Zinc in PDB 6dz8: Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (S75C)

The structure of Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (S75C), PDB code: 6dz8 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)	29.16 / 1.86
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	104.511, 89.730, 77.489, 90.00, 98.09, 90.00
R / Rfree (%)	17.5 / 21.7

The binding sites of Zinc atom in the Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (S75C) (pdb code 6dz8). 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 (S75C), PDB code: 6dz8:
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 (S75C)


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 (S75C) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:65.1 occ:1.00 OE2 A:GLU357 1.7 49.9 1.0 HE2 A:HIS362 1.7 34.0 1.0 NE2 A:HIS362 2.4 28.3 1.0 CD A:GLU357 2.7 46.6 1.0 CE1 A:HIS362 3.2 26.4 1.0 HE1 A:HIS362 3.2 31.6 1.0 O A:HOH619 3.3 52.5 1.0 OE1 A:GLU357 3.3 51.2 1.0 CD2 A:HIS362 3.4 21.6 1.0 HD2 A:HIS362 3.7 25.9 1.0 CG A:GLU357 3.9 39.1 1.0 HG2 A:GLU357 3.9 46.9 1.0 HG11 A:VAL355 4.1 49.3 1.0 HG12 A:VAL355 4.1 49.3 1.0 HG3 A:GLU357 4.2 46.9 1.0 ND1 A:HIS362 4.3 27.1 1.0 CG A:HIS362 4.4 21.0 1.0 HG2 A:PRO376 4.5 31.8 1.0 CG1 A:VAL355 4.5 41.1 1.0 O A:HOH501 4.8 31.0 1.0 HB A:VAL355 4.9 32.8 1.0 HD1 A:HIS362 5.0 32.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (S75C)


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 (S75C) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:52.1 occ:0.36 OE1 A:GLU380 2.0 73.4 1.0 HG2 A:GLU336 2.8 59.4 1.0 CD A:GLU380 3.0 63.9 1.0 HB2 A:GLU380 3.1 46.1 1.0 HB3 A:GLU380 3.2 46.1 1.0 CB A:GLU380 3.5 38.5 1.0 CG A:GLU336 3.5 49.5 1.0 CD A:GLU336 3.6 58.9 1.0 HB2 A:GLU336 3.7 51.6 1.0 CG A:GLU380 3.8 48.7 1.0 OE1 A:GLU336 3.8 60.3 1.0 OE2 A:GLU380 3.9 62.9 1.0 HD2 A:HIS382 3.9 73.7 1.0 CB A:GLU336 4.1 43.0 1.0 OE2 A:GLU336 4.2 65.4 1.0 HG3 A:GLU380 4.3 58.4 1.0 HB3 A:GLU336 4.3 51.6 1.0 HG3 A:GLU336 4.3 59.4 1.0 HG2 A:GLU380 4.5 58.4 1.0 CD2 A:HIS382 4.8 61.4 1.0 CA A:GLU380 4.9 28.8 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (S75C)


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 (S75C) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:36.1 occ:0.57 OE2 B:GLU336 1.9 80.1 1.0 NE2 B:HIS382 2.0 65.0 1.0 CD2 B:HIS382 2.7 58.8 1.0 HD2 B:HIS382 2.7 70.5 1.0 HD1 B:TYR334 3.0 52.8 1.0 CD B:GLU336 3.2 80.0 1.0 CE1 B:HIS382 3.2 65.7 1.0 CD1 B:TYR334 3.4 44.1 1.0 HE1 B:HIS382 3.5 78.9 1.0 HB3 B:TYR334 3.7 78.9 1.0 O B:HOH580 3.8 46.8 1.0 HG2 B:GLU336 3.8 77.7 1.0 CE1 B:TYR334 3.9 73.1 1.0 HE1 B:TYR334 3.9 87.8 1.0 CG B:HIS382 3.9 55.7 1.0 OE1 B:GLU336 4.0 87.3 1.0 CG B:TYR334 4.0 71.0 1.0 CG B:GLU336 4.1 64.7 1.0 ND1 B:HIS382 4.1 62.4 1.0 CB B:TYR334 4.4 65.7 1.0 HG3 B:GLU336 4.5 77.7 1.0 HA B:GLU336 4.7 55.0 1.0 HB2 B:TYR334 4.8 78.9 1.0 CZ B:TYR334 4.9 65.9 1.0 HD1 B:HIS382 4.9 74.9 1.0 CD2 B:TYR334 5.0 66.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of S. Aureus Penicillin Binding Protein 4 (PBP4) Mutant (S75C)


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 (S75C) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:35.1 occ:0.50 OE2 B:GLU357 1.7 48.9 1.0 NE2 B:HIS362 2.3 35.0 1.0 CD B:GLU357 2.8 36.0 1.0 CE1 B:HIS362 3.0 23.9 1.0 HE1 B:HIS362 3.0 28.6 1.0 OE1 B:GLU357 3.3 51.5 1.0 CD2 B:HIS362 3.3 33.7 1.0 O B:HOH651 3.4 48.7 1.0 HD2 B:HIS362 3.6 40.5 1.0 HG2 B:GLU357 3.9 38.4 1.0 HG11 B:VAL355 3.9 37.9 1.0 CG B:GLU357 3.9 32.0 1.0 HG12 B:VAL355 4.0 37.9 1.0 ND1 B:HIS362 4.1 33.4 1.0 HG3 B:GLU357 4.3 38.4 1.0 CG B:HIS362 4.3 28.8 1.0 CG1 B:VAL355 4.4 31.5 1.0 HB B:VAL355 4.6 39.8 1.0 HG2 B:PRO376 4.7 34.4 1.0 O B:HOH524 4.8 38.8 1.0 HD1 B:HIS362 4.9 40.0 1.0

R.Maya-Martinez, J.A.N.Alexander, C.F.Otten, I.Ayala, D.Vollmer, J.Gray, C.M.Bougault, A.Burt, C.Laguri, M.Fonvielle, M.Arthur, N.C.J.Strynadka, W.Vollmer, J.P.Simorre. Recognition of Peptidoglycan Fragments By the Transpeptidase PBP4 Fromstaphylococcus Aureus. Front Microbiol V. 9 3223 2018.
ISSN: ESSN 1664-302X
PubMed: 30713527
DOI: 10.3389/FMICB.2018.03223