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, G. Kennedy, S.D. Krugh, T.R. Turner, D.H. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 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 C10 H13 N4 O7 P 332.207 n PURINE RIBOSIDE-5'-MONOPHOSPHATE RNA linking C9 H13 N2 O9 P 324.181 y URIDINE-5'-MONOPHOSPHATE RNA linking US Biochemistry BICHAW 0033 0006-2960 45 6889 6903 10.1021/bi0524464 16734425 An Alternating Sheared AA Pair and Elements of Stability for a Single Sheared Purine-Purine Pair Flanked by Sheared GA Pairs in RNA 2006 10.2210/pdb2dd1/pdb pdb_00002dd1 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 3272.996 5'-R(*GP*GP*UP*GP*GP*AP*GP*GP*CP*U)-3' 1 syn polymer 3167.991 5'-R(*GP*CP*CP*GP*AP*AP*AP*CP*CP*(P5P))-3' 1 syn polymer no no GGUGGAGGCU GGUGGAGGCU A polyribonucleotide no yes GCCGAAACC(P5P) GCCGAAACCA B polyribonucleotide n n n n n n n n n n n n n n n n n n n n -12.600 1 19 A 1 B 19 -0.868 A_G1:C19_B 1 -14.068 -0.801 -0.205 -0.230 -15.709 1 19 A 2 B 18 1.002 A_G2:C18_B 2 -16.444 -0.375 -0.350 -0.050 -17.940 1 20 A 3 B 17 0.043 A_U3:A17_B 3 -21.714 0.348 -0.292 -0.083 -8.407 9 11 A 4 B 16 0.358 A_G4:A16_B 4 -6.661 6.756 -0.618 -3.907 15.370 A 5 B 15 -36.389 A_G5:A15_B 5 -6.503 7.332 0.046 -6.102 -12.730 9 11 A 6 B 14 -4.787 A_A6:G14_B 6 1.795 -6.788 -0.272 -4.204 3.781 1 19 A 7 B 13 -0.562 A_G7:C13_B 7 -3.645 -0.468 0.004 -0.087 15.349 1 19 A 8 B 12 0.498 A_G8:C12_B 8 -7.496 -0.710 0.133 -0.132 20.853 1 19 A 9 B 11 1.015 A_C9:G11_B 9 -17.727 0.772 -0.439 -0.164 2.936 34.405 A A 1 2 14.219 B B 19 18 3.388 8.318 0.395 -1.613 AA_G1G2:C18C19_BB 1 3.457 -5.909 33.239 -4.005 -0.137 3.113 36.246 A A 2 3 9.408 B B 18 17 3.366 5.821 0.259 -1.427 AA_G2U3:A17C18_BB 2 3.517 -5.685 35.624 -3.110 0.077 3.381 63.075 A A 3 4 1.975 B B 17 16 3.339 2.061 0.718 -0.662 AA_U3G4:A16A17_BB 3 8.668 -8.308 62.507 -0.728 -0.288 2.365 43.660 A A 4 5 6.791 B B 16 15 2.935 5.010 -2.554 -0.209 AA_G4G5:A15A16_BB 4 8.561 -11.603 42.572 -0.675 4.108 4.186 -14.829 A A 5 6 -8.876 B B 15 14 3.926 2.270 1.413 -0.801 AA_G5A6:G14A15_BB 5 -2.575 -10.069 -14.428 0.678 2.724 2.932 52.971 A A 6 7 5.390 B B 14 13 2.993 4.794 -0.482 -0.995 AA_A6G7:C13G14_BB 6 -5.716 6.427 52.481 -1.396 0.206 2.734 28.905 A A 7 8 7.703 B B 13 12 3.001 3.827 -0.014 -1.752 