1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Stuart, J.W. Koshlap, K.M. Guenther, R.H. Agris, P.F. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C10 H16 N3 O8 P 337.223 n 5-METHYLCYTIDINE-5'-MONOPHOSPHATE RNA linking 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 H16 N3 O8 P 337.223 n O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE RNA linking C11 H16 N5 O8 P 377.247 n O2'-METHYLGUANOSINE-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 334 901 918 10.1016/j.jmb.2003.09.058 14643656 Naturally-occurring Modification Restricts the Anticodon Domain Conformational Space of tRNA(Phe). 2003 10.2210/pdb1lux/pdb pdb_00001lux 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 ANTICODON (RESIDUES 27-43) OF TRNA-PHE WITH THREE MODIFIED RESIDUES (OMC at position 32, OMG at 34, M5C at position 40) 5508.404 5'-R(*CP*CP*AP*GP*AP*(OMC)P*UP*(OMG)P*AP*AP*GP*AP*UP*(5MC)P*UP*GP*G)-3' 1 syn polymer no yes CCAGA(OMC)U(OMG)AAGAU(5MC)UGG CCAGACUGAAGAUCUGG A polyribonucleotide n n n n n n n n n n n n n n n n n 8.473 1 19 A 27 A 43 -4.112 A_C27:G43_A 1 -20.951 0.675 0.385 -0.267 11.278 1 19 A 28 A 42 -2.360 A_C28:G42_A 2 -20.714 -0.460 0.059 -0.043 -2.003 1 20 A 29 A 41 -1.510 A_A29:U41_A 3 -16.862 -0.530 -0.090 -0.133 -8.360 1 19 A 30 A 40 -2.090 A_G30:5MC40_A 4 -19.144 0.175 -0.033 -0.039 -5.808 1 20 A 31 A 39 0.074 A_A31:U39_A 5 -21.995 -0.527 -0.062 -0.203 -10.151 A 32 A 38 -2.349 A_OMC32:A38_A 6 -3.011 2.502 0.077 -0.328 2.424 31.774 A A 27 28 13.591 A A 43 42 2.877 7.371 -0.666 -1.830 AA_C27C28:G42G43_AA 1 -2.004 3.695 30.865 -4.454 0.914 2.076 41.373 A A 28 29 31.503 A A 42 41 3.242 21.274 -0.262 -1.486 AA_C28A29:U41G42_AA 2 -0.592 0.877 35.687 -4.108 0.314 1.975 33.495 A A 29 30 27.381 A A 41 40 3.232 15.230 0.243 -2.063 AA_A29G30:5MC40U41_AA 3 -0.592 1.065 29.916 -5.696 -0.503 2.161 32.703 A A 30 31 21.010 A A 40 39 2.991 11.586 0.256 -1.853 AA_G30A31:U395MC40_AA 4 -0.534 0.969 30.630 -4.923 -0.530 2.973 47.730 A A 31 32 8.832 A A 39 38 3.183 7.122 -0.263 -1.194 AA_A31OMC32:A38U39_AA 5 1.680 -2.083 47.198 -2.013 0.451 database_2 pdbx_nmr_software pdbx_nmr_spectrometer 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 2003-09-09 1 1 2008-04-28 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _pdbx_nmr_spectrometer.model _struct_conn.pdbx_leaving_atom_flag NMR SOLUTION STRUCTURE OF THE ANTICODON OF YEAST TRNA-PHE WITH 4 MODIFICATIONS (OMC32 OMG34 1MG37 5MC40) RCSB Y RCSB 2002-05-23 REL REL SEQUENCE WITH NATURALLY OCCURRING MODIFICATIONS SYNTHESIZED USING PHOSPHORAMIDITE CHEMISTRY. sample This structure was determined using standard 2D homonuclear techniques. structures with the least restraint violations, structures with the lowest energy 50 10 2D NOESY DQF-COSY 5.60 1 atm 298 K 271 restraints (258 NOE-Derived, 13 h-bond), 95 dihedral angle global fold by distance geometry. refinement