1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Schmitz, M. 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 Co H18 N6 3 161.116 COBALT HEXAMMINE(III) non-polymer C9 H13 N2 O9 P 324.181 y URIDINE-5'-MONOPHOSPHATE RNA linking UK RNA RNARFU 2122 1355-8382 6 1212 1225 10.1017/S1355838200000881 10999599 Solution structure and metal-ion binding of the P4 element from bacterial RNase P RNA. 2000 10.2210/pdb1f78/pdb pdb_00001f78 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 8633.143 RNASE P RNA RIBOZYME, P4 DOMAIN P4 STEM 1 syn polymer 161.116 COBALT HEXAMMINE(III) 1 syn non-polymer no no GGAAGUCCGGUCUUCGGACCGGCUUCC GGAAGUCCGGUCUUCGGACCGGCUUCC A polyribonucleotide n n n n n n n n n n n n n n n n n n n n n n n n n n n 45.755 1 19 A 1 A 27 -3.047 A_G1:C27_A 1 20.415 -0.273 -0.444 -0.339 7.996 1 19 A 2 A 26 -4.371 A_G2:C26_A 2 -2.819 -0.355 0.073 -0.266 -2.191 1 20 A 3 A 25 -1.003 A_A3:U25_A 3 -21.191 0.200 -0.824 -0.177 -3.528 1 20 A 4 A 24 -2.763 A_A4:U24_A 4 -5.000 0.063 -0.481 0.001 2.700 1 19 A 5 A 23 -2.327 A_G5:C23_A 5 -2.238 -0.222 -1.051 -0.401 -9.964 1 19 A 7 A 22 2.551 A_C7:G22_A 6 30.686 0.147 0.449 -0.186 -8.481 1 19 A 8 A 21 -8.819 A_C8:G21_A 7 7.807 -0.055 -1.097 -0.547 3.745 1 19 A 9 A 20 -4.977 A_G9:C20_A 8 4.757 0.061 -1.285 -0.644 -0.140 1 19 A 10 A 19 9.943 A_G10:C19_A 9 -19.688 -0.375 -1.117 -0.592 4.173 1 20 A 11 A 18 -3.586 A_U11:A18_A 10 -5.740 -0.300 -0.611 0.020 -29.827 1 19 A 12 A 17 -4.459 A_C12:G17_A 11 16.219 0.174 1.970 -0.633 37.976 2 A 13 A 16 -64.596 A_U13:G16_A 12 8.481 1.214 0.287 -5.464 3.910 31.598 A A 1 2 41.964 A A 27 26 5.728 20.922 -0.665 -0.698 AA_G1G2:C26C27_AA 1 -3.669 7.359 23.529 -7.887 0.062 2.785 40.097 A A 2 3 26.656 A A 26 25 3.808 17.634 0.282 -1.553 AA_G2A3:U25C26_AA 2 5.691 -8.603 35.716 -4.424 0.285 4.333 32.447 A A 3 4 -24.651 A A 25 24 4.294 -13.355 0.354 -1.165 AA_A3A4:U24U25_AA 3 -3.587 6.622 29.424 1.171 -1.509 1.900 30.339 A A 4 5 32.974 A A 24 23 3.280 16.371 0.055 -1.657 AA_A4G5:C23U24_AA 4 1.218 -2.453 25.602 -6.010 0.107 2.820 68.926 A A 5 7 42.078 A A 23 22 3.629 44.253 -1.968 -0.643 AA_G5C7:G22C23_AA 5 -13.950 13.264 52.460 -2.474 1.138 3.169 33.549 A A 7 8 25.486 A A 22 21 4.457 14.007 -1.054 -0.781 AA_C7C8:G21G22_AA 6 10.765 -19.587 28.635 -4.261 4.061 3.883 22.710 A A 8 9 -0.870 A A 21 20 3.866 -0.343 0.170 -0.898 AA_C8G9:C20G21_AA 7 0.936 -2.377 22.689 -2.135 -0.032 3.188 29.054 A A 9 10 25.925 A A 20 19 4.017 12.584 0.844 -1.150 AA_G9G10:C19C20_AA 8 1.760 -3.627 26.182 -5.504 -1.233 2.327 38.043 A A 10 11 32.354 A A 19 18 3.218 20.025 -0.890 -1.015 AA_G10U11:A18C19_AA 9 -5.079 8.206 32.120 -3.915 0.767 2.244 41.138 A A 11 12 33.950 A A 18 17 4.218 21.719 -0.641 -2.187 AA_U11C12:G17A18_AA 10 -18.753 29.314 29.794 -5.852 -1.453 2.145 100.094 A A 12 13 -0.140 A A 17 16 2.543 -0.213 2.092 -2.070 AA_C12U13:G16G17_AA 11 -23.362 15.314 98.049 -1.348 -1.632 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2000-10-09 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-16 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id 1F6X shows the structure of the free wildtype P4 stem oligoribonucleotide 1F6Z shows the structure of the free C70U mutant P4 stem oligoribonucleotide RCSB Y RCSB 2000-06-26 REL REL NCO COBALT HEXAMMINE(III) enzymatically synthesized from DNA ologonucleotide template by T7 RNA polymerase sample This structure was determined using standard 2D homonuclear techniques and 13C and 31P heteronuclear techniques at natural abundance. Intermolecular NOE crosspeaks between RNA protons and cobalt (III) hexammine protons and derived intermolecular distance constraints were used to determine the site of cobalt (III) hexammine binding in the complex structure 1 2D NOESY 2D NOESY 2D NOESY 2D NOESY DQF-COSY 31P-1H-COSY 13C-1H-HMQC 100 mM Na 6.5 ambient 288 K 100 mM Na 6.5 ambient 288 K 100 mM Na, 10 mM Mg 6.5 ambient 288 K 100 mM Na, 3 mM Co(NH3)6 6.5 ambient 288 K The average structure is based on superposition of 11 converged structures after refinement. The average RMS deviation between the ensemble and the average structure is 1.7 Angstrom. A total of 266 NOE-derived intramolecular distance constraints, 164 dihedral restraint and 48 distance restraints from hydrogen bonds were used in the refinement. 12 NOE derived intermolecular distance constraints were used to localize the bound cobalt (III) hexammine restrained molecular dynamics and simulated annealing minimized average structure 2 mM P4 RNA; 100 mM sodium chloride; 10 mM phosphate buffer; 90% H2O, 10% D2O 90% H2O/10% D2O 2 mM P4 RNA; 100 mM sodium chloride; 10 mM phosphate buffer; 99.96% D2O 99.96% D2O 2 mM P4 RNA; 100 mM sodium chloride; 10 mM magnesium chloride; 10 mM phosphate buffer; 90% H2O, 10% D2O 90% H2O/10% D2O 2 mM P4 RNA; 100 mM sodium chloride; 3 mM hexammine cobalt chloride; 10 mM phosphate buffer; 90% H2O, 10% D2O 90% H2O/10% D2O Bruker collection XwinNMR 3.1 MSI processing Felix 95 Brunger structure solution X-PLOR 3.84 Brunger refinement X-PLOR 3.84 600 Bruker AMX 500 Bruker DRX NCO 28 2 NCO NCO 28 A G 1 n 1 G 1 A G 2 n 2 G 2 A A 3 n 3 A 3 A A 4 n 4 A 4 A G 5 n 5 G 5 A U 6 n 6 U 6 A C 7 n 7 C 7 A C 8 n 8 C 8 A G 9 n 9 G 9 A G 10 n 10 G 10 A U 11 n 11 U 11 A C 12 n 12 C 12 A U 13 n 13 U 13 A U 14 n 14 U 14 A C 15 n 15 C 15 A G 16 n 16 G 16 A G 17 n 17 G 17 A A 18 n 18 A 18 A C 19 n 19 C 19 A C 20 n 20 C 20 A G 21 n 