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Iron in PDB 1vlb: Structure Refinement of the Aldehyde Oxidoreductase From Desulfovibrio Gigas at 1.28 A

Enzymatic activity of Structure Refinement of the Aldehyde Oxidoreductase From Desulfovibrio Gigas at 1.28 A

All present enzymatic activity of Structure Refinement of the Aldehyde Oxidoreductase From Desulfovibrio Gigas at 1.28 A:
1.2.3.1;

Protein crystallography data

The structure of Structure Refinement of the Aldehyde Oxidoreductase From Desulfovibrio Gigas at 1.28 A, PDB code: 1vlb was solved by J.M.Rebelo, J.M.Dias, R.Huber, J.J.G.Moura, M.J.Romao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.40 / 1.28
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 141.780, 141.780, 160.870, 90.00, 90.00, 120.00
R / Rfree (%) 14.8 / 19.3

Other elements in 1vlb:

The structure of Structure Refinement of the Aldehyde Oxidoreductase From Desulfovibrio Gigas at 1.28 A also contains other interesting chemical elements:

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

Iron Binding Sites:

The binding sites of Iron atom in the Structure Refinement of the Aldehyde Oxidoreductase From Desulfovibrio Gigas at 1.28 A (pdb code 1vlb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure Refinement of the Aldehyde Oxidoreductase From Desulfovibrio Gigas at 1.28 A, PDB code: 1vlb:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1vlb

Go back to Iron Binding Sites List in 1vlb
Iron binding site 1 out of 4 in the Structure Refinement of the Aldehyde Oxidoreductase From Desulfovibrio Gigas at 1.28 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure Refinement of the Aldehyde Oxidoreductase From Desulfovibrio Gigas at 1.28 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe908

b:15.4
occ:1.00
 FE1 A:FES908 0.0 15.4 1.0
S2 A:FES908 2.2 16.9 1.0
S1 A:FES908 2.3 16.9 1.0
SG A:CYS100 2.3 16.2 1.0
SG A:CYS139 2.3 16.5 1.0
FE2 A:FES908 2.7 15.9 1.0
CB A:CYS139 3.3 16.1 1.0
CB A:CYS100 3.4 16.2 1.0
N A:CYS100 3.6 16.0 1.0
CA A:CYS100 3.9 15.9 1.0
O A:HOH4105 3.9 17.1 1.0
N A:GLY101 3.9 15.5 1.0
N A:CYS139 4.1 15.2 1.0
CA A:CYS139 4.3 14.9 1.0
C A:CYS100 4.3 18.6 1.0
N A:PHE102 4.4 15.7 1.0
SG A:CYS137 4.4 16.3 1.0
SG A:CYS103 4.7 16.9 1.0
C A:GLN99 4.8 14.5 1.0
CB A:GLN99 4.8 16.1 1.0
N A:ARG138 4.8 16.7 1.0
N A:CYS103 4.9 15.7 1.0
CA A:GLY101 5.0 15.2 1.0

Iron binding site 2 out of 4 in 1vlb

Go back to Iron Binding Sites List in 1vlb
Iron binding site 2 out of 4 in the Structure Refinement of the Aldehyde Oxidoreductase From Desulfovibrio Gigas at 1.28 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure Refinement of the Aldehyde Oxidoreductase From Desulfovibrio Gigas at 1.28 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe908

b:15.9
occ:1.00
 FE2 A:FES908 0.0 15.9 1.0
S2 A:FES908 2.2 16.9 1.0
S1 A:FES908 2.2 16.9 1.0
SG A:CYS103 2.3 16.9 1.0
SG A:CYS137 2.4 16.3 1.0
FE1 A:FES908 2.7 15.4 1.0
CB A:CYS137 3.4 17.4 1.0
CB A:CYS103 3.4 16.5 1.0
CA A:CYS137 3.8 16.6 1.0
O A:HOH4465 4.1 18.2 1.0
N A:ARG138 4.2 16.7 1.0
N A:CYS103 4.2 15.7 1.0
N A:CYS139 4.3 15.2 1.0
CB A:CYS139 4.3 16.1 1.0
CA A:CYS103 4.4 15.6 1.0
SG A:CYS139 4.4 16.5 1.0
C A:CYS137 4.4 16.7 1.0
CG2 A:THR140 4.6 16.9 1.0
SG A:CYS100 4.6 16.2 1.0
O A:ALA136 4.9 17.8 1.0
CA A:CYS139 4.9 14.9 1.0

