Zinc in PDB 5ty2: Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Nafcillin

The structure of Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Nafcillin, PDB code: 5ty2 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)	46.12 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.850, 92.244, 78.952, 90.00, 98.43, 90.00
R / Rfree (%)	16.9 / 20.5

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

Chlorine	(Cl)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Zinc atom in the Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Nafcillin (pdb code 5ty2). 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 Nafcillin, PDB code: 5ty2:
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 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 S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Nafcillin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:29.2 occ:0.42 OE2 A:GLU357 1.9 32.8 1.0 CD A:GLU357 2.8 27.9 1.0 OE1 A:GLU357 3.1 34.9 1.0 O A:HOH745 3.2 30.5 1.0 CE1 A:HIS362 3.8 31.1 1.0 CG A:GLU357 4.2 28.1 1.0 NE2 A:HIS362 4.2 23.5 1.0 O A:HOH664 4.3 43.5 1.0 ND1 A:HIS362 4.7 27.7 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 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 S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Nafcillin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:73.7 occ:0.70 OE1 A:GLU336 2.5 88.6 1.0 O A:HOH747 3.0 57.1 1.0 OE2 A:GLU336 3.1 93.0 1.0 CD A:GLU336 3.1 87.3 1.0 ZN A:ZN404 3.8 55.7 0.6 NE2 A:HIS382 4.3 0.8 1.0 CG A:GLU336 4.5 75.2 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 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 S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Nafcillin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:55.7 occ:0.60 NE2 A:HIS382 1.8 0.8 1.0 CD2 A:HIS382 1.9 0.7 1.0 OE2 A:GLU336 2.5 93.0 1.0 CE1 A:HIS382 3.1 99.7 1.0 CG A:HIS382 3.2 92.3 1.0 CD2 A:TYR334 3.6 77.5 1.0 CD A:GLU336 3.6 87.3 1.0 ND1 A:HIS382 3.7 95.3 1.0 ZN A:ZN403 3.8 73.7 0.7 CE2 A:TYR334 4.0 78.8 1.0 CG A:TYR334 4.2 77.4 1.0 OE1 A:GLU336 4.4 88.6 1.0 CB A:HIS382 4.4 80.2 1.0 CB A:TYR334 4.6 67.5 1.0 CG A:GLU336 4.6 75.2 1.0 O A:HOH747 4.8 57.1 1.0 CZ A:TYR334 4.9 77.8 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 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 S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) in Complex with Nafcillin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:28.5 occ:0.44 OE2 B:GLU357 1.9 33.1 1.0 O B:HOH762 2.2 33.3 1.0 CD B:GLU357 2.9 32.2 1.0 OE1 B:GLU357 3.2 29.6 1.0 CE1 B:HIS362 3.8 23.8 1.0 NE2 B:HIS362 4.2 23.6 1.0 O B:HOH683 4.2 31.6 1.0 CG B:GLU357 4.3 30.5 1.0 ND1 B:HIS362 4.8 25.5 1.0 O B:HOH775 4.9 42.7 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