Calcium 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:

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

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Staphylococcus Aureus Lipase S116A Inactive Mutant-Psa Complex, PDB code: 8k7q:
Jump to Calcium binding site number: 1; 2;

Calcium 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 Calcium with other atoms in the Ca 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:Ca417 b:54.8 occ:1.00 O A:GLY283 2.3 57.2 1.0 OD2 A:ASP359 2.3 57.2 1.0 OD2 A:ASP351 2.4 50.7 1.0 OD2 A:ASP348 2.4 52.2 1.0 OD2 A:ASP356 2.4 57.2 1.0 O A:HOH598 2.5 51.9 1.0 OD1 A:ASP351 2.7 50.9 1.0 CG A:ASP351 2.9 52.7 1.0 CG A:ASP348 3.2 52.2 1.0 CG A:ASP359 3.3 62.1 1.0 CG A:ASP356 3.5 52.1 1.0 C A:GLY283 3.5 63.8 1.0 CB A:ASP359 3.6 57.9 1.0 OD1 A:ASP348 3.7 47.9 1.0 CB A:ASP356 4.0 50.2 1.0 N A:PHE285 4.1 52.1 1.0 CB A:ASP348 4.1 46.2 1.0 N A:THR284 4.2 52.7 1.0 O A:HOH567 4.2 56.2 1.0 CA A:THR284 4.2 56.0 1.0 CB A:ASP351 4.4 46.8 1.0 O2 A:FMT409 4.4 55.1 1.0 C A:THR284 4.5 50.9 1.0 OD1 A:ASP356 4.5 53.7 1.0 OD1 A:ASP359 4.5 61.4 1.0 CA A:GLY283 4.5 61.7 1.0 N A:ASP348 4.5 43.4 1.0 O A:GLY346 4.6 54.7 1.0 CG A:ARG362 4.6 58.8 1.0 CA A:ASP348 4.9 43.4 1.0 CA A:PHE285 5.0 52.0 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca418 b:50.5 occ:1.00 O B:GLY283 2.3 44.6 1.0 OD2 B:ASP348 2.4 47.9 1.0 OD2 B:ASP359 2.4 51.5 1.0 OD2 B:ASP356 2.4 48.6 1.0 OD2 B:ASP351 2.4 50.6 1.0 O B:HOH523 2.5 49.4 1.0 OD1 B:ASP351 2.7 44.3 1.0 CG B:ASP351 2.9 48.2 1.0 CG B:ASP348 3.2 40.7 1.0 CG B:ASP359 3.4 57.8 1.0 C B:GLY283 3.5 50.2 1.0 CG B:ASP356 3.5 49.4 1.0 CB B:ASP359 3.6 48.9 1.0 OD1 B:ASP348 3.7 44.8 1.0 CB B:ASP356 4.0 47.2 1.0 N B:PHE285 4.1 44.9 1.0 CB B:ASP348 4.1 43.0 1.0 O B:HOH529 4.2 49.4 1.0 CA B:THR284 4.2 47.9 1.0 N B:THR284 4.2 42.2 1.0 O B:HOH531 4.2 44.1 1.0 CB B:ASP351 4.4 41.0 1.0 C B:THR284 4.4 45.5 1.0 OD1 B:ASP356 4.5 51.3 1.0 N B:ASP348 4.5 43.7 1.0 CA B:GLY283 4.5 57.4 1.0 OD1 B:ASP359 4.5 54.8 1.0 O B:GLY346 4.6 47.2 1.0 CG B:ARG362 4.6 46.2 1.0 CA B:ASP348 4.9 45.9 1.0 CA B:PHE285 5.0 48.0 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