Sodium in PDB 5npm: Crystal Structure of Mutant Ribosomal Protein TTHL1 Lacking 8 N- Terminal Residues in Complex with 80NT 23S Rna From Thermus Thermophilus

The structure of Crystal Structure of Mutant Ribosomal Protein TTHL1 Lacking 8 N- Terminal Residues in Complex with 80NT 23S Rna From Thermus Thermophilus, PDB code: 5npm was solved by A.G.Gabdulkhakov, T.V.Tishchenko, N.A.Nevskaya, S.V.Nikonov, M.B.Garber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.34 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.127, 65.532, 119.925, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 24.9

The binding sites of Sodium atom in the Crystal Structure of Mutant Ribosomal Protein TTHL1 Lacking 8 N- Terminal Residues in Complex with 80NT 23S Rna From Thermus Thermophilus (pdb code 5npm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Mutant Ribosomal Protein TTHL1 Lacking 8 N- Terminal Residues in Complex with 80NT 23S Rna From Thermus Thermophilus, PDB code: 5npm:

Sodium binding site 1 out of 1 in the Crystal Structure of Mutant Ribosomal Protein TTHL1 Lacking 8 N- Terminal Residues in Complex with 80NT 23S Rna From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Mutant Ribosomal Protein TTHL1 Lacking 8 N- Terminal Residues in Complex with 80NT 23S Rna From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Na102 b:29.9 occ:1.00 O2' B:A67 2.3 18.0 1.0 OP1 B:C59 2.3 20.1 1.0 OP2 B:C60 2.4 29.1 1.0 O5' B:U68 3.0 28.9 1.0 OP2 B:U68 3.2 33.0 1.0 O5' B:C59 3.5 19.3 1.0 P B:C59 3.5 21.1 1.0 O B:HOH207 3.5 26.3 1.0 C5' B:C59 3.5 22.1 1.0 C2' B:A67 3.6 17.7 1.0 P B:U68 3.7 19.9 1.0 P B:C60 3.8 22.9 1.0 O3' B:A67 4.0 22.1 1.0 C6 B:U68 4.0 14.7 1.0 C5' B:U68 4.1 25.7 1.0 C3' B:A67 4.2 15.4 1.0 O6 B:G61 4.2 30.7 1.0 O3' B:C59 4.2 21.6 1.0 O4' B:U68 4.4 22.6 1.0 OP1 B:C60 4.5 24.0 1.0 C5 B:U68 4.5 19.1 1.0 OP2 B:C59 4.5 25.2 1.0 O3' B:G58 4.5 14.0 1.0 C4' B:C59 4.5 22.1 1.0 C3' B:C59 4.6 22.4 1.0 C1' B:A67 4.7 16.8 1.0 O6 B:G62 4.8 30.0 1.0 C4' B:U68 4.9 18.4 1.0 O5' B:C60 4.9 30.5 1.0

O.S.Kostareva, N.A.Nevskaya, S.V.Tishchenko, A.G.Gabdulkhakov, M.B.Garber, S.V.Nikonov. [Influence of Nonconserved Regions of L1 Protuberance of Thermus Thermophilus Ribosome on the Affinity of L1 Protein to 23S Rrna]. Mol.Biol.(Moscow) V. 52 106 2018.
ISSN: ISSN 0026-8984
PubMed: 29512642
DOI: 10.7868/S0026898418010147