1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Shankar, N. 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 y URIDINE-5'-MONOPHOSPHATE RNA linking US Biochemistry BICHAW 0033 0006-2960 45 11776 11789 10.1021/bi0605787 17002278 The NMR structure of an internal loop from 23S ribosomal RNA differs from its structure in crystals of 50s ribosomal subunits. 2006 10.2210/pdb2h49/pdb pdb_00002h49 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 2894.807 5'-R(*GP*GP*CP*UP*AP*AP*GP*AP*C)-3' 1 syn polymer 2870.783 5'-R(*GP*UP*CP*GP*AP*AP*GP*CP*C)-3' 1 syn polymer no no GGCUAAGAC GGCUAAGAC A polyribonucleotide no no GUCGAAGCC GUCGAAGCC B polyribonucleotide n n n n n n n n n n n n n n n n n n -1.075 1 19 A 1 B 18 -0.659 A_G1:C18_B 1 -3.793 -0.592 -0.128 -0.144 -4.276 1 19 A 2 B 17 1.486 A_G2:C17_B 2 -12.869 -0.414 -0.182 -0.070 -5.460 1 19 A 3 B 16 -1.006 A_C3:G16_B 3 -10.066 0.345 -0.067 -0.071 -8.359 A 4 B 15 7.063 A_U4:A15_B 4 -5.238 4.672 -0.071 -0.543 1.799 6 A 5 B 14 -10.599 A_A5:A14_B 5 -1.789 6.481 -0.403 -4.278 4.935 9 11 A 6 B 13 -2.569 A_A6:G13_B 6 -9.425 -6.789 -0.089 -4.211 2.658 1 19 A 7 B 12 0.415 A_G7:C12_B 7 -12.921 -0.794 0.025 -0.212 -0.376 1 20 A 8 B 11 2.387 A_A8:U11_B 8 -12.741 -0.158 0.193 0.011 -3.697 1 19 A 9 B 10 -0.466 A_C9:G10_B 9 -13.657 0.643 0.242 -0.171 2.918 33.380 A A 1 2 11.660 B B 18 17 3.334 6.655 0.274 -1.837 AA_G1G2:C17C18_BB 1 0.363 -0.636 32.727 -4.264 -0.419 3.122 35.711 A A 2 3 4.251 B B 17 16 3.263 2.604 -0.086 -1.897 AA_G2C3:G16C17_BB 2 -0.241 0.393 35.618 -3.462 0.106 3.336 46.756 A A 3 4 3.059 B B 16 15 3.380 2.425 0.553 -1.388 AA_C3U4:A15G16_BB 3 3.047 -3.843 46.603 -1.957 -0.436 2.910 44.488 A A 4 5 -0.257 B B 15 14 3.041 -0.194 -0.778 -1.428 AA_U4A5:A14A15_BB 4 6.485 -8.593 44.036 -1.870 1.575 3.778 -26.084 A A 5 6 -17.538 B B 14 13 3.074 7.782 0.388 -2.780 AA_A5A6:G13A14_BB 5 -2.894 -6.523 -24.749 3.872 0.010 3.432 63.223 A A 6 7 2.719 B B 13 12 3.491 2.848 0.355 -0.727 AA_A6G7:C12G13_BB 6 -4.166 3.978 63.042 -0.827 -0.534 2.887 34.513 A A 7 8 9.251 B B 12 11 3.220 5.465 0.050 -1.884 AA_G7A8:U11C12_BB 7 -1.557 2.635 34.056 -3.972 -0.311 3.130 39.395 A A 8 9 5.785 B B 11 10 3.266 3.894 -0.164 -1.241 AA_A8C9:G10U11_BB 8 0.638 -0.948 39.204 -2.293 0.318 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 2006-11-21 1 1 2008-05-01 1 2 2011-07-13 1 3 2022-03-09 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name RCSB Y RCSB 2006-05-23 REL REL Synthesized on a DNA/RNA synthesizer sample Synthesized on a DNA/RNA synthesizer sample structures with the least restraint violations,structures with the lowest energy 50 20 6.5 K SILICON