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. 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 C9 H14 N3 O8 P 323.197 n ISOCYTIDINE-5'-MONOPHOSPHATE RNA linking C10 H14 N5 O8 P 363.221 n ISOGUANOSINE-5'-MONOPHOSPHATE RNA linking N 1 N O N 2 N P N 3 N O N 4 N O N 5 N O N 6 N C N 7 R C N 8 N O N 9 S C N 10 N O N 11 R C N 12 N O N 13 R C Y 14 N N Y 15 N C Y 16 N N Y 17 N C Y 18 N C N 19 N N Y 20 N N Y 21 N C Y 22 N N Y 23 N C N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N O N 39 N P N 40 N O N 41 N O N 42 N O N 43 N C N 44 R C N 45 N O N 46 S C N 47 N O N 48 R C N 49 N O N 50 R C N 51 N N N 52 N C N 53 N O N 54 N N N 55 N C N 56 N N N 57 N C N 58 N C N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N O N 74 N P N 75 N O N 76 N O N 77 N O N 78 N C N 79 R C N 80 N O N 81 S C N 82 N O N 83 R C N 84 N O N 85 R C Y 86 N N Y 87 N C Y 88 N N Y 89 N C N 90 N C N 91 N O N 92 N N N 93 N C N 94 N N N 95 N N Y 96 N C N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N P N 112 N O N 113 N O N 114 N O N 115 N O N 116 N O N 117 R C N 118 R C N 119 S C N 120 R C N 121 N C N 122 N O N 123 N O N 124 N N N 125 N C N 126 N N N 127 N C N 128 N O N 129 N N N 130 N C N 131 N C N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H N 144 N H N 145 N H N 146 N P N 147 N O N 148 N O N 149 N O N 150 N O N 151 N O N 152 R C N 153 R C N 154 S C N 155 R C N 156 N C N 157 N O N 158 N O N 159 N N N 160 N O N 161 N C N 162 N C N 163 N N N 164 N C N 165 N N N 166 N C N 167 N N N 168 N C N 169 N N N 170 N H N 171 N H N 172 N H N 173 N H N 174 N H N 175 N H N 176 N H N 177 N H N 178 N H N 179 N H N 180 N H N 181 N H N 182 N H N 183 N H N 1 N sing N 2 N sing N 3 N doub N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing Y 25 N sing Y 26 N sing Y 27 N doub N 28 N sing Y 29 N sing Y 30 N sing Y 31 N doub N 32 N sing Y 33 N doub N 34 N sing N 35 N sing Y 36 N sing Y 37 N doub N 38 N sing Y 39 N sing N 40 N sing N 41 N sing N 42 N doub N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N doub N 67 N sing N 68 N doub N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N doub N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N doub N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N sing Y 100 N sing Y 101 N sing Y 102 N doub N 103 N sing Y 104 N sing N 105 N sing Y 106 N doub N 107 N doub N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N doub N 113 N sing N 114 N sing N 115 N sing N 116 N doub N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N sing N 144 N doub N 145 N sing N 146 N doub N 147 N sing N 148 N sing N 149 N doub N 150 N sing N 151 N sing N 152 N doub N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N doub N 180 N doub N 181 N sing N 182 N sing N 183 N sing N 184 N doub N 185 N sing N 186 N sing N 187 N sing N 188 N doub N 189 N sing N 190 N sing N 191 N sing US J.Phys.Chem.B