Zinc in PDB 8yib: Staphylococcus Aureus Lipase -Psa Complex - Covalent Bonding State

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

The structure of Staphylococcus Aureus Lipase -Psa Complex - Covalent Bonding State, PDB code: 8yib 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)	48.29 / 2.27
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	132.548, 132.548, 249.754, 90, 90, 90
R / Rfree (%)	19.7 / 22.1

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

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

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

Zinc binding site 1 out of 2 in the Staphylococcus Aureus Lipase -Psa Complex - Covalent Bonding State


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 - Covalent Bonding State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn409 b:52.8 occ:1.00 OD2 A:ASP236 2.0 52.7 1.0 OD1 A:ASP64 2.1 50.1 1.0 CE1 A:HIS84 2.1 54.3 1.0 CE1 A:HIS90 2.1 45.1 1.0 OD2 A:ASP64 2.7 49.3 1.0 CG A:ASP64 2.7 53.5 1.0 CG A:ASP236 2.8 48.5 1.0 OD1 A:ASP236 3.0 52.3 1.0 NE2 A:HIS84 3.1 46.9 1.0 NE2 A:HIS90 3.1 52.9 1.0 ND1 A:HIS84 3.1 53.1 1.0 ND1 A:HIS90 3.1 48.2 1.0 OG A:SER61 4.1 50.0 1.0 CB A:ASP236 4.2 45.7 1.0 CB A:ASP64 4.2 45.7 1.0 CD2 A:HIS84 4.2 49.5 1.0 CD2 A:HIS90 4.3 41.5 1.0 CG A:HIS84 4.3 56.3 1.0 CG A:HIS90 4.3 48.7 1.0 CD1 A:TYR63 4.4 50.8 1.0 O A:HOH508 4.5 46.6 1.0 CD2 A:TYR88 4.7 59.6 1.0 CZ2 A:TRP209 4.8 59.5 1.0 N A:ASP64 4.8 51.8 1.0 CA A:ASP64 4.9 51.2 1.0 O A:ASP236 4.9 49.8 1.0 CE1 A:TYR63 4.9 49.9 1.0 CB A:TYR88 5.0 57.9 1.0

Zinc binding site 2 out of 2 in the Staphylococcus Aureus Lipase -Psa Complex - Covalent Bonding State


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 - Covalent Bonding State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn409 b:63.4 occ:1.00 OD2 B:ASP236 2.0 48.7 1.0 OD1 B:ASP64 2.1 58.9 1.0 CE1 B:HIS84 2.1 73.5 1.0 CE1 B:HIS90 2.1 55.0 1.0 CG B:ASP64 2.7 61.1 1.0 OD2 B:ASP64 2.7 62.1 1.0 CG B:ASP236 2.8 53.8 1.0 OD1 B:ASP236 3.0 57.2 1.0 NE2 B:HIS84 3.1 66.5 1.0 NE2 B:HIS90 3.1 61.5 1.0 ND1 B:HIS84 3.1 72.8 1.0 ND1 B:HIS90 3.1 62.3 1.0 OG B:SER61 4.1 64.0 1.0 CB B:ASP64 4.2 57.7 1.0 CD2 B:HIS84 4.2 73.4 1.0 CB B:ASP236 4.3 46.1 1.0 CG B:HIS84 4.3 84.8 1.0 CD2 B:HIS90 4.3 54.8 1.0 CG B:HIS90 4.3 60.2 1.0 CD1 B:TYR63 4.4 62.1 1.0 O B:HOH504 4.5 56.5 1.0 CD2 B:TYR88 4.7 63.0 1.0 CZ2 B:TRP209 4.8 59.8 1.0 N B:ASP64 4.8 58.8 1.0 CA B:ASP64 4.8 56.6 1.0 O B:ASP236 4.9 57.3 1.0 CE1 B:TYR63 4.9 67.9 1.0 CB B:TYR88 5.0 62.0 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