Zinc in PDB 8k7q: Staphylococcus Aureus Lipase S116A Inactive Mutant-Psa Complex

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

The structure of Staphylococcus Aureus Lipase S116A Inactive Mutant-Psa Complex, PDB code: 8k7q was solved by J.Kitadokoro, S.Kamitani, K.Kitadokoro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.00 / 2.02
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	131.348, 131.348, 249.851, 90, 90, 90
R / Rfree (%)	21.8 / 23.9

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

Magnesium	(Mg)	1 atom
Calcium	(Ca)	2 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Zinc atom in the Staphylococcus Aureus Lipase S116A Inactive Mutant-Psa Complex (pdb code 8k7q). 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-Psa Complex, PDB code: 8k7q:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Staphylococcus Aureus Lipase S116A Inactive Mutant-Psa 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 S116A Inactive Mutant-Psa Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn416 b:49.3 occ:1.00 OD2 A:ASP236 1.9 46.6 1.0 OD1 A:ASP64 2.1 46.9 1.0 CE1 A:HIS90 2.1 44.9 1.0 CE1 A:HIS84 2.1 50.8 1.0 CG A:ASP64 2.7 48.1 1.0 CG A:ASP236 2.8 46.0 1.0 OD2 A:ASP64 2.8 47.0 1.0 OD1 A:ASP236 3.0 47.5 1.0 NE2 A:HIS84 3.1 50.9 1.0 ND1 A:HIS90 3.1 49.2 1.0 NE2 A:HIS90 3.1 48.2 1.0 ND1 A:HIS84 3.1 53.1 1.0 OG A:SER61 4.0 44.0 1.0 CB A:ASP236 4.2 42.5 1.0 CB A:ASP64 4.2 44.8 1.0 CD2 A:HIS84 4.2 43.4 1.0 CG A:HIS90 4.3 45.7 1.0 CD2 A:HIS90 4.3 42.6 1.0 CG A:HIS84 4.3 51.0 1.0 CD1 A:TYR63 4.4 47.3 1.0 O A:HOH540 4.5 41.5 1.0 CZ2 A:TRP209 4.7 51.1 1.0 N A:ASP64 4.8 43.1 1.0 CA A:ASP64 4.8 44.7 1.0 CD2 A:TYR88 4.8 47.6 1.0 O A:ASP236 4.9 45.4 1.0 CE1 A:TYR63 4.9 46.9 1.0 CB A:TYR88 4.9 49.4 1.0

Zinc binding site 2 out of 2 in the Staphylococcus Aureus Lipase S116A Inactive Mutant-Psa 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 S116A Inactive Mutant-Psa Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn417 b:58.1 occ:1.00 OD2 B:ASP236 1.9 47.7 1.0 OD1 B:ASP64 2.1 52.1 1.0 CE1 B:HIS84 2.1 67.3 1.0 CE1 B:HIS90 2.1 48.4 1.0 CG B:ASP64 2.8 54.6 1.0 CG B:ASP236 2.8 51.5 1.0 OD2 B:ASP64 2.8 58.6 1.0 OD1 B:ASP236 3.0 50.6 1.0 NE2 B:HIS84 3.1 64.5 1.0 ND1 B:HIS90 3.1 53.3 1.0 ND1 B:HIS84 3.1 65.7 1.0 NE2 B:HIS90 3.1 56.6 1.0 OG B:SER61 4.0 57.5 1.0 CB B:ASP236 4.2 46.8 1.0 CD2 B:HIS84 4.2 63.4 1.0 CB B:ASP64 4.2 48.6 1.0 CG B:HIS84 4.2 63.9 1.0 CG B:HIS90 4.3 54.8 1.0 CD2 B:HIS90 4.3 46.3 1.0 CD1 B:TYR63 4.3 53.6 1.0 O B:HOH507 4.5 53.6 1.0 CZ2 B:TRP209 4.7 51.5 1.0 N B:ASP64 4.8 49.9 1.0 CA B:ASP64 4.8 50.6 1.0 CD2 B:TYR88 4.8 56.9 1.0 CE1 B:TYR63 4.9 57.9 1.0 O B:ASP236 4.9 56.7 1.0 CB B:TYR88 4.9 57.4 1.0

J.Kitadokoro, S.Kamitani, Y.Okuno, T.Hikima, M.Yamamoto, T.Hirokawa, K.Kitadokoro. Crystal Structure of Staphylococcus Aureus Lipase Complex with Unsaturated Petroselinic Acid. Febs Open Bio 2024.
ISSN: ESSN 2211-5463
PubMed: 38757397
DOI: 10.1002/2211-5463.13808