1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Lynch, S.R. Puglisi, J.D. 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 UK J.Mol.Biol. JMOBAK 0070 0022-2836 306 1023 1035 10.1006/jmbi.2000.4419 11237616 Structure of a eukaryotic decoding region A-site RNA. 2001 10.2210/pdb1fyo/pdb pdb_00001fyo 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 EUKARYOTIC DECODING REGION A-SITE RNA 8672.185 FRAGMENT OF 18S RIBOSOMAL RNA 18S RNA - NUCLEOTIDES 1404-1412, 1488-1497 (E. COLI NUMBERS) U1410A, A1490U 1 syn polymer no no GGCGUCGCACCUUCGGGUGAAGUCGCC GGCGUCGCACCUUCGGGUGAAGUCGCC A polyribonucleotide n n n n n n n n n n n n n n n n n n n n n n n n n n n 4.468 1 19 A 1 A 27 -10.190 A_G1:C27_A 1 -9.505 -0.346 0.931 -0.585 -7.136 1 19 A 2 A 26 -5.306 A_G2:C26_A 2 5.946 -0.480 -0.105 -0.395 13.771 1 19 A 3 A 25 -3.873 A_C3:G25_A 3 -14.868 0.478 -0.328 -0.382 3.171 1 19 A 4 A 24 -4.379 A_G4:C24_A 4 -21.376 -0.456 0.363 -0.449 1.432 1 16 A 5 A 23 3.734 A_U5:U23_A 5 -14.194 2.921 0.469 -1.905 -12.313 1 19 A 6 A 22 -0.269 A_C6:G22_A 6 -6.295 0.447 -0.700 -0.606 -9.376 1 19 A 8 A 19 -14.271 A_C8:G19_A 7 -14.682 0.244 1.329 -0.768 9.176 1 20 A 9 A 18 -10.898 A_A9:U18_A 8 -11.114 0.215 1.284 -0.376 14.480 1 19 A 10 A 17 -5.277 A_C10:G17_A 9 -9.947 0.328 0.683 -0.418 26.173 1 19 A 11 A 16 -1.800 A_C11:G16_A 10 -19.205 0.595 -0.718 -0.361 -13.698 A 12 A 15 -78.916 A_U12:G15_A 11 -34.618 2.259 0.119 -4.255 -1.160 169.108 A A 1 2 83.620 A A 27 26 -0.501 163.230 3.634 -1.123 AA_G1G2:C26C27_AA 1 -3.528 1.807 98.569 -0.257 -1.818 2.725 35.931 A A 2 3 6.253 A A 26 25 2.809 3.847 0.344 -0.838 AA_G2C3:G25C26_AA 2 2.781 -4.520 35.626 -1.826 -0.221 2.405 33.642 A A 3 4 21.482 A A 25 24 3.235 12.140 0.552 -1.540 AA_C3G4:C24G25_AA 3 -3.804 6.731 31.209 -4.438 -1.511 3.307 51.698 A A 4 5 -5.918 A A 24 23 3.242 -5.152 0.357 -1.062 AA_G4U5:U23C24_AA 4 -2.553 2.933 51.399 -0.868 -0.582 2.910 36.784 A A 5 6 2.664 A A 23 22 3.325 1.631 -0.087 -1.866 AA_U5C6:G22U23_AA 5 15.613 -25.509 33.372 -3.180 2.271 2.700 33.868 A A 8 9 -16.431 A A 19 18 2.348 -9.451 -0.282 -1.611 AA_C8A9:U18G19_AA 6 -0.368 0.639 32.558 -1.566 0.438 3.534 36.589 A A 9 10 -15.773 A A 18 17 3.238 -9.783 0.361 -1.511 AA_A9C10:G17U18_AA 7 2.325 -3.748 35.226 -0.985 -0.237 3.084 32.676 A A 10 11 -11.518 A A 17 16 2.927 -6.380 0.282 -1.190 AA_C10C11:G16G17_AA 8 7.776 -14.038 31.129 -1.074 0.767 3.271 95.152 A A 11 12 10.489 A A 16 15 3.504 15.426 -0.200 -1.409 AA_C11U12:G15G16_AA 9 10.778 -7.328 93.716 -1.241 0.336 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2001-03-14 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name the eukaryotic decoding region A-site RNA bound to paromomycin the prokaryotic decoding region A site RNA the prokaryotic decoding region A site RNA bound to paromomycin RCSB Y RCSB 2000-10-02 REL This sequence occurs naturally in Tetrahymena thermophila sample structures with the least restraint violations,structures with the lowest energy 100 25 2D NOESY 3D_13C-separated_NOESY 