by simulated annealing using the amber forcefield 1.6 mM RNA, 10 mM cacodylate buffer, pH 5.6, 0.1 mM EDTA Bruker collection XwinNMR Accelrys data analysis Felix 98 Accelrys refinement Discover 98 500 Bruker AVANCE C 27 n 1 C 27 A C 28 n 2 C 28 A A 29 n 3 A 29 A G 30 n 4 G 30 A A 31 n 5 A 31 A OMC 32 n 6 OMC 32 A U 33 n 7 U 33 A OMG 34 n 8 OMG 34 A A 35 n 9 A 35 A A 36 n 10 A 36 A G 37 n 11 G 37 A A 38 n 12 A 38 A U 39 n 13 U 39 A 5MC 40 n 14 5MC 40 A U 41 n 15 U 41 A G 42 n 16 G 42 A G 43 n 17 G 43 A author_defined_assembly 1 monomeric A OMC 32 O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE A OMC 6 C A OMG 34 O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE A OMG 8 G A 5MC 40 5-METHYLCYTIDINE-5'-MONOPHOSPHATE A 5MC 14 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 A 29 0.083 SIDE CHAIN 1 A A 31 0.063 SIDE CHAIN 1 A A 35 0.091 SIDE CHAIN 1 A U 41 0.070 SIDE CHAIN 2 A U 33 0.130 SIDE CHAIN 2 A A 35 0.120 SIDE CHAIN 2 A U 41 0.061 SIDE CHAIN 3 A C 27 0.082 SIDE CHAIN 3 A A 31 0.066 SIDE CHAIN 3 A U 33 0.094 SIDE CHAIN 3 A A 35 0.086 SIDE CHAIN 3 A A 36 0.099 SIDE CHAIN 3 A G 37 0.069 SIDE CHAIN 3 A U 41 0.069 SIDE CHAIN 4 A A 31 0.074 SIDE CHAIN 4 A U 33 0.082 SIDE CHAIN 4 A A 35 0.210 SIDE CHAIN 4 A G 43 0.079 SIDE CHAIN 5 A G 30 0.061 SIDE CHAIN 5 A A 31 0.066 SIDE CHAIN 5 A U 33 0.062 SIDE CHAIN 5 A A 35 0.146 SIDE CHAIN 5 A G 37 0.063 SIDE CHAIN 5 A A 38 0.056 SIDE CHAIN 6 A C 27 0.066 SIDE CHAIN 6 A A 31 0.094 SIDE CHAIN 6 A U 33 0.091 SIDE CHAIN 6 A A 35 0.063 SIDE CHAIN 6 A G 37 0.074 SIDE CHAIN 6 A G 43 0.061 SIDE CHAIN 7 A C 27 0.086 SIDE CHAIN 7 A A 29 0.061 SIDE CHAIN 7 A A 31 0.066 SIDE CHAIN 7 A U 33 0.160 SIDE CHAIN 7 A A 36 0.087 SIDE CHAIN 8 A C 28 0.087 SIDE CHAIN 8 A A 31 0.086 SIDE CHAIN 8 A G 37 0.060 SIDE CHAIN 8 A A 38 0.091 SIDE CHAIN 9 A A 31 0.082 SIDE CHAIN 9 A U 33 0.079 SIDE CHAIN 9 A A 36 0.085 SIDE CHAIN 9 A G 42 0.056 SIDE CHAIN 10 A A 31 0.079 SIDE CHAIN 10 A U 33 0.218 SIDE CHAIN 10 A G 37 0.057 SIDE CHAIN 10 A A 38 0.067 SIDE CHAIN 1 5.97 0.70 108.50 114.47 A A A O4' C1' N1 C C C 27 27 27 N 1 -7.24 1.20 109.10 101.86 A A A C5' C4' O4' U U U 33 33 33 N 1 6.30 0.80 101.50 107.80 A A A C3' C2' C1' U U U 33 33 33 N 1 7.63 0.70 108.50 116.13 A A A O4' C1' N1 U U U 33 33 33 N 1 11.27 1.20 119.70 130.97 A A A C3' O3' P OMG OMG A 34 34 35 Y 1 -11.80 1.90 104.00 92.20 A A A O3' P O5' OMG A A 34 35 35 Y 1 7.97 0.90 109.80 117.77 A A A C5' C4' O4' A A A 35 35 35 N 1 7.70 0.70 108.50 116.20 A A A O4' C1' N9 A A A 35 35 35 N 1 -5.19 0.50 129.30 124.11 A A A N1 C2 N3 A A A 38 38 38 N 1 4.11 0.50 110.60 114.71 A A A C2 N3 C4 A A A 38 38 38 N 1 7.48 0.70 108.50 115.98 A A A O4' C1' N9 G G G 43 43 43 N 2 4.32 0.70 108.50 112.82 A A A O4' C1' N1 C C C 27 27 27 N 2 9.94 1.30 114.00 123.94 A A A N9 C1' C2' A A A 35 35 35 N 2 7.10 0.70 108.50 115.60 A A A