1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Kennedy, S.D. 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/pdb2o83/pdb pdb_00002o83 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*GP*(IC)P*GP*AP*(IG)P*CP*CP*A)-3' 2 syn polymer no yes GG(IC)GA(IG)CCA GGCGAGCCA A,B polyribonucleotide n n n n n n n n n -9.306 1 19 A 1 B 8 -1.883 A_G1:C8_B 1 -19.706 -0.562 0.032 -0.201 -14.242 1 19 A 2 B 7 -1.683 A_G2:C7_B 2 -18.965 -0.190 0.060 -0.092 -9.534 A 3 B 6 -4.400 A_IC3:IG6_B 3 -9.752 -0.292 0.430 0.018 -0.818 8 A 4 B 5 -17.408 A_G4:A5_B 4 -9.988 -0.088 -0.090 1.619 2.564 8 A 5 B 4 -17.385 A_A5:G4_B 5 -10.317 0.090 -0.091 1.620 10.280 A 6 B 3 -4.509 A_IG6:IC3_B 6 -10.932 0.315 0.479 0.011 15.130 1 19 A 7 B 2 -1.806 A_C7:G2_B 7 -20.980 0.203 0.069 -0.101 10.568 1 19 A 8 B 1 -1.901 A_C8:G1_B 8 -21.283 0.548 0.042 -0.195 3.085 36.933 A A 1 2 9.548 B B 8 7 3.341 6.023 0.102 -1.365 AA_G1G2:C7C8_BB 1 0.863 -1.368 36.446 -2.959 -0.046 3.180 33.130 A A 2 3 -0.879 B B 7 6 3.152 -0.501 0.096 -1.834 AA_G2IC3:IG6C7_BB 2 0.489 -0.858 33.123 -3.135 -0.088 2.839 32.024 A A 3 4 1.692 B B 6 5 3.066 0.929 -0.869 -1.534 AA_IC3G4:A5IG6_BB 3 5.350 -9.743 31.572 -2.933 2.452 3.075 26.049 A A 4 5 4.715 B B 5 4 3.215 2.123 0.037 -1.622 AA_G4A5:G4A5_BB 4 0.099 -0.221 25.964 -4.159 -0.056 2.787 31.978 A A 5 6 3.100 B B 4 3 3.056 1.699 0.815 -1.618 AA_A5IG6:IC3G4_BB 5 -5.530 10.091 31.464 -3.213 -2.380 3.185 33.343 A A 6 7 -1.489 B B 3 2 3.138 -0.854 -0.217 -1.817 AA_IG6C7:G2IC3_BB 6 -0.464 0.808 33.329 -3.030 0.303 3.093 37.532 A A 7 8 10.099 B B 2 1 3.339 6.467 -0.151 -1.211 AA_C7C8:G1G2_BB 7 -0.544 0.850 36.987 -2.719 0.164 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 GC(IG)GA(IC)GCA 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 7.1 278 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 600 Varian INOVA 500 Varian INOVA G 1 n 1 G 1 A G 2 n 2 G 2 A IC 3 n 3 IC 3 A G 4 n 4 G 4 A A 5 n 5 A 5 A IG 6 n 6 IG 6 A C 7 n 7 C 7 A C 8 n 8 C 8 A A 9 n 9 A 9 A G 1 n 1 G 1 B G 2 n 2 G 2 B IC 3 n 3 IC 3 B G 4 n 4 G 4 B A 5 n 5 A 5 B IG 6 n 6 IG 6 B C 7 n 7 C 7 B C 8 n 8 C 8 B A 9 n 9 A 9 B author_defined_assembly 2 dimeric A IC 3 ISOCYTIDINE-5'-MONOPHOSPHATE A IC 3 C A IG 6 ISOGUANOSINE-5'-MONOPHOSPHATE A IG 6 G B IC 3 ISOCYTIDINE-5'-MONOPHOSPHATE B IC 3 C B IG 6 ISOGUANOSINE-5'-MONOPHOSPHATE B IG 6 G 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 C 7 0.067 SIDE CHAIN 1 B C 7 0.065 SIDE CHAIN 3 A C 7 0.067 SIDE CHAIN 3 B C 7 0.065 SIDE CHAIN 5 A C 7 0.066 SIDE CHAIN 6 B C 7 0.062 SIDE CHAIN 7 B C 7 0.059 SIDE CHAIN 8 B C 7 0.066 SIDE CHAIN 9 A C 7 0.064 SIDE CHAIN 9 B C 7 0.062 SIDE CHAIN 10 A C 7 0.067 SIDE CHAIN 10 B C 7 0.065 SIDE CHAIN 11 A C 7 0.068 SIDE CHAIN 11 B C 7 0.063 SIDE CHAIN 12 A C 7 0.065 SIDE CHAIN 12 B C 7 0.062 SIDE CHAIN 13 A C 7 0.068 SIDE CHAIN 14 A C 7 0.065 SIDE CHAIN 14 B C 7 0.066 SIDE CHAIN 15 A C 7 0.066 SIDE CHAIN 17 B C 7 0.064 SIDE CHAIN 1 4.22 0.70 108.50 112.72 A A A O4' C1' N9 A A A 5 5 5 N 1 4.20 0.70 108.50 112.70 A A A O4' C1' N1 C C C 7 7 7 N 2 4.25 0.70 108.50 112.75 A A A O4' C1' N1 C C C 7 7 7 N 2 4.85 0.70 108.50 113.35 A A A O4' C1' N1 C C C 8 8 8 N 2 4.37 0.70 