Zinc in PDB 6ksm: Staphylococcus Aureus Lipase -Orlistat Complex

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

The structure of Staphylococcus Aureus Lipase -Orlistat Complex, PDB code: 6ksm 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)	48.18 / 2.23
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	132.510, 132.510, 248.243, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 25.9

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

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Staphylococcus Aureus Lipase -Orlistat Complex (pdb code 6ksm). 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 -Orlistat Complex, PDB code: 6ksm:
Jump to Zinc binding site number: 1; 2;

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


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 -Orlistat Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:68.4 occ:1.00 OD1 A:ASP64 1.7 26.0 1.0 NE2 A:HIS84 1.8 47.5 1.0 OD2 A:ASP236 1.9 14.3 1.0 NE2 A:HIS90 2.3 36.6 1.0 CG A:ASP64 2.7 33.3 1.0 CE1 A:HIS84 2.8 38.3 1.0 CG A:ASP236 2.8 29.4 1.0 CD2 A:HIS84 2.9 42.5 1.0 OD2 A:ASP64 3.0 39.7 1.0 OD1 A:ASP236 3.1 30.6 1.0 CE1 A:HIS90 3.2 30.2 1.0 CD2 A:HIS90 3.2 29.7 1.0 ND1 A:HIS84 3.9 36.0 1.0 CG A:HIS84 4.0 38.5 1.0 OG A:SER61 4.1 34.3 1.0 CB A:ASP64 4.2 29.3 1.0 CB A:ASP236 4.2 32.0 1.0 CD1 A:TYR63 4.3 34.3 1.0 ND1 A:HIS90 4.3 36.1 1.0 CG A:HIS90 4.4 36.1 1.0 CA A:ASP64 4.6 34.4 1.0 N A:ASP64 4.7 34.4 1.0 CE1 A:TYR63 4.7 34.3 1.0 CD2 A:TYR88 4.8 39.2 1.0 O A:ASP236 4.8 47.5 1.0 CZ2 A:TRP209 4.9 37.5 1.0 CD1 A:TYR80 4.9 35.0 1.0

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


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 -Orlistat Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:69.7 occ:1.00 OD2 B:ASP236 1.4 26.0 1.0 OD1 B:ASP64 1.9 52.4 1.0 NE2 B:HIS84 2.1 49.4 1.0 NE2 B:HIS90 2.2 50.1 1.0 CG B:ASP236 2.7 36.1 1.0 CG B:ASP64 2.7 47.7 1.0 CD2 B:HIS84 2.9 46.0 1.0 OD2 B:ASP64 2.9 53.3 1.0 CD2 B:HIS90 3.1 45.7 1.0 CE1 B:HIS90 3.2 45.6 1.0 CE1 B:HIS84 3.2 47.4 1.0 OD1 B:ASP236 3.3 40.9 1.0 CB B:ASP236 4.0 36.4 1.0 OG B:SER61 4.1 47.1 1.0 CG B:HIS84 4.1 49.2 1.0 CB B:ASP64 4.2 46.0 1.0 ND1 B:HIS84 4.2 48.5 1.0 ND1 B:HIS90 4.3 48.8 1.0 CG B:HIS90 4.3 48.0 1.0 CD1 B:TYR63 4.3 42.1 1.0 CA B:ASP64 4.7 46.6 1.0 N B:ASP64 4.7 44.2 1.0 CD1 B:TYR80 4.8 35.6 1.0 CZ2 B:TRP209 4.8 42.6 1.0 CD2 B:TYR88 4.8 47.9 1.0 CE1 B:TYR63 4.9 40.8 1.0 CG B:TYR80 4.9 39.2 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