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

The structure of Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Ceftobiprole, PDB code: 5txi 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)	46.15 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.904, 92.293, 79.519, 90.00, 100.01, 90.00
R / Rfree (%)	17.1 / 20.2

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

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


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 Ceftobiprole within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:32.5 occ:1.00 O A:HOH520 2.2 30.8 1.0 OD1 A:ASP313 2.3 27.2 1.0 CG A:ASP313 3.2 28.1 1.0 OD2 A:ASP313 3.5 29.6 1.0 OE1 A:GLU309 3.9 27.1 1.0 O A:HOH656 4.0 22.2 1.0 O A:GLU309 4.4 18.0 1.0 CB A:ASP313 4.6 19.9 1.0 N A:ASP313 4.7 15.4 1.0 NH1 A:ARG276 4.8 18.3 1.0 CA A:ASP313 4.8 16.8 1.0

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


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 Ceftobiprole within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:29.6 occ:1.00 OD2 A:ASP364 2.0 39.1 1.0 O A:HOH733 2.1 32.0 1.0 CG A:ASP364 2.9 29.6 1.0 OD1 A:ASP364 3.1 30.9 1.0 O A:HOH558 4.0 35.7 1.0 CE A:LYS353 4.2 46.0 1.0 CB A:ASP364 4.3 24.2 1.0 CA A:TYR365 4.4 18.5 1.0 C A:ASP364 4.4 18.4 1.0 N A:TYR365 4.4 19.1 1.0 O A:ASP364 4.5 21.2 1.0 C A:TYR365 4.6 17.7 1.0 N A:PRO366 4.8 19.1 1.0 CD A:PRO366 4.9 19.1 1.0 CA A:ASP364 5.0 20.3 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Ceftobiprole


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 Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Ceftobiprole within 5.0Å range: probe atom residue distance (Å) B Occ B:Na405 b:10.2 occ:1.00 O B:HOH518 2.1 21.6 1.0 O B:HOH700 2.1 36.8 1.0 O B:HOH701 2.1 28.5 1.0 O B:HOH612 2.1 36.8 1.0 OD1 B:ASP313 2.1 24.0 1.0 O B:HOH758 2.3 31.5 1.0 CG B:ASP313 3.1 23.1 1.0 OD2 B:ASP313 3.4 23.5 1.0 OE1 B:GLU309 3.9 24.8 1.0 O B:HOH697 4.2 18.2 1.0 O B:HOH635 4.2 37.1 1.0 O B:GLU309 4.3 15.8 1.0 CB B:ASP313 4.4 20.1 1.0 N B:ASP313 4.6 14.7 1.0 CA B:ASP313 4.6 14.7 1.0 NH1 B:ARG276 4.8 15.0 1.0 C B:PHE312 4.9 18.2 1.0 CB B:PHE312 4.9 13.4 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Ceftobiprole within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:18.6 occ:1.00 OD2 B:ASP364 2.0 34.6 1.0 O B:HOH760 2.1 24.6 1.0 O B:HOH759 2.3 22.2 1.0 CG B:ASP364 2.9 28.1 1.0 OD1 B:ASP364 3.2 28.9 1.0 O B:HOH638 4.1 29.4 1.0 CA B:TYR365 4.3 15.9 1.0 CB B:ASP364 4.3 18.8 1.0 N B:TYR365 4.4 17.0 1.0 CE B:LYS353 4.4 38.9 1.0 C B:ASP364 4.5 21.3 1.0 C B:TYR365 4.5 16.7 1.0 O B:ASP364 4.6 19.7 1.0 N B:PRO366 4.8 17.5 1.0 CD B:PRO366 4.9 19.7 1.0 O B:TYR365 5.0 16.3 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