108.50 112.87 B B B O4' C1' N9 G G G 2 2 2 N 3 4.28 0.70 108.50 112.78 A A A O4' C1' N9 A A A 5 5 5 N 4 4.93 0.70 108.50 113.43 A A A O4' C1' N1 C C C 8 8 8 N 4 4.31 0.70 108.50 112.81 B B B O4' C1' N1 C C C 7 7 7 N 5 4.25 0.70 108.50 112.75 A A A O4' C1' N9 A A A 5 5 5 N 5 4.47 0.70 108.50 112.97 B B B O4' C1' N1 C C C 8 8 8 N 6 4.23 0.70 108.50 112.73 A A A O4' C1' N9 A A A 5 5 5 N 6 4.21 0.70 108.50 112.71 A A A O4' C1' N1 C C C 7 7 7 N 6 4.85 0.70 108.50 113.35 A A A O4' C1' N1 C C C 8 8 8 N 7 4.97 0.70 108.50 113.47 A A A O4' C1' N1 C C C 8 8 8 N 8 4.22 0.70 108.50 112.72 A A A O4' C1' N9 A A A 5 5 5 N 8 4.20 0.70 108.50 112.70 A A A O4' C1' N1 C C C 7 7 7 N 8 4.48 0.70 108.50 112.98 A A A O4' C1' N1 C C C 8 8 8 N 9 4.24 0.70 108.50 112.74 A A A O4' C1' N9 A A A 5 5 5 N 10 4.21 0.70 108.50 112.71 A A A O4' C1' N1 C C C 7 7 7 N 10 4.36 0.70 108.50 112.86 B B B O4' C1' N1 C C C 8 8 8 N 11 4.30 0.70 108.50 112.80 A A A O4' C1' N9 A A A 5 5 5 N 13 4.24 0.70 108.50 112.74 A A A O4' C1' N9 A A A 5 5 5 N 13 4.56 0.70 108.50 113.06 B B B O4' C1' N1 C C C 8 8 8 N 14 4.30 0.70 108.50 112.80 A A A O4' C1' N9 A A A 5 5 5 N 15 4.33 0.70 108.50 112.83 A A A O4' C1' N9 A A A 5 5 5 N 15 4.57 0.70 108.50 113.07 B B B O4' C1' N1 C C C 8 8 8 N 16 4.21 0.70 108.50 112.71 A A A O4' C1' N9 A A A 5 5 5 N 16 5.00 0.70 108.50 113.50 A A A O4' C1' N1 C C C 8 8 8 N 16 4.69 0.70 108.50 113.19 B B B O4' C1' N1 C C C 8 8 8 N 17 4.23 0.70 108.50 112.73 A A A O4' C1' N9 A A A 5 5 5 N 17 4.24 0.70 108.50 112.74 A A A O4' C1' N1 C C C 7 7 7 N 17 4.49 0.70 108.50 112.99 A A A O4' C1' N1 C C C 8 8 8 N 18 4.92 0.70 108.50 113.42 A A A O4' C1' N1 C C C 8 8 8 N 18 4.63 0.70 108.50 113.13 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 1.615 both A G 2 A O3' G 2 1_555 A IC 3 A P IC 3 1_555 covale 1.613 both A IC 3 A O3' IC 3 1_555 A G 4 A P G 4 1_555 covale 1.617 both A A 5 A O3' A 5 1_555 A IG 6 A P IG 6 1_555 covale 1.612 both A IG 6 A O3' IG 6 1_555 A C 7 A P C 7 1_555 covale 1.615 both B G 2 B O3' G 2 1_555 B IC 3 B P IC 3 1_555 covale 1.613 both B IC 3 B O3' IC 3 1_555 B G 4 B P G 4 1_555 covale 1.618 both B A 5 B O3' A 5 1_555 B IG 6 B P IG 6 1_555 covale 1.614 both B IG 6 B O3' IG 6 1_555 B C 7 B P C 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 G 2 A N1 G 2 1_555 B C 7 B N3 C 7 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 B C 7 B O2 C 7 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 B C 7 B N4 C 7 1_555 hydrog IC-IG PAIR A IC 3 A N3 IC 3 1_555 B IG 6 B N1 IG 6 1_555 hydrog TYPE_8_PAIR A G 4 A N1 G 4 1_555 B A 5 B N1 A 5 1_555 hydrog TYPE_8_PAIR A G 4 A O6 G 4 1_555 B A 5 B N6 A 5 1_555 hydrog TYPE_8_PAIR A A 5 A N1 A 5 1_555 B G 4 B N1 G 4 1_555 hydrog TYPE_8_PAIR A A 5 A N6 A 5 1_555 B G 4 B O6 G 4 1_555 hydrog IG-IC PAIR A IG 6 A N1 IG 6 1_555 B IC 3 B N3 IC 3 1_555 hydrog WATSON-CRICK A C 7 A N3 C 7 1_555 B G 2 B N1 G 2 1_555 hydrog WATSON-CRICK A C 7 A N4 C 7 1_555 B G 2 B O6 G 2 1_555 hydrog WATSON-CRICK A C 7 A O2 C 7 1_555 B G 2 B N2 G 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, imino GA pair, isoguanosine, isocytidine 2O83 PDB 1 2O83 1 9 2O83 1 9 2O83 A 1 1 9 1 9 2O83 1 9 2O83 B 1 1 9