Sodium in PDB 5tx9: Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Ceftobiprole

The structure of Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Ceftobiprole, PDB code: 5tx9 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)	32.84 / 1.68
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.882, 92.252, 79.381, 90.00, 100.22, 90.00
R / Rfree (%)	20.8 / 24.1

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

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 Ceftobiprole (pdb code 5tx9). 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 S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Ceftobiprole, PDB code: 5tx9:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) 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 S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Ceftobiprole within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:26.9 occ:1.00 OD2 A:ASP364 2.0 26.0 1.0 O A:HOH767 2.1 27.2 1.0 CG A:ASP364 3.0 20.4 1.0 OD1 A:ASP364 3.3 20.5 1.0 O A:HOH644 3.8 29.7 1.0 CE A:LYS353 4.3 34.4 1.0 CB A:ASP364 4.3 21.4 1.0 CA A:TYR365 4.4 14.7 1.0 C A:ASP364 4.5 17.3 1.0 N A:TYR365 4.5 14.0 1.0 O A:ASP364 4.6 17.7 1.0 C A:TYR365 4.7 14.3 1.0 CD A:LYS353 4.9 34.0 1.0 N A:PRO366 4.9 15.9 1.0 CD A:PRO366 4.9 17.0 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) 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 S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Ceftobiprole within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:51.6 occ:1.00 OD1 A:ASP313 2.3 27.3 1.0 O A:HOH705 2.6 59.4 1.0 CG A:ASP313 3.3 25.2 1.0 OE1 A:GLU309 3.6 18.4 1.0 OD2 A:ASP313 3.7 23.7 1.0 O A:HOH740 3.9 20.3 1.0 O A:GLU309 4.2 16.6 1.0 N A:ASP313 4.5 15.1 1.0 CB A:ASP313 4.6 21.7 1.0 NH1 A:ARG276 4.6 13.4 1.0 CA A:ASP313 4.7 18.7 1.0 CB A:PHE312 4.7 17.3 1.0 CD A:GLU309 4.8 18.1 1.0 C A:PHE312 4.8 16.8 1.0 O A:PHE312 5.0 19.3 1.0 O A:HOH688 5.0 32.8 1.0 CB A:GLU309 5.0 17.2 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) 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 S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Ceftobiprole within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:19.6 occ:1.00 OD2 B:ASP364 2.0 23.2 1.0 O B:HOH788 2.1 21.0 1.0 O B:HOH778 2.2 44.6 1.0 CG B:ASP364 2.9 17.6 1.0 OD1 B:ASP364 3.1 18.6 1.0 O B:HOH605 3.9 28.4 1.0 CB B:ASP364 4.3 15.8 1.0 CA B:TYR365 4.3 16.8 1.0 N B:TYR365 4.3 16.9 1.0 C B:ASP364 4.4 16.3 1.0 CE B:LYS353 4.5 35.7 1.0 C B:TYR365 4.6 15.2 1.0 O B:ASP364 4.6 17.6 1.0 N B:PRO366 4.8 18.5 1.0 O B:HOH713 4.9 41.5 1.0 CD B:PRO366 4.9 19.2 1.0 CA B:ASP364 4.9 15.1 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) 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 S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Ceftobiprole within 5.0Å range: probe atom residue distance (Å) B Occ B:Na405 b:16.8 occ:1.00 O B:HOH545 2.1 20.5 1.0 OD1 B:ASP313 2.2 21.1 1.0 O B:HOH615 2.2 60.5 1.0 O B:HOH789 2.3 51.5 1.0 CG B:ASP313 3.2 21.1 1.0 OD2 B:ASP313 3.4 20.6 1.0 OE1 B:GLU309 3.7 17.7 1.0 O B:HOH715 4.1 16.3 1.0 O B:GLU309 4.4 15.6 1.0 CB B:ASP313 4.5 19.9 1.0 N B:ASP313 4.7 15.4 1.0 NH1 B:ARG276 4.8 15.3 1.0 CA B:ASP313 4.8 16.6 1.0 CD B:GLU309 4.9 16.6 1.0 C B:PHE312 5.0 17.6 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