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 C11 H16 N5 O8 P 377.247 n 1N-METHYLGUANOSINE-5'-MONOPHOSPHATE RNA linking 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/pdb1luu/pdb pdb_00001luu 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 ANTICODON (RESIDUES 27-43) OF TRNA-PHE WITH FOUR MODIFIED RESIDUES (OMC at position 32, OMG at 34, 1MG at 37, and 5MC at position 40) 5522.430 5'-R(*CP*CP*AP*GP*AP*(OMC)P*UP*(OMG)P*AP*AP*(1MG)P*AP*UP*(5MC)P*UP*GP*G)-3' 1 syn polymer no yes CCAGA(OMC)U(OMG)AA(1MG)AU(5MC)UGG CCAGACUGAAGAUCUGG A polyribonucleotide n n n n n n n n n n n n n n n n n 8.735 1 19 A 27 A 43 -3.183 A_C27:G43_A 1 -6.496 -0.211 -0.033 -0.035 15.331 1 19 A 28 A 42 -0.803 A_C28:G42_A 2 -11.798 -0.428 -0.114 -0.008 -3.519 1 20 A 29 A 41 2.525 A_A29:U41_A 3 -11.069 -0.535 -0.594 -0.210 -16.975 1 19 A 30 A 40 -4.456 A_G30:5MC40_A 4 -6.340 0.311 -1.102 -0.177 -16.861 1 20 A 31 A 39 -0.102 A_A31:U39_A 5 3.104 0.035 -0.216 0.043 -8.413 1 A 32 A 38 7.868 A_OMC32:A38_A 6 -0.272 3.709 0.143 -0.805 -47.808 A 34 A 36 165.804 A_OMG34:A36_A 7 1.244 -1.622 -0.685 -5.162 2.383 31.631 A A 27 28 25.382 A A 43 42 3.090 13.417 0.289 -1.014 AA_C27C28:G42G43_AA 1 -0.651 1.231 28.704 -4.044 -0.637 1.896 47.106 A A 28 29 46.517 A A 42 41 4.021 33.620 0.245 -1.432 AA_C28A29:U41G42_AA 2 5.345 -7.395 33.055 -4.791 0.170 3.079 36.794 A A 29 30 22.695 A A 41 40 3.846 13.985 -0.686 -1.266 AA_A29G30:5MC40U41_AA 3 1.407 -2.283 34.090 -4.104 1.298 2.867 34.941 A A 30 31 10.592 A A 40 39 3.400 6.286 0.886 -1.378 AA_G30A31:U395MC40_AA 4 -7.026 11.839 33.684 -3.223 -2.512 2.671 43.990 A A 31 32 17.533 A A 39 38 3.184 12.950 -0.054 -1.339 AA_A31OMC32:A38U39_AA 5 2.599 -3.518 42.054 -2.910 0.298 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 3 MODIFICATIONS (OMC32 OMG34 M5C40) 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 11 2D NOESY DQF-COSY 5.60 1 atm 298 K 269 RESTRAINTS (256 NOE-DERIVED, 13 H-BOND) 96 DIHEDRAL ANGLE. GLOBAL FOLD BY DISTANCE GEOMETRY. REFINEMENT BY SIMULATED ANNEALING USING THE AMBER FORCEFIELD 1 minimized average structure 1.2 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 1MG 37 n 11 1MG 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 1MG 37 1N-METHYLGUANOSINE-5'-MONOPHOSPHATE A 1MG 11 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 C 27 0.088 SIDE CHAIN 1 A C 28 0.075 SIDE CHAIN 1 A A 29 0.079 SIDE CHAIN 1 A G 42 0.076 SIDE CHAIN 2 A C 27 0.086 SIDE CHAIN 2 A C 28 0.057 SIDE CHAIN 2 A A 29 0.073 SIDE CHAIN 2 A U 33 0.059 SIDE CHAIN 2 A A 35 0.071 SIDE CHAIN 2 A U 41 0.069 SIDE CHAIN 2 A G 42 0.073 SIDE CHAIN 