Zinc 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
Sodium	(Na)	3 atoms

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

Zinc binding site 1 out of 4 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 Zinc with other atoms in the Zn 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:Zn402 b:20.7 occ:0.38 O A:HOH782 1.6 28.4 1.0 OE2 A:GLU357 2.0 31.7 1.0 O A:HOH846 2.7 28.6 1.0 CD A:GLU357 2.9 28.5 1.0 OE1 A:GLU357 3.1 28.4 1.0 CE1 A:HIS362 3.8 18.8 1.0 NE2 A:HIS362 4.2 18.1 1.0 CG A:GLU357 4.3 28.2 1.0 O A:HOH711 4.3 28.5 1.0 ND1 A:HIS362 4.8 18.7 1.0

Zinc binding site 2 out of 4 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 Zinc with other atoms in the Zn 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:Zn402 b:25.9 occ:0.45 NE2 B:HIS382 1.6 61.4 1.0 OE2 B:GLU336 2.2 56.1 1.0 OE1 B:GLU336 2.4 57.2 1.0 CE1 B:HIS382 2.5 63.0 1.0 CD B:GLU336 2.6 53.8 1.0 CD2 B:HIS382 2.6 63.3 1.0 ZN B:ZN404 3.4 34.1 0.4 ND1 B:HIS382 3.6 61.1 1.0 CG B:HIS382 3.7 57.7 1.0 CG B:GLU336 4.1 43.7 1.0 CD1 B:TYR334 4.4 38.4 1.0 CE1 B:TYR334 4.4 43.0 1.0 CB B:GLU336 4.8 33.7 1.0

Zinc binding site 3 out of 4 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 Zinc with other atoms in the Zn 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:Zn403 b:21.6 occ:0.38 OE2 B:GLU357 1.9 32.4 1.0 O B:HOH831 2.3 24.8 1.0 CD B:GLU357 2.5 26.7 1.0 OE1 B:GLU357 2.5 27.9 1.0 CG B:GLU357 4.0 24.4 1.0 O B:HOH848 4.0 38.2 1.0 O B:HOH703 4.3 31.3 1.0 CE1 B:HIS362 4.5 19.1 1.0 CB B:GLU357 5.0 25.5 1.0

Zinc binding site 4 out of 4 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 Zinc with other atoms in the Zn binding site number 4 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:Zn404 b:34.1 occ:0.41 CE1 B:HIS382 2.5 63.0 1.0 OE1 B:GLU336 2.5 57.2 1.0 OE1 B:GLU380 3.0 79.8 1.0 CD B:GLU336 3.3 53.8 1.0 NE2 B:HIS382 3.3 61.4 1.0 ZN B:ZN402 3.4 25.9 0.5 ND1 B:HIS382 3.5 61.1 1.0 OE2 B:GLU336 3.9 56.1 1.0 CG B:GLU336 4.1 43.7 1.0 CD B:GLU380 4.3 70.1 1.0 CD2 B:HIS382 4.5 63.3 1.0 CG B:HIS382 4.6 57.7 1.0 CB B:GLU380 4.8 32.9 1.0 CB B:GLU336 4.8 33.7 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