1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Bilbille, Y. Agris, P.F. 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 H13 N2 O9 P 324.181 n PSEUDOURIDINE-5'-MONOPHOSPHATE RNA linking C10 H14 N3 O9 P 351.207 n 5-formylcytidine 5'-(dihydrogen phosphate) RNA linking C9 H13 N2 O9 P 324.181 y URIDINE-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 N N 112 N C N 113 N N N 114 N C N 115 N C N 116 N C N 117 N O N 118 N O N 119 S C N 120 R C N 121 N O N 122 S C N 123 R C N 124 N O N 125 N O N 126 N C N 127 N O N 128 N P N 129 N O N 130 N O N 131 N O 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 P N 146 N N N 147 N C N 148 N O N 149 N N N 150 N C N 151 N N N 152 N C N 153 N C N 154 R C N 155 N C N 156 R C N 157 N O N 158 S C N 159 N O N 160 N O N 161 R C N 162 N O N 163 N C N 164 N O N 165 N O N 166 N O N 167 N O N 168 N H N 169 N H 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 O N 183 N P N 184 N O N 185 N O N 186 N O N 187 N C N 188 R C N 189 N O N 190 S C N 191 N O N 192 R C N 193 N O N 194 R C N 195 N N N 196 N C N 197 N O N 198 N N N 199 N C N 200 N O N 201 N C N 202 N C N 203 N H N 204 N H N 205 N H N 206 N H N 207 N H N 208 N H N 209 N H N 210 N H N 211 N H N 212 N H N 213 N H N 214 N H N 215 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 sing N 117 N sing N 118 N sing N 119 N sing N 120 N doub N 121 N sing N 122 N sing N 123 N sing N 124 N doub N 125 N doub 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 sing N 145 N sing N 146 N doub N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N doub N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N doub N 159 N sing N 160 N doub N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N doub 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 doub 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 sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N sing N 189 N sing N 190 N sing N 191 N doub N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N sing N 201 N sing N 202 N sing N 203 N sing N 204 N sing N 205 N sing N 206 N sing N 207 N sing N 208 N sing N 209 N sing N 210 N sing N 211 N sing N 212 N sing N 213 N sing N 214 N sing N 215 N doub N 216 N sing N 217 N sing N 218 N sing N 219 N doub N 220 N sing N 221 N doub N 222 N sing N 223 N sing To be Published 0353 The Human Mitochondrial tRNAMet ASL structure solved by Nuclear Magnetic Resonance 10.2210/pdb2kry/pdb pdb_00002kry 5405.279 RNA (5'-R(*(PSU)P*CP*GP*GP*GP*CP*CP*(RSQ)P*AP*UP*AP*CP*CP*CP*CP*GP*A)-3') 1 syn polymer no yes (PSU)CGGGCC(RSQ)AUACCCCGA UCGGGCCXAUACCCCGA A polyribonucleotide n n n n n n n n n n n n n n n n n 10.250 1 19 A 2 A 16 -5.395 A_C2:G16_A 1 -25.518 0.392 0.004 -0.174 8.937 1 19 A 3 A 15 -4.953 A_G3:C15_A 2 -12.223 -0.708 0.295 -0.287 -7.328 1 19 A 4 A 14 2.342 A_G4:C14_A 3 -33.738 -0.609 -0.302 -0.383 -25.535 1 19 A 5 A 13 -9.921 A_G5:C13_A 4 -24.982 0.216 0.222 -0.045 -34.716 A 6 A 12 -24.932 A_C6:C12_A 5 17.540 6.088 2.346 -3.326 2.504 35.794 A A 2 3 29.867 A A 16 15 3.227 17.590 -0.414 -0.726 AA_C2G3:C15G16_AA 1 -2.490 4.228 31.200 -3.564 0.336 3.481 40.010 A A 3 4 21.718 A A 15 14 3.857 14.520 0.663 -0.508 AA_G3G4:C14C15_AA 2 4.146 -6.201 37.159 -2.687 -0.414 3.682 43.700 A A 4 5 17.920 A A 14 13 3.895 