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Magnesium in PDB 4us8: Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Benzaldehyde

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

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

Protein crystallography data

The structure of Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Benzaldehyde, PDB code: 4us8 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) 124.04 / 1.49
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 143.229, 143.229, 162.250, 90.00, 90.00, 120.00
R / Rfree (%) 9.109 / 12.215

Other elements in 4us8:

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

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Benzaldehyde (pdb code 4us8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Benzaldehyde, PDB code: 4us8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4us8

Go back to Magnesium Binding Sites List in 4us8
Magnesium binding site 1 out of 4 in the Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Benzaldehyde


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 Benzaldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg915

b:23.7
occ:0.80
 O A:HOH3258 2.0 35.5 1.0
O A:HOH2230 2.0 34.3 1.0
O A:HOH2405 2.0 32.0 1.0
O A:HOH2236 2.1 20.9 1.0
O A:HOH3257 2.1 43.3 1.0
O A:HOH3259 2.2 32.1 1.0
OE2 A:GLU162 4.2 24.8 1.0
O A:HOH2235 4.2 36.4 1.0
O A:LEU85 4.2 13.4 1.0
O A:HOH2084 4.3 38.5 1.0
OE1 A:GLU162 4.4 26.3 1.0
O A:HOH2157 4.4 39.0 1.0
O A:HOH2210 4.5 16.6 1.0
CD A:PRO87 4.5 12.4 1.0
CD A:GLU162 4.7 22.5 1.0
OD1 A:ASN84 4.8 22.4 1.0

Magnesium binding site 2 out of 4 in 4us8

Go back to Magnesium Binding Sites List in 4us8
Magnesium binding site 2 out of 4 in the Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Benzaldehyde


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 Benzaldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg916

b:11.4
occ:0.50
 O A:HOH3195 1.9 27.0 1.0
O A:HOH3263 2.0 21.1 1.0
O A:HOH3261 2.1 23.8 1.0
O A:HOH3260 2.1 29.0 1.0
O A:HOH3193 2.1 25.2 1.0
O A:HOH3262 2.2 27.6 1.0
O A:HOH2713 4.1 40.0 1.0
O A:HOH2669 4.1 24.9 1.0
OD2 A:ASP826 4.1 9.5 0.5
O A:HOH2720 4.2 23.1 1.0
O A:HOH3187 4.3 16.3 1.0
OD1 A:ASP826 4.3 10.6 0.5
O A:HOH2671 4.4 23.4 1.0
O A:HOH2668 4.4 45.1 1.0
O A:HOH3192 4.4 26.3 1.0
O A:HOH3203 4.4 22.5 1.0
CG A:ASP826 4.6 9.1 0.5

Magnesium binding site 3 out of 4 in 4us8

Go back to Magnesium Binding Sites List in 4us8
Magnesium binding site 3 out of 4 in the Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Benzaldehyde


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 Benzaldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg917

b:11.9
occ:1.00
 OD2 A:ASP263 2.0 10.3 1.0
O A:HOH2642 2.1 13.1 1.0
O A:HOH3264 2.1 14.3 1.0
O A:HOH2641 2.1 11.5 1.0
CG A:ASP263 3.1 9.4 1.0
OD1 A:ASP263 3.4 10.0 1.0
O A:HOH2598 3.8 15.6 1.0
O A:HOH2639 4.2 14.1 1.0
CB A:ASP263 4.4 8.8 1.0
O A:HOH2253 4.4 14.7 1.0
O A:HOH2749 4.5 32.8 1.0
CB A:TRP265 4.7 9.5 1.0
O A:HOH2597 4.8 32.9 1.0

Magnesium binding site 4 out of 4 in 4us8

Go back to Magnesium Binding Sites List in 4us8
Magnesium binding site 4 out of 4 in the Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Benzaldehyde


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Benzaldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg918

b:19.3
occ:0.80
 O A:HOH3269 2.1 26.9 1.0
O A:HOH3267 2.1 28.9 1.0
O A:HOH3268 2.1 21.8 1.0
O A:HOH2901 2.1 16.5 1.0
O A:HOH3265 2.1 22.7 1.0
O A:HOH3266 2.2 26.6 1.0
O A:HOH2904 4.0 22.5 1.0
O A:HOH2417 4.2 15.0 1.0
O A:HOH2944 4.2 25.0 1.0
O A:HOH2418 4.2 21.4 1.0
O A:HOH2902 4.3 16.4 1.0
O A:HOH2399 4.3 38.2 1.0
OD1 A:ASP572 4.4 12.8 1.0
O A:HOH2460 4.7 30.8 1.0
O A:HOH2938 4.7 29.2 1.0
OD1 A:ASN511 4.8 15.3 1.0

Reference:

H.D.Correia, J.Marangon, C.D.Brondino, J.J.G.Moura, M.J.Romao, P.J.Gonzalez, T.Santos-Silva. Aromatic Aldehydes at the Active Site of Aldehyde Oxidoreductase From Desulfovibrio Gigas: Reactivity and Molecular Details of the Enzyme-Substrate and Enzyme- Product Interaction. J.Biol.Inorg.Chem. 2014.
ISSN: ESSN 1432-1327
PubMed: 25261288
DOI: 10.1007/S00775-014-1196-4
Page generated: Tue Aug 20 04:58:02 2024

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