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. Ohtsuka, E. Nakamura, H. 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 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 C10 H16 N3 O8 P 337.223 n O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE RNA linking C11 H16 N5 O8 P 377.247 n O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE RNA linking C10 H15 N2 O9 P 338.208 n O2'-METHYLURIDINE 5'-MONOPHOSPHATE RNA linking C9 H13 N2 O9 P 324.181 y URIDINE-5'-MONOPHOSPHATE RNA linking US Biochemistry BICHAW 0033 0006-2960 36 2577 2585 10.1021/bi962297c 9054564 Solution structure of an RNA.2'-O-methylated RNA hybrid duplex containing an RNA.DNA hybrid segment at the center. 1997 10.2210/pdb1nao/pdb pdb_00001nao 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 A SUBSTRATE OF RNASE H 2934.831 RNA (5'-R(*GP*GP*AP*GP*AP*UP*GP*AP*C)-3') 1 syn polymer A SUBSTRATE OF RNASE H 2802.865 DNA/RNA (5'-R(*OMGP*OMUP*OMC)-D(P*AP*TP*CP*T)-R(P*OMCP*OMC)-3') 1 syn polymer no no GGAGAUGAC GGAGAUGAC A polyribonucleotide no yes (OMG)(OMU)(OMC)(DA)(DT)(DC)(DT)(OMC)(OMC) GUCATCTCC B polydeoxyribonucleotide/polyribonucleotide hybrid n n n n n n n n n n n n n n n n n n -2.528 1 19 A 1 B 18 0.259 A_G1:OMC18_B 1 0.759 -0.633 -0.094 -0.327 -1.293 1 19 A 2 B 17 2.598 A_G2:OMC17_B 2 -12.662 -0.895 0.036 -0.376 0.589 1 20 A 3 B 16 -3.118 A_A3:DT16_B 3 0.971 -0.219 -0.326 -0.212 2.800 1 19 A 4 B 15 -0.586 A_G4:DC15_B 4 -5.671 -0.360 0.149 -0.267 -5.205 1 20 A 5 B 14 -3.545 A_A5:DT14_B 5 -5.529 0.057 -0.170 -0.123 8.351 1 20 A 6 B 13 -0.610 A_U6:DA13_B 6 -6.664 0.581 -0.225 -0.276 -6.473 1 19 A 7 B 12 6.064 A_G7:OMC12_B 7 -8.654 -1.023 -0.543 -0.395 2.847 1 20 A 8 B 11 -14.621 A_A8:OMU11_B 8 -4.469 1.480 -0.061 -0.158 6.487 1 19 A 9 B 10 2.063 A_C9:OMG10_B 9 0.254 0.684 -0.274 -0.140 3.687 41.487 A A 1 2 -4.571 B B 18 17 3.528 -3.227 -1.260 -0.522 AA_G1G2:OMC17OMC18_BB 1 -5.407 7.660 41.028 -0.356 1.141 3.752 41.262 A A 2 3 -23.597 B B 17 16 4.061 -16.207 -1.237 0.190 AA_G2A3:DT16OMC17_BB 2 -2.496 3.634 37.995 2.449 1.419 3.925 30.406 A A 3 4 18.620 B B 16 15 4.092 9.606 0.470 0.080 AA_A3G4:DC15DT16_BB 3 0.615 -1.191 28.877 -2.271 -0.740 3.406 43.590 A A 4 5 33.810 B B 15 14 3.812 23.815 -1.454 0.118 AA_G4A5:DT14DC15_BB 4 -3.769 5.352 36.588 -2.620 1.519 2.911 27.049 A A 5 6 -3.806 B B 14 13 2.851 -1.778 0.753 -1.575 AA_A5U6:DA13DT14_BB 5 -1.179 2.523 26.967 -2.969 -1.874 1.906 36.366 A A 6 7 34.320 B B 13 12 3.473 20.254 0.815 -1.759 AA_U6G7:OMC12DA13_BB 6 -2.073 3.512 30.293 -5.370 -1.568 3.132 44.543 A A 7 8 3.869 B B 12 11 3.018 2.929 -2.589 -0.567 AA_G7A8:OMU11OMC12_BB 7 -2.905 3.838 44.361 -1.002 3.164 3.717 28.593 A A 8 9 -7.517 B B 11 10 3.219 -3.693 2.319 -2.049 AA_A8C9:OMG10OMU11_BB 8 3.660 -7.450 28.126 -3.252 -3.808 database_2 pdbx_database_status pdbx_struct_assembly pdbx_struct_oper_list struct_conn repository Initial release Version format compliance Version format compliance Database references Derived calculations Other 1 0 1997-01-27 1 1 2008-03-10 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.process_site _struct_conn.pdbx_dist_value _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 Y BNL 1996-03-29 REL REL 00MM NACL, 50MM NA PHOSPHATE, 3MM EDTA AVERAGED 10 1 7.0 313 K simulated annealing BRUNGER refinement X-PLOR 3.1F 3.1F structure solution X-PLOR 600 Bruker AMX600 G 1 n 1 G 1 A G 2 n 2 G 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 