1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Trempe, J.-F. Gehring, K. 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 C9 H13 F N3 O7 P 325.188 n 4-amino-1-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)pyrimidin-2(1H)-one 2'-FLUORO-2'-DEOXY-CYTIDINE-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 C10 H13 F N5 O7 P 365.212 n 2-AMINO-9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE 2'-FLUORO-2-DEOXY-GUANOSINE-5'-MONOPHOSPHATE DNA linking C10 H14 F N2 O8 P 340.199 n 2'-DEOXY-2'-FLUORO-ARABINO-FURANOSYL THYMINE-5'-PHOSPHATE DNA linking US J.Am.Chem.Soc. JACSAT 0004 0002-7863 123 4896 4903 10.1021/ja003859p 11457316 NMR solution structure of an oligonucleotide hairpin with a 2'F-ANA/RNA stem: implications for RNase H specificity toward DNA/RNA hybrid duplexes. 2001 10.2210/pdb1fc8/pdb pdb_00001fc8 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 3790.341 5'-R(*GP*GP*AP*CP)D(*TP*TP*CP*GP*(GFL)P*(TAF)P*(CFL)P*(CFL))-3' 1 syn polymer RNA/2'F-ANA HAIRPIN no yes GGAC(DT)(DT)(DC)(DG)(GFL)(TAF)(CFL)(CFL) GGACTTCGGTCC A polydeoxyribonucleotide/polyribonucleotide hybrid n n n n n n n n n n n n -4.075 1 19 A 1 A 12 -1.939 A_G1:CFL12_A 1 -4.793 -0.396 0.080 -0.303 1.420 1 19 A 2 A 11 3.196 A_G2:CFL11_A 2 -9.232 -1.075 -0.446 -0.507 10.512 1 20 A 3 A 10 3.408 A_A3:TAF10_A 3 -2.561 -0.051 -0.723 -0.320 14.008 1 19 A 4 A 9 3.096 A_C4:GFL9_A 4 0.533 0.717 -0.343 -0.254 3.595 32.689 A A 1 2 -3.683 A A 12 11 3.480 -2.066 0.592 -1.230 AA_G1G2:CFL11CFL12_AA 1 4.064 -7.243 32.379 -1.797 -0.288 2.891 37.824 A A 2 3 13.456 A A 11 10 3.147 8.650 0.764 -0.733 AA_G2A3:TAF10CFL11_AA 2 -0.796 1.239 36.849 -2.172 -1.275 3.320 33.636 A A 3 4 6.339 A A 10 9 3.546 3.661 0.800 -1.741 AA_A3C4:GFL9TAF10_AA 3 -0.908 1.572 33.430 -3.638 -1.539 database_2 pdbx_struct_assembly pdbx_struct_oper_list struct_conn repository Initial release Version format compliance Version format compliance Database references Derived calculations 1 0 2001-05-30 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag RCSB Y RCSB 2000-07-18 REL REL SOLID PHASE SYNTHESIS; PHOSPHORAMIDITE CHEMISTRY sample This structure was determined using standard 2D homonuclear techniques. RMSD FROM AVERAGE LOWER THAN 0.7 ANGSTROM 5 5 2D NOESY 2D NOESY DQF-COSY 2D 1H-13C HMQC 2D 1H-31P HETCOR 2D 1H-19F HETCOR 0.066 7.2 ambient 293 K SA at 15000K for 15 psec from random coordinates. Refinement from lower energy structure at 3000K fro 9 psec. 5 structures generated. Total of 305 restraints: 98 intraresidue