1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Chen, X. McDowell, J.A. Kierzek, R. Krugh, T.R. Turner, D.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 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 39 8970 8982 10.1021/bi992938e 10913310 Nuclear magnetic resonance spectroscopy and molecular modeling reveal that different hydrogen bonding patterns are possible for G.U pairs: one hydrogen bond for each G.U pair in r(GGCGUGCC)(2) and two for each G.U pair in r(GAGUGCUC)(2). 2000 10.2210/pdb1eka/pdb pdb_00001eka 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 2542.561 RNA (5'-R(*GP*AP*GP*UP*GP*CP*UP*C)-3') 2 syn polymer no no GAGUGCUC GAGUGCUC A,B polyribonucleotide n n n n n n n n -10.745 1 19 A 1 B 8 -0.733 A_G1:C8_B 1 -11.610 -0.542 -0.225 -0.123 -7.188 1 20 A 2 B 7 -0.135 A_A2:U7_B 2 -9.294 0.172 -0.164 0.029 -1.001 1 19 A 3 B 6 -0.690 A_G3:C6_B 3 -9.454 -0.328 -0.059 -0.072 3.017 1 28 A 4 B 5 5.973 A_U4:G5_B 4 -9.007 2.175 -0.198 -0.293 0.413 1 28 A 5 B 4 4.166 A_G5:U4_B 5 -7.854 -2.169 -0.018 -0.311 4.315 1 19 A 6 B 3 -0.521 A_C6:G3_B 6 -10.624 0.331 -0.052 -0.064 11.085 1 20 A 7 B 2 0.161 A_U7:A2_B 7 -9.210 -0.184 -0.228 0.039 18.450 1 19 A 8 B 1 -0.675 A_C8:G1_B 8 -13.024 0.545 -0.432 -0.096 2.834 33.452 A A 1 2 11.709 B B 8 7 3.175 6.693 0.263 -1.492 AA_G1A2:U7C8_BB 1 2.039 -3.568 32.733 -3.619 -0.144 2.730 29.620 A A 2 3 11.021 B B 7 6 3.108 5.602 0.193 -1.747 AA_A2G3:C6U7_BB 2 -0.155 0.305 29.097 -4.483 -0.408 3.280 38.617 A A 3 4 -0.033 B B 6 5 3.261 -0.022 0.598 -1.607 AA_G3U4:G5C6_BB 3 1.393 -2.107 38.593 -2.427 -0.733 3.115 16.049 A A 4 5 10.227 B B 5 4 3.561 2.835 -0.339 -2.313 AA_U4G5:U4G5_BB 4 -1.661 5.989 15.712 -10.407 -0.028 3.275 38.855 A A 5 6 -0.279 B B 4 3 3.260 -0.186 -0.518 -1.584 AA_G5C6:G3U4_BB 5 -0.673 1.012 38.849 -2.359 0.697 2.746 29.678 A A 6 7 10.949 B B 3 2 3.108 5.576 -0.272 -1.667 AA_C6U7:A2G3_BB 6 0.288 -0.565 29.160 -4.313 0.586 2.823 33.218 A A 7 8 11.181 B B 2 1 3.133 6.354 -0.182 -1.393 AA_U7C8:G1A2_BB 7 -0.908 1.598 32.610 -3.414 0.179 database_2 pdbx_struct_assembly pdbx_struct_oper_list repository Initial release Version format compliance Version format compliance Database references Derived calculations 1 0 2000-11-13 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-16 _database_2.pdbx_DOI _database_2.pdbx_database_accession RCSB Y RCSB 2000-03-07 REL REL 1 0.1M 7 ambient 32 K Simulated annealing, Molecular