AA_G7G8:C12C13_BB 7 -3.009 6.057 28.501 -4.260 -0.561 3.014 37.450 A A 8 9 5.246 B B 12 11 3.170 3.364 -0.116 -1.655 AA_G8C9:G11C12_BB 8 0.194 -0.302 37.303 -2.996 0.204 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list struct_conn repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2006-06-13 1 1 2008-04-30 1 2 2011-07-13 1 3 2022-03-09 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _struct_conn.pdbx_leaving_atom_flag 5'gguGGAggcu/3'pccaAAGccg a Single Sheared Purine-Purine Pair Flanked by Sheared GA Pairs, 5'gguGAAggcu/3'pccgAAGccg 3 sheared GA pairs closed by ug wobble and cg WC pairs, 5'gguGGAggcu/3'pccgAAGccg PDBJ Y PDBJ 2006-01-19 REL REL structures with the lowest energy, structures with the least restraint violations 40 24 distance geometry, simulated annealing, molecular dynamics 1 closest to the average 80mM NaCl, 10mM sodium phosphate, 0.5mM Na2EDTA, 2mM total duplex concentrations, pH 5.4, pD 6.8 processing Felix refinement Discover collection VNMR 500 Varian INOVA 600 Varian INOVA G 1 n 1 G 1 A G 2 n 2 G 2 A U 3 n 3 U 3 A G 4 n 4 G 4 A G 5 n 5 G 5 A A 6 n 6 A 6 A G 7 n 7 G 7 A G 8 n 8 G 8 A C 9 n 9 C 9 A U 10 n 10 U 10 A G 11 n 1 G 11 B C 12 n 2 C 12 B C 13 n 3 C 13 B G 14 n 4 G 14 B A 15 n 5 A 15 B A 16 n 6 A 16 B A 17 n 7 A 17 B C 18 n 8 C 18 B C 19 n 9 C 19 B P5P 20 n 10 P5P 20 B author_defined_assembly 2 dimeric B P5P 20 PURINE RIBOSIDE-5'-MONOPHOSPHATE B P5P 10 A 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 G 5 0.062 SIDE CHAIN 2 A G 8 0.063 SIDE CHAIN 2 B A 17 0.065 SIDE CHAIN 3 A G 4 0.050 SIDE CHAIN 3 B G 14 0.064 SIDE CHAIN 4 B G 11 0.058 SIDE CHAIN 4 B A 17 0.059 SIDE CHAIN 6 A G 4 0.063 SIDE CHAIN 7 B A 16 0.069 SIDE CHAIN 7 B A 17 0.063 SIDE CHAIN 8 B G 11 0.069 SIDE CHAIN 8 B A 17 0.054 SIDE CHAIN 9 B G 14 0.055 SIDE CHAIN 10 A G 5 0.068 SIDE CHAIN 10 B G 11 0.063 SIDE CHAIN 10 B A 17 0.071 SIDE CHAIN 11 B A 16 0.067 SIDE CHAIN 11 B A 17 0.074 SIDE CHAIN 12 A G 5 0.063 SIDE CHAIN 13 B G 14 0.056 SIDE CHAIN 14 A G 5 0.092 SIDE CHAIN 14 B G 11 0.057 SIDE CHAIN 14 B A 17 0.064 SIDE CHAIN 15 B A 16 0.081 SIDE CHAIN 15 B A 17 0.097 SIDE CHAIN 16 B G 14 0.061 SIDE CHAIN 17 A G 5 0.053 SIDE CHAIN 17 B A 17 0.063 SIDE CHAIN 18 B A 16 0.075 SIDE CHAIN 18 B A 17 0.104 SIDE CHAIN 19 A G 5 0.071 SIDE