Calcium in PDB 6ksi: Staphylococcus Aureus Lipase - Native

All present enzymatic activity of Staphylococcus Aureus Lipase - Native:
3.1.1.3;

The structure of Staphylococcus Aureus Lipase - Native, PDB code: 6ksi 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)	47.74 / 2.08
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	129.913, 129.913, 251.224, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 25

The structure of Staphylococcus Aureus Lipase - Native also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

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

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


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 - Native within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:66.7 occ:1.00 O A:GLY283 2.3 44.3 1.0 OD2 A:ASP359 2.3 41.8 1.0 OD2 A:ASP348 2.3 39.8 1.0 OD2 A:ASP351 2.5 52.9 1.0 OD2 A:ASP356 2.6 49.2 1.0 OD1 A:ASP351 2.8 47.1 1.0 CG A:ASP351 3.0 50.3 1.0 CG A:ASP348 3.1 38.2 1.0 CG A:ASP359 3.3 47.2 1.0 C A:GLY283 3.5 43.3 1.0 CB A:ASP359 3.6 38.3 1.0 CG A:ASP356 3.6 53.3 1.0 OD1 A:ASP348 3.7 40.1 1.0 N A:PHE285 3.9 43.9 1.0 CB A:ASP348 4.1 37.4 1.0 CB A:ASP356 4.2 53.3 1.0 CA A:THR284 4.2 40.3 1.0 N A:THR284 4.3 37.3 1.0 C A:THR284 4.4 42.0 1.0 OD1 A:ASP359 4.5 45.2 1.0 N A:ASP348 4.5 39.1 1.0 CB A:ASP351 4.5 42.2 1.0 CA A:GLY283 4.6 43.3 1.0 OD1 A:ASP356 4.6 51.6 1.0 CG A:ARG362 4.7 46.5 1.0 O A:GLY346 4.8 46.9 1.0 CA A:PHE285 4.9 40.1 1.0 CA A:ASP348 4.9 35.1 1.0

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


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 - Native within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:61.1 occ:1.00 O B:GLY283 2.5 39.9 1.0 OD2 B:ASP348 2.5 38.2 1.0 OD2 B:ASP351 2.5 45.5 1.0 OD2 B:ASP359 2.5 40.8 1.0 OD2 B:ASP356 2.6 45.6 1.0 OD1 B:ASP351 2.7 39.9 1.0 CG B:ASP351 3.0 42.0 1.0 CG B:ASP348 3.1 41.1 1.0 CG B:ASP359 3.5 46.2 1.0 C B:GLY283 3.6 39.8 1.0 CG B:ASP356 3.6 49.0 1.0 CB B:ASP359 3.6 41.2 1.0 OD1 B:ASP348 3.7 41.4 1.0 N B:PHE285 4.0 42.2 1.0 CB B:ASP348 4.0 38.1 1.0 O B:HOH501 4.1 50.1 1.0 CB B:ASP356 4.1 43.9 1.0 CA B:THR284 4.2 42.5 1.0 N B:THR284 4.3 36.1 1.0 CB B:ASP351 4.4 39.1 1.0 N B:ASP348 4.4 38.0 1.0 C B:THR284 4.5 44.6 1.0 CG B:ARG362 4.5 48.2 1.0 OD1 B:ASP356 4.6 54.8 1.0 CA B:GLY283 4.6 43.8 1.0 OD1 B:ASP359 4.7 45.0 1.0 O B:GLY346 4.7 41.8 1.0 CA B:ASP348 4.9 42.4 1.0 CA B:PHE285 4.9 44.6 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