dynamics, Energy minimization minimized average structure 3.5 mM RNA Oligomer 10 mM phosphate, 80 mM NaCl, 100 D2O 1.5 mM RNA Oligomer 10 mM Phosphate, 80 mM NaCl, 10% D2O, 90 % H2O 500 Varian UNITYPLUS 500 Varian INOVA G 1 n 1 G 1 A A 2 n 2 A 2 A G 3 n 3 G 3 A U 4 n 4 U 4 A G 5 n 5 G 5 A C 6 n 6 C 6 A U 7 n 7 U 7 A C 8 n 8 C 8 A G 1 n 1 G 1 B A 2 n 2 A 2 B G 3 n 3 G 3 B U 4 n 4 U 4 B G 5 n 5 G 5 B C 6 n 6 C 6 B U 7 n 7 U 7 B C 8 n 8 C 8 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 U 7 0.064 SIDE CHAIN 1 B U 7 0.067 SIDE CHAIN 1 5.46 0.70 108.50 113.96 A A A O4' C1' N1 U U U 4 4 4 N 1 4.23 0.70 108.50 112.73 A A A O4' C1' N9 G G G 5 5 5 N 1 4.74 0.70 108.50 113.24 A A A O4' C1' N1 C C C 6 6 6 N 1 5.15 0.70 108.50 113.65 B B B O4' C1' N1 U U U 4 4 4 N 1 4.36 0.70 108.50 112.86 B B B O4' C1' N1 C C C 6 6 6 N minimized average NMR AND MOLECULAR MODELING REVEAL THAT DIFFERENT HYDROGEN BONDING PATTERNS ARE POSSIBLE FOR GU PAIRS: ONE HYDROGEN BOND FOR EACH GU PAIR IN R(GGCGUGCC)2 AND TWO FOR EACH GU PAIR IN R(GAGUGCUC)2 1 N N 1 N N hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 B C 8 B N3 C 8 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 B C 8 B O2 C 8 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 B C 8 B N4 C 8 1_555 hydrog WATSON-CRICK A A 2 A N1 A 2 1_555 B U 7 B N3 U 7 1_555 hydrog WATSON-CRICK A A 2 A N6 A 2 1_555 B U 7 B O4 U 7 1_555 hydrog WATSON-CRICK A G 3 A N1 G 3 1_555 B C 6 B N3 C 6 1_555 hydrog WATSON-CRICK A G 3 A N2 G 3 1_555 B C 6 B O2 C 6 1_555 hydrog WATSON-CRICK A G 3 A O6 G 3 1_555 B C 6 B N4 C 6 1_555 hydrog TYPE_28_PAIR A U 4 A N3 U 4 1_555 B G 5 B O6 G 5 1_555 hydrog TYPE_28_PAIR A U 4 A O2 U 4 1_555 B G 5 B N1 G 5 1_555 hydrog TYPE_28_PAIR A G 5 A N1 G 5 1_555 B U 4 B O2 U 4 1_555 hydrog TYPE_28_PAIR A G 5 A O6 G 5 1_555 B U 4 B N3 U 4 1_555 hydrog WATSON-CRICK A C 6 A N3 C 6 1_555 B G 3 B N1 G 3 1_555 hydrog WATSON-CRICK A C 6 A N4 C 6 1_555 B G 3 B O6 G 3 1_555 hydrog WATSON-CRICK A C 6 A O2 C 6 1_555 B G 3 B N2 G 3 1_555 hydrog WATSON-CRICK A U 7 A N3 U 7 1_555 B A 2 B N1 A 2 1_555 hydrog WATSON-CRICK A U 7 A O4 U 7 1_555 B A 2 B N6 A 2 1_555 hydrog WATSON-CRICK A C 8 A N3 C 8 1_555 B G 1 B N1 G 1 1_555 hydrog WATSON-CRICK A C 8 A N4 C 8 1_555 B G 1 B O6 G 1 1_555 hydrog WATSON-CRICK A C 8 A O2 C 8 1_555 B G 1 B N2 G 1 1_555 RNA RNA, GU Pair, Hydrogen Bonds, Duble Helix 1EKA PDB 1 1EKA 1 8 1EKA 1 8 1EKA A 1 1 8 1 8 1EKA 1 8 1EKA B 1 1 8 1 P 1