Zinc in PDB 5ty7: Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Nafcillin

The structure of Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Nafcillin, PDB code: 5ty7 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)	55.59 / 1.89
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.323, 92.231, 79.061, 90.00, 98.94, 90.00
R / Rfree (%)	18.5 / 22.2

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

Sodium

(Na)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) in Complex with Nafcillin (pdb code 5ty7). 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 Nafcillin, PDB code: 5ty7:
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 Nafcillin


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 Nafcillin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:43.5 occ:0.53 NE2 A:HIS382 2.1 87.0 1.0 OE2 A:GLU336 2.3 77.7 1.0 CE1 A:HIS382 2.8 89.6 1.0 CD2 A:HIS382 3.3 84.9 1.0 ZN A:ZN404 3.3 73.5 0.7 CD A:GLU336 3.5 72.9 1.0 CD1 A:TYR334 3.6 0.9 1.0 ND1 A:HIS382 4.0 88.5 1.0 CG A:TYR334 4.1 0.3 1.0 CE1 A:TYR334 4.1 0.2 1.0 OE1 A:GLU336 4.2 79.0 1.0 CG A:HIS382 4.3 86.0 1.0 CB A:TYR334 4.4 81.3 1.0 CG A:GLU336 4.5 58.7 1.0 CD2 A:TYR334 4.9 0.7 1.0 CZ A:TYR334 4.9 0.4 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 Nafcillin


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 Nafcillin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:32.5 occ:0.43 OE2 A:GLU357 2.0 44.1 1.0 CD A:GLU357 2.9 35.1 1.0 O A:HOH649 3.0 33.4 1.0 OE1 A:GLU357 3.1 41.4 1.0 CE1 A:HIS362 3.9 35.2 1.0 O A:HOH574 4.2 55.0 1.0 CG A:GLU357 4.2 37.8 1.0 NE2 A:HIS362 4.3 31.1 1.0 O A:HOH656 4.8 50.5 1.0 ND1 A:HIS362 4.9 31.2 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 Nafcillin


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 Nafcillin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:73.5 occ:0.65 OE1 A:GLU336 2.5 79.0 1.0 OE2 A:GLU336 2.6 77.7 1.0 CD A:GLU336 2.9 72.9 1.0 ZN A:ZN402 3.3 43.5 0.5 CG A:GLU336 4.4 58.7 1.0 CE1 A:TYR334 5.0 0.2 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 Nafcillin


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 Nafcillin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:36.0 occ:0.45 OE2 B:GLU357 2.0 43.3 1.0 CD B:GLU357 2.9 37.0 1.0 O B:HOH676 3.1 36.3 1.0 OE1 B:GLU357 3.2 39.1 1.0 CE1 B:HIS362 3.9 28.0 1.0 O B:HOH562 4.0 42.5 1.0 CG B:GLU357 4.3 33.6 1.0 NE2 B:HIS362 4.3 29.6 1.0 ND1 B:HIS362 4.9 29.1 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