Sodium in PDB 6c3k: Apo Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R)

The structure of Apo Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R), PDB code: 6c3k 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)	46.28 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.868, 92.561, 79.189, 90.00, 99.30, 90.00
R / Rfree (%)	17.6 / 20.4

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

Zinc	(Zn)	5 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Apo Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) (pdb code 6c3k). 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 S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R), PDB code: 6c3k:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Apo Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R)


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 S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:31.5 occ:1.00 OD2 A:ASP364 2.1 40.1 1.0 O A:HOH770 2.1 37.8 1.0 O A:HOH788 2.3 51.2 1.0 CG A:ASP364 3.0 31.7 1.0 OD1 A:ASP364 3.2 31.3 1.0 HE2 A:LYS353 3.4 80.2 1.0 O A:HOH603 3.7 40.1 1.0 HA A:TYR365 3.7 26.7 1.0 HD3 A:PRO366 4.1 29.7 1.0 CE A:LYS353 4.3 66.8 1.0 CB A:ASP364 4.3 30.3 1.0 CA A:TYR365 4.4 22.2 1.0 N A:TYR365 4.4 21.0 1.0 C A:ASP364 4.4 21.7 1.0 HG3 A:PRO366 4.5 35.7 1.0 O A:ASP364 4.5 23.3 1.0 HB3 A:ASP364 4.5 36.4 1.0 HE3 A:LYS353 4.5 80.2 1.0 C A:TYR365 4.6 21.4 1.0 HG2 A:LYS353 4.7 63.3 1.0 H A:TYR365 4.7 25.2 1.0 HZ1 A:LYS353 4.8 88.4 1.0 N A:PRO366 4.8 20.4 1.0 CD A:PRO366 4.8 24.7 1.0 CA A:ASP364 5.0 24.3 1.0 HB2 A:ASP364 5.0 36.4 1.0

Sodium binding site 2 out of 2 in the Apo Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R)


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 S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:24.9 occ:1.00 OD2 B:ASP364 2.0 38.1 1.0 O B:HOH803 2.1 25.2 1.0 O B:HOH805 2.2 38.9 1.0 O B:HOH791 2.3 22.1 1.0 CG B:ASP364 2.9 29.3 1.0 OD1 B:ASP364 3.2 29.5 1.0 HE2 B:LYS353 3.4 63.5 1.0 HA B:TYR365 3.6 21.8 1.0 O B:HOH563 3.6 39.9 1.0 HD3 B:PRO366 4.1 30.8 1.0 CA B:TYR365 4.2 18.2 1.0 N B:TYR365 4.3 18.4 1.0 CB B:ASP364 4.3 22.5 1.0 CE B:LYS353 4.3 52.9 1.0 C B:ASP364 4.4 22.4 1.0 O B:ASP364 4.5 22.2 1.0 HB3 B:ASP364 4.5 27.1 1.0 C B:TYR365 4.6 19.4 1.0 HE3 B:LYS353 4.6 63.5 1.0 HG3 B:PRO366 4.6 37.1 1.0 H B:TYR365 4.6 22.2 1.0 HG2 B:LYS353 4.7 56.9 1.0 HZ1 B:LYS353 4.7 68.3 1.0 N B:PRO366 4.8 21.9 1.0 CD B:PRO366 4.8 25.6 1.0 CA B:ASP364 5.0 20.7 1.0 HB2 B:ASP364 5.0 27.1 1.0 NZ B:LYS353 5.0 56.9 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