1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Rudisser, S. Tinoco Jr., I. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 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 UK J.Mol.Biol. JMOBAK 0070 0022-2836 295 1211 1232 10.1006/jmbi.1999.3421 10653698 Solution structure of Cobalt(III)hexammine complexed to the GAAA tetraloop, and metal-ion binding to G.A mismatches. 2000 10.2210/pdb1f9l/pdb pdb_00001f9l 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 7175.371 5'-R(*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*AP*AP*AP*GP*AP*UP*GP*GP*CP*GP*CP*CP*)-3' P5ABC DOMAIN 1 syn polymer no no GGCGAAGUCGAAAGAUGGCGCC GGCGAAGUCGAAAGAUGGCGCC A polyribonucleotide n n n n n n n n n n n n n n n n n n n n n n 29.668 1 19 A 1 A 22 -5.981 A_G1:C22_A 1 20.355 -0.014 -0.317 -0.146 2.523 1 19 A 2 A 21 7.136 A_G2:C21_A 2 26.162 -0.430 0.676 -0.396 10.066 1 19 A 3 A 20 3.509 A_C3:G20_A 3 -17.715 0.197 -0.837 -0.282 -3.547 1 19 A 4 A 19 -18.929 A_G4:C19_A 4 -17.763 0.382 0.881 -0.427 -6.105 8 A 5 A 18 -23.184 A_A5:G18_A 5 0.510 0.043 -0.872 1.123 1.811 8 A 6 A 17 -22.412 A_A6:G17_A 6 -5.291 0.107 -0.538 1.247 -4.341 28 A 7 A 16 -5.401 A_G7:U16_A 7 -9.111 -2.147 -0.501 -0.370 2.072 1 20 A 8 A 15 -6.032 A_U8:A15_A 8 -0.802 0.097 -0.353 -0.044 20.290 1 19 A 9 A 14 -3.456 A_C9:G14_A 9 -5.584 0.064 0.008 -0.172 31.387 A 10 A 13 -63.956 A_G10:A13_A 10 7.842 7.104 -1.176 -5.355 5.217 25.467 A A 1 2 -14.160 A A 22 21 6.124 -6.023 1.065 -0.598 AA_G1G2:C21C22_AA 1 -9.796 23.029 22.761 1.811 -7.569 1.951 40.145 A A 2 3 24.399 A A 21 20 2.908 16.037 0.743 -2.087 AA_G2C3:G20C21_AA 2 12.339 -18.774 34.855 -4.503 0.044 4.548 33.340 A A 3 4 -1.565 A A 20 19 3.945 -0.888 -2.712 -1.585 AA_C3G4:C19G20_AA 3 -8.779 15.477 32.183 -2.567 2.797 3.973 28.140 A A 4 5 -11.115 A A 19 18 3.555 -5.245 0.983 -2.023 AA_G4A5:G18C19_AA 4 10.529 -22.315 25.609 -2.676 0.958 2.439 26.968 A A 5 6 17.100 A A 18 17 3.154 7.862 -0.188 -2.046 AA_A5A6:G17G18_AA 5 -0.764 1.663 25.806 -6.144 0.232 3.268 31.738 A A 6 7 19.893 A A 17 16 3.763 10.676 1.859 -0.705 AA_A6G7:U16G17_AA 6 -0.917 1.709 29.918 -3.462 -3.586 2.467 36.531 A A 7 8 17.416 A A 16 15 3.088 10.754 -1.236 -2.032 AA_G7U8:A15U16_AA 7 -2.931 4.747 34.844 -4.535 1.620 3.523 32.981 A A 8 9 -33.885 A A 15 14 3.623 -18.192 0.224 -0.932 AA_U8C9:G14A15_AA 8 -2.490 4.638 27.515 2.063 -0.902 3.156 66.936 A A 9 10 12.322 A A 14 13 4.196 13.447 -3.903 -1.230 AA_C9G10:A13G14_AA 9 13.186 -12.084 64.530 -1.722 4.134 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 2000-07-26 1 1 2008-01-08 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name 2009-07-28 SPRSDE Solution structure of the 22-nucleotide without Cobalt(III)hexammine RCSB Y RCSB 2000-07-11 REL REL The RNA was enzymatically synthesized from a synthetic RNA template using T7 RNA polymerase sample The structure of the complex was determined using 7 NOE constraints between Cobalt(III)Hexammine and the GAAA tetraloop. In addition, the same constraints as for the 22-nucleotide hairpin without