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 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/pdb1dhh/pdb pdb_00001dhh 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 2854.832 DNA/RNA (5'-D(*GP*G)-R(P*AP*GP*AP*U)-D(P*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 RIBONUCLEIC ACID DEOXYRIBONUCLEIC ACID/RIBONUCLEIC ACID DHD DHD no no (DG)(DG)AGAU(DG)(DA)(DC) 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 -2.266 1 19 A 1 B 18 1.153 A_DG1:DC18_B 1 0.102 -0.530 -0.185 -0.306 -3.103 1 19 A 2 B 17 5.848 A_DG2:DC17_B 2 -4.593 -0.694 -0.076 -0.321 2.053 1 20 A 3 B 16 4.670 A_A3:DT16_B 3 -8.970 -0.342 0.180 -0.370 4.345 1 19 A 4 B 15 1.710 A_G4:DC15_B 4 -10.176 -0.225 0.086 -0.303 -3.696 1 20 A 5 B 14 -5.726 A_A5:DT14_B 5 -4.093 -0.412 0.115 -0.242 8.703 1 20 A 6 B 13 10.088 A_U6:DA13_B 6 -7.978 0.165 -0.193 -0.201 -7.184 1 19 A 7 B 12 0.778 A_DG7:DC12_B 7 -1.884 0.161 -0.290 -0.310 0.601 1 20 A 8 B 11 -0.505 A_DA8:DT11_B 8 -1.969 -0.433 0.018 -0.380 2.282 1 19 A 9 B 10 -1.240 A_DC9:DG10_B 9 -0.853 0.615 -0.044 -0.430 3.347 28.942 A A 1 2 -0.678 B B 18 17 3.332 -0.339 0.069 -1.396 AA_DG1DG2:DC17DC18_BB 1 -0.232 0.464 28.939 -2.716 -0.190 3.616 37.415 A A 2 3 2.125 B B 17 16 3.609 1.363 -0.855 0.146 AA_DG2A3:DT16DC17_BB 2 -0.188 0.293 37.390 0.030 1.305 3.357 37.354 A A 3 4 27.227 B B 16 15 3.424 16.843 -0.562 0.707 AA_A3G4:DC15DT16_BB 3 1.801 -2.911 33.415 -1.340 1.139 3.193 33.096 A A 4 5 28.370 B B 15 14 3.484 15.473 -1.226 -0.124 AA_G4A5:DT14DC15_BB 4 -5.761 10.562 28.785 -3.081 1.085 3.067 33.918 A A 5 6 2.628 B B 14 13 2.936 1.527 1.136 -0.056 AA_A5U6:DA13DT14_BB 5 5.184 -8.923 33.497 -0.322 -1.179 3.497 52.301 A A 6 7 44.349 B B 13 12 3.827 35.887 -0.446 0.949 AA_U6DG7:DC12DA13_BB 6 0.601 -0.743 38.689 -2.052 0.558 3.123 27.623 A A 7 8 3.463 B B 12 11 3.234 1.650 -0.319 -1.106 AA_DG7DA8:DT11DC12_BB 7 2.466 -5.174 27.467 -2.708 1.252 3.155 36.240 A A 8 9 4.569 B B 11 10 3.272 2.838 0.419 -1.099 AA_DA8DC9:DG10DT11_BB 8 -1.830 2.946 36.087 -2.159 -0.927 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 1995-10-18 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 A 3 A G 4 n 4 G 4 A A 5 n 5 A 5 A U 6 n 6 U 6 A G 7 n 7 DG 7 A A 8 n 8 DA 8 A C 9 n 9 DC 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 A A 3 0.052 SIDE CHAIN 1 A U 6 0.057 SIDE CHAIN 1 4.06 0.30 108.30 112.36 A A A O4' C1' N9 DG DG DG 1 1 1 N 1 4.39 0.50 113.10 117.49 A A A N7 C8 N9 DG DG DG 1 1 1 N 1 -2.69 0.40 106.40 103.71 A A A C8 N9 C4 DG DG DG 1 1 1 N 1 4.22 0.30 108.30 112.52 A A A O4' C1' N9 DG DG DG 2 2 2 N 1 4.62 0.50 113.10 117.72 A A A N7 C8 N9 DG DG DG 2 2 2 N 1 -2.45 0.40 106.40 