Zinc in PDB 8k7p: Staphylococcus Aureus Lipase -Psa Complex

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

The structure of Staphylococcus Aureus Lipase -Psa Complex, PDB code: 8k7p 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)	48.16 / 2.19
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	132.324, 132.324, 248.636, 90, 90, 90
R / Rfree (%)	19.8 / 21.8

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

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

The binding sites of Zinc atom in the Staphylococcus Aureus Lipase -Psa Complex (pdb code 8k7p). 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 -Psa Complex, PDB code: 8k7p:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Staphylococcus Aureus Lipase -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 -Psa Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn416 b:51.5 occ:1.00 OD2 A:ASP236 2.0 49.9 1.0 OD1 A:ASP64 2.1 48.1 1.0 CE1 A:HIS84 2.1 53.5 1.0 CE1 A:HIS90 2.1 42.8 1.0 CG A:ASP64 2.7 52.5 1.0 OD2 A:ASP64 2.7 48.0 1.0 CG A:ASP236 2.8 52.3 1.0 NE2 A:HIS84 3.0 49.9 1.0 OD1 A:ASP236 3.0 51.1 1.0 NE2 A:HIS90 3.1 49.3 1.0 ND1 A:HIS90 3.1 48.4 1.0 ND1 A:HIS84 3.1 54.6 1.0 OG A:SER61 4.1 47.7 1.0 CD2 A:HIS84 4.2 47.4 1.0 CB A:ASP236 4.2 44.9 1.0 CB A:ASP64 4.2 44.1 1.0 CG A:HIS84 4.3 55.8 1.0 CD2 A:HIS90 4.3 40.9 1.0 CG A:HIS90 4.3 49.0 1.0 CD1 A:TYR63 4.4 47.3 1.0 O A:HOH508 4.5 44.3 1.0 CZ2 A:TRP209 4.7 57.3 1.0 CD2 A:TYR88 4.7 54.5 1.0 N A:ASP64 4.8 47.1 1.0 CA A:ASP64 4.8 48.5 1.0 O A:ASP236 4.9 49.4 1.0 CB A:TYR88 4.9 50.8 1.0 CE1 A:TYR63 4.9 51.2 1.0

Zinc binding site 2 out of 2 in the Staphylococcus Aureus Lipase -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 -Psa Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn417 b:62.1 occ:1.00 OD2 B:ASP236 2.0 49.9 1.0 OD1 B:ASP64 2.0 59.1 1.0 CE1 B:HIS84 2.1 75.1 1.0 CE1 B:HIS90 2.1 53.4 1.0 CG B:ASP64 2.7 60.8 1.0 OD2 B:ASP64 2.7 59.3 1.0 CG B:ASP236 2.8 56.0 1.0 NE2 B:HIS84 3.0 63.8 1.0 OD1 B:ASP236 3.0 56.8 1.0 NE2 B:HIS90 3.1 59.8 1.0 ND1 B:HIS84 3.1 68.1 1.0 ND1 B:HIS90 3.1 59.5 1.0 OG B:SER61 4.0 59.1 1.0 CB B:ASP64 4.2 54.0 1.0 CD2 B:HIS84 4.2 67.0 1.0 CB B:ASP236 4.3 46.4 1.0 CG B:HIS84 4.3 78.0 1.0 CD2 B:HIS90 4.3 55.0 1.0 CG B:HIS90 4.3 59.1 1.0 CD1 B:TYR63 4.4 58.4 1.0 O B:HOH515 4.5 54.3 1.0 CD2 B:TYR88 4.7 61.6 1.0 CZ2 B:TRP209 4.7 56.5 1.0 N B:ASP64 4.8 56.3 1.0 CA B:ASP64 4.8 58.6 1.0 CE1 B:TYR63 4.9 63.9 1.0 O B:ASP236 5.0 58.0 1.0 CB B:TYR88 5.0 62.7 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