Magnesium in PDB 2zyr: A. Fulgidus Lipase with Fatty Acid Fragment and Magnesium

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

The structure of A. Fulgidus Lipase with Fatty Acid Fragment and Magnesium, PDB code: 2zyr 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 / 1.77
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.289, 106.667, 175.885, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 21.4

The binding sites of Magnesium atom in the A. Fulgidus Lipase with Fatty Acid Fragment and Magnesium (pdb code 2zyr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the A. Fulgidus Lipase with Fatty Acid Fragment and Magnesium, PDB code: 2zyr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the A. Fulgidus Lipase with Fatty Acid Fragment and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A. Fulgidus Lipase with Fatty Acid Fragment and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2001 b:31.4 occ:1.00 O A:HOH732 1.8 35.1 1.0 O A:HOH681 2.1 37.2 1.0 O A:HOH682 2.2 26.0 1.0 O A:HOH679 2.2 30.2 1.0 O A:HOH680 2.2 34.1 1.0 NE2 A:HIS158 2.2 21.2 1.0 CE1 A:HIS158 3.2 21.1 1.0 CD2 A:HIS158 3.2 22.1 1.0 O A:HOH683 3.5 34.2 1.0 O A:PHE226 4.1 17.9 1.0 O A:HOH497 4.1 55.2 1.0 O A:HOH496 4.2 36.5 1.0 O A:HOH498 4.2 28.0 1.0 ND1 A:HIS158 4.3 19.5 1.0 CG A:HIS158 4.4 19.7 1.0 O A:ILE227 4.9 20.7 1.0

Magnesium binding site 2 out of 5 in the A. Fulgidus Lipase with Fatty Acid Fragment and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of A. Fulgidus Lipase with Fatty Acid Fragment and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2002 b:59.8 occ:1.00 O A:HOH873 1.9 61.7 1.0 O A:HOH874 2.0 35.3 1.0 O A:HOH872 2.1 37.9 1.0 O A:HOH1138 2.1 65.7 1.0 O A:HOH870 2.4 59.1 1.0 O A:HOH748 4.0 55.6 1.0 OD1 A:ASP243 4.4 27.1 1.0 O A:HOH749 4.4 34.5 1.0 CA A:GLY242 5.0 28.0 1.0

Magnesium binding site 3 out of 5 in the A. Fulgidus Lipase with Fatty Acid Fragment and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of A. Fulgidus Lipase with Fatty Acid Fragment and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2003 b:22.1 occ:1.00 O A:LYS411 2.3 28.9 1.0 O A:ARG406 2.3 23.6 1.0 OD1 A:ASP405 2.4 25.1 1.0 O A:HOH845 2.4 37.1 1.0 OD2 A:ASP409 2.5 27.6 1.0 OD1 A:ASP431 2.5 23.0 1.0 OD2 A:ASP431 2.8 27.2 1.0 CG A:ASP431 3.0 24.1 1.0 CG A:ASP409 3.4 29.9 1.0 C A:ARG406 3.5 26.4 1.0 C A:LYS411 3.5 28.2 1.0 CG A:ASP405 3.6 25.4 1.0 N A:ARG406 3.7 23.7 1.0 OD1 A:ASP409 3.7 32.0 1.0 C A:ASP405 3.9 23.9 1.0 N A:LYS411 4.0 25.5 1.0 CA A:ARG406 4.1 24.3 1.0 CA A:LYS411 4.2 26.3 1.0 CA A:ASP405 4.2 23.0 1.0 OD2 A:ASP405 4.4 26.6 1.0 CB A:LYS411 4.5 25.9 1.0 NE A:ARG406 4.5 29.7 1.0 CB A:ARG406 4.5 23.2 1.0 O A:ASP405 4.5 24.1 1.0 CB A:ASP431 4.5 19.9 1.0 N A:ASP409 4.5 29.4 1.0 CB A:ASP405 4.5 23.0 1.0 N A:SER412 4.6 28.7 1.0 N A:GLY407 4.6 25.6 1.0 CA A:SER412 4.7 29.3 1.0 CB A:ASP409 4.8 30.2 1.0 N A:ALA408 4.8 26.9 1.0 CA A:GLY407 4.9 29.3 1.0 N A:GLY410 4.9 26.0 1.0 CD A:ARG406 4.9 28.0 1.0 N A:ASP413 5.0 31.4 1.0