103.95 A A A C8 N9 C4 DG DG DG 2 2 2 N 1 3.84 0.50 113.80 117.64 A A A N7 C8 N9 A A A 3 3 3 N 1 5.43 0.80 101.50 106.93 A A A C3' C2' C1' G G G 4 4 4 N 1 4.56 0.50 113.10 117.66 A A A N7 C8 N9 G G G 4 4 4 N 1 4.98 0.80 101.50 106.48 A A A C3' C2' C1' A A A 5 5 5 N 1 4.25 0.50 113.80 118.05 A A A N7 C8 N9 A A A 5 5 5 N 1 2.57 0.30 108.30 110.87 A A A O4' C1' N9 DG DG DG 7 7 7 N 1 4.76 0.50 113.10 117.86 A A A N7 C8 N9 DG DG DG 7 7 7 N 1 -2.43 0.40 106.40 103.97 A A A C8 N9 C4 DG DG DG 7 7 7 N 1 2.54 0.30 108.30 110.84 A A A O4' C1' N9 DA DA DA 8 8 8 N 1 3.81 0.50 113.80 117.61 A A A N7 C8 N9 DA DA DA 8 8 8 N 1 3.06 0.30 108.30 111.36 A A A O4' C1' N1 DC DC DC 9 9 9 N 1 2.95 0.30 108.30 111.25 B B B O4' C1' N9 DG DG DG 10 10 10 N 1 4.63 0.50 113.10 117.73 B B B N7 C8 N9 DG DG DG 10 10 10 N 1 -2.58 0.40 106.40 103.82 B B B C8 N9 C4 DG DG DG 10 10 10 N 1 3.33 0.30 108.30 111.63 B B B O4' C1' N1 DT DT DT 11 11 11 N 1 2.52 0.30 108.30 110.82 B B B O4' C1' N1 DC DC DC 12 12 12 N 1 2.30 0.30 108.30 110.60 B B B O4' C1' N9 DA DA DA 13 13 13 N 1 3.76 0.50 113.80 117.56 B B B N7 C8 N9 DA DA DA 13 13 13 N 1 2.36 0.30 108.30 110.66 B B B O4' C1' N1 DT DT DT 14 14 14 N 1 2.79 0.30 108.30 111.09 B B B O4' C1' N1 DC DC DC 15 15 15 N 1 2.59 0.30 108.30 110.89 B B B O4' C1' N1 DT DT DT 16 16 16 N 1 2.65 0.30 108.30 110.95 B B B O4' C1' N1 DC DC DC 17 17 17 N 1 4.29 0.30 108.30 112.59 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(GG)R(AGAU)D(GAC)/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 A 3 A N1 A 3 1_555 B DT 16 B N3 DT 7 1_555 hydrog WATSON-CRICK A A 3 A N6 A 3 1_555 B DT 16 B O4 DT 7 1_555 hydrog WATSON-CRICK A G 4 A N1 G 4 1_555 B DC 15 B N3 DC 6 1_555 hydrog WATSON-CRICK A G 4 A N2 G 4 1_555 B DC 15 B O2 DC 6 1_555 hydrog WATSON-CRICK A G 4 A O6 G 4 1_555 B DC 15 B N4 DC 6 1_555 hydrog WATSON-CRICK A A 5 A N1 A 5 1_555 B DT 14 B N3 DT 5 1_555 hydrog WATSON-CRICK A A 5 A N6 A 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 DG 7 A N1 DG 7 1_555 B DC 12 B N3 DC 3 1_555 hydrog WATSON-CRICK A DG 7 A N2 DG 7 1_555 B DC 12 B O2 DC 3 1_555 hydrog WATSON-CRICK A DG 7 A O6 DG 7 1_555 B DC 12 B N4 DC 3 1_555 hydrog WATSON-CRICK A DA 8 A N1 DA 8 1_555 B DT 11 B N3 DT 2 1_555 hydrog WATSON-CRICK A DA 8 A N6 DA 8 1_555 B DT 11 B O4 DT 2 1_555 hydrog WATSON-CRICK A DC 9 A N3 DC 9 1_555 B DG 10 B N1 DG 1 1_555 hydrog WATSON-CRICK A DC 9 A N4 DC 9 1_555 B DG 10 B O6 DG 1 1_555 hydrog WATSON-CRICK A DC 9 A O2 DC 9 1_555 B DG 10 B N2 DG 1 1_555 DNA-RNA HYBRID DNA/RNA HYBRID IN DNA DUPLEX, DNA-RNA HYBRID 1DHH PDB 1 1DHH 1DHH PDB 2 1DHH 1 9 1DHH 1 9 1DHH A 1 1 9 10 18 1DHH 10 18 1DHH B 2 1 9 1 P 1