1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Salazar, M. Fedoroff, O.Y. Reid, B.R. 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 O7 P 347.221 y ADENOSINE-5'-MONOPHOSPHATE RNA linking C9 H14 N3 O8 P 323.197 y CYTIDINE-5'-MONOPHOSPHATE RNA 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 Biochemistry BICHAW 0033 0006-2960 35 8126 8135 10.1021/bi9528917 8679564 Structure of chimeric duplex junctions: solution conformation of the retroviral Okazaki-like fragment r(ccca)d(AATGA).d(TCATTTGGG) from Moloney murine leukemia virus. 1996 10.2210/pdb1oka/pdb pdb_00001oka 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 2761.820 RNA/DNA CHIMERA (R(CCCA)D(AATGA)(DOT)D(TCATTTGGG)) 1 syn polymer 2772.813 RNA/DNA CHIMERA (R(CCCA)D(AATGA)(DOT)D(TCATTTGGG)) 1 syn polymer no no (DT)(DC)(DA)(DT)(DT)(DT)(DG)(DG)(DG) TCATTTGGG A polydeoxyribonucleotide no no CCCA(DA)(DA)(DT)(DG)(DA) CCCAAATGA B polydeoxyribonucleotide/polyribonucleotide hybrid n n n n n n n n n n n n n n n n n n -10.094 1 20 A 1 B 9 0.068 A_DT1:DA9_B 1 -4.595 0.426 -0.374 -0.152 -10.865 1 19 A 2 B 8 -1.180 A_DC2:DG8_B 2 5.468 0.974 0.253 -0.319 2.331 1 20 A 3 B 7 0.646 A_DA3:DT7_B 3 -4.262 0.630 -0.200 -0.019 0.902 1 20 A 4 B 6 -2.875 A_DT4:DA6_B 4 -6.724 -0.013 -0.361 -0.034 3.397 1 20 A 5 B 5 0.367 A_DT5:DA5_B 5 -2.318 -0.543 0.174 0.021 17.604 1 20 A 6 B 4 2.648 A_DT6:A4_B 6 -16.969 0.271 -0.450 -0.099 1.735 1 19 A 7 B 3 -0.502 A_DG7:C3_B 7 -9.409 -0.101 0.041 -0.021 3.140 1 19 A 8 B 2 -2.876 A_DG8:C2_B 8 -11.145 0.245 0.188 -0.039 -3.150 1 19 A 9 B 1 -1.970 A_DG9:C1_B 9 -13.605 -0.487 -0.072 -0.128 2.959 33.098 A A 1 2 8.838 B B 9 8 3.237 5.011 -0.085 -1.621 AA_DT1DC2:DG8DA9_BB 1 -2.718 4.794 32.616 -3.653 -0.288 3.120 33.320 A A 2 3 -4.610 B B 8 7 3.018 -2.639 -0.352 -1.736 AA_DC2DA3:DT7DG8_BB 2 1.790 -3.126 33.171 -2.615 0.895 3.230 26.874 A A 3 4 0.258 B B 7 6 3.246 0.120 -0.302 -2.162 AA_DA3DT4:DA6DT7_BB 3 0.510 -1.098 26.869 -4.682 0.780 2.800 28.559 A A 4 5 7.716 B B 6 5 3.166 3.782 0.267 -2.069 AA_DT4DT5:DA5DA6_BB 4 -4.177 8.521 28.008 -4.987 -1.415 2.693 36.756 A A 5 6 1.694 B B 5 4 2.765 1.066 -0.255 -1.159 AA_DT5DT6:A4DA5_BB 5 3.737 -5.937 36.557 -1.959 0.831 2.396 33.688 A A 6 7 27.874 B B 4 3 3.406 15.531 -0.310 -1.451 AA_DT6DG7:C3A4_BB 6 -4.155 7.458 29.703 -4.897 -0.106 2.686 33.820 A A 7 8 10.513 B B 3 2 2.987 6.078 -0.366 -1.567 AA_DG7DG8:C2C3_BB 7 -2.710 4.686 33.178 -3.554 0.246 2.569 28.082 A A 8 9 16.033 B B 2 1 