Zinc in PDB 4lxc: The Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans

All present enzymatic activity of The Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans:
3.4.24.75;

The structure of The Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans, PDB code: 4lxc 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)	47.67 / 3.50
Space group	P 43 3 2
Cell size a, b, c (Å), α, β, γ (°)	282.013, 282.013, 282.013, 90.00, 90.00, 90.00
R / Rfree (%)	26.8 / 28.7

The binding sites of Zinc atom in the The Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans (pdb code 4lxc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans, PDB code: 4lxc:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the The Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:36.3 occ:1.00 O1 A:SO4602 1.8 47.4 1.0 ND1 A:HIS362 2.1 33.0 1.0 OD1 A:ASP283 2.1 33.6 1.0 NE2 A:HIS279 2.3 36.9 1.0 OD2 A:ASP283 2.5 38.3 1.0 O3 A:SO4602 2.6 47.4 1.0 CG A:ASP283 2.6 35.5 1.0 S A:SO4602 2.7 47.4 1.0 CE1 A:HIS362 2.9 33.4 1.0 CG A:HIS362 3.1 31.6 1.0 CD2 A:HIS279 3.2 39.1 1.0 CE1 A:HIS279 3.3 36.5 1.0 CB A:HIS362 3.5 31.4 1.0 O2 A:SO4602 3.7 47.4 1.0 O4 A:SO4602 3.8 47.4 1.0 NE2 A:HIS360 3.9 38.8 1.0 NE2 A:HIS362 4.1 32.3 1.0 CB A:ASP283 4.1 35.2 1.0 CD2 A:HIS362 4.1 31.2 1.0 NE2 A:HIS329 4.2 39.1 1.0 CG A:HIS279 4.4 40.0 1.0 ND1 A:HIS279 4.4 38.4 1.0 CD2 A:HIS360 4.5 36.6 1.0 CA A:HIS362 4.5 29.4 1.0 CD2 A:HIS329 4.7 37.9 1.0 CA A:ASP283 4.8 32.5 1.0 N A:ASP283 4.9 32.1 1.0 CE1 A:HIS360 4.9 42.2 1.0

Zinc binding site 2 out of 4 in the The Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:19.2 occ:1.00 NE2 B:HIS279 2.0 20.7 1.0 OD1 B:ASP283 2.0 19.2 1.0 ND1 B:HIS362 2.1 17.1 1.0 CG B:ASP283 2.8 21.0 1.0 OD2 B:ASP283 2.9 22.7 1.0 CE1 B:HIS362 2.9 17.3 1.0 CD2 B:HIS279 2.9 22.3 1.0 CG B:HIS362 3.1 15.8 1.0 CE1 B:HIS279 3.1 20.8 1.0 CB B:HIS362 3.5 15.8 1.0 NE2 B:HIS360 4.0 20.6 1.0 NE2 B:HIS362 4.0 16.2 1.0 CD2 B:HIS362 4.1 15.3 1.0 CG B:HIS279 4.1 23.4 1.0 ND1 B:HIS279 4.1 22.4 1.0 CB B:ASP283 4.3 22.0 1.0 NE2 B:HIS329 4.4 18.3 1.0 CD2 B:HIS360 4.5 20.4 1.0 CA B:HIS362 4.6 15.6 1.0 CA B:ASP283 4.9 20.8 1.0 OH B:TYR270 5.0 26.5 1.0

Zinc binding site 3 out of 4 in the The Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn601 b:62.5 occ:1.00 NE2 C:HIS279 2.0 70.0 1.0 OD1 C:ASP283 2.1 63.7 1.0 ND1 C:HIS362 2.1 58.2 1.0 CD2 C:HIS279 2.6 74.1 1.0 CG C:ASP283 2.9 68.1 1.0 CE1 C:HIS362 2.9 60.1 1.0 OD2 C:ASP283 3.1 71.7 1.0 CG C:HIS362 3.1 53.1 1.0 CE1 C:HIS279 3.2 73.1 1.0 CB C:HIS362 3.5 50.7 1.0 NE2 C:HIS360 3.9 57.1 1.0 CG C:HIS279 3.9 79.8 1.0 NE2 C:HIS362 4.0 56.2 1.0 CD2 C:HIS362 4.1 51.9 1.0 ND1 C:HIS279 4.1 79.0 1.0 CB C:ASP283 4.4 70.3 1.0 NE2 C:HIS329 4.5 48.7 1.0 CA C:HIS362 4.6 50.9 1.0 CD2 C:HIS360 4.6 57.8 1.0 CA C:ASP283 4.9 68.2 1.0 CE1 C:HIS360 5.0 57.0 1.0 N C:ASP283 5.0 71.3 1.0

Zinc binding site 4 out of 4 in the The Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:16.5 occ:1.00 OD1 D:ASP283 2.0 15.7 1.0 NE2 D:HIS279 2.0 17.3 1.0 ND1 D:HIS362 2.1 15.4 1.0 CG D:ASP283 2.7 16.5 1.0 OD2 D:ASP283 2.8 17.6 1.0 CE1 D:HIS362 2.9 15.9 1.0 CD2 D:HIS279 3.0 18.6 1.0 CE1 D:HIS279 3.1 17.2 1.0 CG D:HIS362 3.2 14.8 1.0 CB D:HIS362 3.6 14.7 1.0 NE2 D:HIS360 3.9 17.3 1.0 NE2 D:HIS362 4.1 15.8 1.0 CG D:HIS279 4.1 19.4 1.0 ND1 D:HIS279 4.2 18.5 1.0 CD2 D:HIS362 4.2 15.1 1.0 CB D:ASP283 4.2 16.8 1.0 NE2 D:HIS329 4.4 17.7 1.0 CD2 D:HIS360 4.5 16.8 1.0 CA D:HIS362 4.6 14.3 1.0 CA D:ASP283 4.9 16.0 1.0 CE1 D:HIS360 5.0 18.8 1.0 CD2 D:HIS329 5.0 17.3 1.0 N D:ASP283 5.0 16.1 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