Calcium 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
Magnesium	(Mg)	1 atom
Zinc	(Zn)	2 atoms

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

Calcium binding site 1 out of 2 in the Staphylococcus Aureus Lipase -Psa Complex


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca417 b:60.4 occ:1.00 O A:GLY283 2.3 59.9 1.0 OD2 A:ASP348 2.3 56.8 1.0 OD2 A:ASP351 2.4 53.3 1.0 OD2 A:ASP356 2.4 62.2 1.0 OD2 A:ASP359 2.5 64.6 1.0 O A:HOH539 2.6 53.4 1.0 OD1 A:ASP351 2.6 56.4 1.0 CG A:ASP351 2.9 57.3 1.0 CG A:ASP348 3.1 57.0 1.0 CG A:ASP359 3.4 67.5 1.0 CG A:ASP356 3.5 58.7 1.0 C A:GLY283 3.5 68.7 1.0 OD1 A:ASP348 3.6 53.6 1.0 CB A:ASP359 3.7 62.8 1.0 CB A:ASP356 4.0 53.0 1.0 N A:PHE285 4.1 51.8 1.0 CB A:ASP348 4.1 46.4 1.0 CA A:THR284 4.2 58.3 1.0 N A:THR284 4.2 57.1 1.0 CB A:ASP351 4.4 45.9 1.0 N A:ASP348 4.5 52.1 1.0 C A:THR284 4.5 57.8 1.0 OD1 A:ASP356 4.5 54.2 1.0 O2 A:FMT409 4.5 67.3 1.0 CA A:GLY283 4.6 62.2 1.0 OD1 A:ASP359 4.6 70.1 1.0 O A:GLY346 4.6 61.3 1.0 CG A:ARG362 4.7 56.8 1.0 CA A:ASP348 4.9 48.0 1.0 CA A:PHE285 5.0 53.7 1.0

Calcium binding site 2 out of 2 in the Staphylococcus Aureus Lipase -Psa Complex


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca418 b:56.9 occ:1.00 O B:GLY283 2.4 48.9 1.0 OD2 B:ASP359 2.4 61.4 1.0 OD2 B:ASP348 2.4 55.6 1.0 OD2 B:ASP351 2.4 56.8 1.0 OD2 B:ASP356 2.4 53.7 1.0 O B:HOH518 2.6 52.7 1.0 OD1 B:ASP351 2.7 44.7 1.0 CG B:ASP351 2.9 54.5 1.0 CG B:ASP348 3.1 48.2 1.0 CG B:ASP359 3.4 66.8 1.0 C B:GLY283 3.5 58.7 1.0 CG B:ASP356 3.5 60.3 1.0 CB B:ASP359 3.7 56.6 1.0 OD1 B:ASP348 3.7 48.1 1.0 N B:PHE285 4.1 48.6 1.0 CB B:ASP356 4.1 51.5 1.0 O B:HOH512 4.1 49.8 1.0 CB B:ASP348 4.1 47.0 1.0 N B:THR284 4.2 50.0 1.0 CA B:THR284 4.2 54.6 1.0 O B:HOH527 4.2 59.8 1.0 CB B:ASP351 4.4 42.2 1.0 C B:THR284 4.5 52.2 1.0 N B:ASP348 4.5 51.6 1.0 OD1 B:ASP356 4.5 54.9 1.0 CA B:GLY283 4.6 61.8 1.0 OD1 B:ASP359 4.6 64.6 1.0 CG B:ARG362 4.6 48.7 1.0 O B:GLY346 4.6 54.6 1.0 CA B:ASP348 4.9 47.3 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