JPCBFK 1278 1089-5647 111 6718 6727 10.1021/jp068732m 17411085 Stacking Effects on Local Structure in RNA: Changes in the Structure of Tandem GA Pairs when Flanking GC Pairs are Replaced by isoG-isoC Pairs 2007 10.2210/pdb2o81/pdb pdb_00002o81 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 1 1.0 2909.823 5'-R(*GP*CP*(IG)P*GP*AP*(IC)P*GP*CP*A)-3' 2 syn polymer no yes GC(IG)GA(IC)GCA GCGGACGCA A,B polyribonucleotide n n n n n n n n n -14.544 1 19 A 1 B 8 -1.311 A_G1:C8_B 1 -18.839 -0.535 -0.071 -0.168 -5.412 1 19 A 2 B 7 -0.878 A_C2:G7_B 2 -9.618 0.398 0.174 -0.075 0.311 A 3 B 6 -3.227 A_IG3:IC6_B 3 -6.470 0.288 -0.028 -0.049 12.408 10 A 4 B 5 -29.582 A_G4:A5_B 4 -4.887 7.376 -0.077 -5.554 -12.172 10 A 5 B 4 -29.975 A_A5:G4_B 5 -5.414 -7.388 -0.019 -5.554 0.467 A 6 B 3 -3.107 A_IC6:IG3_B 6 -6.802 -0.248 -0.038 -0.048 6.157 1 19 A 7 B 2 -0.654 A_G7:C2_B 7 -9.749 -0.365 0.167 -0.058 17.228 1 19 A 8 B 1 -1.150 A_C8:G1_B 8 -20.088 0.542 -0.126 -0.154 2.850 36.238 A A 1 2 9.878 B B 8 7 3.041 6.116 0.100 -0.904 AA_G1C2:G7C8_BB 1 -0.861 1.390 35.726 -2.233 -0.270 2.885 33.047 A A 2 3 10.415 B B 7 6 3.147 5.892 0.668 -1.405 AA_C2IG3:IC6G7_BB 2 1.724 -3.047 32.488 -3.398 -0.903 3.281 61.087 A A 3 4 -1.723 B B 6 5 3.103 -1.750 -2.356 -1.509 AA_IG3G4:A5IC6_BB 3 -4.196 4.131 60.934 -1.403 2.123 3.985 -24.525 A A 4 5 -3.307 B B 5 4 3.916 1.404 -0.046 -1.340 AA_G4A5:G4A5_BB 4 -0.172 -0.406 -24.485 2.631 -0.174 3.263 61.345 A A 5 6 -1.398 B B 4 3 3.084 -1.425 2.350 -1.497 AA_A5IC6:IG3G4_BB 5 4.481 -4.395 61.182 -1.402 -2.098 2.861 33.123 A A 6 7 11.654 B B 3 2 3.152 6.599 -0.700 -1.346 AA_IC6G7:C2IG3_BB 6 -1.624 2.868 32.437 -3.394 0.975 2.808 35.964 A A 7 8 10.478 B B 2 1 3.000 6.436 -0.185 -0.795 AA_G7C8:G1C2_BB 7 1.392 -2.267 35.376 -2.108 0.477 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list struct_conn chem_comp_atom chem_comp_bond repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Data collection 1 0 2007-07-10 1 1 2008-05-01 1 2 2011-07-13 1 3 2022-03-16 1 4 2023-12-27 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _struct_conn.pdbx_leaving_atom_flag GG(IC)GA(IG)CCA RCSB Y RCSB 2006-12-11 REL REL structures with the least restraint violations,structures with the lowest energy 20 18 2D NOESY 2D TOCSY DQF-COSY 7.1 303 K simulated annealing, molecular dynamics 1 lowest energy 80 mM NaCl, 10 mM sodium phosphate, 0.5 mM Na2EDTA, pH 7.1, 0.7mM RNA duplex concentration, 90% H2O, 10% D2O 90% H2O/10% D2O Varian collection VNMR 6.1C Delagio, F. processing NMRPipe 2.3 Goddard, T.D.; Kneller, D.G. data analysis Sparky 3.11 Molecular Simulations, Inc. structure solution Discover I2000 Molecular Simulations, Inc. refinement Discover I2000 500 Varian INOVA 600 Varian INOVA G 1 n 1 G 1 A C 2 n 2 C 2 A IG 3 n 3 IG 3 A G 4 n 4 G 4 A A 5 n 5 A 5 A IC 6 n 6 IC 6 A G 7 n 7 G 7 A C 8 n 8 C 8 A A 9 n 9 A 9 A G 1 n 