Sodium in PDB 5ty7: Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Nafcillin

The structure of Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Nafcillin, PDB code: 5ty7 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)	55.59 / 1.89
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.323, 92.231, 79.061, 90.00, 98.94, 90.00
R / Rfree (%)	18.5 / 22.2

The structure of Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Nafcillin also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Nafcillin (pdb code 5ty7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Nafcillin, PDB code: 5ty7:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) 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 Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Nafcillin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:48.1 occ:1.00 OD2 A:ASP364 2.2 49.2 1.0 O A:HOH650 2.2 44.7 1.0 CG A:ASP364 3.1 38.6 1.0 OD1 A:ASP364 3.4 41.4 1.0 CE A:LYS353 3.8 87.1 1.0 CA A:TYR365 4.3 28.6 1.0 C A:ASP364 4.4 34.1 1.0 N A:TYR365 4.4 30.6 1.0 O A:ASP364 4.4 32.3 1.0 CB A:ASP364 4.4 40.9 1.0 C A:TYR365 4.6 26.8 1.0 NZ A:LYS353 4.6 83.5 1.0 CD A:PRO366 4.7 27.9 1.0 N A:PRO366 4.8 26.1 1.0 CD A:LYS353 4.8 89.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Nafcillin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Nafcillin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:27.9 occ:1.00 OD2 B:ASP364 2.0 41.1 1.0 O B:HOH678 2.1 32.6 1.0 O B:HOH668 2.3 33.1 1.0 CG B:ASP364 2.9 33.5 1.0 OD1 B:ASP364 3.2 38.1 1.0 O B:HOH595 3.7 36.5 1.0 CE B:LYS353 4.1 93.2 1.0 CA B:TYR365 4.2 31.4 1.0 CB B:ASP364 4.3 32.8 1.0 N B:TYR365 4.3 29.6 1.0 C B:ASP364 4.3 31.7 1.0 O B:ASP364 4.5 29.4 1.0 C B:TYR365 4.5 31.2 1.0 CD B:PRO366 4.7 33.0 1.0 N B:PRO366 4.7 28.3 1.0 NZ B:LYS353 4.9 97.0 1.0 CA B:ASP364 4.9 31.9 1.0 O B:TYR365 5.0 27.5 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