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Iron in PDB 4c7y: Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Sodium Dithionite and Sodium Sulfide

Enzymatic activity of Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Sodium Dithionite and Sodium Sulfide

All present enzymatic activity of Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Sodium Dithionite and Sodium Sulfide:
1.2.99.7;

Protein crystallography data

The structure of Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Sodium Dithionite and Sodium Sulfide, PDB code: 4c7y 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) 124.06 / 1.57
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 143.250, 143.250, 162.300, 90.00, 90.00, 120.00
R / Rfree (%) 13.44 / 15.792

Other elements in 4c7y:

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

Molybdenum (Mo) 1 atom
Magnesium (Mg) 3 atoms
Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Sodium Dithionite and Sodium Sulfide (pdb code 4c7y). 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 Sodium Dithionite and Sodium Sulfide, PDB code: 4c7y:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4c7y

Go back to Iron Binding Sites List in 4c7y
Iron binding site 1 out of 4 in the Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Sodium Dithionite and Sodium Sulfide


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 Sodium Dithionite and Sodium Sulfide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe908

b:7.5
occ:1.00
 FE1 A:FES908 0.0 7.5 1.0
S2 A:FES908 2.2 8.6 1.0
S1 A:FES908 2.2 7.9 1.0
SG A:CYS103 2.3 7.8 1.0
SG A:CYS137 2.3 6.7 1.0
FE2 A:FES908 2.7 7.2 1.0
CB A:CYS137 3.4 7.4 1.0
CB A:CYS103 3.4 7.2 1.0
CA A:CYS137 3.8 7.2 1.0
O A:HOH2230 4.2 8.4 1.0
N A:CYS103 4.3 7.8 1.0
N A:ARG138 4.3 7.2 1.0
CB A:CYS139 4.3 7.8 1.0
N A:CYS139 4.4 7.1 1.0
CA A:CYS103 4.4 7.4 1.0
C A:CYS137 4.4 7.1 1.0
SG A:CYS139 4.5 8.3 1.0
SG A:CYS100 4.6 6.6 1.0
CG2 A:THR140 4.6 6.6 1.0
O A:ALA136 4.9 7.1 1.0
CA A:CYS139 4.9 7.5 1.0

Iron binding site 2 out of 4 in 4c7y

Go back to Iron Binding Sites List in 4c7y
Iron binding site 2 out of 4 in the Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Sodium Dithionite and Sodium Sulfide


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 Sodium Dithionite and Sodium Sulfide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe908

b:7.2
occ:1.00
 FE2 A:FES908 0.0 7.2 1.0
S2 A:FES908 2.2 8.6 1.0
S1 A:FES908 2.3 7.9 1.0
SG A:CYS100 2.3 6.6 1.0
SG A:CYS139 2.4 8.3 1.0
FE1 A:FES908 2.7 7.5 1.0
CB A:CYS139 3.3 7.8 1.0
CB A:CYS100 3.4 6.9 1.0
N A:CYS100 3.7 6.8 1.0
O A:HOH2781 3.9 8.7 1.0
CA A:CYS100 3.9 7.1 1.0
N A:GLY101 4.0 6.8 1.0
N A:CYS139 4.2 7.1 1.0
C A:CYS100 4.3 7.4 1.0
SG A:CYS137 4.4 6.7 1.0
CA A:CYS139 4.4 7.5 1.0
N A:PHE102 4.5 7.3 1.0
SG A:CYS103 4.7 7.8 1.0
C A:GLN99 4.8 7.0 1.0
CB A:GLN99 4.8 6.9 1.0
N A:CYS103 4.9 7.8 1.0
N A:ARG138 4.9 7.2 1.0
CA A:GLY101 5.0 7.0 1.0

Iron binding site 3 out of 4 in 4c7y

Go back to Iron Binding Sites List in 4c7y
Iron binding site 3 out of 4 in the Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Sodium Dithionite and Sodium Sulfide


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 Sodium Dithionite and Sodium Sulfide 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 10.3 1.0
S2 A:FES909 2.2 10.1 1.0
SG A:CYS60 2.3 11.9 1.0
SG A:CYS48 2.3 10.3 1.0
FE2 A:FES909 2.7 10.7 1.0
CB A:CYS60 3.2 10.4 1.0
CB A:CYS48 3.5 9.4 1.0
N A:CYS60 4.2 10.6 1.0
N A:CYS48 4.3 9.6 1.0
CA A:CYS60 4.3 11.3 1.0
N A:GLY43 4.4 13.5 1.0
CB A:ARG58 4.4 12.5 1.0
SG A:CYS40 4.5 13.9 1.0
CG A:ARG58 4.5 13.9 1.0
CA A:CYS48 4.5 9.2 1.0
CA A:GLY43 4.6 13.2 1.0
N A:GLU41 4.6 12.8 1.0
SG A:CYS45 4.6 11.1 1.0
CA A:GLU41 4.7 14.4 1.0
N A:GLY46 4.9 9.3 1.0
N A:ALA47 4.9 9.3 1.0
N A:GLN42 5.0 14.7 1.0

Iron binding site 4 out of 4 in 4c7y

Go back to Iron Binding Sites List in 4c7y
Iron binding site 4 out of 4 in the Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Sodium Dithionite and Sodium Sulfide


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 Sodium Dithionite and Sodium Sulfide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe909

b:10.7
occ:1.00
 FE2 A:FES909 0.0 10.7 1.0
S2 A:FES909 2.2 10.1 1.0
S1 A:FES909 2.2 10.3 1.0
SG A:CYS45 2.3 11.1 1.0
SG A:CYS40 2.4 13.9 1.0
FE1 A:FES909 2.7 10.1 1.0
CB A:CYS45 3.4 8.4 1.0
N A:CYS45 3.5 10.6 1.0
N A:CYS40 3.5 11.7 1.0
CB A:CYS40 3.6 12.0 1.0
N A:GLU41 3.8 12.8 1.0
CA A:CYS45 3.9 9.9 1.0
N A:GLY46 4.0 9.3 1.0
CA A:CYS40 4.0 12.4 1.0
C A:CYS45 4.2 8.9 1.0
N A:GLN44 4.3 12.9 1.0
SG A:CYS60 4.3 11.9 1.0
C A:CYS40 4.3 15.2 1.0
N A:ALA47 4.4 9.3 1.0
N A:GLY39 4.4 10.2 1.0
N A:GLY43 4.5 13.5 1.0
C A:GLY39 4.5 12.1 1.0
C A:GLN44 4.7 14.1 1.0
SG A:CYS48 4.7 10.3 1.0
N A:GLN42 4.7 14.7 1.0
O A:HOH2106 4.7 22.3 1.0
CA A:GLY39 4.7 11.1 1.0
CA A:GLU41 4.8 14.4 1.0
CA A:GLY43 4.9 13.2 1.0
C A:GLY43 4.9 12.5 1.0
CB A:ALA47 4.9 8.9 1.0
CA A:GLY46 5.0 10.4 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 00:16:31 2024

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