1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Maufrais, C. Fazakerley, G.V. Cadet, J. Boulard, Y. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C6 H12 N O7 P 241.136 N-(2-DEOXY-BETA-D-ERYTHO-PENTOFURANOSYL-5-PHOSPHATE) FORMAMIDE 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 UK Nucleic Acids Res. NARHAD 0389 0305-1048 31 5930 5940 10.1093/nar/gkg803 14530441 Structural study of DNA duplex containing an N-(2-deoxy-beta-D-erythro-pentofuranosyl) formamide frameshift by NMR and restrained molecular dynamics. 2003 10.2210/pdb1osr/pdb pdb_00001osr 2749.826 5'-D(*AP*GP*GP*AP*CP*CP*AP*CP*G)-3' 1 syn polymer 2945.905 5'-D(*CP*GP*TP*GP*GP*(2DF)P*TP*CP*CP*T)-3' 1 syn polymer no no (DA)(DG)(DG)(DA)(DC)(DC)(DA)(DC)(DG) AGGACCACG A polydeoxyribonucleotide no yes (DC)(DG)(DT)(DG)(DG)(2DF)(DT)(DC)(DC)(DT) CGTGGNTCCT B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n -20.071 1 20 A 1 B 19 -10.630 A_DA1:DT19_B 1 -3.873 -0.563 -0.047 -0.192 -12.890 1 19 A 2 B 18 -6.941 A_DG2:DC18_B 2 -10.584 0.609 -0.318 -0.030 -4.452 1 19 A 3 B 17 -4.326 A_DG3:DC17_B 3 -6.491 0.079 0.105 -0.028 -5.201 1 20 A 4 B 16 -7.564 A_DA4:DT16_B 4 0.109 0.490 0.094 0.126 -3.299 1 19 A 5 B 14 -4.528 A_DC5:DG14_B 5 -4.383 -0.036 0.270 0.024 2.696 1 19 A 6 B 13 -3.681 A_DC6:DG13_B 6 -7.327 0.033 0.063 -0.024 7.486 1 20 A 7 B 12 -4.892 A_DA7:DT12_B 7 -3.196 0.168 0.419 0.026 4.372 1 19 A 8 B 11 -6.566 A_DC8:DG11_B 8 -6.209 -0.605 0.493 -0.080 22.312 1 19 A 9 B 10 -8.167 A_DG9:DC10_B 9 -5.550 0.688 1.024 -0.148 3.152 40.415 A A 1 2 -1.462 B B 19 18 3.189 -1.007 -0.178 -0.490 AA_DA1DG2:DC18DT19_BB 1 5.355 -7.774 40.062 -0.600 0.843 2.976 34.206 A A 2 3 -6.132 B B 18 17 2.995 -3.592 -0.033 -0.141 AA_DG2DG3:DC17DC18_BB 2 -4.191 7.154 33.771 0.280 -0.552 3.341 39.995 A A 3 4 -8.891 B B 17 16 3.312 -6.059 -0.051 -0.447 AA_DG3DA4:DT16DC17_BB 3 0.363 -0.533 39.550 0.057 0.118 3.284 32.727 A A 4 5 2.033 B B 16 14 3.304 1.145 0.056 -0.475 AA_DA4DC5:DG14DT16_BB 4 -0.450 0.799 32.705 -1.043 -0.178 3.227 36.053 A A 5 6 -8.271 B B 14 13 3.245 -5.102 0.237 -0.045 AA_DC5DC6:DG13DG14_BB 5 1.317 -2.135 35.678 0.647 -0.197 3.252 40.234 A A 6 7 -4.737 B B 13 12 3.249 -3.253 -0.078 -0.190 AA_DC6DA7:DT12DG13_BB 6 -2.824 4.112 40.013 0.092 -0.206 3.357 31.565 A A 7 8 -1.729 B B 12 11 3.342 -0.941 -0.155 -0.546 AA_DA7DC8:DG11DT12_BB 7 -0.107 0.197 31.551 -0.825 0.264 2.778 41.936 A A 8 9 -12.295 B B 11 10 2.782 -8.723 0.034 -0.359 AA_DC8DG9:DC10DG11_BB 8 -4.677 6.591 