Cobalt(III)hexammine were used. For RNA without Cobalt(III)Hexammine see entry 1EOR. structures with the least restraint violations 50 1 2D NOESY 200 mM NaCl 5.6 ambient 283 K 356 NOE constraints, 16 sugar pucker constraints, 93 torsion angle constraints, 7 constraints between Cobalt(III)Hexammine and the GAAA tetraloop restrained molecular dynamics, 1 minimized average structure 2.8 mM RNA, 10 mM sodium Phosphate, 200 mM NaCl, 0.1 mM EDTA pH 5.6, 3.4 mM Cobalt(III)Hexammine 90% H2O/10% D2O Brunger structure solution X-PLOR 3.1 MSI data analysis Felix 95 Brunger refinement X-PLOR 3.1 600 Bruker AMX 500 Bruker DRX G 1 n 1 G 1 A G 2 n 2 G 2 A C 3 n 3 C 3 A G 4 n 4 G 4 A A 5 n 5 A 5 A A 6 n 6 A 6 A G 7 n 7 G 7 A U 8 n 8 U 8 A C 9 n 9 C 9 A G 10 n 10 G 10 A A 11 n 11 A 11 A A 12 n 12 A 12 A A 13 n 13 A 13 A G 14 n 14 G 14 A A 15 n 15 A 15 A U 16 n 16 U 16 A G 17 n 17 G 17 A G 18 n 18 G 18 A C 19 n 19 C 19 A G 20 n 20 G 20 A C 21 n 21 C 21 A C 22 n 22 C 22 A author_defined_assembly 1 monomeric 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 H61 O6 A G 6 17 1.51 1 A A H61 O6 A G 5 18 1.55 minimized average Solution Structure of a 22-Nucleotide Hairpin Similar to the P5ABC Region of a Group I Ribozyme with Cobalt(III)hexammine Complexed to the GAAA Tetraloop 1 N N hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 A C 22 A N3 C 22 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 A C 22 A O2 C 22 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 A C 22 A N4 C 22 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 A C 21 A N3 C 21 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 A C 21 A O2 C 21 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 A C 21 A N4 C 21 1_555 hydrog WATSON-CRICK A C 3 A N3 C 3 1_555 A G 20 A N1 G 20 1_555 hydrog WATSON-CRICK A C 3 A N4 C 3 1_555 A G 20 A O6 G 20 1_555 hydrog WATSON-CRICK A C 3 A O2 C 3 1_555 A G 20 A N2 G 20 1_555 hydrog WATSON-CRICK A G 4 A N1 G 4 1_555 A C 19 A N3 C 19 1_555 hydrog WATSON-CRICK A G 4 A N2 G 4 1_555 A C 19 A O2 C 19 1_555 hydrog WATSON-CRICK A G 4 A O6 G 4 1_555 A C 19 A N4 C 19 1_555 hydrog TYPE_8_PAIR A A 5 A N1 A 5 1_555 A G 18 A N1 G 18 1_555 hydrog TYPE_8_PAIR A A 5 A N6 A 5 1_555 A G 18 A O6 G 18 1_555 hydrog TYPE_8_PAIR A A 6 A N1 A 6 1_555 A G 17 A N1 G 17 1_555 hydrog TYPE_8_PAIR A A 6 A N6 A 6 1_555 A G 17 A O6 G 17 1_555 hydrog TYPE_28_PAIR A G 7 A N1 G 7 1_555 A U 16 A O2 U 16 1_555 hydrog TYPE_28_PAIR A G 7 A O6 G 7 1_555 A U 16 A N3 U 16 1_555 hydrog WATSON-CRICK A U 8 A N3 U 8 1_555 A A 15 A N1 A 15 1_555 hydrog WATSON-CRICK A U 8 A O4 U 8 1_555 A A 15 A N6 A 15 1_555 hydrog WATSON-CRICK A C 9 A N3 C 9 1_555 A G 14 A N1 G 14 1_555 hydrog WATSON-CRICK A C 9 A N4 C 9 1_555 A G 14 A O6 G 14 1_555 hydrog WATSON-CRICK A C 9 A O2 C 9 1_555 A G 14 A N2 G 14 1_555 hydrog G-A MISPAIR A G 10 A N2 G 10 1_555 A A 13 A N7 A 13 1_555 RNA GA mismatches, GAAA tetraloop, metal-ion binding, Cobalt(III)hexammine, hairpin, P5abc, group I intron, RNA 1F9L PDB 1 1F9L 1 22 1F9L 1 22 1F9L A 1 1 22 1 P 1