Zinc in PDB 6ksi: Staphylococcus Aureus Lipase - Native

All present enzymatic activity of Staphylococcus Aureus Lipase - Native:
3.1.1.3;

The structure of Staphylococcus Aureus Lipase - Native, PDB code: 6ksi was solved by K.Kitadokoro, M.Tanaka, S.Kamitani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.74 / 2.08
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	129.913, 129.913, 251.224, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 25

The structure of Staphylococcus Aureus Lipase - Native also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Staphylococcus Aureus Lipase - Native (pdb code 6ksi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Staphylococcus Aureus Lipase - Native, PDB code: 6ksi:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Staphylococcus Aureus Lipase - Native


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Staphylococcus Aureus Lipase - Native within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:55.7 occ:1.00 OD2 A:ASP236 1.5 25.9 1.0 OD1 A:ASP64 1.6 35.5 1.0 NE2 A:HIS84 2.0 42.7 1.0 NE2 A:HIS90 2.2 39.8 1.0 CG A:ASP236 2.7 33.0 1.0 CG A:ASP64 2.7 39.0 1.0 CE1 A:HIS84 3.0 33.2 1.0 CD2 A:HIS84 3.0 33.8 1.0 OD2 A:ASP64 3.0 41.3 1.0 OD1 A:ASP236 3.0 33.1 1.0 CE1 A:HIS90 3.1 30.8 1.0 CD2 A:HIS90 3.2 34.9 1.0 OG A:SER61 3.9 39.1 1.0 CB A:ASP236 4.1 36.5 1.0 ND1 A:HIS84 4.1 40.2 1.0 CB A:ASP64 4.1 36.0 1.0 CG A:HIS84 4.2 40.6 1.0 CD1 A:TYR63 4.2 35.3 1.0 ND1 A:HIS90 4.3 39.4 1.0 CG A:HIS90 4.3 40.9 1.0 CA A:ASP64 4.7 38.8 1.0 N A:ASP64 4.8 40.2 1.0 CZ2 A:TRP209 4.8 39.4 1.0 CE1 A:TYR63 4.8 34.7 1.0 CD2 A:TYR88 4.9 38.9 1.0 CB A:TYR88 5.0 38.9 1.0 CD1 A:TYR80 5.0 38.5 1.0 O A:ASP236 5.0 41.9 1.0

Zinc binding site 2 out of 2 in the Staphylococcus Aureus Lipase - Native


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Staphylococcus Aureus Lipase - Native within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:63.5 occ:1.00 OD2 B:ASP236 1.6 27.2 1.0 OD1 B:ASP64 2.0 57.6 1.0 NE2 B:HIS84 2.0 50.6 1.0 NE2 B:HIS90 2.2 47.4 1.0 CG B:ASP236 2.7 38.8 1.0 CG B:ASP64 2.8 47.3 1.0 CD2 B:HIS84 2.9 47.6 1.0 OD2 B:ASP64 3.0 53.1 1.0 CD2 B:HIS90 3.1 41.4 1.0 CE1 B:HIS84 3.1 47.8 1.0 OD1 B:ASP236 3.1 41.6 1.0 CE1 B:HIS90 3.2 44.1 1.0 OG B:SER61 4.0 44.6 1.0 CG B:HIS84 4.1 52.6 1.0 ND1 B:HIS84 4.2 50.9 1.0 CB B:ASP236 4.2 36.6 1.0 CD1 B:TYR63 4.2 42.9 1.0 CB B:ASP64 4.2 48.7 1.0 CG B:HIS90 4.3 44.9 1.0 ND1 B:HIS90 4.3 46.4 1.0 CA B:ASP64 4.7 41.3 1.0 N B:ASP64 4.8 43.2 1.0 CE1 B:TYR63 4.8 42.6 1.0 CZ2 B:TRP209 4.8 44.1 1.0 CD2 B:TYR88 4.8 50.9 1.0 CD1 B:TYR80 4.9 42.2 1.0 CG B:TYR63 4.9 45.0 1.0

K.Kitadokoro, M.Tanaka, T.Hikima, Y.Okuno, M.Yamamoto, S.Kamitani. Crystal Structure of Pathogenic Staphylococcus Aureus Lipase Complex with the Anti-Obesity Drug Orlistat. Sci Rep V. 10 5469 2020.
ISSN: ESSN 2045-2322
PubMed: 32214208
DOI: 10.1038/S41598-020-62427-8