1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Nishizaki, T. Iwai, S. Ohkubo, T. Kojima, C. Nakamura, H. Kyogoku, Y. Ohtsuka, E. 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 C10 H14 N5 O8 P 363.221 y GUANOSINE-5'-MONOPHOSPHATE RNA linking C9 H13 N2 O9 P 324.181 y URIDINE-5'-MONOPHOSPHATE RNA linking US Biochemistry BICHAW 0033 0006-2960 35 4016 4025 10.1021/bi9519821 8672435 Solution Strucutres of DNA duplexes containing a DNA x RNA hybrid region, d(GG)r(AGAU)d(GAC) x d(GTCATCTCC) and d(GGAGA)r(UGAC) x d(GTCATCTCC). 1996 10.2210/pdb1drn/pdb pdb_00001drn 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 CRYSTALLIZATION CONDITIONS\: PH 7.0, 298K, 100MM NACL, 50MM NA PHOSPHATE, 3MM EDTA 2854.833 DNA/RNA (5'-D(*GP*GP*AP*GP*A)-R(P*UP*GP*AP*C)-3') 1 syn polymer CRYSTALLIZATION CONDITIONS\: PH 7.0, 298K, 100MM NACL, 50MM NA PHOSPHATE, 3MM EDTA 2666.761 DNA (5'-D(*GP*TP*CP*AP*TP*CP*TP*CP*C)-3') 1 syn polymer DDH DDH no no (DG)(DG)(DA)(DG)(DA)UGAC GGAGAUGAC A polydeoxyribonucleotide/polyribonucleotide hybrid no no (DG)(DT)(DC)(DA)(DT)(DC)(DT)(DC)(DC) GTCATCTCC B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n -0.669 1 19 A 1 B 18 -1.966 A_DG1:DC18_B 1 -3.214 -0.475 0.079 -0.391 -0.117 1 19 A 2 B 17 3.674 A_DG2:DC17_B 2 0.604 -0.476 -0.101 -0.057 -0.582 1 20 A 3 B 16 6.094 A_DA3:DT16_B 3 -2.994 -0.748 -0.035 -0.438 -0.065 1 19 A 4 B 15 2.647 A_DG4:DC15_B 4 -2.404 -1.038 0.034 -0.398 -1.605 1 20 A 5 B 14 5.445 A_DA5:DT14_B 5 -4.396 -0.580 -0.021 -0.345 1.851 1 20 A 6 B 13 0.436 A_U6:DA13_B 6 -1.525 0.465 -0.109 -0.343 -1.969 1 19 A 7 B 12 7.669 A_G7:DC12_B 7 -4.804 -1.334 0.015 -0.452 0.235 1 20 A 8 B 11 -0.771 A_A8:DT11_B 8 -5.307 -0.436 0.063 -0.381 4.268 1 19 A 9 B 10 4.174 A_C9:DG10_B 9 -3.614 1.405 -0.142 -0.496 3.279 33.648 A A 1 2 21.508 B B 18 17 3.488 12.168 0.557 0.212 AA_DG1DG2:DC17DC18_BB 1 -2.911 5.145 31.298 -1.767 -1.473 2.730 30.363 A A 2 3 10.278 B B 17 16 3.086 5.341 -0.057 -1.689 AA_DG2DA3:DT16DC17_BB 2 -4.059 7.811 29.630 -4.192 -0.625 4.025 29.528 A A 3 4 -11.501 B B 16 15 3.930 -5.825 0.180 -0.896 AA_DA3DG4:DC15DT16_BB 3 -0.617 1.217 28.954 -0.236 -0.515 3.043 34.429 A A 4 5 8.671 B B 15 14 3.193 5.114 -0.143 -0.820 AA_DG4DA5:DT14DC15_BB 4 -0.368 0.623 34.056 -2.149 0.186 3.077 35.507 A A 5 6 2.334 B B 14 13 3.118 1.423 0.425 -0.963 AA_DA5U6:DA13DT14_BB 5 -0.126 0.207 35.479 -1.777 -0.714 2.778 23.905 A A 6 7 8.018 B B 13 12 3.046 3.294 0.140 -1.241 AA_U6G7:DC12DA13_BB 6 -4.189 10.197 23.312 -3.964 -1.567 3.443 44.906 A A 7 8 4.117 B B 12 11 3.388 3.141 -0.980 0.221 AA_G7A8:DT11DC12_BB 