Sodium in PDB 5ty2: Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Nafcillin

The structure of Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Nafcillin, PDB code: 5ty2 was solved by J.A.N.Alexander, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.12 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.850, 92.244, 78.952, 90.00, 98.43, 90.00
R / Rfree (%)	16.9 / 20.5

The structure of Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Nafcillin also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Zinc	(Zn)	4 atoms

The binding sites of Sodium atom in the Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Nafcillin (pdb code 5ty2). 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 S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Nafcillin, PDB code: 5ty2:

Sodium binding site 1 out of 1 in the Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Nafcillin


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 S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Nafcillin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:34.7 occ:1.00 OD2 B:ASP364 2.1 32.0 1.0 O B:HOH758 2.2 28.9 1.0 O B:HOH722 2.4 34.8 1.0 CG B:ASP364 3.0 31.3 1.0 NZ B:LYS353 3.2 81.0 1.0 OD1 B:ASP364 3.3 28.6 1.0 O B:HOH696 3.7 41.0 1.0 CA B:TYR365 4.3 22.4 1.0 CB B:ASP364 4.3 23.3 1.0 N B:TYR365 4.4 22.5 1.0 C B:ASP364 4.4 24.1 1.0 O B:ASP364 4.5 23.9 1.0 C B:TYR365 4.6 22.1 1.0 CE B:LYS353 4.7 70.2 1.0 N B:PRO366 4.9 21.7 1.0 CD B:PRO366 4.9 24.5 1.0 CA B:ASP364 5.0 20.8 1.0

J.A.N.Alexander, S.S.Chatterjee, S.M.Hamilton, L.D.Eltis, H.F.Chambers, N.C.J.Strynadka. Structural and Kinetic Analysis of Penicillin-Binding Protein 4 (PBP4)-Mediated Antibiotic Resistance Instaphylococcus Aureus. J. Biol. Chem. 2018.
ISSN: ESSN 1083-351X
PubMed: 30366985
DOI: 10.1074/JBC.RA118.004952