1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Denisov, A.Y. Hannoush, R.N. Gehring, K. Damha, M.J. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C10 H14 N5 O8 P 363.221 GUANOSINE-5'-MONOPHOSPHATE non-polymer 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 H14 N3 O8 P 323.197 CYTIDINE-5'-MONOPHOSPHATE non-polymer 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 C9 H13 N2 O9 P 324.181 URIDINE-5'-MONOPHOSPHATE non-polymer US J.AM.CHEM.SOC. JACSAT 0004 0002-7863 125 11525 11531 10.1021/ja036207k 13129354 A Novel RNA Motif Based on the Structure of Unusually Stable 2',5'-Linked r(UUCG) Loops 2003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 SINGLE WAVELENGTH M x-ray 1 1.0 3804.296 5'-R(*GP*GP*AP*CP*(U25)P*(U25)P*(C25)P*(5GP)P*GP*UP*CP*C)-3' 1 syn polymer no yes GGAC(U5P)(U5P)(C5P)(5GP)GUCC GGACXXXXGUCC A polyribonucleotide n n n n n n n n n n n n -13.203 1 19 A 1 A 12 1.107 A_G1:C12_A 1 -3.782 -0.379 -0.340 -0.326 0.316 1 19 A 2 A 11 4.841 A_G2:C11_A 2 -4.781 -1.287 -0.196 -0.500 9.817 1 20 A 3 A 10 -2.526 A_A3:U10_A 3 -7.317 -0.162 -0.162 -0.402 1.433 1 19 A 4 A 9 5.464 A_C4:G9_A 4 -3.632 0.769 -0.284 -0.191 2.844 31.491 A A 1 2 0.561 A A 12 11 2.858 0.304 -0.104 -1.276 AA_G1G2:C11C12_AA 1 -2.735 5.045 31.374 -2.401 -0.253 2.855 44.156 A A 2 3 14.540 A A 11 10 2.744 10.813 -1.670 0.168 AA_G2A3:U10C11_AA 2 -4.450 5.984 42.655 -0.660 1.858 2.348 38.774 A A 3 4 21.792 A A 10 9 3.111 14.150 1.545 -1.810 AA_A3C4:G9U10_AA 3 2.094 -3.225 36.134 -4.226 -2.106 repository Initial release Version format compliance Version format compliance Non-polymer description 1 0 2003-08-19 1 1 2008-04-28 1 2 2011-07-13 1 3 2011-08-24 CHIMERIC HAIRPIN WITH 2',5'-LINKED RNA LOOP AND DNA STEM COMPOUND NUCLOTIDES 5(U25), 6(U25), 7(C25), 8(5GP) HAS A NON-STANDARD 2'-5' LINKAGE. RCSB Y RCSB 2002-08-07 REL REL Solid phase synthesis, phosphoramidite chemistry sample Structure was determined using standard 2D homo- and heteronuclear techniques: 2D-NOESY, DQF-COSY, TOCSY, H,C-HMQC, H,P-HetCOSY STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS, STRUCTURES WITH THE LOWEST ENERGY 20 10 2D NOESY DQF-COSY 7.0 1 atm 288 K Structures were refined by NMR-restrained molecular dynamics (12 ps, 300-1000 K) with final energy minimization simulated annealing 1 closest to the average, lowest energy 1.5 mM hairpin D2O, H2O/D2O Brunger refinement X-PLOR 