GRAPHICS OCTANE COMPUTER,AMBER 95 FORCE FIELD DISTANCE GEOMETRY, SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS 1 lowest energy 2mM TOTAL DUPLEX CONCENTRATION; 80MM NACL, 10MM SODIUM PHOSPHATE, 0.5MM NA2EDTA, 90% H2O, 10% D2O 90% H2O/10% D2O 2mM TOTAL DUPLEX CONCENTRATION; 80MM NACL, 10MM SODIUM PHOSPHATE, 0.5MM NA2EDTA, 100% D2O 100% D2O T. D. Goddard and D. G. Kneller data analysis Sparky 3.110 F. Delaglio processing NMRDraw 2.3 Molecular Simulations Inc. refinement Discover 98 500 Varian INOVA 600 Varian INOVA G 1 n 1 G 1 A G 2 n 2 G 2 A C 3 n 3 C 3 A U 4 n 4 U 4 A A 5 n 5 A 5 A A 6 n 6 A 6 A G 7 n 7 G 7 A A 8 n 8 A 8 A C 9 n 9 C 9 A G 10 n 1 G 10 B U 11 n 2 U 11 B C 12 n 3 C 12 B G 13 n 4 G 13 B A 14 n 5 A 14 B A 15 n 6 A 15 B G 16 n 7 G 16 B C 17 n 8 C 17 B C 18 n 9 C 18 B author_defined_assembly 2 dimeric 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 8 0.070 SIDE CHAIN 1 B G 10 0.056 SIDE CHAIN 2 A A 8 0.068 SIDE CHAIN 2 B G 10 0.058 SIDE CHAIN 3 A A 8 0.074 SIDE CHAIN 3 B G 10 0.057 SIDE CHAIN 4 A A 8 0.084 SIDE CHAIN 4 B G 10 0.060 SIDE CHAIN 5 A A 8 0.078 SIDE CHAIN 5 B G 10 0.061 SIDE CHAIN 6 A A 8 0.054 SIDE CHAIN 7 A A 8 0.079 SIDE CHAIN 7 B G 10 0.056 SIDE CHAIN 7 B C 17 0.064 SIDE CHAIN 8 A A 8 0.082 SIDE CHAIN 8 B G 10 0.060 SIDE CHAIN 8 B C 17 0.069 SIDE CHAIN 9 A A 5 0.055 SIDE CHAIN 9 A A 8 0.076 SIDE CHAIN 9 B G 10 0.061 SIDE CHAIN 10 A A 5 0.056 SIDE CHAIN 10 A A 8 0.062 SIDE CHAIN 10 B G 10 0.059 SIDE CHAIN 10 B C 17 0.069 SIDE CHAIN 11 A A 8 0.061 SIDE CHAIN 11 B G 10 0.056 SIDE CHAIN 12 A A 8 0.064 SIDE CHAIN 12 B G 10 0.057 SIDE CHAIN 13 A A 8 0.063 SIDE CHAIN 13 B G 10 0.058 SIDE CHAIN 14 A A 8 0.075 SIDE CHAIN 14 B G 10 0.060 SIDE CHAIN 14 B A 15 0.056 SIDE CHAIN 15 A A 8 0.070 SIDE CHAIN 15 B G 10 0.057 SIDE CHAIN 16 A A 8 0.068 SIDE CHAIN 16 B G 10 0.058 SIDE CHAIN 17 A A 8 0.057 SIDE CHAIN 18 A A 8 0.076 SIDE CHAIN 18 B G 10 0.058 SIDE CHAIN 19 A A 8 0.064 SIDE CHAIN 19 B G 10 0.059 SIDE CHAIN 20 A A 8 0.061 SIDE CHAIN 20 B G 10 0.059 SIDE CHAIN 1 4.96 0.70 108.50 113.46 A A A O4' C1' N1 C C C 3 3 3 N 1 4.81 0.70 108.50 113.31 A A A O4' C1' N1 U U U 4 4 4 N 1 4.87 0.70 108.50 113.37 B B B O4' C1' N1 U U U 11 11 11 N 1 5.50 0.70 108.50 114.00 B B B O4' C1' N1 C C C 12 12 12 N 1 4.69 0.70 108.50 113.19 B B B O4' C1' N1 C C C 17 17 17 N 2 5.04 0.70 108.50 113.54 A A A O4' C1' N1 C C C 3 3 3 N 2 5.06 0.70 108.50 113.56 A A A O4' C1' N1 U U U 4 4 4 N 2 4.85 0.70 108.50 113.35 B B B O4' C1' N1 U U U 11 11 11 N 2 5.52 0.70 108.50 114.02 B B B O4' C1' N1 C C C 12 12 12 N 2 4.62 0.70 108.50 113.12 B B B O4' C1' N1 C C C 17 17 17 N 3 5.15 0.70 108.50 