O4' C1' N9 A A A 36 36 36 N 2 6.09 0.90 109.80 115.89 A A A C5' C4' O4' A A A 38 38 38 N 2 -5.17 0.50 129.30 124.13 A A A N1 C2 N3 A A A 38 38 38 N 2 4.07 0.50 110.60 114.67 A A A C2 N3 C4 A A A 38 38 38 N 2 4.26 0.70 108.50 112.76 A A A O4' C1' N1 U U U 41 41 41 N 2 7.43 0.70 108.50 115.93 A A A O4' C1' N9 G G G 43 43 43 N 3 4.79 0.70 108.50 113.29 A A A O4' C1' N1 C C C 27 27 27 N 3 5.55 0.90 109.80 115.35 A A A C5' C4' O4' A A A 35 35 35 N 3 4.81 0.70 108.50 113.31 A A A O4' C1' N9 A A A 35 35 35 N 3 4.72 0.70 108.50 113.22 A A A O4' C1' N9 G G G 37 37 37 N 3 6.44 0.90 109.80 116.24 A A A C5' C4' O4' A A A 38 38 38 N 3 -5.35 0.50 129.30 123.95 A A A N1 C2 N3 A A A 38 38 38 N 3 4.13 0.50 110.60 114.73 A A A C2 N3 C4 A A A 38 38 38 N 3 4.24 0.70 108.50 112.74 A A A O4' C1' N1 U U U 41 41 41 N 3 7.18 0.70 108.50 115.68 A A A O4' C1' N9 G G G 43 43 43 N 4 6.17 0.70 108.50 114.67 A A A O4' C1' N1 C C C 27 27 27 N 4 9.26 1.20 119.70 128.96 A A A C3' O3' P OMG OMG A 34 34 35 Y 4 7.58 0.90 109.80 117.38 A A A C5' C4' O4' A A A 35 35 35 N 4 7.49 0.70 108.50 115.99 A A A O4' C1' N9 A A A 35 35 35 N 4 6.15 0.70 108.50 114.65 A A A O4' C1' N9 A A A 36 36 36 N 4 5.48 0.90 109.80 115.28 A A A C5' C4' O4' A A A 38 38 38 N 4 -5.29 0.50 129.30 124.01 A A A N1 C2 N3 A A A 38 38 38 N 4 4.16 0.50 110.60 114.76 A A A C2 N3 C4 A A A 38 38 38 N 4 4.36 0.70 108.50 112.86 A A A O4' C1' N1 U U U 39 39 39 N 5 4.34 0.70 108.50 112.84 A A A O4' C1' N1 C C C 27 27 27 N 5 8.81 0.70 108.50 117.31 A A A O4' C1' N9 A A A 35 35 35 N 5 4.49 0.70 108.50 112.99 A A A O4' C1' N9 A A A 36 36 36 N 5 5.45 0.70 108.50 113.95 A A A O4' C1' N9 G G G 37 37 37 N 5 5.54 0.90 109.80 115.34 A A A C5' C4' O4' A A A 38 38 38 N 5 -5.33 0.50 129.30 123.97 A A A N1 C2 N3 A A A 38 38 38 N 5 4.35 0.50 110.60 114.95 A A A C2 N3 C4 A A A 38 38 38 N 5 7.51 0.70 108.50 116.01 A A A O4' C1' N9 G G G 43 43 43 N 6 4.28 0.70 108.50 112.78 A A A O4' C1' N1 C C C 27 27 27 N 6 4.38 0.70 108.50 112.88 A A A O4' C1' N1 U U U 33 33 33 N 6 6.54 0.90 109.80 116.34 A A A C5' C4' O4' A A A 35 35 35 N 6 12.23 0.70 108.50 120.73 A A A O4' C1' N9 A A A 35 35 35 N 6 5.50 0.90 109.80 115.30 A A A C5' C4' O4' A A A 38 38 38 N 6 -5.28 0.50 129.30 124.02 A A A N1 C2 N3 A A A 38 38 38 N 6 4.21 0.50 110.60 114.81 A A A C2 N3 C4 A A A 38 38 38 N 6 4.65 0.70 108.50 113.15 A A A O4' C1' N1 U U U 39 39 39 N 7 4.70 0.70 108.50 113.20 A A A O4' C1' N1 C C C 27 27 27 N 7 -4.55 0.70 101.30 96.75 A A A C3' C2' C1' A A A 35 35 35 N 7 -5.33 0.50 129.30 123.97 A A A N1 C2 N3 A A A 38 38 38 N 7 4.23 0.50 110.60 114.83 A A A C2 N3 C4 A A A 38 38 38 N 7 4.49 0.70 108.50 112.99 A A A O4' C1' N1 U U U 39 39 39 N 7 4.50 0.70 108.50 113.00 A A A O4' C1' N1 U U U 41 41 41 N 7 7.27 0.70 108.50 115.77 A A A O4' C1' N9 G G G 43 43 43 N 8 8.25 0.90 109.80 118.05 A A A C5' C4' O4' A A A 29 29 29 N 8 -4.77 0.70 