7 -2.570 3.369 44.732 -0.008 1.039 3.620 40.561 A A 8 9 -0.317 B B 11 10 3.577 -0.220 0.688 -0.701 AA_A8C9:DG10DT11_BB 8 2.953 -4.264 40.457 -0.985 -0.631 database_2 pdbx_database_status pdbx_struct_assembly pdbx_struct_oper_list repository Initial release Version format compliance Version format compliance Database references Derived calculations Other 1 0 1996-04-03 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 MINIMIZED AVERAGE STRUCTURE Y BNL 1995-11-15 REL REL A SUBSTRATE OF RNASE H sample A SUBSTRATE OF RNASE H sample 1 100 mM 50 mM 3 mM 7.0 298 K RMSD BOND DISTANCES 0.0077 ANGSTROMS RMSD BOND ANGLES 1.40 DEGREES NUMBER OF ATOMS USED IN REFINEMENT. NUMBER OF PROTEIN ATOMS 0 NUMBER OF NUCLEIC ACID ATOMS 366 NUMBER OF HETEROGEN ATOMS 0 NUMBER OF SOLVENT ATOMS 0 THE STRUCTURES WAS REFINED BY A COMBINATION OF RESTRAINED MOLECULAR DYNAMICS USING THE X-PLOR (V3.1F) PROGRAM (BRUNGER 1988) AND FULL RELAXATION MATRIX REFINEMENT OF THE TWO-DIMENSIONAL NUCLEAR OVERHAUSER EFFECT SPECTRUM AT 150 MSEC. MOLECULAR DYNAMICS, MATRIX RELAXATION BRUNGER refinement X-PLOR 3.1F G 1 n 1 DG 1 A G 2 n 2 DG 2 A A 3 n 3 DA 3 A G 4 n 4 DG 4 A A 5 n 5 DA 5 A U 6 n 6 U 6 A G 7 n 7 G 7 A A 8 n 8 A 8 A C 9 n 9 C 9 A G 10 n 1 DG 10 B T 11 n 2 DT 11 B C 12 n 3 DC 12 B A 13 n 4 DA 13 B T 14 n 5 DT 14 B C 15 n 6 DC 15 B T 16 n 7 DT 16 B C 17 n 8 DC 17 B C 18 n 9 DC 18 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 2.13 0.30 108.30 110.43 A A A O4' C1' N9 DG DG DG 1 1 1 N 1 4.60 0.50 113.10 117.70 A A A N7 C8 N9 DG DG DG 1 1 1 N 1 -2.65 0.40 106.40 103.75 A A A C8 N9 C4 DG DG DG 1 1 1 N 1 3.36 0.30 108.30 111.66 A A A O4' C1' N9 DG DG DG 2 2 2 N 1 4.38 0.50 113.10 117.48 A A A N7 C8 N9 DG DG DG 2 2 2 N 1 -2.72 0.40 106.40 103.68 A A A C8 N9 C4 DG DG DG 2 2 2 N 1 3.13 0.30 108.30 111.43 A A A O4' C1' N9 DA DA DA 3 3 3 N 1 4.04 0.50 113.80 117.84 A A A N7 C8 N9 DA DA DA 3 3 3 N 1 3.22 0.30 108.30 111.52 A A A O4' C1' N9 DG DG DG 4 4 4 N 1 4.62 0.50 113.10 117.72 A A A N7 C8 N9 DG DG DG 4 4 4 N 1 -2.48 0.40 106.40 103.92 A A A C8 N9 C4 DG DG DG 4 4 4 N 1 3.08 0.30 108.30 111.38 A A A O4' C1' N9 DA DA DA 5 5 5 N 1 4.00 0.50 113.80 117.80 A A A N7 C8 N9 DA DA DA 5 5 5 N 1 5.24 0.80 101.50 106.74 A A A C3' C2' C1' G G G 7 7 7 N 1 4.53 0.70 108.50 113.03 A A A O4' C1' N9 G G G 7 7 7 N 1 4.55 0.50 113.10 117.65 A A A N7 C8 N9 G G G 7 7 7 N 1 -2.52 0.40 106.40 103.88 A A A C8 N9 C4 G G G 7 7 7 N 1 3.90 0.50 113.80 117.70 A A A N7 C8 N9 A A A 8 8 8 N 1 2.82 0.30 108.30 111.12 B B B O4' C1' N9 DG DG DG 10 10 10 N 1 4.70 0.50 113.10 117.80 B B B