Zinc in PDB 5tw8: Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Ceftaroline

The structure of Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Ceftaroline, PDB code: 5tw8 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)	46.08 / 1.72
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.415, 92.165, 79.153, 90.00, 99.23, 90.00
R / Rfree (%)	18.6 / 21.5

The structure of Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Ceftaroline also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Ceftaroline (pdb code 5tw8). 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 Ceftaroline, PDB code: 5tw8:
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 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 Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Ceftaroline within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:27.2 occ:0.34 OE1 A:GLU357 1.9 45.1 1.0 CD A:GLU357 3.0 40.0 1.0 O A:HOH669 3.4 37.0 1.0 OE2 A:GLU357 3.4 43.5 1.0 CE1 A:HIS362 3.8 29.2 1.0 NE2 A:HIS362 4.2 26.1 1.0 CG A:GLU357 4.3 39.5 1.0 O A:HOH684 4.4 39.0 1.0 ND1 A:HIS362 4.7 26.6 1.0 O A:HOH674 5.0 50.9 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 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 Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Ceftaroline within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:32.4 occ:0.37 NE2 A:HIS382 2.0 65.6 1.0 CE1 A:HIS382 2.7 63.3 1.0 OE2 A:GLU336 2.8 76.8 1.0 CD2 A:HIS382 3.2 59.0 1.0 ZN A:ZN404 3.2 74.3 0.8 CD1 A:TYR334 3.7 65.7 1.0 CD A:GLU336 3.8 77.7 1.0 ND1 A:HIS382 3.9 62.5 1.0 CG A:TYR334 4.1 65.1 1.0 CG A:HIS382 4.2 60.5 1.0 CE1 A:TYR334 4.2 63.6 1.0 CB A:TYR334 4.4 54.9 1.0 OE1 A:GLU336 4.4 78.7 1.0 CG A:GLU336 4.7 73.2 1.0 CD2 A:TYR334 5.0 65.8 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 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 Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Ceftaroline within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:74.3 occ:0.75 OE2 A:GLU336 2.4 76.8 1.0 OE1 A:GLU336 2.7 78.7 1.0 CD A:GLU336 2.9 77.7 1.0 ZN A:ZN403 3.2 32.4 0.4 CG A:GLU336 4.4 73.2 1.0 NE2 A:HIS382 4.8 65.6 1.0 CE1 A:TYR334 4.9 63.6 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 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 Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Ceftaroline within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:53.0 occ:0.49 OE1 B:GLU357 1.9 54.0 1.0 CD B:GLU357 2.6 37.6 1.0 O B:HOH694 2.7 37.4 1.0 OE2 B:GLU357 2.8 40.7 1.0 CG B:GLU357 4.1 37.3 1.0 O B:HOH621 4.1 44.7 1.0 O B:HOH701 4.2 45.5 1.0 CE1 B:HIS362 4.2 27.1 1.0 NE2 B:HIS362 4.8 26.0 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