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Iron in PDB 3fc4: Ethylene Glycol Inhibited Form of Aldehyde Oxidoreductase From Desulfovibrio Gigas

Enzymatic activity of Ethylene Glycol Inhibited Form of Aldehyde Oxidoreductase From Desulfovibrio Gigas

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

Protein crystallography data

The structure of Ethylene Glycol Inhibited Form of Aldehyde Oxidoreductase From Desulfovibrio Gigas, PDB code: 3fc4 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) 29.44 / 1.79
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 142.800, 142.800, 161.550, 90.00, 90.00, 120.00
R / Rfree (%) 15.3 / 18.9

Other elements in 3fc4:

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

Molybdenum (Mo) 1 atom
Magnesium (Mg) 3 atoms
Chlorine (Cl) 3 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Ethylene Glycol Inhibited Form of Aldehyde Oxidoreductase From Desulfovibrio Gigas (pdb code 3fc4). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Ethylene Glycol Inhibited Form of Aldehyde Oxidoreductase From Desulfovibrio Gigas, PDB code: 3fc4:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3fc4

Go back to Iron Binding Sites List in 3fc4
Iron binding site 1 out of 4 in the Ethylene Glycol Inhibited Form of Aldehyde Oxidoreductase From Desulfovibrio Gigas


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ethylene Glycol Inhibited Form of Aldehyde Oxidoreductase From Desulfovibrio Gigas within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe908

b:12.3
occ:1.00
 FE1 A:FES908 0.0 12.3 1.0
S2 A:FES908 2.2 14.1 1.0
S1 A:FES908 2.2 13.1 1.0
SG A:CYS100 2.3 13.2 1.0
SG A:CYS139 2.4 13.5 1.0
FE2 A:FES908 2.7 12.8 1.0
CB A:CYS139 3.2 11.7 1.0
CB A:CYS100 3.4 11.9 1.0
N A:CYS100 3.6 12.4 1.0
CA A:CYS100 3.9 12.1 1.0
O A:HOH1255 3.9 11.6 1.0
N A:GLY101 4.0 12.6 1.0
N A:CYS139 4.1 11.9 1.0
CA A:CYS139 4.3 11.7 1.0
C A:CYS100 4.3 12.0 1.0
SG A:CYS137 4.4 14.2 1.0
N A:PHE102 4.4 12.7 1.0
SG A:CYS103 4.7 14.8 1.0
C A:GLN99 4.8 12.8 1.0
CB A:GLN99 4.8 11.8 1.0
N A:ARG138 4.8 12.8 1.0
N A:CYS103 4.9 13.2 1.0
CA A:GLY101 5.0 13.3 1.0

Iron binding site 2 out of 4 in 3fc4

Go back to Iron Binding Sites List in 3fc4
Iron binding site 2 out of 4 in the Ethylene Glycol Inhibited Form of Aldehyde Oxidoreductase From Desulfovibrio Gigas


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ethylene Glycol Inhibited Form of Aldehyde Oxidoreductase From Desulfovibrio Gigas within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe908

b:12.8
occ:1.00
 FE2 A:FES908 0.0 12.8 1.0
S2 A:FES908 2.2 14.1 1.0
S1 A:FES908 2.2 13.1 1.0
SG A:CYS103 2.3 14.8 1.0
SG A:CYS137 2.4 14.2 1.0
FE1 A:FES908 2.7 12.3 1.0
CB A:CYS103 3.4 12.9 1.0
CB A:CYS137 3.4 13.6 1.0
CA A:CYS137 3.7 13.9 1.0
O A:HOH1305 4.2 15.0 1.0
N A:ARG138 4.2 12.8 1.0
N A:CYS103 4.2 13.2 1.0
CB A:CYS139 4.3 11.7 1.0
N A:CYS139 4.3 11.9 1.0
CA A:CYS103 4.4 13.6 1.0
C A:CYS137 4.4 13.4 1.0
SG A:CYS139 4.5 13.5 1.0
SG A:CYS100 4.6 13.2 1.0
CG2 A:THR140 4.7 13.8 1.0
O A:ALA136 4.8 14.7 1.0
CA A:CYS139 4.9 11.7 1.0