1 G 1 B C 2 n 2 C 2 B IG 3 n 3 IG 3 B G 4 n 4 G 4 B A 5 n 5 A 5 B IC 6 n 6 IC 6 B G 7 n 7 G 7 B C 8 n 8 C 8 B A 9 n 9 A 9 B author_defined_assembly 2 dimeric A IG 3 ISOGUANOSINE-5'-MONOPHOSPHATE A IG 3 G A IC 6 ISOCYTIDINE-5'-MONOPHOSPHATE A IC 6 C B IG 3 ISOGUANOSINE-5'-MONOPHOSPHATE B IG 3 G B IC 6 ISOCYTIDINE-5'-MONOPHOSPHATE B IC 6 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 A G 1 0.070 SIDE CHAIN 1 A G 7 0.060 SIDE CHAIN 1 B G 1 0.071 SIDE CHAIN 1 B G 7 0.060 SIDE CHAIN 2 A G 1 0.068 SIDE CHAIN 2 A G 7 0.060 SIDE CHAIN 2 B G 1 0.071 SIDE CHAIN 2 B G 7 0.060 SIDE CHAIN 3 A G 1 0.070 SIDE CHAIN 3 A G 7 0.060 SIDE CHAIN 3 B G 1 0.071 SIDE CHAIN 3 B G 7 0.060 SIDE CHAIN 4 A G 1 0.073 SIDE CHAIN 4 A G 7 0.059 SIDE CHAIN 4 B G 1 0.072 SIDE CHAIN 4 B G 7 0.059 SIDE CHAIN 5 A G 1 0.070 SIDE CHAIN 5 A G 7 0.059 SIDE CHAIN 5 B G 1 0.071 SIDE CHAIN 5 B G 7 0.061 SIDE CHAIN 6 A G 1 0.068 SIDE CHAIN 6 A G 7 0.060 SIDE CHAIN 6 B G 1 0.071 SIDE CHAIN 6 B G 7 0.060 SIDE CHAIN 7 A G 1 0.072 SIDE CHAIN 7 B G 1 0.075 SIDE CHAIN 7 B G 7 0.059 SIDE CHAIN 8 A G 1 0.072 SIDE CHAIN 8 A G 7 0.060 SIDE CHAIN 8 B G 1 0.071 SIDE CHAIN 8 B G 7 0.061 SIDE CHAIN 9 A G 1 0.070 SIDE CHAIN 9 A G 7 0.060 SIDE CHAIN 9 B G 1 0.071 SIDE CHAIN 9 B G 7 0.058 SIDE CHAIN 10 A G 1 0.072 SIDE CHAIN 10 B G 1 0.059 SIDE CHAIN 10 B G 7 0.060 SIDE CHAIN 11 A G 1 0.068 SIDE CHAIN 11 A G 7 0.066 SIDE CHAIN 11 B G 1 0.071 SIDE CHAIN 11 B G 7 0.061 SIDE CHAIN 12 A G 1 0.071 SIDE CHAIN 12 A G 7 0.059 SIDE CHAIN 12 B G 1 0.071 SIDE CHAIN 12 B G 7 0.059 SIDE CHAIN 13 A G 1 0.072 SIDE CHAIN 13 A G 7 0.060 SIDE CHAIN 13 B G 1 0.072 SIDE CHAIN 13 B G 7 0.055 SIDE CHAIN 14 A G 1 0.068 SIDE CHAIN 14 A G 7 0.057 SIDE CHAIN 14 B G 1 0.075 SIDE CHAIN 14 B G 7 0.061 SIDE CHAIN 15 A G 1 0.070 SIDE CHAIN 15 A G 7 0.056 SIDE CHAIN 15 B G 1 0.075 SIDE CHAIN 15 B G 7 0.060 SIDE CHAIN 16 A G 1 0.067 SIDE CHAIN 16 A G 7 0.061 SIDE CHAIN 16 B G 1 0.072 SIDE CHAIN 17 A G 1 0.073 SIDE CHAIN 17 A G 7 0.063 SIDE CHAIN 17 B G 1 0.073 SIDE CHAIN 17 B G 7 0.060 SIDE CHAIN 18 A G 1 0.072 SIDE CHAIN 18 A G 7 0.066 SIDE CHAIN 18 B G 1 0.071 SIDE CHAIN 18 B G 7 0.056 SIDE CHAIN 1 4.61 0.70 108.50 113.11 A A A O4' C1' N1 C C C 2 2 2 N 2 4.56 0.70 108.50 113.06 A A A O4' C1' N1 C C C 2 2 2 N 2 4.24 0.70 108.50 112.74 B B B O4' C1' N1 C C C 2 2 2 N 3 4.65 0.70 108.50 113.15 A A A O4' C1' N1 C C C 2 2 2 N 3 4.24 0.70 108.50 112.74 B B B O4' C1' N1 C C C 2 2 2 N 4 4.55 0.70 108.50 113.05 A A A O4' C1' N1 C C C 2 2 2 N 5 4.62 0.70 108.50 113.12 A A A O4' C1' N1 C C C 2 2 2 N 5 4.20 0.70 108.50 112.70 B B B O4' C1' N1 C C C 2 2 2 N 6 4.63 0.70 108.50 113.13 A A A O4' C1' N1 C C C 2 2 2 N 6 4.22 0.70 108.50 112.72 B B B O4' C1' N1 C C C 2 2 2 N 7 4.58 0.70 108.50 113.08 A A A O4' C1' N1 C C C 2 2 2 N 7 4.36 0.70 108.50 112.86 A A A O4' C1' N1 C C C 8 8 8 N 8 4.48 0.70 108.50 112.98 A