3.160 7.674 0.025 -1.730 AA_DG8DG9:C1C2_BB 8 2.586 -5.403 26.912 -5.182 0.492 database_2 pdbx_database_status pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Other 1 0 1996-11-08 1 1 2008-03-24 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.process_site _pdbx_nmr_software.name Y BNL 1996-04-19 REL REL 7 BIOSYM refinement Discover T 1 n 1 DT 1 A C 2 n 2 DC 2 A A 3 n 3 DA 3 A T 4 n 4 DT 4 A T 5 n 5 DT 5 A T 6 n 6 DT 6 A G 7 n 7 DG 7 A G 8 n 8 DG 8 A G 9 n 9 DG 9 A C 1 n 1 C 1 B C 2 n 2 C 2 B C 3 n 3 C 3 B A 4 n 4 A 4 B A 5 n 5 DA 5 B A 6 n 6 DA 6 B T 7 n 7 DT 7 B G 8 n 8 DG 8 B A 9 n 9 DA 9 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 B C 1 0.081 SIDE CHAIN 1 B A 4 0.075 SIDE CHAIN 1 B DA 5 0.051 SIDE CHAIN 2 B C 1 0.076 SIDE CHAIN 2 B A 4 0.071 SIDE CHAIN 2 B DA 5 0.065 SIDE CHAIN 3 B C 1 0.077 SIDE CHAIN 3 B A 4 0.078 SIDE CHAIN 3 B DA 5 0.059 SIDE CHAIN 4 B C 1 0.081 SIDE CHAIN 4 B A 4 0.071 SIDE CHAIN 4 B DA 5 0.063 SIDE CHAIN 5 B C 1 0.077 SIDE CHAIN 5 B A 4 0.078 SIDE CHAIN 6 B C 1 0.069 SIDE CHAIN 6 B A 4 0.067 SIDE CHAIN 7 B C 1 0.069 SIDE CHAIN 7 B A 4 0.067 SIDE CHAIN 1 3.62 0.30 108.30 111.92 A A A O4' C1' N1 DT DT DT 1 1 1 N 1 5.32 0.30 108.30 113.62 A A A O4' C1' N1 DC DC DC 2 2 2 N 1 3.36 0.30 108.30 111.66 A A A O4' C1' N9 DA DA DA 3 3 3 N 1 5.03 0.30 108.30 113.33 A A A O4' C1' N1 DT DT DT 4 4 4 N 1 5.15 0.30 108.30 113.45 A A A O4' C1' N1 DT DT DT 5 5 5 N 1 -3.67 0.60 122.90 119.23 A A A C6 C5 C7 DT DT DT 5 5 5 N 1 2.82 0.30 108.30 111.12 A A A O4' C1' N1 DT DT DT 6 6 6 N 1 3.55 0.30 108.30 111.85 A A A O4' C1' N9 DG DG DG 7 7 7 N 1 4.18 0.30 108.30 112.48 A A A O4' C1' N9 DG DG DG 8 8 8 N 1 4.31 0.30 108.30 112.61 A A A O4' C1' N9 DG DG DG 9 9 9 N 1 5.13 0.70 108.50 113.63 B B B O4' C1' N1 C C C 2 2 2 N 1 5.00 0.70 108.50 113.50 B B B O4' C1' N1 C C C 3 3 3 N 1 3.27 0.30 108.30 111.57 B B B O4' C1' N9 DA DA DA 5 5 5 N 1 4.91 0.30 108.30 113.21 B B B O4' C1' N9 DA DA DA 6 6 6 N 1 5.94 0.30 108.30 114.24 B B B O4' C1' N1 DT DT DT 7 7 7 N 1 4.17 0.30 108.30 112.47 B B B O4' C1' N9 DG DG DG 8 8 8 N 1 3.62 0.30 108.30 111.92 B B B O4' C1' N9 DA DA DA 9 9 9 N 2 5.06 0.30 108.30 113.36 A A A O4' C1' N1 DT DT DT 1 1 1 N 2 5.42 0.30 108.30 113.72 A A A O4' C1' N1 DC DC DC 2 2 2 N 2 3.84 0.30 108.30 112.14 A A A O4' C1' N9 DA DA DA 3 3 3 N 2 4.92 0.30 108.30 113.22 A A A O4' C1' N1 DT DT DT 4 4 4 N 2 4.89 0.30 108.30 113.19 A A A O4' C1' N1 DT DT DT 5 5 5 N 2 2.62 0.30 108.30 110.92 