Sodium in PDB 4wfa: The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Linezolid

The structure of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Linezolid, PDB code: 4wfa was solved by Z.Eyal, D.Matzov, M.Krupkin, I.Wekselman, E.Zimmerman, H.Rozenberg, A.Bashan, A.E.Yonath, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.88 / 3.39
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	279.922, 279.922, 870.586, 90.00, 90.00, 120.00
R / Rfree (%)	20.2 / 24.3

The structure of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Linezolid also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Magnesium	(Mg)	246 atoms
Manganese	(Mn)	195 atoms

The binding sites of Sodium atom in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Linezolid (pdb code 4wfa). 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 The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Linezolid, PDB code: 4wfa:

Sodium binding site 1 out of 1 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Linezolid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Linezolid within 5.0Å range: probe atom residue distance (Å) B Occ X:Na3367 b:64.5 occ:1.00 OP2 X:G2630 2.6 86.3 1.0 OP2 X:A2629 2.7 0.6 1.0 P X:G2630 3.9 93.0 1.0 P X:A2629 4.0 0.7 1.0 O5' X:G2630 4.1 94.8 1.0 C5' X:G2630 4.3 94.1 1.0 O3' X:C2628 4.3 80.8 1.0 C3' X:C2628 4.4 78.4 1.0 OP1 X:G2630 4.8 95.9 1.0 O2' X:C2628 4.9 87.0 1.0 OP1 X:A2629 4.9 0.4 1.0

Z.Eyal, D.Matzov, M.Krupkin, I.Wekselman, S.Paukner, E.Zimmerman, H.Rozenberg, A.Bashan, A.Yonath. Structural Insights Into Species-Specific Features of the Ribosome From the Pathogen Staphylococcus Aureus. Proc.Natl.Acad.Sci.Usa V. 112 E5805 2015.
ISSN: ESSN 1091-6490
PubMed: 26464510
DOI: 10.1073/PNAS.1517952112