3 A C 27 0.070 SIDE CHAIN 3 A C 28 0.062 SIDE CHAIN 3 A G 30 0.073 SIDE CHAIN 3 A U 33 0.098 SIDE CHAIN 3 A A 35 0.073 SIDE CHAIN 3 A G 42 0.074 SIDE CHAIN 4 A C 27 0.096 SIDE CHAIN 4 A G 30 0.085 SIDE CHAIN 4 A A 35 0.090 SIDE CHAIN 4 A G 42 0.081 SIDE CHAIN 5 A C 27 0.063 SIDE CHAIN 5 A C 28 0.105 SIDE CHAIN 5 A A 29 0.104 SIDE CHAIN 5 A G 30 0.082 SIDE CHAIN 5 A U 33 0.057 SIDE CHAIN 5 A U 41 0.076 SIDE CHAIN 5 A G 42 0.075 SIDE CHAIN 6 A C 27 0.077 SIDE CHAIN 6 A C 28 0.092 SIDE CHAIN 6 A G 30 0.078 SIDE CHAIN 6 A A 35 0.094 SIDE CHAIN 6 A G 42 0.065 SIDE CHAIN 7 A C 27 0.103 SIDE CHAIN 7 A A 29 0.064 SIDE CHAIN 7 A G 42 0.078 SIDE CHAIN 8 A C 27 0.082 SIDE CHAIN 8 A C 28 0.112 SIDE CHAIN 8 A A 29 0.087 SIDE CHAIN 8 A G 30 0.061 SIDE CHAIN 8 A U 33 0.056 SIDE CHAIN 8 A A 38 0.060 SIDE CHAIN 8 A U 41 0.065 SIDE CHAIN 8 A G 42 0.077 SIDE CHAIN 9 A C 27 0.072 SIDE CHAIN 9 A C 28 0.096 SIDE CHAIN 9 A A 29 0.061 SIDE CHAIN 9 A G 30 0.078 SIDE CHAIN 9 A G 42 0.075 SIDE CHAIN 10 A C 27 0.086 SIDE CHAIN 10 A C 28 0.115 SIDE CHAIN 10 A G 30 0.066 SIDE CHAIN 10 A U 41 0.067 SIDE CHAIN 10 A G 42 0.083 SIDE CHAIN 11 A C 27 0.068 SIDE CHAIN 11 A C 28 0.070 SIDE CHAIN 11 A G 30 0.059 SIDE CHAIN 11 A G 42 0.068 SIDE CHAIN 11 A G 43 0.064 SIDE CHAIN 1 4.35 0.70 108.50 112.85 A A A O4' C1' N1 U U U 33 33 33 N 1 6.42 0.70 108.50 114.92 A A A O4' C1' N9 A A A 36 36 36 N 1 -5.59 0.50 129.30 123.71 A A A N1 C2 N3 A A A 38 38 38 N 1 4.25 0.50 110.60 114.85 A A A C2 N3 C4 A A A 38 38 38 N 2 9.93 1.30 114.00 123.93 A A A N9 C1' C2' A A A 35 35 35 N 2 4.34 0.70 108.50 112.84 A A A O4' C1' N9 A A A 35 35 35 N 2 5.24 0.70 108.50 113.74 A A A O4' C1' N9 A A A 36 36 36 N 2 -5.36 0.50 129.30 123.94 A A A N1 C2 N3 A A A 38 38 38 N 2 3.81 0.50 110.60 114.41 A A A C2 N3 C4 A A A 38 38 38 N 3 9.87 1.30 114.00 123.87 A A A N9 C1' C2' A A A 35 35 35 N 3 -5.50 0.50 129.30 123.80 A A A N1 C2 N3 A A A 38 38 38 N 3 3.80 0.50 110.60 114.40 A A A C2 N3 C4 A A A 38 38 38 N 4 6.39 0.70 108.50 114.89 A A A O4' C1' N1 U U U 33 33 33 N 4 10.62 1.30 114.00 124.62 A A A N9 C1' C2' A A A 35 35 35 N 4 6.77 0.70 108.50 115.27 A A A O4' C1' N9 A A A 35 35 35 N 4 -2.99 0.40 105.80 102.81 A A A C8 N9 C4 A A A 35 35 35 N 4 -6.13 0.70 109.70 103.57 A A A C1' O4' C4' A A A 38 38 38 N 4 5.73 0.70 108.50 114.23 A A A O4' C1' N9 A A A 38 38 38 N 4 -5.44 0.50 129.30 123.86 A A A N1 C2 N3 A A A 38 38 38 N 4 3.72 0.50 110.60 114.32 A A A C2 N3 C4 A A A 38 38 38 N 5 4.28 0.70 108.50 112.78 A A A O4' C1' N9 A A A 36 36 36 N 5 -5.41 0.50 129.30 123.89 A A A N1 C2 N3 A A A 38 38 38 N 5 3.94 0.50 110.60 114.54 A A