1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Znosko, B.M. Burkard, M.E. Krugh, T.R. Turner, D.H. 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 C10 H13 N4 O7 P 332.207 n PURINE RIBOSIDE-5'-MONOPHOSPHATE RNA linking C9 H13 N2 O9 P 324.181 y URIDINE-5'-MONOPHOSPHATE RNA linking US Biochemistry BICHAW 0033 0006-2960 41 14978 14987 10.1021/bi0203278 12475247 Molecular Recognition in Purine-Rich Internal Loops: Thermodynamic, Structural, and Dynamic Consequences of Purine for Adenine Substitutions in 5'(rGGCAAGCCU)2 2002 US Biochemistry BICHAW 0033 0006-2960 41 14969 14977 10.1021/bi020326f Sheared Aanti-Aanti Base Pairs in a Destabilizing 2x2 Internal Loop: The NMR Structure of 5'(rGGCAAGCCU)2 2002 10.2210/pdb1mv2/pdb pdb_00001mv2 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 2855.769 5'-R(*GP*GP*CP*AP*(P5P)P*GP*CP*CP*U)-3' 2 syn polymer no yes GGCA(P5P)GCCU GGCAAGCCU A,B polyribonucleotide n n n n n n n n n -6.723 1 19 A 1 B 8 -0.667 A_G1:C8_B 1 -8.508 -0.652 -0.333 -0.192 -13.081 1 19 A 2 B 7 0.191 A_G2:C7_B 2 -13.856 -0.435 -0.151 -0.081 -12.957 1 19 A 3 B 6 -2.853 A_C3:G6_B 3 -8.064 0.333 0.259 -0.051 9.956 1 19 A 6 B 3 -2.591 A_G6:C3_B 4 -7.073 -0.400 0.297 -0.075 14.477 1 19 A 7 B 2 0.323 A_C7:G2_B 5 -12.610 0.438 -0.103 -0.072 10.203 1 19 A 8 B 1 -0.560 A_C8:G1_B 6 -9.322 0.636 -0.396 -0.181 3.012 33.421 A A 1 2 10.734 B B 8 7 3.413 6.140 -0.003 -1.939 AA_G1G2:C7C8_BB 1 -0.333 0.583 32.867 -4.378 -0.050 3.036 36.958 A A 2 3 6.081 B B 7 6 3.232 3.848 -0.289 -1.799 AA_G2C3:G6C7_BB 2 -0.138 0.219 36.764 -3.337 0.438 3.024 36.425 A A 6 7 4.550 B B 3 2 3.162 2.841 0.202 -1.702 AA_G6C7:G2C3_BB 3 -0.112 0.179 36.317 -3.096 -0.337 2.923 32.968 A A 7 8 11.379 B B 2 1 3.351 6.418 -0.037 -1.935 AA_C7C8:G1G2_BB 4 0.459 -0.814 32.351 -4.467 0.141 database_2 pdbx_nmr_software 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 2002-12-18 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 _struct_conn.pdbx_leaving_atom_flag 1YFV IS Tandem, sheared GA pairs in the same stem, determined by 2D NMR 1GID IS Tandem, sheared AA pairs in the J4/5 loop of Tetrahymena thermophila, determined by x-ray crystallography 1MUV IS the Tandem, sheared AA pairs, in 5'(rGGCAAGCCU)2 1mv1 is The tandem, sheared PA Pairs in 5'(rGGCPAGCCU)2 1mv6 is The tandem, Sheared PP Pairs in 5'(rGGCPPGCCU)2 RCSB Y RCSB 2002-09-24 REL REL 1 2D NOESY 90% H2O, 10% D2O 6.5 ambient 273 K 99.996% D2O 7.7 ambient 303 K The structure is based on a total of 71 interproton distance restraints per strand, 18 hydrogen bond restraints, and 59 dihedral angle restraints per strand. simulated annealing, energy minimization 1 closest to the average 1mM RNA, 80 mM