40.802 0.282 -0.467 database_2 pdbx_nmr_software pdbx_nmr_spectrometer pdbx_struct_assembly pdbx_struct_oper_list struct_conn repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2003-10-14 1 1 2008-04-29 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _pdbx_nmr_spectrometer.model _struct_conn.pdbx_leaving_atom_flag RCSB Y RCSB 2003-03-20 REL THE STRUCTURES WERE DETERMINED USING PROTON NMR FOLLOWED BY DISTANCE RESTRAINED MOLECULAR DYNAMICS SIMULATIONS. TWO REPRESENTATIVE STRUCTURES OF THE TWO ISOMER CIS AND TRANS FOR THE FORMAMIDE RESIDUE ARE PRESENTED. 2 NOESY COSY DQFCOSY TOCSY HSQC 1H-31P 10 mM PHOSPHATE BUFFER, 150 mM NACL, 0.2 mM EDTA 6.5 AMBIENT 290 K 10 mM PHOSPHATE BUFFER, 150 mM NACL, 0.2 mM EDTA 5.5 AMBIENT 278 K MOLECULAR MODELING; SIMULATED ANNEALING; RESTRAINED MOLECULAR DYNAMICS SIMULATIONS 2 those which were used to initiate molecular dynamic simulations 2 MM DNA, 10 MM PHOSPHATE BUFFER, 50 MM NACL, 0.2 MM EDTA 99.9% D2O 2 MM DNA, 10 MM PHOSPHATE BUFFER, 50 MM NACL, 0.2 MM EDTA 90% H2O/10% D2O KOLLMAN refinement Amber LEBRET refinement MORCAD Koradi, Wuthrich refinement MOLMOL 2.6 BRUKER processing XwinNMR 2.5 600 Bruker AVANCE 500 Bruker AVANCE A 1 n 1 DA 1 A G 2 n 2 DG 2 A G 3 n 3 DG 3 A A 4 n 4 DA 4 A C 5 n 5 DC 5 A C 6 n 6 DC 6 A A 7 n 7 DA 7 A C 8 n 8 DC 8 A G 9 n 9 DG 9 A C 10 n 1 DC 10 B G 11 n 2 DG 11 B T 12 n 3 DT 12 B G 13 n 4 DG 13 B G 14 n 5 DG 14 B 2DF 15 n 6 2DF 15 B T 16 n 7 DT 16 B C 17 n 8 DC 17 B C 18 n 9 DC 18 B T 19 n 10 DT 19 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 1 A DA 1 0.064 SIDE CHAIN 1 A DG 9 0.059 SIDE CHAIN 1 B DC 18 0.064 SIDE CHAIN 2 A DA 1 0.078 SIDE CHAIN 1 3.09 0.30 108.30 111.39 A A A O4' C1' N9 DA DA DA 1 1 1 N 1 1.94 0.30 108.30 110.24 A A A O4' C1' N9 DG DG DG 2 2 2 N 1 1.92 0.30 108.30 110.22 A A A O4' C1' N9 DA DA DA 4 4 4 N 1 2.27 0.30 108.30 110.57 A A A O4' C1' N1 DC DC DC 6 6 6 N 1 2.39 0.30 108.30 110.69 B B B O4' C1' N1 DC DC DC 10 10 10 N 1 2.39 0.30 108.30 110.69 B B B O4' C1' N1 DT DT DT 12 12 12 N 1 -3.70 0.60 122.90 119.20 B B B C6 C5 C7 DT DT DT 12 12 12 N 1 2.31 0.30 108.30 110.61 B B B O4' C1' N1 DT DT DT 16 16 16 N 1 2.28 0.30 108.30 110.58 B B B O4' C1' N1 DC DC DC 18 18 18 N 1 2.95 0.30 108.30 111.25 B B B O4' C1' N1 DT DT DT 19 19 19 N 2 3.43 0.30 108.30 111.73 A A A O4' C1' N9 DA DA DA 1 1 1 N 2 2.11 0.30 108.30 110.41 A A A O4' C1' N9 DG DG DG 2 2 2 N 2 2.13 0.30 108.30 110.43 A A A O4' C1' N9 DA DA DA 4 4 4 N 2 2.70 0.30 108.30 