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 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/pdb1mv6/pdb pdb_00001mv6 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 2840.755 5'-R(*GP*GP*CP*(P5P)P*(P5P)P*GP*CP*CP*U)-3' 2 syn polymer no yes GGC(P5P)(P5P)GCCU GGCAAGCCU A,B polyribonucleotide n n n n n n n n n -8.258 1 19 A 1 B 8 -1.243 A_G1:C8_B 1 -4.544 -0.619 -0.293 -0.173 -4.460 1 19 A 2 B 7 -0.432 A_G2:C7_B 2 -10.259 -0.370 -0.115 -0.075 -2.369 1 19 A 3 B 6 1.559 A_C3:G6_B 3 -15.275 0.717 0.046 -0.181 -5.724 1 19 A 6 B 3 0.836 A_G6:C3_B 4 -16.838 -0.554 -0.324 -0.185 -6.205 1 19 A 7 B 2 -1.054 A_C7:G2_B 5 -5.706 0.445 0.019 -0.086 7.224 1 19 A 8 B 1 -0.765 A_C8:G1_B 6 -2.004 0.573 -0.295 -0.150 2.891 31.134 A A 1 2 8.600 B B 8 7 3.195 4.600 -0.021 -1.874 AA_G1G2:C7C8_BB 1 -0.294 0.549 30.799 -4.313 -0.013 3.022 33.639 A A 2 3 5.888 B B 7 6 3.209 3.402 0.085 -1.741 AA_G2C3:G6C7_BB 2 -0.310 0.537 33.470 -3.539 -0.195 2.951 33.743 A A 6 7 8.572 B B 3 2 3.257 4.957 0.111 -1.857 AA_G6C7:G2C3_BB 3 -1.465 2.534 33.356 -3.966 -0.418 2.878 28.262 A A 7 8 3.669 B B 2 1 2.998 1.790 0.074 -1.817 AA_C7C8:G1G2_BB 4 1.640 -3.363 28.159 -4.096 0.190 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 the Tandem, sheared GA pairs in the same stem, determined by 2D NMR 1gid is the Tandem, sheared AA pairs in the J4/5 loop of Tetrahymena thermophila, determined by x-ray crystallography 1mUV is The tandem, sheared AA Pairs with same stem 1MV1 IS THE Tandem, Sheared PA Pairs in 5'(rGGCPAGCCU)2 1mv2 is The tandem, Face-to-Face AP Pairs in 5'(rGGCAPGCCU)2 RCSB Y RCSB 2002-09-24 REL REL Random Structures to show variety 33 3 2D NOESY 90% H2O, 10% D2O 6.5 ambient 273 K 99.996% D2O 7.7 ambient 303 K total of 63 interproton distance restraints per strand, 18 hydrogen bond restraints, and 50 dihedral angle restraints per strand. simulated annealing, energy minimization 3 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 P 4 n 4 P5P 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 P 4 n 4 P5P 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 4 PURINE RIBOSIDE-5'-MONOPHOSPHATE A P5P 4 A A P5P 5 PURINE RIBOSIDE-5'-MONOPHOSPHATE A P5P 5 A B P5P 4 PURINE RIBOSIDE-5'-MONOPHOSPHATE B P5P 4 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 5.75 0.70 108.50 114.25 A A A O4' C1' N1 C C C 3 3 3 N 1 4.97 0.70 108.50 113.47 A A A O4' C1' N1 C C C 7 7 7 N 1 5.20 0.70 108.50 113.70 A A A O4' C1' N1 C C C 8 8 8 N 1 4.68 0.70 108.50 113.18 B B B O4' C1' N1 C C C 3 3 3 N 1 4.69 0.70 108.50 113.19 B B B O4' C1' N1 C C C 7 7 7 N 1 4.88 0.70 108.50 113.38 B B B O4' C1' N1 C C C 8 8 8 N 1 4.26 0.70 108.50 112.76 B B B O4' C1' N1 U U U 9 9 9 N 2 5.24 0.70 108.50 113.74 A A A O4' C1' N1 C C C 3 3 3 N 2 5.19 0.70 108.50 113.69 A A A O4' C1' N1 C C C 7 7 7 N 2 5.12 0.70 108.50 113.62 A A A O4' C1' N1 C C C 8 8 8 N 2 5.42 0.70 108.50 113.92 B B B O4' C1' N1 C C C 3 3 3 N 2 4.28 0.70 108.50 112.78 B B B O4' C1' N9 G G G 6 6 6 N 2 4.98 0.70 108.50 113.48 B B B O4' C1' N1 C C C 7 7 7 N 2 4.93 0.70 108.50 113.43 B B B O4' C1' N1 C C C 8 8 8 N 3 5.82 0.70 108.50 114.32 A A A O4' C1' N1 C C C 3 3 3 N 3 5.47 0.70 108.50 113.97 A A A O4' C1' N1 C C C 7 7 7 N 3 5.18 0.70 108.50 113.68 A A A O4' C1' N1 C C C 8 8 8 N 3 4.53 0.70 108.50 113.03 B B B O4' C1' N1 C C C 3 3 3 N 3 4.99 0.70 108.50 113.49 B B B O4' C1' N1 C C C 7 7 7 N 3 5.32 0.70 108.50 113.82 B B B O4' C1' N1 C C C 8 8 8 N 3 4.68 0.70 108.50 113.18 B B B O4' C1' N1 U U U 9 9 9 N The tandem, Sheared PP Pairs in 5'(rGGCPPGCCU)2 1 N N 1 N N covale 1.614 both A C 3 A O3' C 3 1_555 A P5P 4 A P P5P 4 1_555 covale 1.614 both A P5P 4 A O3' P5P 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 1.619 both B C 3 B O3' C 3 1_555 B P5P 4 B P P5P 4 1_555 covale 1.614 both B P5P 4 B O3' P5P 4 1_555 B P5P 5 B P P5P 5 1_555 covale 1.618 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 1MV6 PDB 1 1MV6 1 9 1MV6 1 9 1MV6 A 1 1 9 1 9 1MV6 1 9 1MV6 B 1 1 9