Calcium in PDB 6ksl: Staphylococcus Aureus Lipase - S116A Inactive Mutant

All present enzymatic activity of Staphylococcus Aureus Lipase - S116A Inactive Mutant:
3.1.1.3;

The structure of Staphylococcus Aureus Lipase - S116A Inactive Mutant, PDB code: 6ksl was solved by K.Kitadokoro, M.Tanaka, S.Kamitani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.81 / 2.59
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	164.209, 164.209, 233.053, 90.00, 90.00, 120.00
R / Rfree (%)	24.9 / 26.8

The structure of Staphylococcus Aureus Lipase - S116A Inactive Mutant also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Calcium atom in the Staphylococcus Aureus Lipase - S116A Inactive Mutant (pdb code 6ksl). 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, PDB code: 6ksl:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Staphylococcus Aureus Lipase - S116A Inactive Mutant


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:78.0 occ:1.00 OD2 A:ASP351 2.3 64.8 1.0 OD2 A:ASP348 2.4 70.8 1.0 OD1 A:ASP351 2.5 65.0 1.0 O A:GLY283 2.5 72.3 1.0 OD2 A:ASP356 2.6 61.4 1.0 OD2 A:ASP359 2.7 76.8 1.0 CG A:ASP351 2.8 66.4 1.0 CG A:ASP348 3.1 65.3 1.0 C A:GLY283 3.6 64.8 1.0 CG A:ASP359 3.6 82.3 1.0 OD1 A:ASP348 3.7 65.9 1.0 CG A:ASP356 3.8 69.5 1.0 CB A:ASP359 3.9 80.5 1.0 CB A:ASP348 3.9 65.6 1.0 CA A:THR284 4.2 59.9 1.0 N A:ASP348 4.2 67.5 1.0 N A:THR284 4.3 63.4 1.0 CB A:ASP351 4.3 67.8 1.0 N A:PHE285 4.4 64.3 1.0 CB A:ASP356 4.4 69.3 1.0 CG A:ARG362 4.6 67.4 1.0 CA A:ASP348 4.7 63.5 1.0 C A:THR284 4.7 66.0 1.0 CA A:GLY283 4.7 73.0 1.0 OD1 A:ASP359 4.7 85.6 1.0 OD1 A:ASP356 4.8 75.7 1.0 O A:GLY346 4.8 65.6 1.0

Calcium binding site 2 out of 2 in the Staphylococcus Aureus Lipase - S116A Inactive Mutant


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:80.0 occ:1.00 O B:GLY283 2.3 75.0 1.0 OD2 B:ASP348 2.4 66.8 1.0 OD2 B:ASP351 2.5 73.2 1.0 OD2 B:ASP356 2.6 76.1 1.0 OD2 B:ASP359 2.6 84.9 1.0 OD1 B:ASP351 2.6 69.2 1.0 CG B:ASP351 2.9 62.6 1.0 CG B:ASP348 3.1 62.3 1.0 C B:GLY283 3.5 66.0 1.0 CG B:ASP359 3.5 83.1 1.0 OD1 B:ASP348 3.8 62.8 1.0 CG B:ASP356 3.8 75.5 1.0 CB B:ASP359 3.8 79.4 1.0 CB B:ASP348 4.0 63.2 1.0 CA B:THR284 4.2 63.2 1.0 N B:THR284 4.3 60.9 1.0 N B:ASP348 4.3 58.1 1.0 CB B:ASP356 4.4 73.2 1.0 CB B:ASP351 4.4 55.2 1.0 N B:PHE285 4.4 63.4 1.0 CA B:GLY283 4.5 70.5 1.0 OD1 B:ASP359 4.6 88.2 1.0 C B:THR284 4.6 63.6 1.0 CG B:ARG362 4.6 67.6 1.0 OD1 B:ASP356 4.7 70.8 1.0 CA B:ASP348 4.7 54.0 1.0 O B:GLY346 4.9 67.4 1.0

K.Kitadokoro, M.Tanaka, T.Hikima, Y.Okuno, M.Yamamoto, S.Kamitani. Crystal Structure of Pathogenic Staphylococcus Aureus Lipase Complex with the Anti-Obesity Drug Orlistat. Sci Rep V. 10 5469 2020.
ISSN: ESSN 2045-2322
PubMed: 32214208
DOI: 10.1038/S41598-020-62427-8