113.65 A A A O4' C1' N1 C C C 3 3 3 N 3 4.88 0.70 108.50 113.38 A A A O4' C1' N1 U U U 4 4 4 N 3 4.99 0.70 108.50 113.49 B B B O4' C1' N1 U U U 11 11 11 N 3 5.53 0.70 108.50 114.03 B B B O4' C1' N1 C C C 12 12 12 N 3 4.68 0.70 108.50 113.18 B B B O4' C1' N1 C C C 17 17 17 N 4 5.21 0.70 108.50 113.71 A A A O4' C1' N1 C C C 3 3 3 N 4 4.77 0.70 108.50 113.27 A A A O4' C1' N1 U U U 4 4 4 N 4 4.65 0.70 108.50 113.15 A A A O4' C1' N1 C C C 9 9 9 N 4 5.01 0.70 108.50 113.51 B B B O4' C1' N1 U U U 11 11 11 N 4 5.48 0.70 108.50 113.98 B B B O4' C1' N1 C C C 12 12 12 N 4 4.81 0.70 108.50 113.31 B B B O4' C1' N1 C C C 17 17 17 N 5 4.96 0.70 108.50 113.46 A A A O4' C1' N1 C C C 3 3 3 N 5 4.74 0.70 108.50 113.24 A A A O4' C1' N1 U U U 4 4 4 N 5 4.65 0.70 108.50 113.15 A A A O4' C1' N1 C C C 9 9 9 N 5 4.91 0.70 108.50 113.41 B B B O4' C1' N1 U U U 11 11 11 N 5 5.41 0.70 108.50 113.91 B B B O4' C1' N1 C C C 12 12 12 N 5 4.63 0.70 108.50 113.13 B B B O4' C1' N1 C C C 17 17 17 N 6 4.42 0.70 108.50 112.92 A A A O4' C1' N1 C C C 3 3 3 N 6 4.29 0.70 108.50 112.79 A A A O4' C1' N1 U U U 4 4 4 N 6 5.10 0.70 108.50 113.60 B B B O4' C1' N1 U U U 11 11 11 N 6 5.38 0.70 108.50 113.88 B B B O4' C1' N1 C C C 12 12 12 N 6 4.61 0.70 108.50 113.11 B B B O4' C1' N1 C C C 17 17 17 N 7 4.91 0.70 108.50 113.41 A A A O4' C1' N1 C C C 3 3 3 N 7 6.05 0.70 108.50 114.55 A A A O4' C1' N1 U U U 4 4 4 N 7 4.71 0.70 108.50 113.21 A A A O4' C1' N1 C C C 9 9 9 N 7 4.89 0.70 108.50 113.39 B B B O4' C1' N1 U U U 11 11 11 N 7 5.21 0.70 108.50 113.71 B B B O4' C1' N1 C C C 12 12 12 N 7 4.99 0.70 108.50 113.49 B B B O4' C1' N1 C C C 17 17 17 N 7 5.13 0.70 108.50 113.63 B B B O4' C1' N1 C C C 18 18 18 N 8 4.87 0.70 108.50 113.37 A A A O4' C1' N1 C C C 3 3 3 N 8 4.91 0.70 108.50 113.41 A A A O4' C1' N1 U U U 4 4 4 N 8 4.63 0.70 108.50 113.13 A A A O4' C1' N1 C C C 9 9 9 N 8 4.96 0.70 108.50 113.46 B B B O4' C1' N1 U U U 11 11 11 N 8 5.45 0.70 108.50 113.95 B B B O4' C1' N1 C C C 12 12 12 N 8 4.94 0.70 108.50 113.44 B B B O4' C1' N1 C C C 17 17 17 N 8 4.92 0.70 108.50 113.42 B B B O4' C1' N1 C C C 18 18 18 N 9 5.02 0.70 108.50 113.52 A A A O4' C1' N1 C C C 3 3 3 N 9 4.55 0.70 108.50 113.05 A A A O4' C1' N1 U U U 4 4 4 N 9 4.65 0.70 108.50 113.15 A A A O4' C1' N1 C C C 9 9 9 N 9 4.90 0.70 108.50 113.40 B B B O4' C1' N1 U U U 11 11 11 N 9 5.40 0.70 108.50 113.90 B B B O4' C1' N1 C C C 12 12 12 N 9 4.68 0.70 108.50 113.18 B B B O4' C1' N1 C C C 17 17 17 N 10 5.15 0.70 108.50 113.65 A A A O4' C1' N1 C C C 3 3 3 N 10 4.54 0.70 108.50 113.04 A A A O4' C1' N1 U U U 4 4 4 N 10 4.75 0.70 108.50 113.25 B B B O4' C1' N1 U U U 11 11 11 N 10 5.28 0.70 