CHAIN 20 A G 4 0.069 SIDE CHAIN 20 A G 5 0.057 SIDE CHAIN 21 B G 14 0.057 SIDE CHAIN 21 B A 16 0.060 SIDE CHAIN 21 B A 17 0.060 SIDE CHAIN 22 B G 11 0.069 SIDE CHAIN 22 B A 16 0.052 SIDE CHAIN 22 B A 17 0.055 SIDE CHAIN 22 B C 19 0.066 SIDE CHAIN 23 A G 5 0.058 SIDE CHAIN 24 A G 5 0.060 SIDE CHAIN 24 B A 16 0.056 SIDE CHAIN 1 5.71 0.70 108.50 114.21 A A A O4' C1' N1 U U U 3 3 3 N 1 4.89 0.70 108.50 113.39 A A A O4' C1' N1 C C C 9 9 9 N 1 4.49 0.70 108.50 112.99 B B B O4' C1' N1 C C C 12 12 12 N 1 4.35 0.70 108.50 112.85 B B B O4' C1' N1 C C C 13 13 13 N 2 5.81 0.70 108.50 114.31 A A A O4' C1' N1 U U U 3 3 3 N 2 4.77 0.70 108.50 113.27 A A A O4' C1' N1 C C C 9 9 9 N 2 4.56 0.70 108.50 113.06 B B B O4' C1' N1 C C C 12 12 12 N 2 4.55 0.70 108.50 113.05 B B B O4' C1' N1 C C C 13 13 13 N 2 4.22 0.70 108.50 112.72 B B B O4' C1' N1 C C C 19 19 19 N 3 5.76 0.70 108.50 114.26 A A A O4' C1' N1 U U U 3 3 3 N 3 4.96 0.70 108.50 113.46 A A A O4' C1' N1 C C C 9 9 9 N 3 4.35 0.70 108.50 112.85 B B B O4' C1' N1 C C C 12 12 12 N 4 5.40 0.70 108.50 113.90 A A A O4' C1' N1 U U U 3 3 3 N 4 4.67 0.70 108.50 113.17 B B B O4' C1' N1 C C C 12 12 12 N 4 4.90 0.70 108.50 113.40 B B B O4' C1' N1 C C C 13 13 13 N 5 5.46 0.70 108.50 113.96 A A A O4' C1' N1 U U U 3 3 3 N 5 5.16 0.70 108.50 113.66 A A A O4' C1' N9 G G G 7 7 7 N 5 5.03 0.70 108.50 113.53 A A A O4' C1' N1 C C C 9 9 9 N 5 4.55 0.70 108.50 113.05 B B B O4' C1' N1 C C C 12 12 12 N 5 5.18 0.70 108.50 113.68 B B B O4' C1' N1 C C C 13 13 13 N 5 4.32 0.70 108.50 112.82 B B B O4' C1' N1 C C C 19 19 19 N 6 5.95 0.70 108.50 114.45 A A A O4' C1' N1 U U U 3 3 3 N 6 4.85 0.70 108.50 113.35 A A A O4' C1' N1 C C C 9 9 9 N 6 4.24 0.70 108.50 112.74 B B B O4' C1' N1 C C C 12 12 12 N 6 4.26 0.70 108.50 112.76 B B B O4' C1' N1 C C C 13 13 13 N 6 4.26 0.70 108.50 112.76 B B B O4' C1' N1 C C C 19 19 19 N 7 5.95 0.70 108.50 114.45 A A A O4' C1' N1 U U U 3 3 3 N 7 4.96 0.70 108.50 113.46 A A A O4' C1' N1 C C C 9 9 9 N 7 5.03 0.70 108.50 113.53 B B B O4' C1' N1 C C C 12 12 12 N 7 5.07 0.70 108.50 113.57 B B B O4' C1' N1 C C C 13 13 13 N 7 4.21 0.70 108.50 112.71 B B B O4' C1' N1 C C C 19 19 19 N 8 5.98 0.70 108.50 114.48 A A A O4' C1' N1 U U U 3 3 3 N 8 4.92 0.70 108.50 113.42 A A A O4' C1' N9 G G G 7 7 7 N 8 4.35 0.70 108.50 112.85 