Calcium 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:

Zinc	(Zn)	2 atoms
Magnesium	(Mg)	1 atom
Chlorine	(Cl)	4 atoms

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Staphylococcus Aureus Lipase -Psa Complex - Covalent Bonding State, PDB code: 8yib:
Jump to Calcium binding site number: 1; 2;

Calcium 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 Calcium with other atoms in the Ca 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:Ca410 b:62.1 occ:1.00 O A:GLY283 2.3 65.8 1.0 OD2 A:ASP348 2.3 59.1 1.0 OD2 A:ASP351 2.4 56.5 1.0 OD2 A:ASP359 2.4 68.9 1.0 OD2 A:ASP356 2.5 67.4 1.0 OD1 A:ASP351 2.6 58.0 1.0 O A:HOH547 2.6 56.1 1.0 CG A:ASP351 2.8 59.4 1.0 CG A:ASP348 3.1 60.9 1.0 CG A:ASP359 3.4 67.6 1.0 C A:GLY283 3.5 72.8 1.0 CG A:ASP356 3.5 64.6 1.0 OD1 A:ASP348 3.6 57.9 1.0 CB A:ASP359 3.7 66.2 1.0 N A:PHE285 4.0 53.0 1.0 CB A:ASP356 4.1 57.0 1.0 CB A:ASP348 4.1 48.1 1.0 N A:THR284 4.2 61.8 1.0 CA A:THR284 4.2 60.7 1.0 CB A:ASP351 4.4 49.5 1.0 N A:ASP348 4.5 50.5 1.0 C A:THR284 4.5 56.9 1.0 CA A:GLY283 4.5 69.6 1.0 OD1 A:ASP356 4.5 60.1 1.0 OD1 A:ASP359 4.6 74.6 1.0 O A:GLY346 4.6 63.2 1.0 O2 A:FMT415 4.7 76.3 1.0 CG A:ARG362 4.7 62.3 1.0 CA A:ASP348 4.9 50.1 1.0 CA A:PHE285 5.0 55.4 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca410 b:57.7 occ:1.00 O B:GLY283 2.3 55.0 1.0 OD2 B:ASP359 2.4 65.0 1.0 OD2 B:ASP348 2.4 56.1 1.0 OD2 B:ASP351 2.4 58.3 1.0 OD2 B:ASP356 2.5 54.7 1.0 O B:HOH524 2.6 59.1 1.0 OD1 B:ASP351 2.7 48.9 1.0 CG B:ASP351 2.9 56.2 1.0 CG B:ASP348 3.2 50.3 1.0 CG B:ASP359 3.4 63.8 1.0 C B:GLY283 3.4 62.9 1.0 CG B:ASP356 3.5 63.2 1.0 OD1 B:ASP348 3.7 52.6 1.0 CB B:ASP359 3.7 58.4 1.0 N B:PHE285 4.0 47.5 1.0 CB B:ASP356 4.1 51.0 1.0 CB B:ASP348 4.2 52.8 1.0 N B:THR284 4.2 49.8 1.0 O B:HOH511 4.2 49.5 1.0 CA B:THR284 4.2 58.4 1.0 O B:HOH517 4.2 57.4 1.0 CB B:ASP351 4.4 43.8 1.0 N B:ASP348 4.5 53.0 1.0 C B:THR284 4.5 54.1 1.0 CA B:GLY283 4.5 62.2 1.0 OD1 B:ASP359 4.5 65.1 1.0 OD1 B:ASP356 4.6 59.9 1.0 O B:GLY346 4.6 57.8 1.0 CG B:ARG362 4.6 52.7 1.0 CA B:ASP348 4.9 50.1 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