A A A O4' C1' N1 DT DT DT 6 6 6 N 2 3.73 0.30 108.30 112.03 A A A O4' C1' N9 DG DG DG 7 7 7 N 2 4.65 0.30 108.30 112.95 A A A O4' C1' N9 DG DG DG 8 8 8 N 2 4.36 0.30 108.30 112.66 A A A O4' C1' N9 DG DG DG 9 9 9 N 2 4.87 0.70 108.50 113.37 B B B O4' C1' N1 C C C 2 2 2 N 2 4.40 0.70 108.50 112.90 B B B O4' C1' N1 C C C 3 3 3 N 2 3.53 0.30 108.30 111.83 B B B O4' C1' N9 DA DA DA 5 5 5 N 2 5.03 0.30 108.30 113.33 B B B O4' C1' N9 DA DA DA 6 6 6 N 2 5.68 0.30 108.30 113.98 B B B O4' C1' N1 DT DT DT 7 7 7 N 2 4.06 0.30 108.30 112.36 B B B O4' C1' N9 DG DG DG 8 8 8 N 2 3.51 0.30 108.30 111.81 B B B O4' C1' N9 DA DA DA 9 9 9 N 3 4.06 0.30 108.30 112.36 A A A O4' C1' N1 DT DT DT 1 1 1 N 3 5.26 0.30 108.30 113.56 A A A O4' C1' N1 DC DC DC 2 2 2 N 3 4.23 0.30 108.30 112.53 A A A O4' C1' N9 DA DA DA 3 3 3 N 3 4.98 0.30 108.30 113.28 A A A O4' C1' N1 DT DT DT 4 4 4 N 3 5.21 0.30 108.30 113.51 A A A O4' C1' N1 DT DT DT 5 5 5 N 3 2.83 0.30 108.30 111.13 A A A O4' C1' N1 DT DT DT 6 6 6 N 3 3.47 0.30 108.30 111.77 A A A O4' C1' N9 DG DG DG 7 7 7 N 3 4.01 0.30 108.30 112.31 A A A O4' C1' N9 DG DG DG 8 8 8 N 3 4.19 0.30 108.30 112.49 A A A O4' C1' N9 DG DG DG 9 9 9 N 3 4.55 0.70 108.50 113.05 B B B O4' C1' N1 C C C 1 1 1 N 3 5.47 0.70 108.50 113.97 B B B O4' C1' N1 C C C 2 2 2 N 3 4.60 0.70 108.50 113.10 B B B O4' C1' N1 C C C 3 3 3 N 3 3.33 0.30 108.30 111.63 B B B O4' C1' N9 DA DA DA 5 5 5 N 3 4.61 0.30 108.30 112.91 B B B O4' C1' N9 DA DA DA 6 6 6 N 3 5.13 0.30 108.30 113.43 B B B O4' C1' N1 DT DT DT 7 7 7 N 3 4.74 0.30 108.30 113.04 B B B O4' C1' N9 DG DG DG 8 8 8 N 3 3.32 0.30 108.30 111.62 B B B O4' C1' N9 DA DA DA 9 9 9 N 4 3.86 0.30 108.30 112.16 A A A O4' C1' N1 DT DT DT 1 1 1 N 4 5.65 0.30 108.30 113.95 A A A O4' C1' N1 DC DC DC 2 2 2 N 4 3.56 0.30 108.30 111.86 A A A O4' C1' N9 DA DA DA 3 3 3 N 4 4.97 0.30 108.30 113.27 A A A O4' C1' N1 DT DT DT 4 4 4 N 4 4.89 0.30 108.30 113.19 A A A O4' C1' N1 DT DT DT 5 5 5 N 4 2.63 0.30 108.30 110.93 A A A O4' C1' N1 DT DT DT 6 6 6 N 4 3.29 0.30 108.30 111.59 A A A O4' C1' N9 DG DG DG 7 7 7 N 4 4.51 0.30 108.30 112.81 A A A O4' C1' N9 DG DG DG 8 8 8 N 4 4.26 0.30 108.30 112.56 A A A O4' C1' N9 DG DG DG 9 9 9 N 4 6.74 0.70 108.50 115.24 B B B O4' C1' N1 C C C 1 1 1 N 4 5.72 0.70 108.50 114.22 B B B O4' C1' N1 C C C 2 2 2 N 4 4.85 0.70 108.50 113.35 B B B O4' C1' N1 C C C 3 3 3 N 4 3.36 0.30 108.30 111.66 B B B O4' C1' N9 DA DA DA 5 5 5 N 4 4.85 0.30 108.30 113.15 B B B O4' C1' N9 