N7 C8 N9 DG DG DG 10 10 10 N 1 -2.59 0.40 106.40 103.81 B B B C8 N9 C4 DG DG DG 10 10 10 N 1 2.96 0.30 108.30 111.26 B B B O4' C1' N1 DT DT DT 11 11 11 N 1 2.22 0.30 108.30 110.52 B B B O4' C1' N1 DC DC DC 12 12 12 N 1 3.63 0.30 108.30 111.93 B B B O4' C1' N9 DA DA DA 13 13 13 N 1 3.80 0.50 113.80 117.60 B B B N7 C8 N9 DA DA DA 13 13 13 N 1 -3.68 0.60 122.90 119.22 B B B C6 C5 C7 DT DT DT 14 14 14 N 1 2.90 0.30 108.30 111.20 B B B O4' C1' N1 DC DC DC 15 15 15 N 1 2.28 0.30 108.30 110.58 B B B O4' C1' N1 DT DT DT 16 16 16 N 1 2.80 0.30 108.30 111.10 B B B O4' C1' N1 DC DC DC 17 17 17 N 1 2.42 0.30 108.30 110.72 B B B O4' C1' N1 DC DC DC 18 18 18 N model building X-PLOR refinement X-PLOR phasing X-PLOR NMR SOLUTION STRUCTURE OF THE DNA DUPLEX CONTAINING DNA/RNA HYBRID REGION, D(GGAGA)R(UGAC)/D(GTCATCTCC) 1 N N 2 N N hydrog WATSON-CRICK A DG 1 A N1 DG 1 1_555 B DC 18 B N3 DC 9 1_555 hydrog WATSON-CRICK A DG 1 A N2 DG 1 1_555 B DC 18 B O2 DC 9 1_555 hydrog WATSON-CRICK A DG 1 A O6 DG 1 1_555 B DC 18 B N4 DC 9 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 B DC 17 B N3 DC 8 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B DC 17 B O2 DC 8 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B DC 17 B N4 DC 8 1_555 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 B DT 16 B N3 DT 7 1_555 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 B DT 16 B O4 DT 7 1_555 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 B DC 15 B N3 DC 6 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B DC 15 B O2 DC 6 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 B DC 15 B N4 DC 6 1_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 B DT 14 B N3 DT 5 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 B DT 14 B O4 DT 5 1_555 hydrog WATSON-CRICK A U 6 A N3 U 6 1_555 B DA 13 B N1 DA 4 1_555 hydrog WATSON-CRICK A U 6 A O4 U 6 1_555 B DA 13 B N6 DA 4 1_555 hydrog WATSON-CRICK A G 7 A N1 G 7 1_555 B DC 12 B N3 DC 3 1_555 hydrog WATSON-CRICK A G 7 A N2 G 7 1_555 B DC 12 B O2 DC 3 1_555 hydrog WATSON-CRICK A G 7 A O6 G 7 1_555 B DC 12 B N4 DC 3 1_555 hydrog WATSON-CRICK A A 8 A N1 A 8 1_555 B DT 11 B N3 DT 2 1_555 hydrog WATSON-CRICK A A 8 A N6 A 8 1_555 B DT 11 B O4 DT 2 1_555 hydrog WATSON-CRICK A C 9 A N3 C 9 1_555 B DG 10 B N1 DG 1 1_555 hydrog WATSON-CRICK A C 9 A N4 C 9 1_555 B DG 10 B O6 DG 1 1_555 hydrog WATSON-CRICK A C 9 A O2 C 9 1_555 B DG 10 B N2 DG 1 1_555 DNA-RNA HYBRID DOUBLE HELIX, DNA/RNA HYBRID, DNA-RNA HYBRID 1DRN PDB 1 1DRN 1DRN PDB 2 1DRN 1 9 1DRN 1 9 1DRN A 1 1 9 10 18 1DRN 10 18 1DRN B 2 1 9 1 P 1