Zinc in PDB 4qpb: Catalytic Domain of the Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans Crystallized in the Absence of Phosphate

All present enzymatic activity of Catalytic Domain of the Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans Crystallized in the Absence of Phosphate:
3.4.24.75;

The structure of Catalytic Domain of the Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans Crystallized in the Absence of Phosphate, PDB code: 4qpb was solved by I.Sabala, E.Jagielska, P.T.Bardelang, H.Czapinska, S.O.Dahms, J.A.Sharpe, R.James, M.E.Than, N.R.Thomas, M.Bochtler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.99 / 1.78
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	34.289, 107.318, 34.307, 90.00, 97.63, 90.00
R / Rfree (%)	21 / 24.4

The binding sites of Zinc atom in the Catalytic Domain of the Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans Crystallized in the Absence of Phosphate (pdb code 4qpb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Catalytic Domain of the Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans Crystallized in the Absence of Phosphate, PDB code: 4qpb:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Catalytic Domain of the Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans Crystallized in the Absence of Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Catalytic Domain of the Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans Crystallized in the Absence of Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:14.3 occ:1.00 OD1 A:ASP283 2.0 7.7 1.0 ND1 A:HIS362 2.1 5.6 1.0 O A:HOH598 2.2 17.4 1.0 O A:HOH595 2.2 14.0 1.0 NE2 A:HIS279 2.2 6.3 1.0 O A:HOH530 2.7 22.9 1.0 CG A:ASP283 2.9 8.3 1.0 CE1 A:HIS362 3.0 12.3 1.0 OD2 A:ASP283 3.0 9.3 1.0 CG A:HIS362 3.1 6.7 1.0 CE1 A:HIS279 3.2 7.7 1.0 CD2 A:HIS279 3.2 7.5 1.0 CB A:HIS362 3.5 6.2 1.0 NE2 A:HIS360 4.1 9.2 1.0 NE2 A:HIS362 4.1 9.2 1.0 CD2 A:HIS362 4.2 8.7 1.0 O A:HOH599 4.3 20.6 1.0 ND1 A:HIS279 4.3 9.2 1.0 CB A:ASP283 4.3 10.3 1.0 CG A:HIS279 4.4 8.5 1.0 CA A:HIS362 4.4 6.6 1.0 CD2 A:HIS360 4.6 6.9 1.0 N A:ASP283 4.8 9.5 1.0 CA A:ASP283 4.8 9.4 1.0 NE2 A:HIS329 4.8 11.8 1.0 O A:HOH502 4.8 10.7 1.0 C A:VAL282 4.9 9.6 1.0

Zinc binding site 2 out of 2 in the Catalytic Domain of the Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans Crystallized in the Absence of Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Catalytic Domain of the Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans Crystallized in the Absence of Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:14.1 occ:1.00 OD1 B:ASP283 2.1 10.4 1.0 ND1 B:HIS362 2.1 10.3 1.0 NE2 B:HIS279 2.3 4.0 1.0 O B:HOH614 2.3 13.7 1.0 O B:HOH616 2.4 20.9 1.0 CG B:ASP283 2.8 8.9 1.0 OD2 B:ASP283 2.9 8.6 1.0 CE1 B:HIS362 3.1 11.5 1.0 CG B:HIS362 3.2 7.8 1.0 O B:HOH518 3.2 27.3 1.0 CE1 B:HIS279 3.2 10.3 1.0 CD2 B:HIS279 3.3 10.9 1.0 CB B:HIS362 3.5 6.3 1.0 NE2 B:HIS360 4.1 10.8 1.0 NE2 B:HIS362 4.2 7.3 1.0 O B:HOH590 4.2 26.4 1.0 CD2 B:HIS362 4.3 9.2 1.0 ND1 B:HIS279 4.3 10.5 1.0 CB B:ASP283 4.3 10.4 1.0 CA B:HIS362 4.4 7.4 1.0 CG B:HIS279 4.4 8.8 1.0 CD2 B:HIS360 4.6 14.4 1.0 NE2 B:HIS329 4.7 10.4 1.0 N B:ASP283 4.8 11.1 1.0 CA B:ASP283 4.8 9.6 1.0 O B:HOH503 4.8 6.9 1.0 C B:VAL282 5.0 10.0 1.0

I.Sabala, E.Jagielska, P.T.Bardelang, H.Czapinska, S.O.Dahms, J.A.Sharpe, R.James, M.E.Than, N.R.Thomas, M.Bochtler. Crystal Structure of the Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans. Febs J. V. 281 4112 2014.
ISSN: ISSN 1742-464X
PubMed: 25039253
DOI: 10.1111/FEBS.12929