21 G 21 A G 22 n 22 G 22 A C 23 n 23 C 23 A U 24 n 24 U 24 A U 25 n 25 U 25 A C 26 n 26 C 26 A C 27 n 27 C 27 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 minimized average SOLUTION STRUCTURE OF RNASE P RNA (M1 RNA) P4 STEM OLIGORIBONUCLEOTIDE COMPLEXED WITH COBALT (III) HEXAMINE, NMR, MINIMIZED AVERAGE STRUCTURE 1 N N 2 N N hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 A C 27 A N3 C 27 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 A C 27 A O2 C 27 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 A C 27 A N4 C 27 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 A C 26 A N3 C 26 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 A C 26 A O2 C 26 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 A C 26 A N4 C 26 1_555 hydrog WATSON-CRICK A A 3 A N1 A 3 1_555 A U 25 A N3 U 25 1_555 hydrog WATSON-CRICK A A 3 A N6 A 3 1_555 A U 25 A O4 U 25 1_555 hydrog WATSON-CRICK A A 4 A N1 A 4 1_555 A U 24 A N3 U 24 1_555 hydrog WATSON-CRICK A A 4 A N6 A 4 1_555 A U 24 A O4 U 24 1_555 hydrog WATSON-CRICK A G 5 A N1 G 5 1_555 A C 23 A N3 C 23 1_555 hydrog WATSON-CRICK A G 5 A N2 G 5 1_555 A C 23 A O2 C 23 1_555 hydrog WATSON-CRICK A G 5 A O6 G 5 1_555 A C 23 A N4 C 23 1_555 hydrog WATSON-CRICK A C 7 A N3 C 7 1_555 A G 22 A N1 G 22 1_555 hydrog WATSON-CRICK A C 7 A N4 C 7 1_555 A G 22 A O6 G 22 1_555 hydrog WATSON-CRICK A C 7 A O2 C 7 1_555 A G 22 A N2 G 22 1_555 hydrog WATSON-CRICK A C 8 A N3 C 8 1_555 A G 21 A N1 G 21 1_555 hydrog WATSON-CRICK A C 8 A N4 C 8 1_555 A G 21 A O6 G 21 1_555 hydrog WATSON-CRICK A C 8 A O2 C 8 1_555 A G 21 A N2 G 21 1_555 hydrog WATSON-CRICK A G 9 A N1 G 9 1_555 A C 20 A N3 C 20 1_555 hydrog WATSON-CRICK A G 9 A N2 G 9 1_555 A C 20 A O2 C 20 1_555 hydrog WATSON-CRICK A G 9 A O6 G 9 1_555 A C 20 A N4 C 20 1_555 hydrog WATSON-CRICK A G 10 A N1 G 10 1_555 A C 19 A N3 C 19 1_555 hydrog WATSON-CRICK A G 10 A N2 G 10 1_555 A C 19 A O2 C 19 1_555 hydrog WATSON-CRICK A G 10 A O6 G 10 1_555 A C 19 A N4 C 19 1_555 hydrog WATSON-CRICK A U 11 A N3 U 11 1_555 A A 18 A N1 A 18 1_555 hydrog WATSON-CRICK A U 11 A O4 U 11 1_555 A A 18 A N6 A 18 1_555 hydrog WATSON-CRICK A C 12 A N3 C 12 1_555 A G 17 A N1 G 17 1_555 hydrog WATSON-CRICK A C 12 A N4 C 12 1_555 A G 17 A O6 G 17 1_555 hydrog WATSON-CRICK A C 12 A O2 C 12 1_555 A G 17 A N2 G 17 1_555 hydrog U-G MISPAIR A U 13 A O2 U 13 1_555 A G 16 A N1 G 16 1_555 RNA RIBONUCLEASE P, RIBOZYME, TRANSFER RNA PROCESSING, P4 STEM, METAL BINDING SITE, METAL COMPLEX, COBALT (III) HEXAMMINE COMPLEX, RNA 1F78 PDB 1 1F78 1 27 1F78 1 27 1F78 A 1 1 27 BINDING SITE FOR RESIDUE NCO A 28 A NCO 28 Software 3 A G 5 A G 5 3 1_555 A C 8 A C 8 3 1_555 A G 21 A G 21 3 1_555 1 P 1