Calcium in PDB 7v6d: Structure of Lipase B From Lasiodiplodia Theobromae

The structure of Structure of Lipase B From Lasiodiplodia Theobromae, PDB code: 7v6d was solved by B.Xue, H.F.Zhang, G.K.T.Nguyen, W.S.Yew, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.70 / 2.50
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	65.428, 162.639, 166.674, 90, 90, 90
R / Rfree (%)	19.2 / 24.3

The binding sites of Calcium atom in the Structure of Lipase B From Lasiodiplodia Theobromae (pdb code 7v6d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Lipase B From Lasiodiplodia Theobromae, PDB code: 7v6d:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Lipase B From Lasiodiplodia Theobromae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Lipase B From Lasiodiplodia Theobromae within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:36.0 occ:1.00 O A:ALA386 2.3 32.7 1.0 O A:HIS389 2.3 36.8 1.0 O A:GLY391 2.3 29.5 1.0 O A:HOH662 2.4 36.0 1.0 OD2 A:ASP257 2.4 34.0 1.0 O A:HOH675 2.6 31.2 1.0 OD1 A:ASP257 2.6 38.2 1.0 CG A:ASP257 2.8 36.8 1.0 C A:ALA386 3.5 33.3 1.0 C A:GLY391 3.5 32.1 1.0 C A:HIS389 3.5 33.5 1.0 N A:GLY391 3.6 34.3 1.0 C A:ASP390 3.8 34.5 1.0 CA A:GLY391 4.1 32.5 1.0 CA A:ASP390 4.1 33.7 1.0 CA A:ALA386 4.1 35.6 1.0 N A:ASP390 4.3 31.7 1.0 CB A:ASP257 4.4 33.7 1.0 O A:ASP390 4.5 42.0 1.0 N A:LEU387 4.5 36.4 1.0 N A:HIS389 4.5 33.5 1.0 N A:PRO392 4.5 33.0 1.0 O A:SER256 4.6 38.4 1.0 CA A:HIS389 4.6 32.4 1.0 CB A:ALA386 4.6 35.0 1.0 CA A:LEU387 4.8 32.9 1.0 CA A:PRO392 4.8 31.1 1.0 C A:LEU387 5.0 33.8 1.0 C A:SER256 5.0 35.3 1.0

Calcium binding site 2 out of 2 in the Structure of Lipase B From Lasiodiplodia Theobromae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Lipase B From Lasiodiplodia Theobromae within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:52.3 occ:1.00 O B:ALA386 2.3 47.3 1.0 O B:HIS389 2.3 53.1 1.0 O B:HOH626 2.3 41.1 1.0 O B:HOH618 2.3 52.7 1.0 O B:GLY391 2.4 47.4 1.0 OD1 B:ASP257 2.4 55.1 1.0 OD2 B:ASP257 2.9 54.6 1.0 CG B:ASP257 3.0 53.2 1.0 C B:ALA386 3.5 50.3 1.0 N B:GLY391 3.5 57.5 1.0 C B:HIS389 3.5 53.5 1.0 C B:GLY391 3.5 52.4 1.0 C B:ASP390 3.8 53.4 1.0 CA B:ASP390 4.0 52.9 1.0 CA B:GLY391 4.0 51.0 1.0 CA B:ALA386 4.2 51.6 1.0 N B:ASP390 4.2 55.9 1.0 O B:ASP390 4.4 52.9 1.0 CB B:ASP257 4.5 51.6 1.0 N B:HIS389 4.5 55.0 1.0 N B:LEU387 4.5 49.0 1.0 CA B:HIS389 4.6 55.1 1.0 N B:PRO392 4.6 52.4 1.0 CA B:LEU387 4.7 52.1 1.0 CB B:ALA386 4.7 48.8 1.0 O B:SER256 4.8 51.0 1.0 C B:LEU387 4.9 52.4 1.0 CA B:PRO392 5.0 51.2 1.0

A.M.J.Ng, R.L.Yang, H.F.Zhang, B.Xue, W.S.Yew, G.K.T.Nguyen. A Novel Lipase From Lasiodiplodia Theobromae Efficiently Hydrolyses C8-C10 Methyl Esters For the Preparation of Medium-Chain Triglycerides Precursors Int J Mol Sci V. 22 2021.
ISSN: ESSN 1422-0067
DOI: 10.3390/IJMS221910339