-METHYL CARBOCYCLIC THYMIDINE 5'-MONOPHOSPHATE DNA linking US J.Biomol.Struct.Dyn. JBSDD6 0646 0739-1102 16 547 568 10052613 The solution conformation of a carbocyclic analog of the Dickerson-Drew dodecamer: comparison with its own X-ray structure and that of the NMR structure of the native counterpart. 1998 10.2210/pdb1dau/pdb pdb_00001dau 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 3687.500 DNA (5'-D(*CP*GP*CP*GP*AP*AP*(T32)P*(T32)P*CP*GP*CP*G)-3') 2 syn polymer no yes (DC)(DG)(DC)(DG)(DA)(DA)(T32)(T32)(DC)(DG)(DC)(DG) CGCGAATTCGCG A,B polydeoxyribonucleotide n n n n n n n n n n n n 6.703 1 19 A 1 B 24 5.498 A_DC1:DG24_B 1 -28.705 -0.078 -0.617 -0.057 5.641 1 19 A 2 B 23 -1.123 A_DG2:DC23_B 2 -1.098 -0.167 0.474 0.010 -0.118 1 19 A 3 B 22 -2.077 A_DC3:DG22_B 3 -7.451 0.862 0.201 -0.187 10.393 1 19 A 4 B 21 0.092 A_DG4:DC21_B 4 5.457 -0.116 0.180 0.064 -11.665 1 20 A 5 B 20 -2.333 A_DA5:T3220_B 5 -3.588 0.679 -1.003 -0.046 -2.625 1 20 A 6 B 19 -0.194 A_DA6:T3219_B 6 1.878 0.445 -0.717 0.044 2.630 1 20 A 7 B 18 -0.188 A_T327:DA18_B 7 1.901 -0.444 -0.718 0.044 11.663 1 20 A 8 B 17 -2.338 A_T328:DA17_B 8 -3.600 -0.679 -1.003 -0.046 -10.397 1 19 A 9 B 16 0.085 A_DC9:DG16_B 9 5.477 0.117 0.181 0.064 0.125 1 19 A 10 B 15 -2.073 A_DG10:DC15_B 10 -7.440 -0.863 0.202 -0.187 -5.636 1 19 A 11 B 14 -1.116 A_DC11:DG14_B 11 -1.097 0.167 0.474 0.010 -6.694 1 19 A 12 B 13 5.484 A_DG12:DC13_B 12 -28.714 0.079 -0.617 -0.057 3.178 38.423 A A 1 2 19.962 B B 24 23 3.437 12.691 -0.336 -0.032 AA_DC1DG2:DC23DG24_BB 1 -11.921 18.751 34.385 -1.744 -1.083 3.350 40.788 A A 2 3 5.763 B B 23 22 3.443 4.009 0.065 -0.820 AA_DG2DC3:DG22DC23_BB 2 1.761 -2.532 40.563 -1.636 0.109 2.972 24.847 A A 3 4 0.185 B B 22 21 3.003 0.080 0.428 -1.045 AA_DC3DG4:DC21DG22_BB 3 -1.376 3.199 24.809 -2.450 -1.373 3.513 42.023 A A 4 5 12.818 B B 21 20 3.979 9.054 -0.109 -1.273 AA_DG4DA5:T3220DC21_BB 4 9.365 -13.259 40.041 -2.879 1.294 3.132 28.789 A A 5 6 1.248 B B 20 19 3.202 0.620 0.432 -0.963 AA_DA5DA6:T3219T3220_BB 5 -2.505 5.045 28.676 -2.072 -1.413 3.150 24.917 A A 6 7 4.561 B B 19 18 3.286 1.966 0.000 -1.622 AA_DA6T327:DA18T3219_BB 6 0.010 -0.024 24.841 -4.340 0.002 3.133 28.784 A A 7 8 1.262 B B 18 17 3.202 0.627 -0.432 -0.963 AA_T327T328:DA17DA18_BB 7 2.498 -5.031 28.671 -2.073 1.412 3.513 42.031 A A 8 9 12.827 B B 17 16 3.980 9.061 0.109 -1.273 AA_T328DC9:DG16DA17_BB 8 -9.368 13.261 40.046 -2.879 -1.294 2.971 24.840 A A 9 10 0.163 B B 16 15 3.002 0.070 -0.427 -1.045 AA_DC9DG10:DC15DG16_BB 9 1.370 -3.186 24.803 -2.449 1.371 3.351 40.787 A A 10 11 5.758 B B 15 14 3.443 4.006 -0.065 -0.820 AA_DG10DC11:DG14DC15_BB 10 -1.748 2.513 40.562 -1.636 -0.108 3.178 38.428 A A 11 12 19.963 B B 14 13 3.437 12.694 0.335 -0.032 AA_DC11DG12:DC13DG14_BB 11 11.915 -18.738 34.392 -1.744 1.082 database_2 pdbx_database_status pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list struct_conn repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Other 1 0 1998-05-27 1 1 2008-03-24 1 2 2011-07-13 1 3 2022-02-16 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.process_site _pdbx_nmr_software.name _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id MINIMIZED AVERAGE STRUCTURE Y BNL 1998-01-21 REL LOWEST ENERGY, BEST AGREEMENT WITH NOE VOLUMES 9 1 NOESY DQF-COSY 7.0 293 K REFINEMENT DETAILS CAN BE FOUND IN THE PAPER. RESTRAINED MD PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMAN refinement Amber 4.1 structure solution AURELIA structure solution Amber structure solution MARDIGRAS 600 Bruker DRX 600 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 T32 7 n 7 T32 7 A T32 8 n 8 T32 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 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 T32 19 n 7 T32 19 B T32 20 n 8 T32 20 B DC 21 n 9 DC 21 B DG 22 n 10 DG 22 B DC 23 n 11 DC 23 B DG 24 n 12 DG 24 B author_defined_assembly 2 dimeric A T32 7 A T32 7 DT A T32 8 A T32 8 DT B T32 19 B T32 7 DT B T32 20 B T32 8 DT 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 4.13 0.30 108.30 112.43 A A A O4' C1' N1 DC DC DC 1 1 1 N 1 4.03 0.60 106.00 110.03 A A A O4' C4' C3' DC DC DC 3 3 3 N 1 4.08 0.30 108.30 112.38 A A A O4' C1' N9 DG DG DG 4 4 4 N 1 1.83 0.30 108.30 110.13 A A A O4' C1' N9 DA DA DA 6 6 6 N 1 3.76 0.60 106.00 109.76 A A A O4' C4' C3' DC DC DC 9 9 9 N 1 5.13 0.30 108.30 113.43 A A A O4' C1' N9 DG DG DG 10 10 10 N 1 6.33 0.60 106.00 112.33 A A A O4' C4' C3' DC DC DC 11 11 11 N 1 4.12 0.30 108.30 112.42 B B B O4' C1' N1 DC DC DC 13 13 13 N 1 4.04 0.60 106.00 110.04 B B B O4' C4' C3' DC DC DC 15 15 15 N 1 4.12 0.30 108.30 112.42 B B B O4' C1' N9 DG DG DG 16 16 16 N 1 1.83 0.30 108.30 110.13 B B B O4' C1' N9 DA DA DA 18 18 18 N 1 3.76 0.60 106.00 109.76 B B B O4' C4' C3' DC DC DC 21 21 21 N 1 5.17 0.30 108.30 113.47 B B B O4' C1' N9 DG DG DG 22 22 22 N 1 6.35 0.60 106.00 112.35 B B B O4' C4' C3' DC DC DC 23 23 23 N refinement AMBER Analog of dickerson-drew DNA dodecamer with 6'-alpha-methyl carbocyclic thymidines, NMR, minimized average structure 1 N N 1 N N covale 1.616 both A DA 6 A O3' DA 6 1_555 A T32 7 A P T32 7 1_555 covale 1.611 one A T32 7 A O3' T32 7 1_555 A T32 8 A P T32 8 1_555 covale 1.621 one A T32 8 A O3' T32 8 1_555 A DC 9 A P DC 9 1_555 covale 1.617 both B DA 18 B O3' DA 6 1_555 B T32 19 B P T32 7 1_555 covale 1.612 one B T32 19 B O3' T32 7 1_555 B T32 20 B P T32 8 1_555 covale 1.620 one B T32 20 B O3' T32 8 1_555 B DC 21 B P DC 9 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 DC 21 B N3 DC 9 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B DC 21 B O2 DC 9 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 B DC 21 B N4 DC 9 1_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 B T32 20 B N3 T32 8 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 B T32 20 B O4 T32 8 1_555 hydrog WATSON-CRICK A DA 6 A N1 DA 6 1_555 B T32 19 B N3 T32 7 1_555 hydrog WATSON-CRICK A DA 6 A N6 DA 6 1_555 B T32 19 B O4 T32 7 1_555 hydrog DA-T32 PAIR A DA 6 A N1 DA 6 1_555 B T32 20 B N3 T32 8 1_555 hydrog WATSON-CRICK A T32 7 A N3 T32 7 1_555 B DA 18 B N1 DA 6 1_555 hydrog WATSON-CRICK A T32 7 A O4 T32 7 1_555 B DA 18 B N6 DA 6 1_555 hydrog WATSON-CRICK A T32 8 A N3 T32 8 1_555 B DA 17 B N1 DA 5 1_555 hydrog WATSON-CRICK A T32 8 A O4 T32 8 1_555 B DA 17 B N6 DA 5 1_555 hydrog T32-DA PAIR A T32 8 A N3 T32 8 1_555 B DA 18 B N1 DA 6 1_555 hydrog WATSON-CRICK A DC 9 A N3 DC 9 1_555 B DG 16 B N1 DG 4 1_555 hydrog WATSON-CRICK A DC 9 A N4 DC 9 1_555 B DG 16 B O6 DG 4 1_555 hydrog WATSON-CRICK A DC 9 A O2 DC 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 DNA, CARBOCYCLIC, DODECAMER, DEOXYRIBONUCLEIC ACID, MINIMIZED AVERAGE STRUCTURE 1DAU PDB 1 1DAU 1 12 1DAU 1 12 1DAU A 1 1 12 13 24 1DAU 13 24 1DAU B 1 1 12 1 P 1