G 7 A A 8 n 8 A 8 A C 9 n 9 C 9 A OMG 10 n 1 OMG 10 B OMU 11 n 2 OMU 11 B OMC 12 n 3 OMC 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 OMC 17 n 8 OMC 17 B OMC 18 n 9 OMC 18 B author_defined_assembly 2 dimeric B OMG 10 O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE B OMG 1 G B OMU 11 O2'-METHYLURIDINE 5'-MONOPHOSPHATE B OMU 2 U B OMC 12 O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE B OMC 3 C B OMC 17 O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE B OMC 8 C B OMC 18 O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE B OMC 9 C 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 5.17 0.80 101.50 106.67 A A A C3' C2' C1' G G G 1 1 1 N 1 4.37 0.50 113.10 117.47 A A A N7 C8 N9 G G G 1 1 1 N 1 -2.47 0.40 106.40 103.93 A A A C8 N9 C4 G G G 1 1 1 N 1 4.56 0.50 113.10 117.66 A A A N7 C8 N9 G G G 2 2 2 N 1 3.82 0.50 113.80 117.62 A A A N7 C8 N9 A A A 3 3 3 N 1 4.52 0.50 113.10 117.62 A A A N7 C8 N9 G G G 4 4 4 N 1 -2.59 0.40 106.40 103.81 A A A C8 N9 C4 G G G 4 4 4 N 1 4.25 0.50 113.80 118.05 A A A N7 C8 N9 A A A 5 5 5 N 1 5.28 0.80 101.50 106.78 A A A C3' C2' C1' U U U 6 6 6 N 1 4.93 0.70 108.50 113.43 A A A O4' C1' N1 U U U 6 6 6 N 1 4.94 0.80 101.50 106.44 A A A C3' C2' C1' G G G 7 7 7 N 1 4.43 0.50 113.10 117.53 A A A N7 C8 N9 G G G 7 7 7 N 1 3.73 0.50 113.80 117.53 A A A N7 C8 N9 A A A 8 8 8 N 1 2.51 0.30 108.30 110.81 B B B O4' C1' N9 DA DA DA 13 13 13 N 1 4.05 0.50 113.80 117.85 B B B N7 C8 N9 DA DA DA 13 13 13 N 1 3.31 0.30 108.30 111.61 B B B O4' C1' N1 DT DT DT 14 14 14 N 1 3.40 0.30 108.30 111.70 B B B O4' C1' N1 DC DC DC 15 15 15 N 1 3.16 0.30 108.30 111.46 B B B O4' C1' N1 DT DT DT 16 16 16 N model building X-PLOR 3.1 refinement X-PLOR 3.1 phasing X-PLOR 3.1 SOLUTION STRUCTURE OF AN RNA 2'-O-METHYLATED RNA DUPLEX CONTAINING AN RNA/DNA HYBRID SEGMENT AT THE CENTER, NMR, MINIMIZED AVERAGE STRUCTURE 1 N N 2 N N covale 1.618 both B OMG 10 B O3' OMG 1 1_555 B OMU 11 B P OMU 2 1_555 covale 1.609 both B OMU 11 B O3' OMU 2 1_555 B OMC 12 B P OMC 3 1_555 covale 1.617 both B OMC 12 B O3' OMC 3 1_555 B DA 13 B P DA 4 1_555 covale 1.621 both B DT 16 B O3' DT 7 1_555 B OMC 17 B P OMC 8 1_555 covale 1.615 both B OMC 17 B O3' OMC 8 1_555 B OMC 18 B P OMC 9 1_555 hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 B OMC 18 B N3 OMC 9 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 B OMC 18 B O2 OMC 9 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 B OMC 18 B N4 OMC 9 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 B OMC 17 B N3 OMC 8 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 B OMC 17 B O2 OMC 8 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 B OMC 17 B N4 OMC 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 G 7 A N1 G 7 1_555 B OMC 12 B N3 OMC 3 1_555 hydrog WATSON-CRICK A G 7 A N2 G 7 1_555 B OMC 12 B O2 OMC 3 1_555 hydrog WATSON-CRICK A G 7 A O6 G 7 1_555 B OMC 12 B N4 OMC 3 1_555 hydrog WATSON-CRICK A A 8 A N1 A 8 1_555 B OMU 11 B N3 OMU 2 1_555 hydrog WATSON-CRICK A A 8 A N6 A 8 1_555 B OMU 11 B O4 OMU 2 1_555 hydrog WATSON-CRICK A C 9 A N3 C 9 1_555 B OMG 10 B N1 OMG 1 1_555 hydrog WATSON-CRICK A C 9 A N4 C 9 1_555 B OMG 10 B O6 OMG 1 1_555 hydrog WATSON-CRICK A C 9 A O2 C 9 1_555 B OMG 10 B N2 OMG 1 1_555 DNA-RNA HYBRID DNA/RNA DUPLEX, DNA-RNA HYBRID 1NAO PDB 1 1NAO 1NAO PDB 2 1NAO 1 9 1NAO 1 9 1NAO A 1 1 9 10 18 1NAO 10 18 1NAO B 2 1 9 1 P 1