13.121 -0.589 -0.315 AA_G4G5:C13C14_AA 3 -5.221 7.130 41.461 -1.921 0.195 3.522 65.583 A A 5 6 10.126 A A 13 12 3.677 10.896 -0.904 -1.348 AA_G5C6:C12C13_AA 4 -9.484 8.813 64.147 -1.743 0.401 chem_comp_atom chem_comp_bond database_2 pdbx_nmr_software pdbx_nmr_spectrometer struct_conn repository Initial release Version format compliance Non-polymer description Data collection Database references Derived calculations 1 0 2010-08-18 1 1 2011-07-13 1 2 2016-02-17 1 3 2024-05-01 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _pdbx_nmr_spectrometer.model _struct_conn.pdbx_leaving_atom_flag BMRB Y RCSB 2009-12-23 REL REL structures with the lowest energy 100 10 2D 1H-1H NOESY 2D 1H-1H NOESY 2D DQF-COSY 2D 1H-1H COSY 2D 1H-1H TOCSY 2D 1H-13C HSQC 2D 1H-31P HETCOR 1.0 mM 1 mM 20 6.8 ambient 298 K simulated annealing 1 lowest energy 1.0 mM RNA (5'-R(*(PSU)P*CP*GP*GP*GP*CP*CP*(RSQ)P*AP*UP*AP*CP*CP*CP*CP*GP*A)-3')-1, 90% H2O/10% D2O 90% H2O/10% D2O 1 mM RNA (5'-R(*(PSU)P*CP*GP*GP*GP*CP*CP*(RSQ)P*AP*UP*AP*CP*CP*CP*CP*GP*A)-3')-2, 100% D2O 100% D2O Bruker Biospin collection XwinNMR Bruker Biospin collection TopSpin Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax data analysis NMRDraw Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax processing NMRPipe Goddard peak picking Sparky Goddard chemical shift assignment Sparky Goddard data analysis Sparky Brunger, Adams, Clore, Gros, Nilges and Read structure solution CNS 1.21 Koradi, Billeter and Wuthrich data analysis MOLMOL Brunger, Adams, Clore, Gros, Nilges and Read refinement CNS 1.21 600 Varian INOVA Varian INOVA 500 Bruker AVANCE Bruker Avance PSU 1 n 1 PSU 1 A C 2 n 2 C 2 A G 3 n 3 G 3 A G 4 n 4 G 4 A G 5 n 5 G 5 A C 6 n 6 C 6 A C 7 n 7 C 7 A RSQ 8 n 8 RSQ 8 A A 9 n 9 A 9 A U 10 n 10 U 10 A A 11 n 11 A 11 A C 12 n 12 C 12 A C 13 n 13 C 13 A C 14 n 14 C 14 A C 15 n 15 C 15 A G 16 n 16 G 16 A A 17 n 17 A 17 A author_defined_assembly 1 monomeric A PSU 1 PSEUDOURIDINE-5'-MONOPHOSPHATE A PSU 1 U A RSQ 8 A RSQ 8 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 Solution structure of the human mitochondrial tRNAMet ASL containing the 5-formylcytidine modification in position 34 1 N N covale 1.609 both A PSU 1 A O3' PSU 1 1_555 A C 2 A P C 2 1_555 covale 1.611 both A C 7 A O3' C 7 1_555 A RSQ 8 A P RSQ 8 1_555 hydrog WATSON-CRICK A C 2 A N3 C 2 1_555 A G 16 A N1 G 16 1_555 hydrog WATSON-CRICK A C 2 A N4 C 2 1_555 A G 16 A O6 G 16 1_555 hydrog WATSON-CRICK A C 2 A O2 C 2 1_555 A G 16 A N2 G 16 1_555 hydrog WATSON-CRICK A G 3 A N1 G 3 1_555 A C 15 A N3 C 15 1_555 hydrog WATSON-CRICK A G 3 A N2 G 3 1_555 A C 15 A O2 C 15 1_555 hydrog WATSON-CRICK A G 3 A O6 G 3 1_555 A C 15 A N4 C 15 1_555 hydrog WATSON-CRICK A G 4 A N1 G 4 1_555 A C 14 A N3 C 14 1_555 hydrog WATSON-CRICK A G 4 A N2 G 4 1_555 A C 14 A O2 C 14 1_555 hydrog WATSON-CRICK A G 4 A O6 G 4 1_555 A C 14 A N4 C 14 1_555 hydrog WATSON-CRICK A G 5 A N1 G 5 1_555 A C 13 A N3 C 13 1_555 hydrog WATSON-CRICK A G 5 A N2 G 5 1_555 A C 13 A O2 C 13 1_555 hydrog WATSON-CRICK A G 5 A O6 G 5 1_555 A C 13 A N4 C 13 1_555 hydrog C-C MISPAIR A C 6 A O2 C 6 1_555 A C 12 A N4 C 12 1_555 RNA RNA, tRNA, 5-formylcytidine, ASL, modification 2KRY PDB 1 2KRY UCGGGCCXAUACCCCGA 1 17 2KRY 1 17 2KRY A 1 1 17