Sodium in PDB 6c39: Apo Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4)

The structure of Apo Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4), PDB code: 6c39 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)	46.20 / 1.69
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.358, 92.403, 79.230, 90.00, 99.23, 90.00
R / Rfree (%)	16.1 / 19.6

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

Zinc

(Zn)

5 atoms

The binding sites of Sodium atom in the Apo Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) (pdb code 6c39). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Apo Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4), PDB code: 6c39:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Apo Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Apo Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:49.1 occ:1.00 O A:HOH751 2.2 46.3 1.0 OD2 A:ASP364 2.2 39.2 1.0 O A:HOH756 2.5 36.9 1.0 CG A:ASP364 3.1 30.2 1.0 HE2 A:LYS353 3.3 66.7 1.0 OD1 A:ASP364 3.4 33.3 1.0 HA A:TYR365 3.5 24.7 1.0 O A:HOH549 3.6 39.9 1.0 HD3 A:PRO366 4.0 26.8 1.0 CA A:TYR365 4.2 20.6 1.0 CE A:LYS353 4.3 55.6 1.0 N A:TYR365 4.3 18.6 1.0 C A:ASP364 4.3 21.6 1.0 HG3 A:PRO366 4.4 39.8 1.0 O A:ASP364 4.4 24.1 1.0 CB A:ASP364 4.4 27.5 1.0 HE3 A:LYS353 4.4 66.7 1.0 C A:TYR365 4.5 19.7 1.0 HB3 A:ASP364 4.5 33.0 1.0 HG2 A:LYS353 4.6 56.8 1.0 H A:TYR365 4.7 22.4 1.0 N A:PRO366 4.7 20.1 1.0 CD A:PRO366 4.7 22.3 1.0 HZ1 A:LYS353 4.8 77.3 1.0 CA A:ASP364 5.0 23.3 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Apo Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:26.1 occ:1.00 OD2 B:ASP364 2.1 38.4 1.0 O B:HOH777 2.2 28.9 1.0 O B:HOH775 2.3 27.9 1.0 CG B:ASP364 3.0 27.0 1.0 OD1 B:ASP364 3.2 27.7 1.0 HE2 B:LYS353 3.5 58.0 1.0 O B:HOH672 3.5 43.7 1.0 HA B:TYR365 3.6 24.0 1.0 HD3 B:PRO366 4.0 29.0 1.0 CA B:TYR365 4.2 20.0 1.0 N B:TYR365 4.3 21.9 1.0 CE B:LYS353 4.3 48.3 1.0 CB B:ASP364 4.4 18.8 1.0 C B:ASP364 4.4 21.1 1.0 HE3 B:LYS353 4.4 58.0 1.0 O B:ASP364 4.5 21.7 1.0 HB3 B:ASP364 4.5 22.6 1.0 C B:TYR365 4.5 20.5 1.0 HG3 B:PRO366 4.6 34.9 1.0 HG2 B:LYS353 4.6 43.5 1.0 H B:TYR365 4.6 26.4 1.0 CD B:PRO366 4.8 24.1 1.0 N B:PRO366 4.8 21.3 1.0 HZ1 B:LYS353 4.8 67.3 1.0 CA B:ASP364 5.0 19.8 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 Analyses of Penicillin-Binding Protein 4 (PBP4)-Mediated Antibiotic Resistance Instaphylococcus Aureus. J. Biol. Chem. V. 293 19854 2018.
ISSN: ESSN 1083-351X
PubMed: 30366985
DOI: 10.1074/JBC.RA118.004952