Zinc in PDB 6c3k: Apo Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R)

The structure of Apo Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R), PDB code: 6c3k 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 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.868, 92.561, 79.189, 90.00, 99.30, 90.00
R / Rfree (%)	17.6 / 20.4

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

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

The binding sites of Zinc atom in the Apo Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) (pdb code 6c3k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Apo Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R), PDB code: 6c3k:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Apo Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Apo Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:31.3 occ:0.47 NE2 A:HIS382 1.9 70.3 1.0 OE2 A:GLU336 2.5 67.0 1.0 CE1 A:HIS382 2.6 70.5 1.0 HE1 A:HIS382 2.6 84.6 1.0 CD2 A:HIS382 3.1 67.2 1.0 HD2 A:TYR334 3.2 94.7 1.0 ZN A:ZN403 3.2 44.2 0.5 HD2 A:HIS382 3.5 80.6 1.0 CD2 A:TYR334 3.6 78.8 1.0 HB3 A:TYR334 3.6 75.7 1.0 CD A:GLU336 3.6 67.0 1.0 ND1 A:HIS382 3.8 70.0 1.0 CG A:TYR334 4.1 77.6 1.0 CG A:HIS382 4.1 67.7 1.0 CE2 A:TYR334 4.2 81.6 1.0 HE2 A:TYR334 4.2 98.0 1.0 CB A:TYR334 4.3 63.0 1.0 OE1 A:GLU336 4.3 67.0 1.0 HG2 A:GLU336 4.5 76.0 1.0 HD1 A:HIS382 4.5 84.0 1.0 O A:HOH789 4.5 53.3 1.0 HB2 A:TYR334 4.6 75.7 1.0 CG A:GLU336 4.7 63.3 1.0

Zinc binding site 2 out of 5 in the Apo Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Apo Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:24.3 occ:0.34 OE2 A:GLU357 1.8 36.9 1.0 O A:HOH774 2.3 33.9 1.0 CD A:GLU357 2.4 30.6 1.0 OE1 A:GLU357 2.5 32.5 1.0 HE1 A:HIS362 3.8 29.1 1.0 CG A:GLU357 3.9 32.0 1.0 O A:HOH791 4.1 44.7 1.0 HG3 A:GLU357 4.1 38.5 1.0 O A:HOH622 4.2 35.5 1.0 HG2 A:GLU357 4.3 38.5 1.0 CE1 A:HIS362 4.5 24.3 1.0 HB2 A:GLU357 4.8 39.0 1.0 CB A:GLU357 4.9 32.5 1.0 HB3 A:GLU357 5.0 39.0 1.0

Zinc binding site 3 out of 5 in the Apo Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Apo Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:44.2 occ:0.52 O A:HOH789 2.2 53.3 1.0 O A:HOH806 2.6 66.5 1.0 OE2 A:GLU336 2.6 67.0 1.0 OE1 A:GLU336 2.7 67.0 1.0 CD A:GLU336 3.0 67.0 1.0 ZN A:ZN401 3.2 31.3 0.5 HE2 A:TYR334 4.2 98.0 1.0 CG A:GLU336 4.4 63.3 1.0 HG3 A:GLU336 4.7 76.0 1.0 CE2 A:TYR334 4.7 81.6 1.0 HD2 A:TYR334 4.7 94.7 1.0 NE2 A:HIS382 4.8 70.3 1.0 HG2 A:GLU336 4.9 76.0 1.0 HB3 A:GLU336 5.0 63.9 1.0 CD2 A:TYR334 5.0 78.8 1.0

Zinc binding site 4 out of 5 in the Apo Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Apo Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:22.8 occ:0.31 OE2 B:GLU357 1.9 34.9 1.0 CD B:GLU357 2.5 28.0 1.0 OE1 B:GLU357 2.5 30.2 1.0 O B:HOH802 3.2 31.6 1.0 HE1 B:HIS362 3.8 26.8 1.0 CG B:GLU357 3.9 26.7 1.0 O B:HOH810 4.0 38.4 1.0 HG3 B:GLU357 4.1 32.0 1.0 O B:HOH648 4.2 28.5 1.0 HG2 B:GLU357 4.3 32.0 1.0 CE1 B:HIS362 4.5 22.3 1.0 HB2 B:GLU357 4.9 30.1 1.0 CB B:GLU357 4.9 25.0 1.0 O B:HOH771 4.9 49.7 1.0 HB3 B:GLU357 5.0 30.1 1.0

Zinc binding site 5 out of 5 in the Apo Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Apo Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (E183A, F241R) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:20.4 occ:0.55 O B:HOH517 2.0 25.3 1.0 O B:HOH733 2.1 28.9 1.0 O B:HOH697 2.1 27.5 1.0 O B:HOH789 2.1 30.0 1.0 OD1 B:ASP313 2.1 29.0 1.0 O B:HOH601 2.2 39.5 1.0 CG B:ASP313 3.1 26.3 1.0 OD2 B:ASP313 3.4 24.7 1.0 OE1 B:GLU309 3.9 23.2 1.0 O B:HOH675 4.0 40.7 1.0 O B:HOH741 4.1 21.2 1.0 HH12 B:ARG276 4.2 23.8 1.0 HA B:ASP313 4.3 20.9 1.0 O B:GLU309 4.3 19.5 1.0 HB3 B:PHE312 4.4 21.4 1.0 CB B:ASP313 4.4 20.9 1.0 HH11 B:ARG276 4.5 23.8 1.0 HB3 B:GLU309 4.5 22.1 1.0 HB2 B:PHE312 4.5 21.4 1.0 N B:ASP313 4.6 18.8 1.0 O B:HOH817 4.7 40.4 1.0 NH1 B:ARG276 4.7 19.8 1.0 CA B:ASP313 4.7 17.5 1.0 H B:ASP313 4.8 22.6 1.0 C B:PHE312 4.8 20.4 1.0 HA B:GLU309 4.9 20.0 1.0 CB B:PHE312 4.9 17.8 1.0 O B:PHE312 4.9 22.8 1.0 HB3 B:ASP313 5.0 25.1 1.0 HB2 B:ASP313 5.0 25.1 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 Analyses of Penicillin-Binding Protein 4 (PBP4)-Mediated Antibiotic Resistance Instaphylococcus Aureus. J. Biol. Chem. V. 293 19854 2018.
ISSN: ESSN 1083-351X
PubMed: 30366985
DOI: 10.1074/JBC.RA118.004952