A A A O4' C1' N1 U U U 10 10 10 N 8 4.48 0.70 108.50 112.98 B B B O4' C1' N1 C C C 12 12 12 N 8 4.66 0.70 108.50 113.16 B B B O4' C1' N1 C C C 13 13 13 N 8 4.25 0.70 108.50 112.75 B B B O4' C1' N1 C C C 19 19 19 N 9 6.04 0.70 108.50 114.54 A A A O4' C1' N1 U U U 3 3 3 N 9 4.94 0.70 108.50 113.44 A A A O4' C1' N1 C C C 9 9 9 N 9 4.54 0.70 108.50 113.04 B B B O4' C1' N1 C C C 12 12 12 N 9 4.49 0.70 108.50 112.99 B B B O4' C1' N1 C C C 13 13 13 N 9 5.29 0.70 108.50 113.79 B B B O4' C1' N1 C C C 19 19 19 N 10 5.80 0.70 108.50 114.30 A A A O4' C1' N1 U U U 3 3 3 N 10 4.45 0.70 108.50 112.95 A A A O4' C1' N1 C C C 9 9 9 N 10 4.43 0.70 108.50 112.93 B B B O4' C1' N1 C C C 12 12 12 N 10 4.99 0.70 108.50 113.49 B B B O4' C1' N1 C C C 13 13 13 N 11 5.80 0.70 108.50 114.30 A A A O4' C1' N1 U U U 3 3 3 N 11 5.05 0.70 108.50 113.55 A A A O4' C1' N1 C C C 9 9 9 N 11 4.52 0.70 108.50 113.02 B B B O4' C1' N1 C C C 12 12 12 N 11 4.87 0.70 108.50 113.37 B B B O4' C1' N1 C C C 13 13 13 N 12 6.06 0.70 108.50 114.56 A A A O4' C1' N1 U U U 3 3 3 N 12 4.74 0.70 108.50 113.24 A A A O4' C1' N1 C C C 9 9 9 N 12 4.50 0.70 108.50 113.00 B B B O4' C1' N1 C C C 12 12 12 N 12 4.53 0.70 108.50 113.03 B B B O4' C1' N1 C C C 13 13 13 N 12 4.53 0.70 108.50 113.03 B B B O4' C1' N1 C C C 19 19 19 N 13 5.96 0.70 108.50 114.46 A A A O4' C1' N1 U U U 3 3 3 N 13 4.72 0.70 108.50 113.22 A A A O4' C1' N1 C C C 9 9 9 N 13 4.54 0.70 108.50 113.04 B B B O4' C1' N1 C C C 12 12 12 N 13 4.47 0.70 108.50 112.97 B B B O4' C1' N1 C C C 13 13 13 N 13 4.48 0.70 108.50 112.98 B B B O4' C1' N1 C C C 19 19 19 N 14 5.93 0.70 108.50 114.43 A A A O4' C1' N1 U U U 3 3 3 N 14 5.34 0.70 108.50 113.84 A A A O4' C1' N9 G G G 7 7 7 N 14 5.15 0.70 108.50 113.65 A A A O4' C1' N1 C C C 9 9 9 N 14 4.54 0.70 108.50 113.04 B B B O4' C1' N1 C C C 12 12 12 N 14 5.33 0.70 108.50 113.83 B B B O4' C1' N1 C C C 13 13 13 N 14 4.30 0.70 108.50 112.80 B B B O4' C1' N1 C C C 19 19 19 N 15 4.45 0.70 108.50 112.95 A A A O4' C1' N9 G G G 2 2 2 N 15 6.40 0.70 108.50 114.90 A A A O4' C1' N1 U U U 3 3 3 N 15 5.02 0.70 108.50 113.52 A A A O4' C1' N1 C C C 9 9 9 N 15 4.53 0.70 108.50 113.03 B B B O4' C1' N1 C C C 12 12 12 N 15 5.23 0.70 108.50 113.73 B B B O4' C1' N1 C C C 13 13 13 N 15 4.23 0.70 108.50 112.73 B B B O4' C1' N9 A A