NOE-derived distance constraints, 94 sequential NOE-derived distance constraints, 3 long range NOE-derived distance constraints, 15 distance restraints from hydrogen bonds, 91 dihedral angle restraints, 4 planarity constraints for base pairs Distance geometry, simulated annealing 3 closest to the average 0.5 mM Oligonucleotide hairpin; 90% H2O, 10% D2O 90% H2O/10% D2O 0.5 mM Oligonucleotide hairpin; D2O D2O BRUNGER structure solution X-PLOR 3.843 BRUNGER refinement X-PLOR 3.843 500 Bruker DRX 400 Bruker DMX 750 Varian UNITYPLUS G 1 n 1 G 1 A G 2 n 2 G 2 A A 3 n 3 A 3 A C 4 n 4 C 4 A T 5 n 5 DT 5 A T 6 n 6 DT 6 A C 7 n 7 DC 7 A G 8 n 8 DG 8 A +G 9 n 9 GFL 9 A +T 10 n 10 TAF 10 A +C 11 n 11 CFL 11 A +C 12 n 12 CFL 12 A author_defined_assembly 1 monomeric A GFL 9 A GFL 9 DG A TAF 10 A TAF 10 DT A CFL 11 A CFL 11 DC A CFL 12 A CFL 12 DC 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 2 A A HO2' O4' C DT 4 5 1.56 3 A A O2 H22 DT DG 6 8 1.60 1 4.72 0.50 113.10 117.82 A A A N7 C8 N9 G G G 1 1 1 N 1 -2.52 0.40 106.40 103.88 A A A C8 N9 C4 G G G 1 1 1 N 1 4.71 0.50 113.10 117.81 A A A N7 C8 N9 G G G 2 2 2 N 1 -2.72 0.40 106.40 103.68 A A A C8 N9 C4 G G G 2 2 2 N 1 3.68 0.50 113.80 117.48 A A A N7 C8 N9 A A A 3 3 3 N 1 2.23 0.30 108.30 110.53 A A A O4' C1' N1 DT DT DT 5 5 5 N 1 2.24 0.30 108.30 110.54 A A A O4' C1' N1 DT DT DT 6 6 6 N 1 2.19 0.30 108.30 110.49 A A A O4' C1' N9 DG DG DG 8 8 8 N 1 4.96 0.50 113.10 118.06 A A A N7 C8 N9 DG DG DG 8 8 8 N 2 4.68 0.50 113.10 117.78 A A A N7 C8 N9 G G G 1 1 1 N 2 -2.46 0.40 106.40 103.94 A A A C8 N9 C4 G G G 1 1 1 N 2 4.76 0.50 113.10 117.86 A A A N7 C8 N9 G G G 2 2 2 N 2 -2.62 0.40 106.40 103.78 A A A C8 N9 C4 G G G 2 2 2 N 2 3.76 0.50 113.80 117.56 A A A N7 C8 N9 A A A 3 3 3 N 2 2.01 0.30 108.30 110.31 A A A O4' C1' N1 DT DT DT 6 6 6 N 2 2.60 0.30 108.30 110.90 A A A O4' C1' N9 DG DG DG 8 8 8 N 2 4.93 0.50 113.10 118.03 A A A N7 C8 N9 DG DG DG 8 8 8 N 3 4.67 0.50 113.10 117.77 A A A N7 C8 N9 G G G 1 1 1 N 3 -2.52 0.40 106.40 103.88 A A A C8 N9 C4 G G G 1 1 1 N 3 4.59 0.50 113.10 117.69 A A A N7 C8 N9 G G G 2 2 2 N 3 -2.68 0.40 106.40 103.72 A A A C8 N9 C4 G G G 2 2 2 N 3 3.74 0.50 113.80 117.54 A A A N7 C8 N9 A A A 3 3 3 N 3 2.71 0.30 108.30 111.01 A A A O4' C1' N1 DT DT DT 6 6 6 N 3 2.64 0.30 108.30 110.94 A A A O4' C1' N1 DC DC DC 7 7 7 N 3 2.39 0.30 108.30 110.69 A A A O4' C1' N9 DG DG DG 8 8 8 N 3 4.88 0.50 113.10 117.98 A A A N7 C8 N9 DG DG DG 8 8 8 N 3 -2.47 0.40 106.40 103.93 A A A C8 N9 C4 DG DG DG 8 8 8 N 4 4.70 0.50 