Iron binding site 3 out of 4 in 3fc4

Go back to Iron Binding Sites List in 3fc4
Iron binding site 3 out of 4 in the Ethylene Glycol Inhibited Form of Aldehyde Oxidoreductase From Desulfovibrio Gigas


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ethylene Glycol Inhibited Form of Aldehyde Oxidoreductase From Desulfovibrio Gigas within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe909

b:16.5
occ:1.00
 FE1 A:FES909 0.0 16.5 1.0
S1 A:FES909 2.2 16.7 1.0
S2 A:FES909 2.2 16.8 1.0
SG A:CYS45 2.3 18.0 1.0
SG A:CYS40 2.4 19.8 1.0
FE2 A:FES909 2.8 16.7 1.0
CB A:CYS45 3.3 15.9 1.0
N A:CYS45 3.5 17.0 1.0
N A:CYS40 3.5 17.9 1.0
CB A:CYS40 3.7 18.2 1.0
CA A:CYS45 3.8 16.1 1.0
N A:GLU41 3.8 17.3 1.0
N A:GLY46 3.9 15.2 1.0
CA A:CYS40 4.0 17.8 1.0
C A:CYS45 4.2 15.9 1.0
N A:GLN44 4.2 18.5 1.0
SG A:CYS60 4.4 17.7 1.0
C A:CYS40 4.4 18.1 1.0
N A:ALA47 4.4 15.2 1.0
N A:GLY39 4.4 15.7 1.0
N A:GLY43 4.5 19.4 1.0
C A:GLY39 4.5 17.3 1.0
N A:GLN42 4.6 20.0 1.0
C A:GLN44 4.6 18.0 1.0
O A:HOH1550 4.6 24.4 1.0
SG A:CYS48 4.7 16.4 1.0
CA A:GLY39 4.7 16.5 1.0
CA A:GLU41 4.8 19.2 1.0
C A:GLY43 4.9 18.6 1.0
CA A:GLY43 4.9 18.8 1.0
CB A:ALA47 4.9 14.9 1.0
CA A:GLY46 4.9 15.1 1.0
CA A:GLN44 5.0 18.6 1.0

Iron binding site 4 out of 4 in 3fc4

Go back to Iron Binding Sites List in 3fc4
Iron binding site 4 out of 4 in the Ethylene Glycol Inhibited Form of Aldehyde Oxidoreductase From Desulfovibrio Gigas


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Ethylene Glycol Inhibited Form of Aldehyde Oxidoreductase From Desulfovibrio Gigas within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe909

b:16.7
occ:1.00
 FE2 A:FES909 0.0 16.7 1.0
S1 A:FES909 2.2 16.7 1.0
S2 A:FES909 2.2 16.8 1.0
SG A:CYS48 2.3 16.4 1.0
SG A:CYS60 2.3 17.7 1.0
FE1 A:FES909 2.8 16.5 1.0
CB A:CYS60 3.2 17.5 1.0
CB A:CYS48 3.5 15.5 1.0
N A:CYS60 4.2 17.1 1.0
N A:CYS48 4.3 15.7 1.0
CA A:CYS60 4.3 17.7 1.0
CB A:ARG58 4.3 15.9 1.0
N A:GLY43 4.4 19.4 1.0
CA A:CYS48 4.5 15.2 1.0
CG A:ARG58 4.5 16.5 1.0
SG A:CYS40 4.5 19.8 1.0
CA A:GLY43 4.6 18.8 1.0
N A:GLU41 4.6 17.3 1.0
SG A:CYS45 4.6 18.0 1.0
CA A:GLU41 4.8 19.2 1.0
N A:GLY46 4.9 15.2 1.0
N A:GLN42 4.9 20.0 1.0
N A:ALA47 4.9 15.2 1.0

Reference:

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
Page generated: Sun Aug 4 10:01:13 2024

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