Calcium in PDB 2zyi: A. Fulgidus Lipase with Fatty Acid Fragment and Calcium

All present enzymatic activity of A. Fulgidus Lipase with Fatty Acid Fragment and Calcium:
3.1.1.3;

The structure of A. Fulgidus Lipase with Fatty Acid Fragment and Calcium, PDB code: 2zyi was solved by C.K.Chen, T.P.Ko, R.T.Guo, A.H.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.445, 105.375, 117.002, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 23.8

The binding sites of Calcium atom in the A. Fulgidus Lipase with Fatty Acid Fragment and Calcium (pdb code 2zyi). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the A. Fulgidus Lipase with Fatty Acid Fragment and Calcium, PDB code: 2zyi:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the A. Fulgidus Lipase with Fatty Acid Fragment and Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of A. Fulgidus Lipase with Fatty Acid Fragment and Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca700 b:21.7 occ:1.00 OD1 A:ASP405 2.3 18.1 1.0 O A:LYS411 2.4 23.5 1.0 OD1 A:ASP431 2.4 14.9 1.0 OD2 A:ASP431 2.4 16.6 1.0 O A:HOH517 2.5 19.2 1.0 O A:ARG406 2.5 25.7 1.0 OD2 A:ASP409 2.6 25.7 1.0 CG A:ASP431 2.8 16.4 1.0 CG A:ASP409 3.3 27.9 1.0 OD1 A:ASP409 3.4 28.2 1.0 CG A:ASP405 3.5 19.7 1.0 C A:ARG406 3.5 24.5 1.0 C A:LYS411 3.5 24.6 1.0 N A:ARG406 3.6 21.5 1.0 C A:ASP405 4.0 18.2 1.0 CA A:ARG406 4.0 23.5 1.0 N A:LYS411 4.1 22.8 1.0 NE A:ARG406 4.2 27.1 1.0 CA A:LYS411 4.3 24.2 1.0 CB A:ARG406 4.3 24.0 1.0 CB A:ASP431 4.3 16.5 1.0 CA A:ASP405 4.3 19.9 1.0 OD2 A:ASP405 4.3 22.7 1.0 OD2 A:ASP413 4.5 44.0 1.0 CB A:LYS411 4.5 26.4 1.0 O A:ASP405 4.5 18.0 1.0 CB A:ASP405 4.5 19.6 1.0 N A:ASP413 4.5 30.5 1.0 N A:SER412 4.6 23.6 1.0 N A:ASP409 4.6 24.5 1.0 N A:GLY407 4.7 25.0 1.0 CA A:SER412 4.7 25.8 1.0 CB A:ASP409 4.8 25.2 1.0 N A:ALA408 4.8 22.1 1.0 CD A:ARG406 4.9 27.4 1.0

Calcium binding site 2 out of 2 in the A. Fulgidus Lipase with Fatty Acid Fragment and Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of A. Fulgidus Lipase with Fatty Acid Fragment and Calcium within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca700 b:19.3 occ:1.00 OD1 B:ASP405 2.4 17.0 1.0 O B:HOH664 2.4 17.5 1.0 OD2 B:ASP409 2.4 22.3 1.0 O B:LYS411 2.4 24.3 1.0 O B:ARG406 2.4 19.0 1.0 OD1 B:ASP431 2.5 14.9 1.0 OD2 B:ASP431 2.5 19.8 1.0 CG B:ASP431 2.8 18.4 1.0 CG B:ASP409 3.3 23.5 1.0 C B:ARG406 3.5 20.9 1.0 OD1 B:ASP409 3.5 24.8 1.0 C B:LYS411 3.5 26.2 1.0 N B:ARG406 3.7 19.9 1.0 CG B:ASP405 3.7 18.5 1.0 C B:ASP405 4.0 17.3 1.0 CA B:ARG406 4.0 19.1 1.0 N B:LYS411 4.0 25.3 1.0 CA B:LYS411 4.2 26.6 1.0 OD2 B:ASP413 4.3 46.7 1.0 CB B:ARG406 4.3 19.4 1.0 CA B:ASP405 4.3 18.4 1.0 NE B:ARG406 4.4 23.1 1.0 CB B:ASP431 4.4 17.2 1.0 CB B:LYS411 4.4 29.7 1.0 O B:ASP405 4.5 17.1 1.0 OD2 B:ASP405 4.5 20.2 1.0 N B:ASP413 4.5 32.6 1.0 N B:ASP409 4.5 23.0 1.0 N B:SER412 4.6 25.0 1.0 CB B:ASP405 4.6 18.1 1.0 N B:GLY407 4.6 20.5 1.0 CB B:ASP409 4.7 18.5 1.0 CA B:SER412 4.8 28.1 1.0 N B:ALA408 4.9 24.9 1.0 CA B:GLY407 4.9 21.3 1.0 CD B:ARG406 4.9 23.4 1.0 N B:GLY410 5.0 23.1 1.0 CG B:ASP413 5.0 43.6 1.0

C.K.Chen, G.C.Lee, T.P.Ko, R.T.Guo, L.M.Huang, H.J.Liu, Y.F.Ho, J.F.Shaw, A.H.Wang. Structure of the Alkalohyperthermophilic Archaeoglobus Fulgidus Lipase Contains A Unique C-Terminal Domain Essential For Long-Chain Substrate Binding. J.Mol.Biol. V. 390 672 2009.
ISSN: ISSN 0022-2836
PubMed: 19447113
DOI: 10.1016/J.JMB.2009.05.017