Zinc in PDB 6c39: Apo Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4)

The structure of Apo Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4), PDB code: 6c39 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)	46.20 / 1.69
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.358, 92.403, 79.230, 90.00, 99.23, 90.00
R / Rfree (%)	16.1 / 19.6

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

Sodium

(Na)

2 atoms

The binding sites of Zinc atom in the Apo Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) (pdb code 6c39). 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 Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4), PDB code: 6c39:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Apo Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4)


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 Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:37.0 occ:0.44 OE2 A:GLU357 1.9 31.8 1.0 O A:HOH761 2.5 36.6 1.0 CD A:GLU357 2.6 26.9 1.0 OE1 A:GLU357 2.8 34.9 1.0 HE1 A:HIS362 3.5 35.1 1.0 CG A:GLU357 4.1 30.6 1.0 CE1 A:HIS362 4.2 29.2 1.0 O A:HOH614 4.2 34.1 1.0 O A:HOH775 4.4 54.5 1.0 HG2 A:GLU357 4.4 36.8 1.0 HG3 A:GLU357 4.4 36.8 1.0 NE2 A:HIS362 4.7 22.6 1.0

Zinc binding site 2 out of 5 in the Apo Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4)


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 Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:29.1 occ:0.51 NE2 A:HIS382 1.9 53.0 1.0 OE2 A:GLU336 2.2 60.2 1.0 CE1 A:HIS382 2.9 46.3 1.0 CD2 A:HIS382 2.9 40.3 1.0 HE1 A:HIS382 3.1 55.6 1.0 HD2 A:HIS382 3.1 48.3 1.0 CD A:GLU336 3.4 54.7 1.0 HB2 A:TYR334 3.7 49.4 1.0 HB3 A:TYR334 3.9 49.4 1.0 OE1 A:GLU336 3.9 55.3 1.0 ND1 A:HIS382 4.0 70.7 1.0 CG A:HIS382 4.1 58.7 1.0 CB A:TYR334 4.2 41.3 1.0 HG2 A:GLU336 4.4 62.6 1.0 CG A:GLU336 4.5 52.2 1.0 HD1 A:HIS382 4.8 84.9 1.0 HG3 A:GLU336 4.9 62.6 1.0 CG A:TYR334 4.9 65.4 1.0

Zinc binding site 3 out of 5 in the Apo Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4)


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 Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:54.6 occ:0.63 OE1 B:GLU336 2.4 83.1 1.0 HD2 B:HIS382 3.0 98.9 1.0 CD B:GLU336 3.1 58.7 1.0 HE2 B:HIS382 3.4 91.5 1.0 OE2 B:GLU336 3.6 63.0 1.0 CD2 B:HIS382 3.7 82.4 1.0 HG2 B:GLU336 3.7 65.1 1.0 NE2 B:HIS382 3.8 76.3 1.0 CG B:GLU336 4.0 54.2 1.0 OE1 B:GLU380 4.1 66.8 1.0 OE2 B:GLU380 4.1 88.9 1.0 HB3 B:GLU380 4.1 37.4 1.0 HB2 B:GLU380 4.2 37.4 1.0 CD B:GLU380 4.2 71.9 1.0 HB2 B:GLU336 4.3 40.7 1.0 CB B:GLU380 4.6 31.2 1.0 CB B:GLU336 4.7 33.9 1.0 HG3 B:GLU336 4.8 65.1 1.0 CG B:HIS382 5.0 73.4 1.0

Zinc binding site 4 out of 5 in the Apo Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4)


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 Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:17.7 occ:0.54 O B:HOH701 2.0 27.4 1.0 O B:HOH516 2.0 21.1 1.0 O B:HOH711 2.1 28.4 1.0 OD1 B:ASP313 2.1 28.2 1.0 O B:HOH769 2.1 30.6 1.0 O B:HOH608 2.3 29.2 1.0 CG B:ASP313 3.1 33.5 1.0 OD2 B:ASP313 3.4 27.7 1.0 OE1 B:GLU309 3.9 27.5 1.0 O B:HOH710 4.0 19.5 1.0 O B:HOH840 4.0 39.9 1.0 O B:HOH793 4.1 61.3 1.0 O B:HOH660 4.2 38.2 1.0 HH12 B:ARG276 4.2 21.0 1.0 HA B:ASP313 4.3 20.6 1.0 O B:GLU309 4.3 18.1 1.0 O B:HOH778 4.3 38.9 1.0 HB3 B:PHE312 4.4 23.0 1.0 CB B:ASP313 4.4 21.1 1.0 HB3 B:GLU309 4.4 19.6 1.0 HH11 B:ARG276 4.5 21.0 1.0 HB2 B:PHE312 4.5 23.0 1.0 N B:ASP313 4.6 15.6 1.0 CA B:ASP313 4.7 17.2 1.0 NH1 B:ARG276 4.7 17.5 1.0 H B:ASP313 4.8 18.7 1.0 C B:PHE312 4.8 23.4 1.0 HA B:GLU309 4.8 17.7 1.0 CB B:PHE312 4.9 19.1 1.0 O B:PHE312 4.9 21.0 1.0 HB2 B:ASP313 5.0 25.4 1.0 HB3 B:ASP313 5.0 25.4 1.0

Zinc binding site 5 out of 5 in the Apo Crystal Structure of Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4)


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 Wild-Type S. Aureus Penicillin Binding Protein 4 (PBP4) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:26.1 occ:0.38 OE2 B:GLU357 1.9 31.0 1.0 O B:HOH779 2.1 35.0 1.0 CD B:GLU357 2.9 29.0 1.0 HE1 B:HIS362 3.2 33.9 1.0 OE1 B:GLU357 3.2 29.7 1.0 CE1 B:HIS362 3.7 28.3 1.0 NE2 B:HIS362 4.2 21.8 1.0 O B:HOH683 4.2 34.9 1.0 CG B:GLU357 4.3 34.0 1.0 HG2 B:GLU357 4.4 40.9 1.0 HG3 B:GLU357 4.6 40.9 1.0 ND1 B:HIS362 4.7 26.6 1.0 O B:HOH786 4.9 42.7 1.0 HG11 B:VAL355 4.9 33.5 1.0 O B:HOH783 4.9 44.0 1.0 HD1 B:HIS362 5.0 31.9 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