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Iron in PDB 1ffv: Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava

Protein crystallography data

The structure of Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava, PDB code: 1ffv was solved by P.Haenzelmann, H.Dobbek, L.Gremer, R.Huber, O.Meyer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.373, 193.793, 218.755, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 23.7

Other elements in 1ffv:

The structure of Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava also contains other interesting chemical elements:

Molybdenum (Mo) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava (pdb code 1ffv). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava, PDB code: 1ffv:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 1ffv

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Iron binding site 1 out of 8 in the Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1907

b:23.4
occ:1.00
 FE1 A:FES1907 0.0 23.4 1.0
S2 A:FES1907 2.2 23.9 1.0
S1 A:FES1907 2.2 23.2 1.0
SG A:CYS138 2.3 24.0 1.0
SG A:CYS101 2.3 23.8 1.0
FE2 A:FES1907 2.7 24.3 1.0
CB A:CYS138 3.4 23.8 1.0
CB A:CYS101 3.4 24.2 1.0
N A:CYS101 3.7 24.8 1.0
O B:HOH1924 3.8 26.0 1.0
N A:GLY102 3.9 24.8 1.0
CA A:CYS101 4.0 24.6 1.0
N A:CYS138 4.1 24.0 1.0
N A:PHE103 4.2 24.4 1.0
C A:CYS101 4.3 24.9 1.0
SG A:CYS136 4.4 22.7 1.0
CA A:CYS138 4.4 23.9 1.0
N A:CYS104 4.7 24.2 1.0
SG A:CYS104 4.7 23.9 1.0
CB A:PHE103 4.7 23.4 1.0
N A:ARG137 4.7 23.9 1.0
C A:GLN100 4.8 24.8 1.0
CA A:GLY102 4.8 24.7 1.0
CA A:PHE103 4.9 24.1 1.0
N A:GLN100 4.9 25.4 1.0
C A:GLY102 5.0 24.6 1.0

Iron binding site 2 out of 8 in 1ffv

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Iron binding site 2 out of 8 in the Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1907

b:24.3
occ:1.00
 FE2 A:FES1907 0.0 24.3 1.0
S1 A:FES1907 2.2 23.2 1.0
S2 A:FES1907 2.2 23.9 1.0
SG A:CYS104 2.3 23.9 1.0
SG A:CYS136 2.3 22.7 1.0
FE1 A:FES1907 2.7 23.4 1.0
CB A:CYS104 3.3 24.2 1.0
CB A:CYS136 3.4 23.8 1.0
CA A:CYS136 3.8 23.5 1.0
N A:CYS104 4.0 24.2 1.0
N A:ARG137 4.1 23.9 1.0
CA A:CYS104 4.2 24.2 1.0
N A:CYS138 4.3 24.0 1.0
O A:HOH1919 4.4 18.6 1.0
SG A:CYS138 4.4 24.0 1.0
C A:CYS136 4.4 23.7 1.0
CB A:CYS138 4.4 23.8 1.0
SG A:CYS101 4.8 23.8 1.0
C A:CYS104 4.8 24.3 1.0
CG2 A:THR139 4.8 23.7 1.0
N A:THR105 4.9 24.5 1.0
O A:LEU135 4.9 23.8 1.0
CA A:CYS138 4.9 23.9 1.0
N A:THR139 5.0 24.5 1.0

Iron binding site 3 out of 8 in 1ffv

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Iron binding site 3 out of 8 in the Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1908

b:26.1
occ:1.00
 FE1 A:FES1908 0.0 26.1 1.0
S1 A:FES1908 2.2 25.4 1.0
S2 A:FES1908 2.3 26.2 1.0
SG A:CYS47 2.3 25.4 1.0
SG A:CYS42 2.3 25.5 1.0
FE2 A:FES1908 2.7 26.5 1.0
CB A:CYS47 3.5 25.3 1.0
N A:CYS42 3.5 23.5 1.0
CB A:CYS42 3.5 24.7 1.0
N A:CYS47 3.6 24.9 1.0
O A:CYS42 3.7 24.8 1.0
N A:GLY48 3.7 24.5 1.0
CA A:CYS47 3.9 25.1 1.0
CA A:CYS42 3.9 24.3 1.0
C A:CYS42 4.0 24.6 1.0
N A:GLY41 4.2 22.9 1.0
O C:HOH1935 4.2 33.4 1.0
C A:GLY41 4.3 23.3 1.0
C A:CYS47 4.3 25.1 1.0
N A:HIS46 4.3 25.2 1.0
SG A:CYS62 4.3 25.7 1.0
C A:HIS46 4.6 25.2 1.0
CA A:GLY41 4.6 22.9 1.0
CA A:SER45 4.6 25.3 1.0
SG A:CYS50 4.6 25.4 1.0
C A:SER45 4.7 25.3 1.0
N A:ALA49 4.7 24.5 1.0
N A:SER45 4.7 25.4 1.0
CA A:GLY48 4.8 24.1 1.0
CA A:HIS46 5.0 25.0 1.0

