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Iron 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
Magnesium (Mg) 3 atoms
Chlorine (Cl) 3 atoms
Sodium (Na) 2 atoms

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 4 binding sites of Iron where determined in the Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Hydrogen Peroxide, PDB code: 4c80:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4c80

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


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 Hydrogen Peroxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe908

b:8.7
occ:1.00
 FE1 A:FES908 0.0 8.7 1.0
S2 A:FES908 2.2 8.9 1.0
S1 A:FES908 2.2 8.8 1.0
SG A:CYS103 2.3 9.5 1.0
SG A:CYS137 2.4 8.5 1.0
FE2 A:FES908 2.7 8.4 1.0
CB A:CYS137 3.4 8.6 1.0
CB A:CYS103 3.4 9.0 1.0
CA A:CYS137 3.8 8.3 1.0
O A:HOH2210 4.2 9.8 1.0
N A:ARG138 4.2 8.3 1.0
N A:CYS103 4.3 8.3 1.0
CB A:CYS139 4.3 8.6 1.0
N A:CYS139 4.3 8.2 1.0
CA A:CYS103 4.4 8.5 1.0
SG A:CYS139 4.4 8.9 1.0
C A:CYS137 4.5 8.3 1.0
CG2 A:THR140 4.6 9.5 1.0
SG A:CYS100 4.6 8.4 1.0
O A:ALA136 4.8 9.4 1.0
CA A:CYS139 4.9 8.6 1.0

Iron binding site 2 out of 4 in 4c80

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


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 Hydrogen Peroxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe908

b:8.4
occ:1.00
 FE2 A:FES908 0.0 8.4 1.0
S2 A:FES908 2.2 8.9 1.0
S1 A:FES908 2.3 8.8 1.0
SG A:CYS100 2.3 8.4 1.0
SG A:CYS139 2.3 8.9 1.0
FE1 A:FES908 2.7 8.7 1.0
CB A:CYS139 3.3 8.6 1.0
CB A:CYS100 3.4 9.3 1.0
N A:CYS100 3.7 8.8 1.0
O A:HOH2684 3.9 9.1 1.0
CA A:CYS100 3.9 9.1 1.0
N A:GLY101 4.0 8.5 1.0
N A:CYS139 4.1 8.2 1.0
CA A:CYS139 4.3 8.6 1.0
C A:CYS100 4.4 8.9 1.0
SG A:CYS137 4.4 8.5 1.0
N A:PHE102 4.4 8.3 1.0
SG A:CYS103 4.6 9.5 1.0
C A:GLN99 4.8 8.4 1.0
CB A:GLN99 4.8 8.8 1.0
N A:ARG138 4.9 8.3 1.0
N A:CYS103 4.9 8.3 1.0
CA A:GLY101 5.0 8.7 1.0

Iron binding site 3 out of 4 in 4c80

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


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 Hydrogen Peroxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe909

b:11.8
occ:1.00
 FE1 A:FES909 0.0 11.8 1.0
S1 A:FES909 2.2 11.8 1.0
S2 A:FES909 2.2 12.1 1.0
SG A:CYS48 2.3 11.2 1.0
SG A:CYS60 2.3 12.9 1.0
FE2 A:FES909 2.7 12.0 1.0
CB A:CYS60 3.2 12.7 1.0
CB A:CYS48 3.4 10.6 1.0
N A:CYS60 4.2 11.9 1.0
N A:CYS48 4.3 9.7 1.0
CA A:CYS60 4.3 12.4 1.0
N A:GLY43 4.3 13.7 1.0
CB A:ARG58 4.4 13.2 1.0
SG A:CYS40 4.5 13.7 1.0
CA A:CYS48 4.5 9.6 1.0
CG A:ARG58 4.5 14.4 1.0
CA A:GLY43 4.5 14.3 1.0
N A:GLU41 4.6 12.3 1.0
SG A:CYS45 4.6 11.9 1.0
CA A:GLU41 4.7 13.3 1.0
N A:ALA47 4.9 9.8 1.0
N A:GLN42 4.9 13.3 1.0
N A:GLY46 4.9 10.9 1.0

Iron binding site 4 out of 4 in 4c80

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


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 Hydrogen Peroxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe909

b:12.0
occ:1.00
 FE2 A:FES909 0.0 12.0 1.0
S1 A:FES909 2.2 11.8 1.0
S2 A:FES909 2.2 12.1 1.0
SG A:CYS45 2.3 11.9 1.0
SG A:CYS40 2.4 13.7 1.0
FE1 A:FES909 2.7 11.8 1.0
CB A:CYS45 3.4 11.8 1.0
N A:CYS40 3.5 12.0 1.0
N A:CYS45 3.5 11.2 1.0
CB A:CYS40 3.6 12.5 1.0
N A:GLU41 3.8 12.3 1.0
CA A:CYS45 3.9 11.3 1.0
N A:GLY46 4.0 10.9 1.0
CA A:CYS40 4.0 12.9 1.0
C A:CYS45 4.2 11.3 1.0
N A:GLN44 4.3 12.0 1.0
C A:CYS40 4.3 13.1 1.0
SG A:CYS60 4.3 12.9 1.0
N A:ALA47 4.4 9.8 1.0
N A:GLY43 4.4 13.7 1.0
N A:GLY39 4.5 10.9 1.0
C A:GLY39 4.5 12.5 1.0
N A:GLN42 4.6 13.3 1.0
C A:GLN44 4.6 12.6 1.0
O A:HOH2096 4.7 21.2 1.0
SG A:CYS48 4.7 11.2 1.0
CA A:GLU41 4.8 13.3 1.0
CA A:GLY39 4.8 12.2 1.0
CA A:GLY43 4.8 14.3 1.0
C A:GLY43 4.9 14.1 1.0
CB A:ALA47 4.9 10.6 1.0
CA A:GLY46 4.9 10.6 1.0
CA A:GLN44 5.0 12.7 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: Mon Aug 5 00:17:51 2024

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