111.00 A A A O4' C1' N1 DC DC DC 6 6 6 N 2 2.25 0.30 108.30 110.55 B B B O4' C1' N1 DC DC DC 10 10 10 N 2 2.74 0.30 108.30 111.04 B B B O4' C1' N1 DT DT DT 12 12 12 N 2 2.68 0.30 108.30 110.98 B B B O4' C1' N1 DT DT DT 16 16 16 N 2 2.07 0.30 108.30 110.37 B B B O4' C1' N1 DC DC DC 18 18 18 N 2 2.89 0.30 108.30 111.19 B B B O4' C1' N1 DT DT DT 19 19 19 N Structural study of dna duplex containaing a n-(2-deoxy-beta-erytho-pentofuranosyl) formamide frameshift by nmr and restrained molecular dynamics 1 N N 2 N N covale 1.622 both B DG 14 B O3' DG 5 1_555 B 2DF 15 B P 2DF 6 1_555 covale 1.611 both B 2DF 15 B O3' 2DF 6 1_555 B DT 16 B P DT 7 1_555 hydrog WATSON-CRICK A DA 1 A N1 DA 1 1_555 B DT 19 B N3 DT 10 1_555 hydrog WATSON-CRICK A DA 1 A N6 DA 1 1_555 B DT 19 B O4 DT 10 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 B DC 18 B N3 DC 9 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B DC 18 B O2 DC 9 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B DC 18 B N4 DC 9 1_555 hydrog WATSON-CRICK A DG 3 A N1 DG 3 1_555 B DC 17 B N3 DC 8 1_555 hydrog WATSON-CRICK A DG 3 A N2 DG 3 1_555 B DC 17 B O2 DC 8 1_555 hydrog WATSON-CRICK A DG 3 A O6 DG 3 1_555 B DC 17 B N4 DC 8 1_555 hydrog WATSON-CRICK A DA 4 A N1 DA 4 1_555 B DT 16 B N3 DT 7 1_555 hydrog WATSON-CRICK A DA 4 A N6 DA 4 1_555 B DT 16 B O4 DT 7 1_555 hydrog WATSON-CRICK A DC 5 A N3 DC 5 1_555 B DG 14 B N1 DG 5 1_555 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 B DG 14 B O6 DG 5 1_555 hydrog WATSON-CRICK A DC 5 A O2 DC 5 1_555 B DG 14 B N2 DG 5 1_555 hydrog WATSON-CRICK A DC 6 A N3 DC 6 1_555 B DG 13 B N1 DG 4 1_555 hydrog WATSON-CRICK A DC 6 A N4 DC 6 1_555 B DG 13 B O6 DG 4 1_555 hydrog WATSON-CRICK A DC 6 A O2 DC 6 1_555 B DG 13 B N2 DG 4 1_555 hydrog WATSON-CRICK A DA 7 A N1 DA 7 1_555 B DT 12 B N3 DT 3 1_555 hydrog WATSON-CRICK A DA 7 A N6 DA 7 1_555 B DT 12 B O4 DT 3 1_555 hydrog WATSON-CRICK A DC 8 A N3 DC 8 1_555 B DG 11 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 8 A N4 DC 8 1_555 B DG 11 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 8 A O2 DC 8 1_555 B DG 11 B N2 DG 2 1_555 hydrog WATSON-CRICK A DG 9 A N1 DG 9 1_555 B DC 10 B N3 DC 1 1_555 hydrog WATSON-CRICK A DG 9 A N2 DG 9 1_555 B DC 10 B O2 DC 1 1_555 hydrog WATSON-CRICK A DG 9 A O6 DG 9 1_555 B DC 10 B N4 DC 1 1_555 DNA MODIFIED BASE, MUTAGENESIS, DEOXYRIBONUCLEIC ACID, DNA 1OSR PDB 1 1OSR 1OSR PDB 2 1OSR 1 9 1OSR 1 9 1OSR A 1 1 9 10 19 1OSR 10 19 1OSR B 2 1 10 1 P 1