Iron binding site 4 out of 8 in 1ffv

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Iron binding site 4 out of 8 in the Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1908

b:26.5
occ:1.00
 FE2 A:FES1908 0.0 26.5 1.0
S1 A:FES1908 2.2 25.4 1.0
S2 A:FES1908 2.2 26.2 1.0
SG A:CYS50 2.3 25.4 1.0
SG A:CYS62 2.3 25.7 1.0
FE1 A:FES1908 2.7 26.1 1.0
CB A:CYS62 3.2 25.1 1.0
CB A:CYS50 3.4 24.7 1.0
O C:HOH1935 4.0 33.4 1.0
N A:CYS62 4.3 24.8 1.0
N A:CYS50 4.4 24.3 1.0
CB A:LYS60 4.4 23.9 1.0
CA A:CYS62 4.4 25.0 1.0
SG A:CYS47 4.4 25.4 1.0
N A:GLY48 4.5 24.5 1.0
CA A:CYS50 4.5 24.0 1.0
SG A:CYS42 4.6 25.5 1.0
O A:CYS42 4.7 24.8 1.0
CA A:GLY48 4.8 24.1 1.0
N A:ALA49 4.8 24.5 1.0
CA A:SER45 4.8 25.3 1.0
CG A:LYS60 4.9 23.3 1.0
CD A:LYS60 5.0 22.9 1.0

Iron binding site 5 out of 8 in 1ffv

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Iron binding site 5 out of 8 in the Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1909

b:25.4
occ:1.00
 FE1 D:FES1909 0.0 25.4 1.0
S2 D:FES1909 2.2 24.7 1.0
S1 D:FES1909 2.2 24.6 1.0
SG D:CYS138 2.3 25.3 1.0
SG D:CYS101 2.4 24.6 1.0
FE2 D:FES1909 2.7 25.6 1.0
CB D:CYS138 3.4 24.4 1.0
CB D:CYS101 3.5 24.8 1.0
N D:CYS101 3.6 24.0 1.0
CA D:CYS101 3.9 24.4 1.0
O E:HOH1930 3.9 31.8 1.0
N D:GLY102 4.0 24.4 1.0
N D:CYS138 4.1 24.2 1.0
N D:PHE103 4.2 23.9 1.0
C D:CYS101 4.3 24.1 1.0
SG D:CYS136 4.4 24.5 1.0
CA D:CYS138 4.4 24.7 1.0
N D:CYS104 4.6 23.2 1.0
SG D:CYS104 4.7 24.0 1.0
CB D:PHE103 4.7 22.9 1.0
C D:GLN100 4.8 24.1 1.0
N D:ARG137 4.8 24.6 1.0
CA D:GLY102 4.9 23.8 1.0
CA D:PHE103 4.9 23.6 1.0
N D:GLN100 5.0 24.3 1.0
C D:GLY102 5.0 24.1 1.0

Iron binding site 6 out of 8 in 1ffv

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Iron binding site 6 out of 8 in the Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1909

