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/pdb1f7i/pdb pdb_00001f7i 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 8634.127 RNASE P RNA RIBOZYME, P4 DOMAIN P4 STEM C70U 1 syn polymer 161.116 COBALT HEXAMMINE(III) 1 syn non-polymer no no GGAAGUUCGGUCUUCGGACCGGCUUCC GGAAGUUCGGUCUUCGGACCGGCUUCC 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 5.257 1 19 A 2 A 26 -6.246 A_G2:C26_A 1 -0.087 -0.262 0.923 -0.404 0.962 1 20 A 3 A 25 -4.170 A_A3:U25_A 2 -20.400 0.032 -0.309 -0.067 4.215 1 20 A 4 A 24 -4.362 A_A4:U24_A 3 -1.324 0.000 -0.857 -0.175 -12.717 1 19 A 5 A 23 -0.309 A_G5:C23_A 4 -21.848 -0.153 -0.655 -0.159 -10.792 1 28 A 6 A 22 5.509 A_U6:G22_A 5 -4.345 2.374 0.000 -0.387 -14.353 1 19 A 8 A 21 -0.809 A_C8:G21_A 6 -15.367 0.076 -0.386 -0.381 15.446 1 19 A 9 A 20 -3.726 A_G9:C20_A 7 5.856 -0.262 1.140 -0.381 -3.353 1 19 A 10 A 19 8.957 A_G10:C19_A 8 -24.941 -0.402 -0.913 -0.484 0.902 1 20 A 11 A 18 -2.333 A_U11:A18_A 9 -29.223 0.038 -0.631 -0.307 -5.664 1 19 A 12 A 17 -1.172 A_C12:G17_A 10 -8.396 0.484 0.105 -0.219 17.843 6 A 13 A 16 -81.303 A_U13:G16_A 11 -12.041 1.423 0.049 -5.467 3.787 32.926 A A 2 3 6.820 A A 26 25 4.005 3.825 0.273 -1.360 AA_G2A3:U25C26_AA 1 7.451 -13.284 31.871 -3.190 1.057 3.994 35.314 A A 3 4 -9.046 A A 25 24 3.842 -5.466 0.402 -1.249 AA_A3A4:U24U25_AA 2 0.859 -1.421 34.891 -1.084 -0.510 4.630 29.334 A A 4 5 6.685 A A 24 23 4.753 3.376 0.583 -1.066 AA_A4G5:C23U24_AA 3 1.962 -3.886 29.079 -3.153 -0.541 2.177 44.525 A A 5 6 32.155 A A 23 22 3.119 23.258 0.923 -0.959 AA_G5U6:G22C23_AA 4 -1.730 2.392 38.196 -3.151 -1.358 2.122 32.777 A A 6 8 46.457 A A 22 21 3.933 23.142 0.643 -0.909 AA_U6C8:G21G22_AA 5 9.793 -19.658 21.216 -6.143 0.778 1.975 33.939 A A 8 9 20.863 A A 21 20 2.422 11.790 -0.427 -0.965 AA_C8G9:C20G21_AA 6 -8.987 15.902 30.617 -2.994 -0.290 3.172 44.946 A A 9 10 44.450 A A 20 19 4.150 30.475 1.398 -0.154 AA_G9G10:C19C20_AA 7 13.516 -19.713 30.585 -3.952 -0.165 2.440 39.882 A A 10 11 21.311 A A 19 18 2.913 14.237 -0.415 -0.893 AA_G10U11:A18C19_AA 8 -1.432 2.143 37.325 -2.702 0.468 2.911 33.885 A A 11 12 27.382 A A 18 17 3.599 15.357 -0.599 -0.813 AA_U11C12:G17A18_AA 9 -4.493 8.011 29.967 -4.016 0.261 3.082 102.888 A A 12 13 -1.088 A A 17 16 3.499 -1.696 2.667 -1.806 AA_C12U13:G16G17_AA 10 -21.255 13.641 101.274 -1.129 -2.022 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 contains the average complex structure calculated from this ensemble RCSB Y RCSB 2000-06-27 REL REL NCO COBALT HEXAMMINE(III) synthesized from DNA oligonucleotide template by T7 RNA polymerase sample This structure was determined using standard 2D homonuclear techniques and 13C and 31P heteronuclear techniques at natural abundance. Distance constraints derived from intermolecular NOE crosspeaks between RNA protons and cobalt (III) hexammine protons were used to determine the site of cobalt (III) hexammine binding in the complex structure structures with the least restraint violations 50 12 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 structures are based on a total of 268 NOE derived distance constraints, 171 dihedral restraints and 49 distance restraints from hydrogen bonds. 12 NOE derived intermolecular distance constraints were used to localize the bound cobalt(III) hexammine. The 12 structures with lowest NOE and dihedral angle violation energies are presented restrained molecular dynamics; simulated annealing 7 closest to the average 2 mM P4m RNA; 100 mM sodium chloride; 10 mM phosphate buffer; 90% H2O, 10% D2O 90% H2O/10% D2O 2 mM P4m RNA; 100 mM sodium chloride; 10 mM phosphate buffer; 99.96% D2O 99.96% D2O 2 mM P4m RNA; 100 mM sodium chloride; 10 mM magnesium chloride; 10 mM phosphate buffer; 90% H2O, 10% D2O 90% H2O/10% D2O 2 mM P4m 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 3.841 Brunger refinement X-PLOR 3.841 600 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 U 7 n 7 U 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 1 A A H41 O6 C G 8 21 1.59 9 A A HO2' O5' U C 14 15 1.46 10 A A O6 H41 G C 2 26 1.59 SOLUTION STRUCTURE OF THE RNASE P RNA (M1 RNA) P4 STEM C70U MUTANT OLIGORIBONUCLEOTIDE COMPLEXED WITH COBALT (III) HEXAMINE ,NMR, ENSEMBLE OF 12 STRUCTURES 1 N N 2 N N 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 TYPE_28_PAIR A U 6 A N3 U 6 1_555 A G 22 A O6 G 22 1_555 hydrog TYPE_28_PAIR A U 6 A O2 U 6 1_555 A G 22 A N1 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, C70U MUTANT, METAL BINDING SITE, METAL COMPLEX, COBALT (III) HEXAMMINE COMPLEX, RNA 1F7I PDB 1 1F7I 1 27 1F7I 1 27 1F7I A 1 1 27 BINDING SITE FOR RESIDUE NCO A 28 A NCO 28 Software 4 A G 5 A G 5 4 1_555 A U 6 A U 6 4 1_555 A G 21 A G 21 4 1_555 A G 22 A G 22 4 1_555 1 P 1