3D_15N-separated_NOESY 4D_13C-separated_NOESY DQF-COSY 10 mM 6.3 1 atm 298 K 682 NOEs, 129 dihedral constraints, 36 Hydrogen bonds simulated annealing molecular dynamics 12 3 mM decoding site RNA, 13C/15N, 10 mM phosphate pH 6.3, 90% H20/10% D20, 100% D20 90% H2O/10% D20; 100% D2O Brunger refinement X-PLOR 3.83 Brunger structure solution X-PLOR 3.83 processing VNMR 6.1 processing Felix 6.1 500 Varian INOVA 800 Varian INOVA G 1 n 1 G 1 A G 2 n 2 G 2 A C 3 n 3 C 3 A G 4 n 4 G 4 A U 5 n 5 U 5 A C 6 n 6 C 6 A G 7 n 7 G 7 A C 8 n 8 C 8 A A 9 n 9 A 9 A C 10 n 10 C 10 A C 11 n 11 C 11 A U 12 n 12 U 12 A U 13 n 13 U 13 A C 14 n 14 C 14 A G 15 n 15 G 15 A G 16 n 16 G 16 A G 17 n 17 G 17 A U 18 n 18 U 18 A G 19 n 19 G 19 A A 20 n 20 A 20 A A 21 n 21 A 21 A G 22 n 22 G 22 A U 23 n 23 U 23 A C 24 n 24 C 24 A G 25 n 25 G 25 A C 26 n 26 C 26 A C 27 n 27 C 27 A author_defined_assembly 1 monomeric 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 A O2' H5'' A A 20 21 1.41 1 A A HO2' O6 U G 12 15 1.58 1 A A O6 H41 G C 2 26 1.59 1 A A H41 O6 C G 6 22 1.59 1 A A H41 O6 C G 3 25 1.60 2 A A O2' H5'' A A 20 21 1.42 2 A A HO2' O6 U G 12 15 1.58 2 A A O6 H41 G C 1 27 1.59 2 A A H41 O6 C G 6 22 1.60 2 A A H41 O6 C G 3 25 1.60 2 A A O6 H41 G C 2 26 1.60 3 A A O2' H5'' A A 20 21 1.46 3 A A HO2' O4' U C 5 6 1.57 3 A A O6 H41 G C 1 27 1.59 4 A A O2' H5'' A A 20 21 1.43 4 A A O2' H8 A A 20 21 1.57 4 A A H41 O6 C G 6 22 1.59 4 A A O6 H41 G C 1 27 1.59 4 A A H41 O6 C G 11 16 1.60 4 A A H41 O6 C G 3 25 1.60 5 A A O2' H5'' A A 20 21 1.41 5 A A H41 O6 C G 6 22 1.59 5 A A O6 H41 G C 1 27 1.60 6 A A O2' H5'' A A 20 21 1.44 6 A A HO2' O4' A A 20 21 1.45 6 A A H41 O6 C G 3 25 1.58 7 A A O2' H5'' A A 20 21 1.41 7 A A H41 O6 C G 6 22 1.59 7 A A O6 H41 G C 1 27 1.59 7 A A O2' H8 A G 21 22 1.60 8 A A O2' H5'' A A 20 21 1.47 8 A A HO2' O4' U C 5 6 1.57 8 A A O2' H8 A A 20 21 1.58 8 A A O6 H41 G C 1 27 1.59 9 A A O2' H5'' A A 20 21 1.44 9 A A HO2' O4' A A 20 21 1.47 9 A A O6 H41 G C 2 26 1.60 10 A A O2' H5'' A A 20 21 1.42 10 A A O2' H8 A A 20 21 1.59 10 A A O6 H41 G C 1 27 1.59 10 A A H41 O6 C G 6 22 1.59 10 A A H41 O6 C G 3 25 1.60 11 A A O2' H5'' A A 20 21 1.42 11 A A H41 O6 C G 6 22 1.58 11 A A O2' H8 A A 20 21 1.58 11 A A HO2' O6 U G 12 15 1.59 12 A A O2' H5'' A A 20 21 1.44 12 A A O6 H41 G C 1 27 1.59 12 A A H41 O6 C G 11 16 1.60 12 A A H41 O6 C G 3 25 1.60 12 A A H41 O6 C G 6 22 1.60 12 A A O2' H8 A A 20 21 1.60 13 A A O2' H5'' A A 20 21 1.44 13 A A H41 O6 C G 6 22 1.59 13 A A O2' H8 A A 20 21 1.59 13 A A O6 H41 G C 1 27 1.59 13 A A H41 O6 C G 11 16 1.59 14 A A O2' H5'' A A 20 21 1.41 14 A A O6 H41 G C 1 27 1.60 15 A A O2' H5'' A A 20 21 1.41 15 A A H41 O6 C G 6 22 1.58 15 A A O6 H41 G C 1 27 1.60 15 A A H41 O6 C G 11 16 1.60 16 A A O2' H5'' A A 20 21 1.44 16 A A HO2' O4' A A 20 21 1.58 16 A A O6 H41 G C 2 26 1.59 17 A A O2' H5'' A A 20 21 1.41 17 A A H41 O6 C G 6 22 1.58 17 A A O2' H8 A A 20 21 1.58 17 A A O6 H41 G C 1 27 1.60 17 A A O6 H41 G C 2 26 1.60 18 A A O2' H5'' A A 20 21 