Sodium in PDB 5tw4: Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Ceftaroline

The structure of Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Ceftaroline, PDB code: 5tw4 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 / 1.57
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.696, 92.562, 79.592, 90.00, 99.75, 90.00
R / Rfree (%)	15.6 / 17.7

The structure of Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Ceftaroline 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 Ceftaroline (pdb code 5tw4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Ceftaroline, PDB code: 5tw4:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Ceftaroline


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 Ceftaroline within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:24.4 occ:1.00 OD2 A:ASP364 2.1 34.8 1.0 O A:HOH833 2.1 27.1 1.0 O A:HOH845 2.3 47.8 1.0 CG A:ASP364 2.9 29.4 1.0 OD1 A:ASP364 3.1 30.7 1.0 O A:HOH633 4.0 33.4 1.0 CB A:ASP364 4.3 22.4 1.0 CA A:TYR365 4.3 16.6 1.0 C A:ASP364 4.3 17.8 1.0 N A:TYR365 4.3 16.1 1.0 O A:ASP364 4.5 19.4 1.0 C A:TYR365 4.6 16.4 1.0 N A:PRO366 4.8 16.3 1.0 CA A:ASP364 4.9 18.8 1.0 CD A:PRO366 4.9 17.2 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Ceftaroline


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 S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Ceftaroline within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:17.0 occ:1.00 OD2 B:ASP364 2.0 30.0 1.0 O B:HOH829 2.2 20.8 1.0 O B:HOH815 2.3 42.8 1.0 CG B:ASP364 2.9 25.7 1.0 OD1 B:ASP364 3.1 26.9 1.0 O B:HOH607 4.2 31.7 1.0 CA B:TYR365 4.3 17.1 1.0 CB B:ASP364 4.3 21.5 1.0 N B:TYR365 4.3 17.1 1.0 C B:ASP364 4.4 17.8 1.0 CE B:LYS353 4.5 55.2 1.0 C B:TYR365 4.5 17.3 1.0 O B:ASP364 4.6 18.8 1.0 N B:PRO366 4.8 18.9 1.0 CD B:PRO366 4.9 20.9 1.0 NZ B:LYS353 5.0 62.4 1.0 CA B:ASP364 5.0 18.5 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Ceftaroline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Ceftaroline within 5.0Å range: probe atom residue distance (Å) B Occ B:Na407 b:31.6 occ:1.00 O B:HOH802 2.1 37.0 1.0 OD1 B:ASP313 2.4 27.2 1.0 CG B:ASP313 3.3 24.3 1.0 OD2 B:ASP313 3.7 27.4 1.0 OE1 B:GLU309 3.7 20.9 1.0 O B:HOH761 4.0 19.2 1.0 O B:HOH696 4.0 49.7 1.0 O B:GLU309 4.2 13.8 1.0 NH1 B:ARG276 4.6 14.3 1.0 CB B:ASP313 4.6 19.6 1.0 N B:ASP313 4.7 13.9 1.0 CA B:ASP313 4.8 15.8 1.0 CB B:PHE312 4.8 14.4 1.0 CD B:GLU309 4.9 19.7 1.0 C B:PHE312 4.9 14.7 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