Magnesium binding site 4 out of 5 in the A. Fulgidus Lipase with Fatty Acid Fragment and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of A. Fulgidus Lipase with Fatty Acid Fragment and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2004 b:36.3 occ:1.00 O B:LYS411 2.1 53.6 1.0 OD1 B:ASP405 2.1 40.1 1.0 O B:ARG406 2.2 41.6 1.0 OD2 B:ASP409 2.6 52.2 1.0 OD1 B:ASP431 2.6 40.6 1.0 O B:HOH804 2.8 46.0 1.0 OD2 B:ASP431 2.9 42.3 1.0 CG B:ASP431 3.1 41.5 1.0 C B:LYS411 3.3 55.3 1.0 C B:ARG406 3.3 42.2 1.0 CG B:ASP405 3.4 40.3 1.0 CG B:ASP409 3.4 52.6 1.0 N B:ARG406 3.5 39.0 1.0 OD1 B:ASP409 3.6 51.1 1.0 C B:ASP405 3.7 38.5 1.0 N B:LYS411 3.9 54.9 1.0 CA B:ARG406 3.9 40.4 1.0 CA B:LYS411 4.0 55.6 1.0 CA B:ASP405 4.0 38.5 1.0 OD2 B:ASP405 4.2 40.5 1.0 CB B:LYS411 4.2 56.4 1.0 O B:ASP405 4.3 38.7 1.0 CB B:ASP405 4.3 39.5 1.0 CB B:ARG406 4.4 40.3 1.0 N B:ASP409 4.4 51.5 1.0 N B:SER412 4.4 55.0 1.0 N B:GLY407 4.4 43.3 1.0 CD B:ARG406 4.5 40.5 1.0 NE B:ARG406 4.6 41.9 1.0 N B:ALA408 4.6 48.7 1.0 CB B:ASP431 4.6 40.5 1.0 CA B:GLY407 4.7 46.4 1.0 CB B:ASP409 4.7 52.2 1.0 N B:GLY410 4.7 53.1 1.0 CA B:SER412 4.8 55.3 1.0 N B:ASP413 4.8 57.4 1.0 C B:GLY407 4.9 48.4 1.0 CA B:ASP409 4.9 52.5 1.0 C B:GLY410 5.0 54.5 1.0

Magnesium binding site 5 out of 5 in the A. Fulgidus Lipase with Fatty Acid Fragment and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of A. Fulgidus Lipase with Fatty Acid Fragment and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2005 b:38.2 occ:1.00 O B:HOH1236 1.9 49.9 1.0 O B:HOH727 2.1 34.8 1.0 O B:HOH1235 2.2 44.1 1.0 O B:HOH867 2.2 42.0 1.0 NE2 B:HIS158 2.3 23.8 1.0 O B:HOH726 2.5 52.1 1.0 CE1 B:HIS158 3.2 23.2 1.0 CD2 B:HIS158 3.3 25.3 1.0 O B:HOH728 3.9 47.2 1.0 O B:PHE226 4.3 20.8 1.0 O B:HOH723 4.3 54.6 1.0 O B:HOH709 4.4 45.5 1.0 ND1 B:HIS158 4.4 22.4 1.0 CG B:HIS158 4.5 21.7 1.0 O B:HOH725 4.6 33.3 1.0 O B:ILE227 4.9 22.9 1.0 CG B:PRO175 5.0 27.6 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