Calcium in PDB 6ksm: Staphylococcus Aureus Lipase -Orlistat Complex

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

The structure of Staphylococcus Aureus Lipase -Orlistat Complex, PDB code: 6ksm 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)	48.18 / 2.23
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	132.510, 132.510, 248.243, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 25.9

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

Zinc

(Zn)

2 atoms

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

Calcium binding site 1 out of 2 in the Staphylococcus Aureus Lipase -Orlistat 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 -Orlistat Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:75.6 occ:1.00 OD2 A:ASP348 2.3 42.1 1.0 O A:GLY283 2.4 49.7 1.0 OD2 A:ASP351 2.4 46.5 1.0 OD2 A:ASP359 2.5 48.5 1.0 OD1 A:ASP351 2.6 46.8 1.0 OD2 A:ASP356 2.8 56.7 1.0 CG A:ASP351 2.9 42.7 1.0 CG A:ASP348 3.1 38.5 1.0 CG A:ASP359 3.4 55.5 1.0 OD1 A:ASP348 3.6 41.1 1.0 C A:GLY283 3.6 51.3 1.0 CB A:ASP359 3.7 53.1 1.0 CG A:ASP356 3.7 58.2 1.0 N A:PHE285 3.9 41.6 1.0 CB A:ASP356 4.1 54.8 1.0 CB A:ASP348 4.2 35.5 1.0 CA A:THR284 4.2 43.4 1.0 N A:THR284 4.3 44.0 1.0 C A:THR284 4.4 41.3 1.0 CB A:ASP351 4.5 37.9 1.0 N A:ASP348 4.5 35.1 1.0 OD1 A:ASP359 4.6 60.1 1.0 CG A:ARG362 4.7 50.0 1.0 OD1 A:ASP356 4.7 62.6 1.0 CA A:GLY283 4.8 51.0 1.0 O A:GLY346 4.8 53.2 1.0 CA A:PHE285 4.9 41.2 1.0 CA A:ASP348 4.9 34.1 1.0

Calcium binding site 2 out of 2 in the Staphylococcus Aureus Lipase -Orlistat 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 -Orlistat Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:64.7 occ:1.00 O B:GLY283 2.4 44.0 1.0 OD2 B:ASP359 2.4 52.9 1.0 OD2 B:ASP351 2.4 40.4 1.0 OD2 B:ASP356 2.5 54.4 1.0 OD2 B:ASP348 2.5 38.9 1.0 OD1 B:ASP351 2.7 39.7 1.0 CG B:ASP351 2.9 41.2 1.0 CG B:ASP348 3.2 37.0 1.0 CG B:ASP359 3.5 51.3 1.0 C B:GLY283 3.5 45.0 1.0 CG B:ASP356 3.6 49.5 1.0 OD1 B:ASP348 3.7 36.4 1.0 CB B:ASP359 3.8 44.8 1.0 CB B:ASP348 4.0 32.0 1.0 N B:PHE285 4.0 37.5 1.0 O B:HOH506 4.2 52.1 1.0 CA B:THR284 4.2 44.7 1.0 CB B:ASP356 4.2 46.0 1.0 N B:THR284 4.2 39.2 1.0 N B:ASP348 4.3 35.9 1.0 O B:HOH501 4.4 55.2 1.0 C B:THR284 4.4 38.3 1.0 CB B:ASP351 4.4 35.3 1.0 CG B:ARG362 4.5 41.0 1.0 OD1 B:ASP356 4.5 47.6 1.0 O B:GLY346 4.5 42.3 1.0 OD1 B:ASP359 4.6 51.7 1.0 CA B:GLY283 4.6 49.2 1.0 CA B:ASP348 4.8 36.1 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