b:25.6
occ:1.00
 FE2 D:FES1909 0.0 25.6 1.0
S1 D:FES1909 2.2 24.6 1.0
S2 D:FES1909 2.2 24.7 1.0
SG D:CYS104 2.3 24.0 1.0
SG D:CYS136 2.3 24.5 1.0
FE1 D:FES1909 2.7 25.4 1.0
CB D:CYS104 3.3 23.4 1.0
CB D:CYS136 3.5 24.6 1.0
CA D:CYS136 3.8 24.1 1.0
N D:CYS104 4.0 23.2 1.0
N D:ARG137 4.1 24.6 1.0
CA D:CYS104 4.2 23.6 1.0
O D:HOH1960 4.3 23.9 1.0
N D:CYS138 4.4 24.2 1.0
SG D:CYS138 4.4 25.3 1.0
C D:CYS136 4.4 24.4 1.0
CB D:CYS138 4.5 24.4 1.0
CG2 D:THR139 4.7 24.9 1.0
C D:CYS104 4.8 23.7 1.0
N D:THR105 4.8 23.8 1.0
SG D:CYS101 4.8 24.6 1.0
O D:LEU135 4.9 24.6 1.0
N D:THR139 5.0 25.1 1.0
CA D:CYS138 5.0 24.7 1.0

Iron binding site 7 out of 8 in 1ffv

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Iron binding site 7 out of 8 in the Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1910

b:26.9
occ:1.00
 FE1 D:FES1910 0.0 26.9 1.0
S2 D:FES1910 2.3 25.5 1.0
S1 D:FES1910 2.3 24.9 1.0
SG D:CYS42 2.3 24.5 1.0
SG D:CYS47 2.3 24.8 1.0
FE2 D:FES1910 2.7 25.2 1.0
CB D:CYS47 3.5 24.9 1.0
CB D:CYS42 3.6 24.8 1.0
N D:CYS42 3.6 24.1 1.0
N D:CYS47 3.6 25.3 1.0
CA D:CYS47 3.9 24.9 1.0
N D:GLY48 3.9 24.7 1.0
O D:CYS42 3.9 25.6 1.0
CA D:CYS42 4.0 24.4 1.0
N D:GLY41 4.1 23.2 1.0
C D:CYS42 4.1 25.1 1.0
C D:GLY41 4.2 23.6 1.0
C D:CYS47 4.3 24.8 1.0
O F:HOH1931 4.3 27.8 1.0
SG D:CYS62 4.4 24.5 1.0
N D:HIS46 4.4 25.5 1.0
CA D:GLY41 4.5 23.1 1.0
N D:ALA49 4.6 23.5 1.0
C D:HIS46 4.7 25.6 1.0
SG D:CYS50 4.7 24.6 1.0
CA D:SER45 4.7 26.1 1.0
C D:SER45 4.7 25.9 1.0
N D:SER45 4.7 26.4 1.0
CA D:GLY48 4.9 24.1 1.0
O D:GLY41 5.0 23.8 1.0

Iron binding site 8 out of 8 in 1ffv

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Iron binding site 8 out of 8 in the Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1910

b:25.2
occ:1.00
 FE2 D:FES1910 0.0 25.2 1.0
S1 D:FES1910 2.2 24.9 1.0
S2 D:FES1910 2.2 25.5 1.0
SG D:CYS50 2.3 24.6 1.0
SG D:CYS62 2.3 24.5 1.0
FE1 D:FES1910 2.7 26.9 1.0
CB D:CYS62 3.2 24.1 1.0
CB D:CYS50 3.5 24.4 1.0
O F:HOH1931 4.1 27.8 1.0
N D:CYS62 4.3 24.5 1.0
N D:CYS50 4.3 23.9 1.0
CA D:CYS62 4.4 24.6 1.0
CB D:LYS60 4.4 24.8 1.0
SG D:CYS47 4.4 24.8 1.0
N D:GLY48 4.5 24.7 1.0
SG D:CYS42 4.5 24.5 1.0
CA D:CYS50 4.5 24.2 1.0
N D:ALA49 4.8 23.5 1.0
CA D:GLY48 4.8 24.1 1.0
CA D:SER45 4.9 26.1 1.0
CD D:LYS60 4.9 23.9 1.0

Reference:

P.Hanzelmann, H.Dobbek, L.Gremer, R.Huber, O.Meyer. The Effect of Intracellular Molybdenum in Hydrogenophaga Pseudoflava on the Crystallographic Structure of the Seleno-Molybdo-Iron-Sulfur Flavoenzyme Carbon Monoxide Dehydrogenase. J.Mol.Biol. V. 301 1221 2000.
ISSN: ISSN 0022-2836
PubMed: 10966817
DOI: 10.1006/JMBI.2000.4023
Page generated: Sun Dec 13 14:13:43 2020

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