3.851 Brunger data analysis X-PLOR 500 Bruker DRX 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 U5P 5 n 5 U5P 5 A U5P 6 n 6 U5P 6 A C5P 7 n 7 C5P 7 A 5GP 8 n 8 5GP 8 A G 9 n 9 G 9 A U 10 n 10 U 10 A C 11 n 11 C 11 A C 12 n 12 C 12 A author_defined_assembly 1 monomeric 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 H21 O2 G C 1 12 1.56 2 A A H21 O2 G C 1 12 1.57 2 A A O2 H21 C G 4 9 1.60 3 A A H21 O2 G C 2 11 1.59 3 A A O2 H21 C G 4 9 1.60 4 A A O2 H21 C G 4 9 1.57 4 A A O2 HN1 U5P 5GP 5 8 1.60 5 A A H21 O2 G C 1 12 1.58 5 A A HO2' O4' C C 11 12 1.59 5 A A O2 H21 C G 4 9 1.59 5 A A O2 HN1 U5P 5GP 5 8 1.60 6 A A H21 O2 G C 2 11 1.56 6 A A HN3 O6 U5P 5GP 5 8 1.57 6 A A HO3' O2P C5P 5GP 7 8 1.59 6 A A H61 O4 A U 3 10 1.59 7 A A O2 H21 C G 4 9 1.56 7 A A H21 O2 G C 2 11 1.57 7 A A H21 O2 G C 1 12 1.58 8 A A HO2' O5' G A 2 3 1.54 8 A A O2 H21 C G 4 9 1.56 8 A A HO2' O4' G G 1 2 1.57 8 A A O2 HN1 U5P 5GP 5 8 1.59 8 A A H21 O2 G C 1 12 1.60 9 A A O2 H21 C G 4 9 1.58 9 A A O2 HN1 U5P 5GP 5 8 1.60 10 A A HO3' O2P C5P 5GP 7 8 1.54 10 A A HO2' O4' U C 10 11 1.57 10 A A HO2' O4' C C 11 12 1.57 10 A A HN3 O6 U5P 5GP 5 8 1.60 1 A A O3' P U5P U5P 5 6 3.08 1 A A O3' P U5P C5P 6 7 4.18 1 A A O3' P C5P 5GP 7 8 4.15 1 A A O3' P 5GP G 8 9 3.55 2 A A O3' P U5P U5P 5 6 3.23 2 A A O3' P U5P C5P 6 7 4.20 2 A A O3' P C5P 5GP 7 8 4.14 2 A A O3' P 5GP G 8 9 3.52 3 A A O3' P U5P U5P 5 6 3.20 3 A A O3' P U5P C5P 6 7 4.17 3 A A O3' P C5P 5GP 7 8 4.11 3 A A O3' P 5GP G 8 9 3.52 4 A A O3' P U5P U5P 5 6 3.04 4 A A O3' P U5P C5P 6 7 4.18 4 A A O3' P C5P 5GP 7 8 4.15 4 A A O3' P 5GP G 8 9 3.50 5 A A O3' P U5P U5P 5 6 3.21 5 A A O3' P U5P C5P 6 7 4.20 5 A A O3' P C5P 5GP 7 8 4.15 5 A A O3' P 5GP G 8 9 3.52 6 A A O3' P U5P U5P 5 6 3.27 6 A A O3' P U5P C5P 6 7 4.18 6 A A O3' P C5P 5GP 7 8 3.07 6 A A O3' P 5GP G 8 9 3.52 7 A A O3' P U5P U5P 5 6 3.06 7 A A O3' P U5P C5P 6 7 4.19 7 A A O3' P C5P 5GP 7 8 4.15 7 A A O3' P 5GP G 8 9 3.53 8 A A O3' P U5P U5P 5 6 3.05 8 A A O3' P U5P C5P 6 7 4.18 8 A A O3' P C5P 5GP 7 8 4.15 8 A A O3' P 5GP G 8 9 3.48 9 A A O3' P U5P U5P 5 6 3.07 9 A A O3' P U5P C5P 6 7 4.18 9 A A O3' P C5P 5GP 7 8 4.16 9 A A O3' P 5GP G 8 9 3.43 10 A A O3' P U5P U5P 5 6 3.18 10 A A O3' P U5P C5P 6 7 4.19 10 A A O3' P C5P 5GP 7 8 3.06 10 A A O3' P 5GP G 8 9 3.52 1 4.44 0.50 113.10 117.54 A A A N7 C8 N9 G G G 1 1 1 N 1 -2.40 0.40 106.40 104.00 A A A C8 N9 