Iron binding site 3 out of 4 in 1vlb

Go back to Iron Binding Sites List in 1vlb
Iron binding site 3 out of 4 in the Structure Refinement of the Aldehyde Oxidoreductase From Desulfovibrio Gigas at 1.28 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure Refinement of the Aldehyde Oxidoreductase From Desulfovibrio Gigas at 1.28 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe909

b:17.1
occ:1.00
 FE1 A:FES909 0.0 17.1 1.0
S2 A:FES909 2.3 18.9 1.0
S1 A:FES909 2.3 18.8 1.0
SG A:CYS45 2.3 18.4 1.0
SG A:CYS40 2.4 19.2 1.0
FE2 A:FES909 2.7 17.0 1.0
CB A:CYS45 3.4 18.3 1.0
N A:CYS40 3.5 18.2 1.0
N A:CYS45 3.5 19.4 1.0
CB A:CYS40 3.6 18.9 1.0
N A:GLU41 3.8 18.6 1.0
CA A:CYS45 3.8 17.8 1.0
CA A:CYS40 3.9 16.7 1.0
N A:GLY46 4.0 17.2 1.0
C A:CYS45 4.2 16.9 1.0
N A:GLN44 4.2 19.9 1.0
C A:CYS40 4.3 18.3 1.0
SG A:CYS60 4.3 18.7 1.0
N A:GLY43 4.4 19.1 1.0
N A:ALA47 4.4 18.0 1.0
C A:GLY39 4.4 18.0 1.0
N A:GLY39 4.5 18.0 1.0
N A:GLN42 4.5 20.7 1.0
C A:GLN44 4.6 17.9 1.0
CA A:GLY39 4.7 18.1 1.0
SG A:CYS48 4.7 17.9 1.0
CA A:GLU41 4.7 18.8 1.0
CA A:GLY43 4.8 19.0 1.0
O A:HOH4200 4.8 23.2 1.0
C A:GLY43 4.9 16.8 1.0
CA A:GLN44 4.9 20.8 1.0
CB A:ALA47 4.9 18.0 1.0
CA A:GLY46 5.0 17.6 1.0

Iron binding site 4 out of 4 in 1vlb

Go back to Iron Binding Sites List in 1vlb
Iron binding site 4 out of 4 in the Structure Refinement of the Aldehyde Oxidoreductase From Desulfovibrio Gigas at 1.28 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure Refinement of the Aldehyde Oxidoreductase From Desulfovibrio Gigas at 1.28 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe909

b:17.0
occ:1.00
 FE2 A:FES909 0.0 17.0 1.0
S1 A:FES909 2.2 18.8 1.0
S2 A:FES909 2.2 18.9 1.0
SG A:CYS60 2.3 18.7 1.0
SG A:CYS48 2.3 17.9 1.0
FE1 A:FES909 2.7 17.1 1.0
CB A:CYS60 3.2 20.3 1.0
CB A:CYS48 3.5 18.9 1.0
N A:CYS60 4.2 18.3 1.0
N A:CYS48 4.3 16.5 1.0
CA A:CYS60 4.3 19.0 1.0
N A:GLY43 4.3 19.1 1.0
CB A:ARG58 4.3 17.9 1.0
SG A:CYS40 4.4 19.2 1.0
CG A:ARG58 4.5 20.7 1.0
CA A:GLY43 4.5 19.0 1.0
CA A:CYS48 4.5 17.3 1.0
SG A:CYS45 4.6 18.4 1.0
N A:GLU41 4.6 18.6 1.0
CA A:GLU41 4.7 18.8 1.0
N A:GLN42 4.9 20.7 1.0
N A:GLY46 4.9 17.2 1.0
N A:ALA47 5.0 18.0 1.0

Reference:

J.M.Rebelo, J.M.Dias, R.Huber, J.J.G.Moura, M.J.Romao. Structure Refinement of the Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop) at 1.28 A J.Biol.Inorg.Chem. V. 6 791 2001.
ISSN: ISSN 0949-8257
PubMed: 11713686
DOI: 10.1007/S007750100255
Page generated: Sat Aug 3 16:14:38 2024

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