101.30 96.53 A A A C3' C2' C1' A A A 35 35 35 N 8 4.73 0.70 108.50 113.23 A A A O4' C1' N9 A A A 35 35 35 N 8 5.42 0.70 108.50 113.92 A A A O4' C1' N9 G G G 37 37 37 N 8 -5.30 0.50 129.30 124.00 A A A N1 C2 N3 A A A 38 38 38 N 8 4.28 0.50 110.60 114.88 A A A C2 N3 C4 A A A 38 38 38 N 9 6.25 0.70 108.50 114.75 A A A O4' C1' N1 C C C 27 27 27 N 9 4.90 0.70 108.50 113.40 A A A O4' C1' N9 G G G 37 37 37 N 9 6.43 0.90 109.80 116.23 A A A C5' C4' O4' A A A 38 38 38 N 9 -5.11 0.50 129.30 124.19 A A A N1 C2 N3 A A A 38 38 38 N 9 4.17 0.50 110.60 114.77 A A A C2 N3 C4 A A A 38 38 38 N 9 4.47 0.70 108.50 112.97 A A A O4' C1' N1 U U U 41 41 41 N 10 5.92 0.70 108.50 114.42 A A A O4' C1' N1 C C C 27 27 27 N 10 6.41 0.70 108.50 114.91 A A A O4' C1' N1 U U U 33 33 33 N 10 6.44 0.90 109.80 116.24 A A A C5' C4' O4' A A A 35 35 35 N 10 -4.59 0.70 109.70 105.11 A A A C1' O4' C4' A A A 35 35 35 N 10 7.57 0.70 108.50 116.07 A A A O4' C1' N9 A A A 35 35 35 N 10 -5.04 0.50 129.30 124.26 A A A N1 C2 N3 A A A 38 38 38 N 10 4.28 0.50 110.60 114.88 A A A C2 N3 C4 A A A 38 38 38 N 9 A A N1 C2 A A 38 38 0.055 0.009 1.339 1.394 N 10 A A N1 C2 A A 38 38 0.055 0.009 1.339 1.394 N NMR SOLUTION STRUCTURE OF THE ANTICODON OF YEAST TRNA-PHE WITH 3 MODIFICATIONS (OMC32 OMG34 M5C40) 1 N N covale 1.618 both A A 31 A O3' A 5 1_555 A OMC 32 A P OMC 6 1_555 covale 1.620 both A OMC 32 A O3' OMC 6 1_555 A U 33 A P U 7 1_555 covale 1.633 both A U 33 A O3' U 7 1_555 A OMG 34 A P OMG 8 1_555 covale 1.586 both A OMG 34 A O3' OMG 8 1_555 A A 35 A P A 9 1_555 covale 1.618 both A U 39 A O3' U 13 1_555 A 5MC 40 A P 5MC 14 1_555 covale 1.612 both A 5MC 40 A O3' 5MC 14 1_555 A U 41 A P U 15 1_555 hydrog WATSON-CRICK A C 27 A N3 C 1 1_555 A G 43 A N1 G 17 1_555 hydrog WATSON-CRICK A C 27 A N4 C 1 1_555 A G 43 A O6 G 17 1_555 hydrog WATSON-CRICK A C 27 A O2 C 1 1_555 A G 43 A N2 G 17 1_555 hydrog WATSON-CRICK A C 28 A N3 C 2 1_555 A G 42 A N1 G 16 1_555 hydrog WATSON-CRICK A C 28 A N4 C 2 1_555 A G 42 A O6 G 16 1_555 hydrog WATSON-CRICK A C 28 A O2 C 2 1_555 A G 42 A N2 G 16 1_555 hydrog WATSON-CRICK A A 29 A N1 A 3 1_555 A U 41 A N3 U 15 1_555 hydrog WATSON-CRICK A A 29 A N6 A 3 1_555 A U 41 A O4 U 15 1_555 hydrog WATSON-CRICK A G 30 A N1 G 4 1_555 A 5MC 40 A N3 5MC 14 1_555 hydrog WATSON-CRICK A G 30 A N2 G 4 1_555 A 5MC 40 A O2 5MC 14 1_555 hydrog WATSON-CRICK A G 30 A O6 G 4 1_555 A 5MC 40 A N4 5MC 14 1_555 hydrog WATSON-CRICK A A 31 A N1 A 5 1_555 A U 39 A N3 U 13 1_555 hydrog WATSON-CRICK A A 31 A N6 A 5 1_555 A U 39 A O4 U 13 1_555 hydrog OMC-A MISPAIR A OMC 32 A N3 OMC 6 1_555 A A 38 A N6 A 12 1_555 hydrog WATSON-CRICK A U 33 A N3 U 7 1_555 A A 38 A N1 A 12 1_555 hydrog WATSON-CRICK A U 33 A O4 U 7 1_555 A A 38 A N6 A 12 1_555 RNA TRNA, ANTICODON STEM LOOP, TRNA DOMAIN, RNA HAIRPIN, 2'-O-METHYL, M5C, RNA 1LUX PDB 1 1LUX 27 43 1LUX 27 43 1LUX A 1 1 17