A C2 N3 C4 A A A 38 38 38 N 6 6.88 0.70 108.50 115.38 A A A O4' C1' N1 U U U 33 33 33 N 6 11.00 1.30 114.00 125.00 A A A N9 C1' C2' A A A 35 35 35 N 6 6.80 0.70 108.50 115.30 A A A O4' C1' N9 A A A 35 35 35 N 6 -2.96 0.40 105.80 102.84 A A A C8 N9 C4 A A A 35 35 35 N 6 -4.42 0.70 109.70 105.28 A A A C1' O4' C4' A A A 38 38 38 N 6 -5.66 0.50 129.30 123.64 A A A N1 C2 N3 A A A 38 38 38 N 6 3.67 0.50 110.60 114.27 A A A C2 N3 C4 A A A 38 38 38 N 6 4.21 0.70 108.50 112.71 A A A O4' C1' N1 U U U 41 41 41 N 7 6.48 0.70 108.50 114.98 A A A O4' C1' N9 A A A 36 36 36 N 7 -5.51 0.50 129.30 123.79 A A A N1 C2 N3 A A A 38 38 38 N 7 3.86 0.50 110.60 114.46 A A A C2 N3 C4 A A A 38 38 38 N 8 4.32 0.70 108.50 112.82 A A A O4' C1' N1 U U U 33 33 33 N 8 4.27 0.70 108.50 112.77 A A A O4' C1' N9 A A A 36 36 36 N 8 -5.27 0.50 129.30 124.03 A A A N1 C2 N3 A A A 38 38 38 N 8 3.83 0.50 110.60 114.43 A A A C2 N3 C4 A A A 38 38 38 N 8 4.23 0.70 108.50 112.73 A A A O4' C1' N1 U U U 41 41 41 N 9 6.37 0.70 108.50 114.87 A A A O4' C1' N9 A A A 36 36 36 N 9 -5.44 0.50 129.30 123.86 A A A N1 C2 N3 A A A 38 38 38 N 9 3.78 0.50 110.60 114.38 A A A C2 N3 C4 A A A 38 38 38 N 10 4.59 0.70 108.50 113.09 A A A O4' C1' N9 A A A 36 36 36 N 10 -5.37 0.50 129.30 123.93 A A A N1 C2 N3 A A A 38 38 38 N 10 3.86 0.50 110.60 114.46 A A A C2 N3 C4 A A A 38 38 38 N 11 4.82 0.70 108.50 113.32 A A A O4' C1' N1 U U U 33 33 33 N 11 7.38 0.70 108.50 115.88 A A A O4' C1' N9 A A A 36 36 36 N 11 -5.57 0.50 129.30 123.73 A A A N1 C2 N3 A A A 38 38 38 N 11 3.67 0.50 110.60 114.27 A A A C2 N3 C4 A A A 38 38 38 N 5 A A C6 N1 A A 38 38 0.042 0.007 1.351 1.393 N 8 A A N1 C2 A A 38 38 0.055 0.009 1.339 1.394 N 8 A A C6 N1 A A 38 38 0.043 0.007 1.351 1.394 N minimized average NMR SOLUTION STRUCTURE OF THE ANTICODON OF YEAST TRNA-PHE WITH 4 MODIFICATIONS (OMC32 OMG34 1MG37 5MC40) 1 N N covale 1.614 both A A 31 A O3' A 5 1_555 A OMC 32 A P OMC 6 1_555 covale 1.610 both A OMC 32 A O3' OMC 6 1_555 A U 33 A P U 7 1_555 covale 1.616 both A U 33 A O3' U 7 1_555 A OMG 34 A P OMG 8 1_555 covale 1.612 both A OMG 34 A O3' OMG 8 1_555 A A 35 A P A 9 1_555 covale 1.609 both A A 36 A O3' A 10 1_555 A 1MG 37 A P 1MG 11 1_555 covale 1.616 both A 1MG 37 A O3' 1MG 11 1_555 A A 38 A P A 12 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 1.619 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 O2 OMC 6 1_555 A A 38 A N6 A 12 1_555 hydrog OMG-A MISPAIR A OMG 34 A O6 OMG 8 1_555 A A 36 A N6 A 10 1_555 RNA TRNA, ANTICODON STEM LOOP, TRNA DOMAIN, RNA HAIRPIN, 1MG, 2'-O-METHYL, 5MC, RNA 1LUU PDB 1 1LUU 27 43 1LUU 27 43 1LUU A 1 1 17