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Magnesium in PDB 4c80: Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Hydrogen Peroxide

Enzymatic activity of Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Hydrogen Peroxide

All present enzymatic activity of Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Hydrogen Peroxide:
1.2.99.7;

Protein crystallography data

The structure of Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Hydrogen Peroxide, PDB code: 4c80 was solved by H.D.Correia, M.J.Romao, T.Santos-Silva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 123.89 / 1.50
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 143.057, 143.057, 162.292, 90.00, 90.00, 120.00
R / Rfree (%) 10.325 / 13.362

Other elements in 4c80:

The structure of Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Hydrogen Peroxide also contains other interesting chemical elements:

Molybdenum (Mo) 1 atom
Iron (Fe) 4 atoms
Chlorine (Cl) 3 atoms
Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Hydrogen Peroxide (pdb code 4c80). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Hydrogen Peroxide, PDB code: 4c80:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4c80

Go back to Magnesium Binding Sites List in 4c80
Magnesium binding site 1 out of 3 in the Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Hydrogen Peroxide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Hydrogen Peroxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg915

b:12.9
occ:1.00
 OE2 A:GLU903 2.1 13.7 1.0
O A:HOH3074 2.1 12.6 1.0
O A:HOH3077 2.1 15.3 1.0
O A:HOH3085 2.1 14.9 1.0
OE2 A:GLU899 2.2 12.7 1.0
CD A:GLU903 3.1 16.9 1.0
CD A:GLU899 3.2 13.5 1.0
CG A:GLU899 3.6 12.4 1.0
CG A:GLU903 3.6 14.6 1.0
O A:HOH3073 3.7 16.3 1.0
O A:HOH3075 3.9 31.6 1.0
OE1 A:GLU903 4.2 22.4 1.0
O A:HOH3076 4.3 35.1 1.0
OE1 A:GLU899 4.3 16.3 1.0
O A:HOH3082 4.6 41.3 1.0
O A:HOH3071 4.9 23.5 1.0

Magnesium binding site 2 out of 3 in 4c80

Go back to Magnesium Binding Sites List in 4c80
Magnesium binding site 2 out of 3 in the Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Hydrogen Peroxide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Hydrogen Peroxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg916

b:24.8
occ:1.00
 O A:HOH3096 2.0 28.6 1.0
O A:HOH3094 2.1 22.8 1.0
O A:HOH3095 2.1 23.7 1.0
O A:HOH3097 2.1 27.0 1.0
O A:HOH2769 2.1 17.9 1.0
O A:HOH3093 2.1 28.0 1.0
O A:HOH2771 4.0 24.9 1.0
O A:HOH2355 4.2 16.5 1.0
O A:HOH2808 4.2 26.1 1.0
O A:HOH2768 4.3 17.3 1.0
O A:HOH2356 4.3 23.1 1.0
OD1 A:ASP572 4.4 14.0 1.0
OD1 A:ASN511 4.7 15.5 1.0
O A:HOH2801 4.7 30.7 1.0
O A:HOH2390 4.8 30.9 1.0

Magnesium binding site 3 out of 3 in 4c80

Go back to Magnesium Binding Sites List in 4c80
Magnesium binding site 3 out of 3 in the Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Hydrogen Peroxide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Hydrogen Peroxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg917

b:25.5
occ:0.80
 O A:HOH3098 2.0 37.0 1.0
O A:HOH2187 2.0 36.7 1.0
O A:HOH3100 2.0 32.2 1.0
O A:HOH2326 2.0 32.4 1.0
O A:HOH2192 2.1 21.6 1.0
O A:HOH3099 2.2 40.2 1.0
O A:HOH2191 4.2 34.2 1.0
O A:LEU85 4.2 14.9 1.0
OE2 A:GLU162 4.2 25.4 1.0
O A:HOH2077 4.4 36.6 1.0
OE1 A:GLU162 4.4 27.8 1.0
O A:HOH2172 4.5 18.4 1.0
O A:HOH2630 4.5 37.5 1.0
CD A:PRO87 4.6 13.5 1.0
CD A:GLU162 4.8 24.4 1.0
OD1 A:ASN84 4.8 22.5 1.0

Reference:

J.Marangon, H.D.Correia, C.D.Brondino, J.J.G.Moura, M.J.Romao, P.J.Gonzalez, T.Santos-Silva. Kinetic and Structural Studies of Aldehyde Oxidoreductase From Desulfovibrio Gigas Reveal A Dithiolene-Based Chemistry For Enzyme Activation and Inhibition By H2O2. Plos One V. 8 83234 2013.
ISSN: ISSN 1932-6203
PubMed: 24391748
DOI: 10.1371/JOURNAL.PONE.0083234
Page generated: Thu Aug 15 16:44:45 2024

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