A A O4' C1' N1 C C C 2 2 2 N 8 4.27 0.70 108.50 112.77 B B B O4' C1' N1 C C C 2 2 2 N 9 4.62 0.70 108.50 113.12 A A A O4' C1' N1 C C C 2 2 2 N 9 4.27 0.70 108.50 112.77 B B B O4' C1' N1 C C C 2 2 2 N 10 4.51 0.70 108.50 113.01 A A A O4' C1' N1 C C C 2 2 2 N 10 5.02 0.70 108.50 113.52 A A A O4' C1' N1 C C C 8 8 8 N 10 4.31 0.70 108.50 112.81 B B B O4' C1' N1 C C C 2 2 2 N 11 4.57 0.70 108.50 113.07 A A A O4' C1' N1 C C C 2 2 2 N 12 4.58 0.70 108.50 113.08 A A A O4' C1' N1 C C C 2 2 2 N 12 4.21 0.70 108.50 112.71 B B B O4' C1' N1 C C C 2 2 2 N 13 4.55 0.70 108.50 113.05 A A A O4' C1' N1 C C C 2 2 2 N 13 4.24 0.70 108.50 112.74 B B B O4' C1' N1 C C C 2 2 2 N 13 4.33 0.70 108.50 112.83 B B B O4' C1' N1 C C C 8 8 8 N 14 4.52 0.70 108.50 113.02 A A A O4' C1' N1 C C C 2 2 2 N 14 4.28 0.70 108.50 112.78 A A A O4' C1' N1 C C C 8 8 8 N 15 4.57 0.70 108.50 113.07 A A A O4' C1' N1 C C C 2 2 2 N 15 4.21 0.70 108.50 112.71 B B B O4' C1' N1 C C C 2 2 2 N 16 4.58 0.70 108.50 113.08 A A A O4' C1' N1 C C C 2 2 2 N 16 4.27 0.70 108.50 112.77 B B B O4' C1' N1 C C C 2 2 2 N 16 4.43 0.70 108.50 112.93 B B B O4' C1' N1 C C C 8 8 8 N 17 4.60 0.70 108.50 113.10 A A A O4' C1' N1 C C C 2 2 2 N 17 4.36 0.70 108.50 112.86 A A A O4' C1' N1 C C C 8 8 8 N 17 4.22 0.70 108.50 112.72 B B B O4' C1' N1 C C C 2 2 2 N 18 4.55 0.70 108.50 113.05 A A A O4' C1' N1 C C C 2 2 2 N 18 4.33 0.70 108.50 112.83 B B B O4' C1' N1 C C C 8 8 8 N The Structure of Tandem GA RNA Pairs When Flanking Pairs are isoG-isoC Pairs 1 N N 1 N N covale 1.616 both A C 2 A O3' C 2 1_555 A IG 3 A P IG 3 1_555 covale 1.616 both A IG 3 A O3' IG 3 1_555 A G 4 A P G 4 1_555 covale 1.619 both A A 5 A O3' A 5 1_555 A IC 6 A P IC 6 1_555 covale 1.616 both A IC 6 A O3' IC 6 1_555 A G 7 A P G 7 1_555 covale 1.617 both B C 2 B O3' C 2 1_555 B IG 3 B P IG 3 1_555 covale 1.617 both B IG 3 B O3' IG 3 1_555 B G 4 B P G 4 1_555 covale 1.620 both B A 5 B O3' A 5 1_555 B IC 6 B P IC 6 1_555 covale 1.615 both B IC 6 B O3' IC 6 1_555 B G 7 B P G 7 1_555 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 C 2 A N3 C 2 1_555 B G 7 B N1 G 7 1_555 hydrog WATSON-CRICK A C 2 A N4 C 2 1_555 B G 7 B O6 G 7 1_555 hydrog WATSON-CRICK A C 2 A O2 C 2 1_555 B G 7 B N2 G 7 1_555 hydrog IG-IC PAIR A IG 3 A N1 IG 3 1_555 B IC 6 B N3 IC 6 1_555 hydrog G-A MISPAIR A G 4 A N2 G 4 1_555 B A 5 B N7 A 5 1_555 hydrog A-G MISPAIR A A 5 A N7 A 5 1_555 B G 4 B N2 G 4 1_555 hydrog IC-IG PAIR A IC 6 A N3 IC 6 1_555 B IG 3 B N1 IG 3 1_555 hydrog WATSON-CRICK A G 7 A N1 G 7 1_555 B C 2 B N3 C 2 1_555 hydrog WATSON-CRICK A G 7 A N2 G 7 1_555 B C 2 B O2 C 2 1_555 hydrog WATSON-CRICK A G 7 A O6 G 7 1_555 B C 2 B N4 C 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, Thermodynamics, secondary structure prediction, sheared GA pair, isoguanosine, isocytidine 2O81 PDB 1 2O81 1 9 2O81 1 9 2O81 A 1 1 9 1 9 2O81 1 9 2O81 B 1 1 9