DA DA DA 6 6 6 N 4 5.47 0.30 108.30 113.77 B B B O4' C1' N1 DT DT DT 7 7 7 N 4 3.49 0.30 108.30 111.79 B B B O4' C1' N9 DG DG DG 8 8 8 N 4 4.00 0.30 108.30 112.30 B B B O4' C1' N9 DA DA DA 9 9 9 N 5 5.09 0.30 108.30 113.39 A A A O4' C1' N1 DT DT DT 1 1 1 N 5 5.29 0.30 108.30 113.59 A A A O4' C1' N1 DC DC DC 2 2 2 N 5 3.40 0.30 108.30 111.70 A A A O4' C1' N9 DA DA DA 3 3 3 N 5 4.45 0.30 108.30 112.75 A A A O4' C1' N1 DT DT DT 4 4 4 N 5 5.13 0.30 108.30 113.43 A A A O4' C1' N1 DT DT DT 5 5 5 N 5 2.74 0.30 108.30 111.04 A A A O4' C1' N1 DT DT DT 6 6 6 N 5 3.64 0.30 108.30 111.94 A A A O4' C1' N9 DG DG DG 7 7 7 N 5 4.17 0.30 108.30 112.47 A A A O4' C1' N9 DG DG DG 8 8 8 N 5 4.23 0.30 108.30 112.53 A A A O4' C1' N9 DG DG DG 9 9 9 N 5 5.08 0.70 108.50 113.58 B B B O4' C1' N1 C C C 2 2 2 N 5 4.83 0.70 108.50 113.33 B B B O4' C1' N1 C C C 3 3 3 N 5 2.94 0.30 108.30 111.24 B B B O4' C1' N9 DA DA DA 5 5 5 N 5 5.52 0.30 108.30 113.82 B B B O4' C1' N9 DA DA DA 6 6 6 N 5 5.00 0.30 108.30 113.30 B B B O4' C1' N1 DT DT DT 7 7 7 N 5 3.74 0.30 108.30 112.04 B B B O4' C1' N9 DG DG DG 8 8 8 N 5 3.09 0.30 108.30 111.39 B B B O4' C1' N9 DA DA DA 9 9 9 N 6 5.12 0.30 108.30 113.42 A A A O4' C1' N1 DT DT DT 1 1 1 N 6 5.09 0.30 108.30 113.39 A A A O4' C1' N1 DC DC DC 2 2 2 N 6 4.31 0.30 108.30 112.61 A A A O4' C1' N9 DA DA DA 3 3 3 N 6 5.81 0.30 108.30 114.11 A A A O4' C1' N1 DT DT DT 4 4 4 N 6 5.49 0.30 108.30 113.79 A A A O4' C1' N1 DT DT DT 5 5 5 N 6 3.61 0.30 108.30 111.91 A A A O4' C1' N1 DT DT DT 6 6 6 N 6 3.42 0.30 108.30 111.72 A A A O4' C1' N9 DG DG DG 7 7 7 N 6 3.65 0.30 108.30 111.95 A A A O4' C1' N9 DG DG DG 8 8 8 N 6 4.51 0.30 108.30 112.81 A A A O4' C1' N9 DG DG DG 9 9 9 N 6 4.54 0.70 108.50 113.04 B B B O4' C1' N1 C C C 1 1 1 N 6 5.51 0.70 108.50 114.01 B B B O4' C1' N1 C C C 2 2 2 N 6 5.46 0.70 108.50 113.96 B B B O4' C1' N1 C C C 3 3 3 N 6 3.75 0.30 108.30 112.05 B B B O4' C1' N9 DA DA DA 5 5 5 N 6 5.71 0.30 108.30 114.01 B B B O4' C1' N9 DA DA DA 6 6 6 N 6 4.97 0.30 108.30 113.27 B B B O4' C1' N1 DT DT DT 7 7 7 N 6 3.70 0.30 108.30 112.00 B B B O4' C1' N9 DG DG DG 8 8 8 N 6 3.72 0.30 108.30 112.02 B B B O4' C1' N9 DA DA DA 9 9 9 N 7 5.12 0.30 108.30 113.42 A A A O4' C1' N1 DT DT DT 1 1 1 N 7 5.09 0.30 108.30 113.39 A A A O4' C1' N1 DC DC DC 2 2 2 N 7 4.31 0.30 108.30 112.61 A A A O4' C1' N9 DA DA DA 3 3 3 N 7 5.81 0.30 108.30 114.11 A A A O4' C1' N1 DT DT DT 4 4 4 N 7 5.49 0.30 108.30 113.79 A A A O4' C1' N1 DT