NaCl, 10mM phosphate buffer, 0.5mM EDTA; 90% H2O, 10% D2O 90% H2O/10% D2O 2mM RNA, 80 mM NaCl, 10mM phosphate buffer, 0.5mM EDTA; 99.996% D2O 99.996% D2O Varian collection VNMR 5.2 MSI data analysis Felix 2000 MSI structure solution Discover 95.0 MSI refinement Discover 95.0 500 Varian INOVA G 1 n 1 G 1 A G 2 n 2 G 2 A C 3 n 3 C 3 A A 4 n 4 A 4 A P 5 n 5 P5P 5 A G 6 n 6 G 6 A C 7 n 7 C 7 A C 8 n 8 C 8 A U 9 n 9 U 9 A G 1 n 1 G 1 B G 2 n 2 G 2 B C 3 n 3 C 3 B A 4 n 4 A 4 B P 5 n 5 P5P 5 B G 6 n 6 G 6 B C 7 n 7 C 7 B C 8 n 8 C 8 B U 9 n 9 U 9 B author_defined_assembly 2 dimeric A P5P 5 PURINE RIBOSIDE-5'-MONOPHOSPHATE A P5P 5 A B P5P 5 PURINE RIBOSIDE-5'-MONOPHOSPHATE B P5P 5 A 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 G 6 0.062 SIDE CHAIN 1 B G 6 0.068 SIDE CHAIN 1 4.39 0.70 108.50 112.89 A A A O4' C1' N9 A A A 4 4 4 N 1 4.22 0.70 108.50 112.72 A A A O4' C1' N1 C C C 7 7 7 N 1 4.72 0.70 108.50 113.22 A A A O4' C1' N1 C C C 8 8 8 N 1 4.47 0.70 108.50 112.97 B B B O4' C1' N1 C C C 7 7 7 N 1 4.67 0.70 108.50 113.17 B B B O4' C1' N1 C C C 8 8 8 N The tandem, Face-to-Face AP Pairs in 5'(rGGCAPGCCU)2 1 N N 1 N N covale 1.617 both A A 4 A O3' A 4 1_555 A P5P 5 A P P5P 5 1_555 covale 1.618 both A P5P 5 A O3' P5P 5 1_555 A G 6 A P G 6 1_555 covale 1.616 both B A 4 B O3' A 4 1_555 B P5P 5 B P P5P 5 1_555 covale 1.619 both B P5P 5 B O3' P5P 5 1_555 B G 6 B P G 6 1_555 hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 B C 8 B N3 C 8 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 B C 8 B O2 C 8 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 B C 8 B N4 C 8 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 B C 7 B N3 C 7 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 B C 7 B O2 C 7 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 B C 7 B N4 C 7 1_555 hydrog WATSON-CRICK A C 3 A N3 C 3 1_555 B G 6 B N1 G 6 1_555 hydrog WATSON-CRICK A C 3 A N4 C 3 1_555 B G 6 B O6 G 6 1_555 hydrog WATSON-CRICK A C 3 A O2 C 3 1_555 B G 6 B N2 G 6 1_555 hydrog WATSON-CRICK A G 6 A N1 G 6 1_555 B C 3 B N3 C 3 1_555 hydrog WATSON-CRICK A G 6 A N2 G 6 1_555 B C 3 B O2 C 3 1_555 hydrog WATSON-CRICK A G 6 A O6 G 6 1_555 B C 3 B N4 C 3 1_555 hydrog WATSON-CRICK A C 7 A N3 C 7 1_555 B G 2 B N1 G 2 1_555 hydrog WATSON-CRICK A C 7 A N4 C 7 1_555 B G 2 B O6 G 2 1_555 hydrog WATSON-CRICK A C 7 A O2 C 7 1_555 B G 2 B N2 G 2 1_555 hydrog WATSON-CRICK A C 8 A N3 C 8 1_555 B G 1 B N1 G 1 1_555 hydrog WATSON-CRICK A C 8 A N4 C 8 1_555 B G 1 B O6 G 1 1_555 hydrog WATSON-CRICK A C 8 A O2 C 8 1_555 B G 1 B N2 G 1 1_555 RNA ribonucleic acid, duplex, tandem mismatch, purine, RNA 1MV2 PDB 1 1MV2 1 9 1MV2 1 9 1MV2 A 1 1 9 1 9 1MV2 1 9 1MV2 B 1 1 9