Zinc 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
Sodium	(Na)	4 atoms

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4;

Zinc 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 Zinc with other atoms in the Zn 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:Zn403 b:25.2 occ:0.42 OE2 A:GLU357 2.0 35.6 1.0 CD A:GLU357 2.9 31.1 1.0 OE1 A:GLU357 3.2 36.6 1.0 O A:HOH743 3.5 28.6 1.0 CE1 A:HIS362 3.8 22.6 1.0 NE2 A:HIS362 4.1 18.7 1.0 O A:HOH651 4.3 31.2 1.0 CG A:GLU357 4.3 30.2 1.0 ND1 A:HIS362 4.8 21.4 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn404 b:25.2 occ:0.52 NE2 A:HIS382 1.8 49.6 1.0 OE2 A:GLU336 2.3 60.6 1.0 CE1 A:HIS382 2.7 49.2 1.0 CD2 A:HIS382 3.0 45.8 1.0 ZN A:ZN405 3.3 55.3 0.6 CD A:GLU336 3.3 56.4 1.0 CD2 A:TYR334 3.6 61.8 1.0 OE1 A:GLU336 3.8 59.8 1.0 ND1 A:HIS382 3.9 48.6 1.0 CG A:TYR334 4.0 60.0 1.0 CG A:HIS382 4.0 45.1 1.0 CB A:TYR334 4.2 50.5 1.0 CE2 A:TYR334 4.2 64.1 1.0 CG A:GLU336 4.5 47.6 1.0 CD1 A:TYR334 4.9 65.6 1.0

Zinc 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 Zinc with other atoms in the Zn 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 A:Zn405 b:55.3 occ:0.63 OE1 A:GLU336 2.7 59.8 1.0 OE2 A:GLU336 2.9 60.6 1.0 CD A:GLU336 3.1 56.4 1.0 ZN A:ZN404 3.3 25.2 0.5 CG A:GLU336 4.6 47.6 1.0 CE2 A:TYR334 4.8 64.1 1.0 NE2 A:HIS382 4.9 49.6 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn403 b:21.1 occ:0.35 OE2 B:GLU357 1.9 34.1 1.0 O B:HOH757 2.4 29.4 1.0 CD B:GLU357 2.5 29.6 1.0 OE1 B:GLU357 2.5 29.7 1.0 O B:HOH772 3.9 34.4 1.0 CG B:GLU357 3.9 27.4 1.0 O B:HOH664 4.3 34.2 1.0 CE1 B:HIS362 4.6 20.6 1.0 CB B:GLU357 4.9 25.3 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