A 16 16 16 N 15 4.27 0.70 108.50 112.77 B B B O4' C1' N1 C C C 19 19 19 N 16 5.78 0.70 108.50 114.28 A A A O4' C1' N1 U U U 3 3 3 N 16 4.61 0.70 108.50 113.11 A A A O4' C1' N1 C C C 9 9 9 N 16 4.58 0.70 108.50 113.08 B B B O4' C1' N1 C C C 12 12 12 N 16 4.50 0.70 108.50 113.00 B B B O4' C1' N1 C C C 13 13 13 N 17 5.84 0.70 108.50 114.34 A A A O4' C1' N1 U U U 3 3 3 N 17 5.07 0.70 108.50 113.57 A A A O4' C1' N1 C C C 9 9 9 N 17 4.56 0.70 108.50 113.06 B B B O4' C1' N1 C C C 12 12 12 N 17 5.13 0.70 108.50 113.63 B B B O4' C1' N1 C C C 13 13 13 N 17 5.01 0.70 108.50 113.51 B B B O4' C1' N1 C C C 19 19 19 N 18 4.27 0.70 108.50 112.77 A A A O4' C1' N9 G G G 2 2 2 N 18 5.79 0.70 108.50 114.29 A A A O4' C1' N1 U U U 3 3 3 N 18 5.00 0.70 108.50 113.50 A A A O4' C1' N1 C C C 9 9 9 N 18 4.50 0.70 108.50 113.00 B B B O4' C1' N1 C C C 12 12 12 N 18 4.79 0.70 108.50 113.29 B B B O4' C1' N1 C C C 13 13 13 N 19 5.70 0.70 108.50 114.20 A A A O4' C1' N1 U U U 3 3 3 N 19 5.06 0.70 108.50 113.56 A A A O4' C1' N1 C C C 9 9 9 N 19 4.45 0.70 108.50 112.95 B B B O4' C1' N1 C C C 12 12 12 N 19 4.99 0.70 108.50 113.49 B B B O4' C1' N1 C C C 13 13 13 N 20 5.65 0.70 108.50 114.15 A A A O4' C1' N1 U U U 3 3 3 N 20 4.69 0.70 108.50 113.19 A A A O4' C1' N9 G G G 7 7 7 N 20 5.04 0.70 108.50 113.54 A A A O4' C1' N1 C C C 9 9 9 N 20 4.55 0.70 108.50 113.05 B B B O4' C1' N1 C C C 12 12 12 N 20 5.14 0.70 108.50 113.64 B B B O4' C1' N1 C C C 13 13 13 N 20 4.59 0.70 108.50 113.09 B B B O4' C1' N1 C C C 19 19 19 N 21 6.11 0.70 108.50 114.61 A A A O4' C1' N1 U U U 3 3 3 N 21 4.97 0.70 108.50 113.47 A A A O4' C1' N1 C C C 9 9 9 N 21 4.50 0.70 108.50 113.00 B B B O4' C1' N1 C C C 12 12 12 N 21 4.48 0.70 108.50 112.98 B B B O4' C1' N1 C C C 13 13 13 N 21 4.31 0.70 108.50 112.81 B B B O4' C1' N1 C C C 19 19 19 N 22 5.52 0.70 108.50 114.02 A A A O4' C1' N1 U U U 3 3 3 N 22 4.33 0.70 108.50 112.83 A A A O4' C1' N9 G G G 7 7 7 N 22 5.01 0.70 108.50 113.51 A A A O4' C1' N1 C C C 9 9 9 N 22 4.67 0.70 108.50 113.17 A A A O4' C1' N1 U U U 10 10 10 N 22 4.45 0.70 108.50 112.95 B B B O4' C1' N1 C C C 12 12 12 N 22 5.24 0.70 108.50 113.74 B B B O4' C1' N1 C C C 13 13 13 N 23 5.83 0.70 108.50 114.33 A A A O4' C1' N1 U U U 3 3 3 N 23 4.83 0.70 108.50 113.33 A A A O4' C1' N1 C C C 9 9 9 N 23 4.46 