Magnesium in PDB 3fah: Glycerol Inhibited Form of Aldehyde Oxidoreductase From Desulfovibrio Gigas

All present enzymatic activity of Glycerol Inhibited Form of Aldehyde Oxidoreductase From Desulfovibrio Gigas:
1.2.99.7;

The structure of Glycerol Inhibited Form of Aldehyde Oxidoreductase From Desulfovibrio Gigas, PDB code: 3fah was solved by T.Santos-Silva, M.J.Romao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.98 / 1.72
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	142.560, 142.560, 161.880, 90.00, 90.00, 120.00
R / Rfree (%)	16 / 19.1

The structure of Glycerol Inhibited Form of Aldehyde Oxidoreductase From Desulfovibrio Gigas also contains other interesting chemical elements:

Molybdenum	(Mo)	1 atom
Iron	(Fe)	4 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Magnesium atom in the Glycerol Inhibited Form of Aldehyde Oxidoreductase From Desulfovibrio Gigas (pdb code 3fah). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Glycerol Inhibited Form of Aldehyde Oxidoreductase From Desulfovibrio Gigas, PDB code: 3fah:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Glycerol Inhibited Form of Aldehyde Oxidoreductase From Desulfovibrio Gigas


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Glycerol Inhibited Form of Aldehyde Oxidoreductase From Desulfovibrio Gigas within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg919 b:40.0 occ:1.00 O A:HOH1846 2.1 27.9 1.0 O A:HOH941 2.1 36.9 1.0 O A:HOH942 2.2 34.2 1.0 O A:HOH940 2.2 24.0 1.0 O A:HOH1843 2.3 32.0 1.0 O A:HOH1422 2.3 20.6 1.0 O A:HOH1634 4.1 26.4 1.0 O A:HOH1460 4.2 20.9 1.0 O A:HOH1487 4.2 19.1 1.0 O A:HOH1656 4.2 26.9 1.0 O A:HOH1545 4.3 27.4 1.0 OD2 A:ASP572 4.5 23.6 1.0 O A:HOH1824 4.5 32.8 1.0 ND2 A:ASN511 4.8 23.4 1.0 O A:HOH2002 4.9 32.8 1.0 O A:HOH1810 5.0 43.1 1.0

Magnesium binding site 2 out of 3 in the Glycerol Inhibited Form of Aldehyde Oxidoreductase From Desulfovibrio Gigas


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Glycerol Inhibited Form of Aldehyde Oxidoreductase From Desulfovibrio Gigas within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg917 b:18.2 occ:1.00 OE2 A:GLU903 2.0 24.2 1.0 OE2 A:GLU899 2.1 22.2 1.0 O A:HOH956 2.1 16.3 1.0 O A:HOH1468 2.1 18.2 1.0 O A:HOH1389 2.2 18.3 1.0 CD A:GLU903 3.1 26.8 1.0 CD A:GLU899 3.1 22.6 1.0 CG A:GLU899 3.5 21.8 1.0 CG A:GLU903 3.5 24.5 1.0 O A:HOH1729 3.8 33.5 1.0 OE1 A:GLU903 4.2 31.5 1.0 OE1 A:GLU899 4.2 24.6 1.0 O A:HOH960 4.8 24.4 1.0

Magnesium binding site 3 out of 3 in the Glycerol Inhibited Form of Aldehyde Oxidoreductase From Desulfovibrio Gigas


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Glycerol Inhibited Form of Aldehyde Oxidoreductase From Desulfovibrio Gigas within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg915 b:36.6 occ:1.00 O A:HOH995 2.0 39.5 1.0 O A:HOH1080 2.1 46.7 1.0 O A:HOH994 2.2 27.3 1.0 O A:HOH1103 2.2 36.8 1.0 O A:HOH1102 2.3 42.9 1.0 O A:HOH1894 2.4 35.1 1.0 OE1 A:GLU162 4.1 32.4 1.0 O A:LEU85 4.2 24.0 1.0 OE2 A:GLU162 4.3 31.8 1.0 CD A:PRO87 4.5 24.0 1.0 O A:HOH1079 4.5 37.9 1.0 O A:HOH2024 4.6 44.8 1.0 O A:HOH1334 4.6 21.8 1.0 CD A:GLU162 4.7 33.1 1.0 OD1 A:ASN84 4.9 29.9 1.0 O A:HOH1811 5.0 46.2 1.0

T.Santos-Silva, F.Ferroni, A.Thapper, J.Marangon, P.J.Gonzalez, A.C.Rizzi, I.Moura, J.J.Moura, M.J.Romao, C.D.Brondino. Kinetic, Structural, and Epr Studies Reveal That Aldehyde Oxidoreductase From Desulfovibrio Gigas Does Not Need A Sulfido Ligand For Catalysis and Give Evidence For A Direct Mo-C Interaction in A Biological System. J.Am.Chem.Soc. V. 131 7990 2009.
ISSN: ISSN 0002-7863
PubMed: 19459677
DOI: 10.1021/JA809448R