C4 G G G 1 1 1 N 1 4.84 0.50 113.10 117.94 A A A N7 C8 N9 G G G 2 2 2 N 1 -2.53 0.40 106.40 103.87 A A A C8 N9 C4 G G G 2 2 2 N 1 4.30 0.50 113.80 118.10 A A A N7 C8 N9 A A A 3 3 3 N 1 4.40 0.50 113.10 117.50 A A A N7 C8 N9 G G G 9 9 9 N 1 -2.44 0.40 106.40 103.96 A A A C8 N9 C4 G G G 9 9 9 N 2 4.36 0.50 113.10 117.46 A A A N7 C8 N9 G G G 1 1 1 N 2 4.90 0.50 113.10 118.00 A A A N7 C8 N9 G G G 2 2 2 N 2 -2.57 0.40 106.40 103.83 A A A C8 N9 C4 G G G 2 2 2 N 2 4.20 0.50 113.80 118.00 A A A N7 C8 N9 A A A 3 3 3 N 2 4.43 0.50 113.10 117.53 A A A N7 C8 N9 G G G 9 9 9 N 2 -2.54 0.40 106.40 103.86 A A A C8 N9 C4 G G G 9 9 9 N 3 4.77 0.50 113.10 117.87 A A A N7 C8 N9 G G G 1 1 1 N 3 -2.58 0.40 106.40 103.82 A A A C8 N9 C4 G G G 1 1 1 N 3 4.54 0.50 113.10 117.64 A A A N7 C8 N9 G G G 2 2 2 N 3 -2.53 0.40 106.40 103.87 A A A C8 N9 C4 G G G 2 2 2 N 3 4.00 0.50 113.80 117.80 A A A N7 C8 N9 A A A 3 3 3 N 3 4.47 0.50 113.10 117.57 A A A N7 C8 N9 G G G 9 9 9 N 3 -2.63 0.40 106.40 103.77 A A A C8 N9 C4 G G G 9 9 9 N 4 4.73 0.50 113.10 117.83 A A A N7 C8 N9 G G G 1 1 1 N 4 -2.59 0.40 106.40 103.81 A A A C8 N9 C4 G G G 1 1 1 N 4 4.49 0.50 113.10 117.59 A A A N7 C8 N9 G G G 2 2 2 N 4 -2.45 0.40 106.40 103.95 A A A C8 N9 C4 G G G 2 2 2 N 4 3.90 0.50 113.80 117.70 A A A N7 C8 N9 A A A 3 3 3 N 4 4.41 0.50 113.10 117.51 A A A N7 C8 N9 G G G 9 9 9 N 4 -2.45 0.40 106.40 103.95 A A A C8 N9 C4 G G G 9 9 9 N 5 4.35 0.50 113.10 117.45 A A A N7 C8 N9 G G G 1 1 1 N 5 4.87 0.50 113.10 117.97 A A A N7 C8 N9 G G G 2 2 2 N 5 -2.53 0.40 106.40 103.87 A A A C8 N9 C4 G G G 2 2 2 N 5 4.37 0.50 113.80 118.17 A A A N7 C8 N9 A A A 3 3 3 N 5 4.46 0.50 113.10 117.56 A A A N7 C8 N9 G G G 9 9 9 N 5 -2.49 0.40 106.40 103.91 A A A C8 N9 C4 G G G 9 9 9 N 6 4.81 0.50 113.10 117.91 A A A N7 C8 N9 G G G 1 1 1 N 6 -2.63 0.40 106.40 103.77 A A A C8 N9 C4 G G G 1 1 1 N 6 4.54 0.50 113.10 117.64 A A A N7 C8 N9 G G G 2 2 2 N 6 -2.56 0.40 106.40 103.84 A A A C8 N9 C4 G G G 2 2 2 N 6 3.93 0.50 113.80 117.73 A A A N7 C8 N9 A A A 3 3 3 N 6 4.50 0.50 113.10 117.60 A A A N7 C8 N9 G G G 9 9 9 N 6 -2.60 0.40 106.40 103.80 A A A C8 N9 C4 G G G 9 9 9 N 7 4.49 0.50 113.10 117.59 A A A N7 C8 N9 G G G 1 1 1 N 7 4.78 0.50 113.10 117.88 A A A N7 C8 N9 G G G 2 2 2 N 7 -2.43 0.40 106.40 103.97 A A A C8 N9 C4 G G G 2 2 2 N 7 4.29 0.50 113.80 118.09 A A A N7 C8 N9 A A A 3 3 3 N 7 4.26 0.50 113.10 117.36 A A A N7 C8 