1.44 18 A A HO2' O4' A A 20 21 1.54 18 A A H41 O6 C G 6 22 1.58 18 A A O6 H41 G C 1 27 1.60 19 A A O2' H5'' A A 20 21 1.41 19 A A H41 O6 C G 11 16 1.59 19 A A O2' H8 A A 20 21 1.59 19 A A O6 H41 G C 1 27 1.60 20 A A O2' H5'' A A 20 21 1.45 21 A A O2' H5'' A A 20 21 1.43 21 A A O6 H41 G C 1 27 1.59 21 A A H41 O6 C G 3 25 1.59 21 A A O6 H41 G C 2 26 1.60 22 A A O2' H5'' A A 20 21 1.44 22 A A HO2' O4' A A 20 21 1.51 22 A A O6 H41 G C 1 27 1.59 22 A A H41 O6 C G 6 22 1.59 23 A A O2' H5'' A A 20 21 1.42 23 A A H41 O6 C G 3 25 1.58 23 A A O6 H41 G C 1 27 1.60 24 A A O2' H5'' A A 20 21 1.42 24 A A O2' H8 A G 21 22 1.47 24 A A H41 O6 C G 6 22 1.56 25 A A O2' H5'' A A 20 21 1.42 25 A A O2' H8 A A 20 21 1.57 25 A A HO2' O6 U G 12 15 1.57 25 A A H41 O6 C G 6 22 1.58 25 A A HO2' O4' G C 2 3 1.60 EUKARYOTIC DECODING REGION A-SITE RNA 1 N N hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 A C 27 A N3 C 27 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 A C 27 A O2 C 27 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 A C 27 A N4 C 27 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 A C 26 A N3 C 26 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 A C 26 A O2 C 26 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 A C 26 A N4 C 26 1_555 hydrog WATSON-CRICK A C 3 A N3 C 3 1_555 A G 25 A N1 G 25 1_555 hydrog WATSON-CRICK A C 3 A N4 C 3 1_555 A G 25 A O6 G 25 1_555 hydrog WATSON-CRICK A C 3 A O2 C 3 1_555 A G 25 A N2 G 25 1_555 hydrog WATSON-CRICK A G 4 A N1 G 4 1_555 A C 24 A N3 C 24 1_555 hydrog WATSON-CRICK A G 4 A N2 G 4 1_555 A C 24 A O2 C 24 1_555 hydrog WATSON-CRICK A G 4 A O6 G 4 1_555 A C 24 A N4 C 24 1_555 hydrog TYPE_16_PAIR A U 5 A N3 U 5 1_555 A U 23 A O4 U 23 1_555 hydrog TYPE_16_PAIR A U 5 A O2 U 5 1_555 A U 23 A N3 U 23 1_555 hydrog WATSON-CRICK A C 6 A N3 C 6 1_555 A G 22 A N1 G 22 1_555 hydrog WATSON-CRICK A C 6 A N4 C 6 1_555 A G 22 A O6 G 22 1_555 hydrog WATSON-CRICK A C 6 A O2 C 6 1_555 A G 22 A N2 G 22 1_555 hydrog WATSON-CRICK A C 8 A N3 C 8 1_555 A G 19 A N1 G 19 1_555 hydrog WATSON-CRICK A C 8 A N4 C 8 1_555 A G 19 A O6 G 19 1_555 hydrog WATSON-CRICK A C 8 A O2 C 8 1_555 A G 19 A N2 G 19 1_555 hydrog C-A MISPAIR A C 8 A O2 C 8 1_555 A A 20 A N6 A 20 1_555 hydrog A-G MISPAIR A A 9 A N6 A 9 1_555 A G 17 A O6 G 17 1_555 hydrog WATSON-CRICK A A 9 A N1 A 9 1_555 A U 18 A N3 U 18 1_555 hydrog WATSON-CRICK A A 9 A N6 A 9 1_555 A U 18 A O4 U 18 1_555 hydrog WATSON-CRICK A C 10 A N3 C 10 1_555 A G 17 A N1 G 17 1_555 hydrog WATSON-CRICK A C 10 A N4 C 10 1_555 A G 17 A O6 G 17 1_555 hydrog WATSON-CRICK A C 10 A O2 C 10 1_555 A G 17 A N2 G 17 1_555 hydrog WATSON-CRICK A C 11 A N3 C 11 1_555 A G 16 A N1 G 16 1_555 hydrog WATSON-CRICK A C 11 A N4 C 11 1_555 A G 16 A O6 G 16 1_555 hydrog WATSON-CRICK A C 11 A O2 C 11 1_555 A G 16 A N2 G 16 1_555 hydrog U-G MISPAIR A U 12 A O2 U 12 1_555 A G 15 A N1 G 15 1_555 RNA stem-internal loop-stem-tetraloop RNA, G-A base pair, bulged A, RNA 1FYO PDB 1 1FYO 1 27 1FYO 1 27 1FYO A 1 1 27 1 P 1