0.70 108.50 112.96 B B B O4' C1' N1 C C C 12 12 12 N 23 4.22 0.70 108.50 112.72 B B B O4' C1' N1 C C C 13 13 13 N 23 4.26 0.70 108.50 112.76 B B B O4' C1' N1 C C C 19 19 19 N 24 5.91 0.70 108.50 114.41 A A A O4' C1' N1 U U U 3 3 3 N 24 4.93 0.70 108.50 113.43 A A A O4' C1' N1 C C C 9 9 9 N 24 4.39 0.70 108.50 112.89 B B B O4' C1' N1 C C C 12 12 12 N 24 4.23 0.70 108.50 112.73 B B B O4' C1' N1 C C C 13 13 13 N 24 4.20 0.70 108.50 112.70 B B B O4' C1' N1 C C C 19 19 19 N Three consecutive sheared GA pairs in 5'GGUGGAGGCU/3'PCCAAAGCCG 1 N N 2 N N covale 1.615 both B C 19 B O3' C 9 1_555 B P5P 20 B P P5P 10 1_555 hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 B C 19 B N3 C 9 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 B C 19 B O2 C 9 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 B C 19 B N4 C 9 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 B C 18 B N3 C 8 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 B C 18 B O2 C 8 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 B C 18 B N4 C 8 1_555 hydrog WATSON-CRICK A U 3 A N3 U 3 1_555 B A 17 B N1 A 7 1_555 hydrog WATSON-CRICK A U 3 A O4 U 3 1_555 B A 17 B N6 A 7 1_555 hydrog TYPE_11_PAIR A G 4 A N2 G 4 1_555 B A 16 B N7 A 6 1_555 hydrog TYPE_11_PAIR A G 4 A N3 G 4 1_555 B A 16 B N6 A 6 1_555 hydrog G-A MISPAIR A G 5 A N2 G 5 1_555 B A 15 B N7 A 5 1_555 hydrog TYPE_11_PAIR A A 6 A N6 A 6 1_555 B G 14 B N3 G 4 1_555 hydrog TYPE_11_PAIR A A 6 A N7 A 6 1_555 B G 14 B N2 G 4 1_555 hydrog WATSON-CRICK A G 7 A N1 G 7 1_555 B C 13 B N3 C 3 1_555 hydrog WATSON-CRICK A G 7 A N2 G 7 1_555 B C 13 B O2 C 3 1_555 hydrog WATSON-CRICK A G 7 A O6 G 7 1_555 B C 13 B N4 C 3 1_555 hydrog WATSON-CRICK A G 8 A N1 G 8 1_555 B C 12 B N3 C 2 1_555 hydrog WATSON-CRICK A G 8 A N2 G 8 1_555 B C 12 B O2 C 2 1_555 hydrog WATSON-CRICK A G 8 A O6 G 8 1_555 B C 12 B N4 C 2 1_555 hydrog WATSON-CRICK A C 9 A N3 C 9 1_555 B G 11 B N1 G 1 1_555 hydrog WATSON-CRICK A C 9 A N4 C 9 1_555 B G 11 B O6 G 1 1_555 hydrog WATSON-CRICK A C 9 A O2 C 9 1_555 B G 11 B N2 G 1 1_555 RNA Three consecutive sheared GA pairs, thermodynamics of molecular recognition, K-turn motif, A-minor motif, secondary structure of RNA, RNA 2DD1 PDB 1 2DD1 2DD1 PDB 2 2DD1 1 10 2DD1 1 10 2DD1 A 1 1 10 11 20 2DD1 11 20 2DD1 B 2 1 10