108.50 113.78 B B B O4' C1' N1 C C C 12 12 12 N 10 5.06 0.70 108.50 113.56 B B B O4' C1' N1 C C C 17 17 17 N 10 5.09 0.70 108.50 113.59 B B B O4' C1' N1 C C C 18 18 18 N 11 5.02 0.70 108.50 113.52 A A A O4' C1' N1 C C C 3 3 3 N 11 4.77 0.70 108.50 113.27 A A A O4' C1' N1 U U U 4 4 4 N 11 4.81 0.70 108.50 113.31 B B B O4' C1' N1 U U U 11 11 11 N 11 5.45 0.70 108.50 113.95 B B B O4' C1' N1 C C C 12 12 12 N 11 4.61 0.70 108.50 113.11 B B B O4' C1' N1 C C C 17 17 17 N 12 5.12 0.70 108.50 113.62 A A A O4' C1' N1 C C C 3 3 3 N 12 4.29 0.70 108.50 112.79 A A A O4' C1' N1 U U U 4 4 4 N 12 4.88 0.70 108.50 113.38 B B B O4' C1' N1 U U U 11 11 11 N 12 5.43 0.70 108.50 113.93 B B B O4' C1' N1 C C C 12 12 12 N 12 4.63 0.70 108.50 113.13 B B B O4' C1' N1 C C C 17 17 17 N 13 4.94 0.70 108.50 113.44 A A A O4' C1' N1 C C C 3 3 3 N 13 4.65 0.70 108.50 113.15 A A A O4' C1' N1 U U U 4 4 4 N 13 4.83 0.70 108.50 113.33 B B B O4' C1' N1 U U U 11 11 11 N 13 6.01 0.70 108.50 114.51 B B B O4' C1' N1 C C C 12 12 12 N 13 4.56 0.70 108.50 113.06 B B B O4' C1' N1 C C C 17 17 17 N 14 5.11 0.70 108.50 113.61 A A A O4' C1' N1 C C C 3 3 3 N 14 5.38 0.70 108.50 113.88 A A A O4' C1' N1 U U U 4 4 4 N 14 4.66 0.70 108.50 113.16 A A A O4' C1' N1 C C C 9 9 9 N 14 4.84 0.70 108.50 113.34 B B B O4' C1' N1 U U U 11 11 11 N 14 5.23 0.70 108.50 113.73 B B B O4' C1' N1 C C C 12 12 12 N 14 7.64 1.20 119.70 127.34 B B B C3' O3' P G G A 13 13 14 Y 14 4.63 0.70 108.50 113.13 B B B O4' C1' N1 C C C 17 17 17 N 15 4.96 0.70 108.50 113.46 A A A O4' C1' N1 C C C 3 3 3 N 15 4.68 0.70 108.50 113.18 A A A O4' C1' N1 U U U 4 4 4 N 15 7.45 1.20 119.70 127.15 A A A C3' O3' P A A A 5 5 6 Y 15 4.91 0.70 108.50 113.41 B B B O4' C1' N1 U U U 11 11 11 N 15 5.53 0.70 108.50 114.03 B B B O4' C1' N1 C C C 12 12 12 N 15 5.03 0.70 108.50 113.53 B B B O4' C1' N1 C C C 17 17 17 N 15 5.11 0.70 108.50 113.61 B B B O4' C1' N1 C C C 18 18 18 N 16 5.03 0.70 108.50 113.53 A A A O4' C1' N1 C C C 3 3 3 N 16 4.90 0.70 108.50 113.40 A A A O4' C1' N1 U U U 4 4 4 N 16 4.88 0.70 108.50 113.38 B B B O4' C1' N1 U U U 11 11 11 N 16 5.38 0.70 108.50 113.88 B B B O4' C1' N1 C C C 12 12 12 N 16 4.76 0.70 108.50 113.26 B B B O4' C1' N1 C C C 17 17 17 N 17 4.46 0.70 108.50 112.96 A A A O4' C1' N1 C C C 3 3 3 N 17 4.63 0.70 108.50 113.13 A A A O4' C1' N1 U U U 4 4 4 N 17 5.02 0.70 108.50 113.52 B B B O4' C1' N1 U U U 11 11 11 N 17 5.42 0.70 108.50 113.92 B B B O4' C1' N1 C C C 12 12 12 N 17 7.65 1.20 119.70 127.35 B B B C3' O3' P G G A 13 13 14 Y 17 4.60 0.70 108.50 113.10 B B B O4' C1' N1 C C C 17 17 17 N 18 5.11 0.70 108.50 113.61 A A A O4' C1' N1 C C C 3 3 3 N 18 4.72 0.70 108.50 