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Iron 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
Magnesium (Mg) 4 atoms
Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 4 binding sites of Iron where determined in the Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Benzaldehyde, PDB code: 4us8:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4us8

Go back to Iron Binding Sites List in 4us8
Iron 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 Iron with other atoms in the Fe 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:Fe908

b:7.1
occ:1.00
 FE1 A:FES908 0.0 7.1 1.0
S1 A:FES908 2.2 7.4 1.0
S2 A:FES908 2.2 7.3 1.0
SG A:CYS103 2.3 8.1 1.0
SG A:CYS137 2.4 7.2 1.0
FE2 A:FES908 2.7 6.7 1.0
CB A:CYS137 3.4 7.2 1.0
CB A:CYS103 3.4 7.4 1.0
CA A:CYS137 3.8 6.6 1.0
O A:HOH2255 4.2 7.4 1.0
N A:CYS103 4.2 6.7 1.0
N A:ARG138 4.2 6.3 1.0
CB A:CYS139 4.3 7.0 1.0
N A:CYS139 4.4 6.6 1.0
CA A:CYS103 4.4 6.7 1.0
SG A:CYS139 4.4 7.6 1.0
C A:CYS137 4.5 6.5 1.0
CG2 A:THR140 4.6 7.6 1.0
SG A:CYS100 4.6 7.0 1.0
O A:ALA136 4.9 7.4 1.0
CA A:CYS139 4.9 6.5 1.0

Iron binding site 2 out of 4 in 4us8

Go back to Iron Binding Sites List in 4us8
Iron 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 Iron with other atoms in the Fe 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:Fe908

b:6.7
occ:1.00
 FE2 A:FES908 0.0 6.7 1.0
S1 A:FES908 2.3 7.4 1.0
S2 A:FES908 2.3 7.3 1.0
SG A:CYS100 2.3 7.0 1.0
SG A:CYS139 2.4 7.6 1.0
FE1 A:FES908 2.7 7.1 1.0
CB A:CYS139 3.3 7.0 1.0
CB A:CYS100 3.4 7.2 1.0
N A:CYS100 3.7 6.3 1.0
O A:HOH2814 3.9 7.8 1.0
CA A:CYS100 3.9 6.8 1.0
N A:GLY101 4.0 6.0 1.0
N A:CYS139 4.2 6.6 1.0
CA A:CYS139 4.3 6.5 1.0
C A:CYS100 4.3 6.6 1.0
SG A:CYS137 4.4 7.2 1.0
N A:PHE102 4.4 6.1 1.0
SG A:CYS103 4.6 8.1 1.0
C A:GLN99 4.8 6.6 1.0
CB A:GLN99 4.9 7.3 1.0
N A:ARG138 4.9 6.3 1.0
N A:CYS103 4.9 6.7 1.0
CA A:GLY101 5.0 7.2 1.0

Iron binding site 3 out of 4 in 4us8

Go back to Iron Binding Sites List in 4us8
Iron 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 Iron with other atoms in the Fe 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:Fe909

b:10.1
occ:1.00
 FE1 A:FES909 0.0 10.1 1.0
S1 A:FES909 2.2 10.2 1.0
S2 A:FES909 2.2 10.2 1.0
SG A:CYS60 2.3 11.6 1.0
SG A:CYS48 2.3 9.8 1.0
FE2 A:FES909 2.7 10.2 1.0
CB A:CYS60 3.2 10.3 1.0
CB A:CYS48 3.4 9.4 1.0
N A:CYS60 4.2 9.9 1.0
N A:CYS48 4.3 8.1 1.0
CA A:CYS60 4.3 10.0 1.0
N A:GLY43 4.3 11.1 1.0
CB A:ARG58 4.4 10.7 1.0
SG A:CYS40 4.4 11.8 1.0
CA A:CYS48 4.5 8.1 1.0
CG A:ARG58 4.6 12.9 1.0
CA A:GLY43 4.6 11.7 1.0
N A:GLU41 4.6 10.4 1.0
SG A:CYS45 4.6 10.3 1.0
CA A:GLU41 4.7 11.2 1.0
N A:GLN42 4.9 11.8 1.0
N A:ALA47 4.9 8.2 1.0
N A:GLY46 4.9 8.2 1.0

Iron binding site 4 out of 4 in 4us8

Go back to Iron Binding Sites List in 4us8
Iron 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 Iron with other atoms in the Fe 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:Fe909

b:10.2
occ:1.00
 FE2 A:FES909 0.0 10.2 1.0
S1 A:FES909 2.2 10.2 1.0
S2 A:FES909 2.3 10.2 1.0
SG A:CYS45 2.3 10.3 1.0
SG A:CYS40 2.4 11.8 1.0
FE1 A:FES909 2.7 10.1 1.0
CB A:CYS45 3.4 10.0 1.0
N A:CYS40 3.5 9.6 1.0
N A:CYS45 3.5 9.5 1.0
CB A:CYS40 3.6 10.9 1.0
N A:GLU41 3.8 10.4 1.0
CA A:CYS45 3.9 10.0 1.0
CA A:CYS40 3.9 10.1 1.0
N A:GLY46 4.0 8.2 1.0
C A:CYS45 4.2 8.9 1.0
N A:GLN44 4.2 9.9 1.0
C A:CYS40 4.3 10.6 1.0
SG A:CYS60 4.3 11.6 1.0
N A:ALA47 4.4 8.2 1.0
N A:GLY43 4.4 11.1 1.0
N A:GLY39 4.4 8.9 1.0
C A:GLY39 4.5 10.7 1.0
N A:GLN42 4.6 11.8 1.0
C A:GLN44 4.7 10.6 1.0
SG A:CYS48 4.7 9.8 1.0
CA A:GLY39 4.8 10.5 1.0
O A:HOH2109 4.8 19.0 1.0
CA A:GLU41 4.8 11.2 1.0
CA A:GLY43 4.9 11.7 1.0
C A:GLY43 4.9 11.7 1.0
CB A:ALA47 4.9 9.1 1.0
CA A:GLY46 4.9 8.2 1.0
CA A:GLN44 5.0 10.7 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: Mon Aug 5 14:05:32 2024

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