DT DT 5 5 5 N 7 3.61 0.30 108.30 111.91 A A A O4' C1' N1 DT DT DT 6 6 6 N 7 3.42 0.30 108.30 111.72 A A A O4' C1' N9 DG DG DG 7 7 7 N 7 3.65 0.30 108.30 111.95 A A A O4' C1' N9 DG DG DG 8 8 8 N 7 4.51 0.30 108.30 112.81 A A A O4' C1' N9 DG DG DG 9 9 9 N 7 4.54 0.70 108.50 113.04 B B B O4' C1' N1 C C C 1 1 1 N 7 5.51 0.70 108.50 114.01 B B B O4' C1' N1 C C C 2 2 2 N 7 5.46 0.70 108.50 113.96 B B B O4' C1' N1 C C C 3 3 3 N 7 3.75 0.30 108.30 112.05 B B B O4' C1' N9 DA DA DA 5 5 5 N 7 5.71 0.30 108.30 114.01 B B B O4' C1' N9 DA DA DA 6 6 6 N 7 4.97 0.30 108.30 113.27 B B B O4' C1' N1 DT DT DT 7 7 7 N 7 3.70 0.30 108.30 112.00 B B B O4' C1' N9 DG DG DG 8 8 8 N 7 3.72 0.30 108.30 112.02 B B B O4' C1' N9 DA DA DA 9 9 9 N refinement AMBER RNA/DNA CHIMERA, NMR 1 N N 2 N N hydrog WATSON-CRICK A DT 1 A N3 DT 1 1_555 B DA 9 B N1 DA 9 1_555 hydrog WATSON-CRICK A DT 1 A O4 DT 1 1_555 B DA 9 B N6 DA 9 1_555 hydrog WATSON-CRICK A DC 2 A N3 DC 2 1_555 B DG 8 B N1 DG 8 1_555 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 B DG 8 B O6 DG 8 1_555 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 B DG 8 B N2 DG 8 1_555 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 B DT 7 B N3 DT 7 1_555 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 B DT 7 B O4 DT 7 1_555 hydrog WATSON-CRICK A DT 4 A N3 DT 4 1_555 B DA 6 B N1 DA 6 1_555 hydrog WATSON-CRICK A DT 4 A O4 DT 4 1_555 B DA 6 B N6 DA 6 1_555 hydrog WATSON-CRICK A DT 5 A N3 DT 5 1_555 B DA 5 B N1 DA 5 1_555 hydrog WATSON-CRICK A DT 5 A O4 DT 5 1_555 B DA 5 B N6 DA 5 1_555 hydrog WATSON-CRICK A DT 6 A N3 DT 6 1_555 B A 4 B N1 A 4 1_555 hydrog WATSON-CRICK A DT 6 A O4 DT 6 1_555 B A 4 B N6 A 4 1_555 hydrog WATSON-CRICK A DG 7 A N1 DG 7 1_555 B C 3 B N3 C 3 1_555 hydrog WATSON-CRICK A DG 7 A N2 DG 7 1_555 B C 3 B O2 C 3 1_555 hydrog WATSON-CRICK A DG 7 A O6 DG 7 1_555 B C 3 B N4 C 3 1_555 hydrog WATSON-CRICK A DG 8 A N1 DG 8 1_555 B C 2 B N3 C 2 1_555 hydrog WATSON-CRICK A DG 8 A N2 DG 8 1_555 B C 2 B O2 C 2 1_555 hydrog WATSON-CRICK A DG 8 A O6 DG 8 1_555 B C 2 B N4 C 2 1_555 hydrog WATSON-CRICK A DG 9 A N1 DG 9 1_555 B C 1 B N3 C 1 1_555 hydrog WATSON-CRICK A DG 9 A N2 DG 9 1_555 B C 1 B O2 C 1 1_555 hydrog WATSON-CRICK A DG 9 A O6 DG 9 1_555 B C 1 B N4 C 1 1_555 DNA-RNA HYBRID RNA-DNA, CHIMERA, RNASE H, REVERSE TRANSCRIPTASE, OKAZAKI FRAGMENT, DNA-RNA COMPLEX, DNA-RNA HYBRID 1OKA PDB 1 1OKA 1OKA PDB 2 1OKA 1 9 1OKA 1 9 1OKA A 1 1 9 1 9 1OKA 1 9 1OKA B 2 1 9 1 P 1