113.22 A A A O4' C1' N1 U U U 4 4 4 N 18 4.90 0.70 108.50 113.40 B B B O4' C1' N1 U U U 11 11 11 N 18 5.53 0.70 108.50 114.03 B B B O4' C1' N1 C C C 12 12 12 N 18 5.11 0.70 108.50 113.61 B B B O4' C1' N1 C C C 17 17 17 N 19 4.99 0.70 108.50 113.49 A A A O4' C1' N1 C C C 3 3 3 N 19 4.79 0.70 108.50 113.29 A A A O4' C1' N1 U U U 4 4 4 N 19 4.77 0.70 108.50 113.27 B B B O4' C1' N1 U U U 11 11 11 N 19 5.34 0.70 108.50 113.84 B B B O4' C1' N1 C C C 12 12 12 N 19 4.63 0.70 108.50 113.13 B B B O4' C1' N1 C C C 17 17 17 N 20 5.04 0.70 108.50 113.54 A A A O4' C1' N1 C C C 3 3 3 N 20 4.52 0.70 108.50 113.02 A A A O4' C1' N1 U U U 4 4 4 N 20 7.50 1.20 119.70 127.20 A A A C3' O3' P A A A 5 5 6 Y 20 4.71 0.70 108.50 113.21 B B B O4' C1' N1 U U U 11 11 11 N 20 5.34 0.70 108.50 113.84 B B B O4' C1' N1 C C C 12 12 12 N 20 4.55 0.70 108.50 113.05 B B B O4' C1' N1 C C C 17 17 17 N The NMR Structure of an Internal Loop from 23S Ribosomal RNA of Deinococcus radiodurans Differs from the Structure in the Crystal of the Ribosomal Subunit 1 N N 2 N N hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 B C 18 B N3 C 9 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 B C 18 B O2 C 9 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 B C 18 B N4 C 9 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 B C 17 B N3 C 8 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 B C 17 B O2 C 8 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 B C 17 B N4 C 8 1_555 hydrog WATSON-CRICK A C 3 A N3 C 3 1_555 B G 16 B N1 G 7 1_555 hydrog WATSON-CRICK A C 3 A N4 C 3 1_555 B G 16 B O6 G 7 1_555 hydrog WATSON-CRICK A C 3 A O2 C 3 1_555 B G 16 B N2 G 7 1_555 hydrog U-A PAIR A U 4 A O2 U 4 1_555 B A 15 B N6 A 6 1_555 hydrog A-A MISPAIR A A 5 A N3 A 5 1_555 B A 14 B N6 A 5 1_555 hydrog TYPE_11_PAIR A A 6 A N6 A 6 1_555 B G 13 B N3 G 4 1_555 hydrog TYPE_11_PAIR A A 6 A N7 A 6 1_555 B G 13 B N2 G 4 1_555 hydrog WATSON-CRICK A G 7 A N1 G 7 1_555 B C 12 B N3 C 3 1_555 hydrog WATSON-CRICK A G 7 A N2 G 7 1_555 B C 12 B O2 C 3 1_555 hydrog WATSON-CRICK A G 7 A O6 G 7 1_555 B C 12 B N4 C 3 1_555 hydrog WATSON-CRICK A A 8 A N1 A 8 1_555 B U 11 B N3 U 2 1_555 hydrog WATSON-CRICK A A 8 A N6 A 8 1_555 B U 11 B O4 U 2 1_555 hydrog WATSON-CRICK A C 9 A N3 C 9 1_555 B G 10 B N1 G 1 1_555 hydrog WATSON-CRICK A C 9 A N4 C 9 1_555 B G 10 B O6 G 1 1_555 hydrog WATSON-CRICK A C 9 A O2 C 9 1_555 B G 10 B N2 G 1 1_555 RNA RNA INTERNAL LOOP 5'cUAAg3'/3'gAAGc5', COMPARISON BETWEEN CRYSTAL STRUCTURE AND NMR STRUCTURE, THERMODYNAMICS OF INTERNAL LOOP, RNA 2H49 PDB 1 2H49 2H49 PDB 2 2H49 1 9 2H49 1 9 2H49 A 1 1 9 10 18 2H49 10 18 2H49 B 2 1 9