N9 G G G 9 9 9 N 7 -2.40 0.40 106.40 104.00 A A A C8 N9 C4 G G G 9 9 9 N 8 4.48 0.50 113.10 117.58 A A A N7 C8 N9 G G G 1 1 1 N 8 -2.43 0.40 106.40 103.97 A A A C8 N9 C4 G G G 1 1 1 N 8 4.81 0.50 113.10 117.91 A A A N7 C8 N9 G G G 2 2 2 N 8 -2.47 0.40 106.40 103.93 A A A C8 N9 C4 G G G 2 2 2 N 8 4.17 0.50 113.80 117.97 A A A N7 C8 N9 A A A 3 3 3 N 8 4.25 0.50 113.10 117.35 A A A N7 C8 N9 G G G 9 9 9 N 8 -2.51 0.40 106.40 103.89 A A A C8 N9 C4 G G G 9 9 9 N 9 4.53 0.50 113.10 117.63 A A A N7 C8 N9 G G G 1 1 1 N 9 -2.54 0.40 106.40 103.86 A A A C8 N9 C4 G G G 1 1 1 N 9 4.98 0.50 113.10 118.08 A A A N7 C8 N9 G G G 2 2 2 N 9 -2.60 0.40 106.40 103.80 A A A C8 N9 C4 G G G 2 2 2 N 9 4.23 0.50 113.80 118.03 A A A N7 C8 N9 A A A 3 3 3 N 9 4.45 0.50 113.10 117.55 A A A N7 C8 N9 G G G 9 9 9 N 9 -2.52 0.40 106.40 103.88 A A A C8 N9 C4 G G G 9 9 9 N 10 4.49 0.50 113.10 117.59 A A A N7 C8 N9 G G G 1 1 1 N 10 4.82 0.50 113.10 117.92 A A A N7 C8 N9 G G G 2 2 2 N 10 4.28 0.50 113.80 118.08 A A A N7 C8 N9 A A A 3 3 3 N 10 4.27 0.50 113.10 117.37 A A A N7 C8 N9 G G G 9 9 9 N 10 -2.44 0.40 106.40 103.96 A A A C8 N9 C4 G G G 9 9 9 N 5'-R(*GP*GP*AP*CP*(U25)P*(U25)P*(C25)P*(5GP)P*GP*UP*CP*C)-3' Chimeric hairpin with 2',5'-linked RNA loop and RNA stem 1 N N covale 1.615 A C 4 A O3' C 4 1_555 A U5P 5 A P U5P 5 1_555 covale 1.610 A U5P 5 A O2' U5P 5 1_555 A U5P 6 A P U5P 6 1_555 covale 1.614 A U5P 6 A O2' U5P 6 1_555 A C5P 7 A P C5P 7 1_555 covale 1.619 A C5P 7 A O2' C5P 7 1_555 A 5GP 8 A P 5GP 8 1_555 covale 1.615 A 5GP 8 A O2' 5GP 8 1_555 A G 9 A P G 9 1_555 hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 A C 12 A N3 C 12 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 A C 12 A O2 C 12 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 A C 12 A N4 C 12 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 A C 11 A N3 C 11 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 A C 11 A O2 C 11 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 A C 11 A N4 C 11 1_555 hydrog WATSON-CRICK A A 3 A N1 A 3 1_555 A U 10 A N3 U 10 1_555 hydrog WATSON-CRICK A A 3 A N6 A 3 1_555 A U 10 A O4 U 10 1_555 hydrog WATSON-CRICK A C 4 A N3 C 4 1_555 A G 9 A N1 G 9 1_555 hydrog WATSON-CRICK A C 4 A N4 C 4 1_555 A G 9 A O6 G 9 1_555 hydrog WATSON-CRICK A C 4 A O2 C 4 1_555 A G 9 A N2 G 9 1_555 RNA Hairpin, (2', 5')-RNA, RNA 1ME1 PDB 1 1ME1 1 12 1ME1 1 12 1ME1 A 1 1 12