113.10 117.80 A A A N7 C8 N9 G G G 1 1 1 N 4 -2.54 0.40 106.40 103.86 A A A C8 N9 C4 G G G 1 1 1 N 4 4.63 0.50 113.10 117.73 A A A N7 C8 N9 G G G 2 2 2 N 4 -2.70 0.40 106.40 103.70 A A A C8 N9 C4 G G G 2 2 2 N 4 3.67 0.50 113.80 117.47 A A A N7 C8 N9 A A A 3 3 3 N 4 1.97 0.30 108.30 110.27 A A A O4' C1' N1 DT DT DT 5 5 5 N 4 2.88 0.30 108.30 111.18 A A A O4' C1' N1 DC DC DC 7 7 7 N 4 3.17 0.30 108.30 111.47 A A A O4' C1' N9 DG DG DG 8 8 8 N 4 4.83 0.50 113.10 117.93 A A A N7 C8 N9 DG DG DG 8 8 8 N 5 4.56 0.50 113.10 117.66 A A A N7 C8 N9 G G G 1 1 1 N 5 -2.50 0.40 106.40 103.90 A A A C8 N9 C4 G G G 1 1 1 N 5 4.53 0.50 113.10 117.63 A A A N7 C8 N9 G G G 2 2 2 N 5 -2.67 0.40 106.40 103.73 A A A C8 N9 C4 G G G 2 2 2 N 5 3.76 0.50 113.80 117.56 A A A N7 C8 N9 A A A 3 3 3 N 5 4.21 0.70 108.50 112.71 A A A O4' C1' N1 C C C 4 4 4 N 5 2.01 0.30 108.30 110.31 A A A O4' C1' N1 DT DT DT 5 5 5 N 5 1.89 0.30 108.30 110.19 A A A O4' C1' N1 DT DT DT 6 6 6 N 5 2.44 0.30 108.30 110.74 A A A O4' C1' N1 DC DC DC 7 7 7 N 5 3.15 0.30 108.30 111.45 A A A O4' C1' N9 DG DG DG 8 8 8 N 5 4.67 0.50 113.10 117.77 A A A N7 C8 N9 DG DG DG 8 8 8 N NMR SOLUTION STRUCTURE OF A CHIMERIC OLIGONUCLEOTIDE HAIRPIN R(GGAC)D(TTCG)2'F-A(GTCC) 1 N N covale 1.619 both A DG 8 A O3' DG 8 1_555 A GFL 9 A P GFL 9 1_555 covale 1.623 one A GFL 9 A O3' GFL 9 1_555 A TAF 10 A P TAF 10 1_555 covale 1.622 one A TAF 10 A O3' TAF 10 1_555 A CFL 11 A P CFL 11 1_555 covale 1.616 one A CFL 11 A O3' CFL 11 1_555 A CFL 12 A P CFL 12 1_555 hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 A CFL 12 A N3 CFL 12 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 A CFL 12 A O2 CFL 12 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 A CFL 12 A N4 CFL 12 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 A CFL 11 A N3 CFL 11 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 A CFL 11 A O2 CFL 11 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 A CFL 11 A N4 CFL 11 1_555 hydrog WATSON-CRICK A A 3 A N1 A 3 1_555 A TAF 10 A N3 TAF 10 1_555 hydrog WATSON-CRICK A A 3 A N6 A 3 1_555 A TAF 10 A O4 TAF 10 1_555 hydrog WATSON-CRICK A C 4 A N3 C 4 1_555 A GFL 9 A N1 GFL 9 1_555 hydrog WATSON-CRICK A C 4 A N4 C 4 1_555 A GFL 9 A O6 GFL 9 1_555 hydrog WATSON-CRICK A C 4 A O2 C 4 1_555 A GFL 9 A N2 GFL 9 1_555 hydrog DT-GFL MISPAIR A DT 5 A O2 DT 5 1_555 A GFL 9 A N1 GFL 9 1_555 RNA/DNA CHIMERA 2'F-ARABINONUCLEIC ACID, RNA, DNA, HYBRID DUPLEX, HAIRPIN, RNA-DNA CHIMERA COMPLEX 1FC8 PDB 1 1FC8 1 12 1FC8 1 12 1FC8 A 1 1 12 1 P 1