Zinc in PDB 6ksl: Staphylococcus Aureus Lipase - S116A Inactive Mutant

All present enzymatic activity of Staphylococcus Aureus Lipase - S116A Inactive Mutant:
3.1.1.3;

The structure of Staphylococcus Aureus Lipase - S116A Inactive Mutant, PDB code: 6ksl 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)	48.81 / 2.59
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	164.209, 164.209, 233.053, 90.00, 90.00, 120.00
R / Rfree (%)	24.9 / 26.8

The structure of Staphylococcus Aureus Lipase - S116A Inactive Mutant also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Staphylococcus Aureus Lipase - S116A Inactive Mutant (pdb code 6ksl). 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 - S116A Inactive Mutant, PDB code: 6ksl:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Staphylococcus Aureus Lipase - S116A Inactive Mutant


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 - S116A Inactive Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:69.7 occ:1.00 NE2 A:HIS90 1.8 53.7 1.0 OD1 A:ASP64 1.8 48.3 1.0 OD2 A:ASP236 2.1 46.1 1.0 CE1 A:HIS90 2.5 55.2 1.0 CG A:ASP64 2.5 47.7 1.0 NE2 A:HIS84 2.5 48.4 1.0 OD2 A:ASP64 2.6 78.3 1.0 CD2 A:HIS90 2.9 56.7 1.0 CG A:ASP236 3.0 46.6 1.0 OD1 A:ASP236 3.2 53.3 1.0 CD2 A:HIS84 3.2 53.2 1.0 CE1 A:HIS84 3.6 53.4 1.0 ND1 A:HIS90 3.6 47.1 1.0 CG A:HIS90 3.9 53.4 1.0 CB A:ASP64 4.0 54.0 1.0 OG A:SER61 4.1 45.5 1.0 CB A:ASP236 4.4 48.5 1.0 CA A:ASP64 4.5 53.9 1.0 CG A:HIS84 4.5 58.3 1.0 CD1 A:TYR63 4.6 56.3 1.0 N A:ASP64 4.6 54.5 1.0 ND1 A:HIS84 4.7 61.6 1.0 CZ2 A:TRP209 4.8 45.0 1.0 O A:ASP236 4.8 61.2 1.0 CD2 A:TYR88 4.9 59.1 1.0 CD1 A:TYR80 4.9 57.4 1.0 CG A:TYR80 5.0 56.9 1.0

Zinc binding site 2 out of 2 in the Staphylococcus Aureus Lipase - S116A Inactive Mutant


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 - S116A Inactive Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:75.5 occ:1.00 OD1 B:ASP64 2.0 47.3 1.0 OD2 B:ASP236 2.0 52.7 1.0 NE2 B:HIS90 2.0 50.1 1.0 NE2 B:HIS84 2.2 58.2 1.0 CG B:ASP64 2.6 48.8 1.0 CG B:ASP236 2.8 47.9 1.0 CE1 B:HIS90 2.8 47.4 1.0 OD2 B:ASP64 2.8 69.3 1.0 OD1 B:ASP236 2.9 46.3 1.0 CD2 B:HIS84 3.1 64.1 1.0 CD2 B:HIS90 3.2 57.5 1.0 CE1 B:HIS84 3.3 68.7 1.0 OG B:SER61 4.0 57.4 1.0 ND1 B:HIS90 4.0 50.7 1.0 CB B:ASP64 4.0 56.7 1.0 CB B:ASP236 4.2 51.5 1.0 CG B:HIS90 4.2 57.2 1.0 CG B:HIS84 4.3 68.4 1.0 ND1 B:HIS84 4.3 74.6 1.0 CD1 B:TYR63 4.4 64.9 1.0 CA B:ASP64 4.5 53.2 1.0 N B:ASP64 4.6 62.8 1.0 CD2 B:TYR88 4.7 62.8 1.0 O B:ASP236 4.8 56.7 1.0 CZ2 B:TRP209 4.9 55.5 1.0 CE1 B:TYR63 4.9 69.5 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