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Iron in PDB 1ffu: Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor

Protein crystallography data

The structure of Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor, PDB code: 1ffu 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 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.235, 193.884, 218.290, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 24.5

Iron Binding Sites:

The binding sites of Iron atom in the Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor (pdb code 1ffu). 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 Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor, PDB code: 1ffu:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 1ffu

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Iron binding site 1 out of 8 in the Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor


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 Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1907

b:24.1
occ:1.00
FE1 A:FES1907 0.0 24.1 1.0
S1 A:FES1907 2.2 25.0 1.0
S2 A:FES1907 2.2 25.1 1.0
SG A:CYS101 2.3 25.2 1.0
SG A:CYS138 2.4 25.8 1.0
FE2 A:FES1907 2.7 26.1 1.0
CB A:CYS101 3.3 25.8 1.0
CB A:CYS138 3.5 25.4 1.0
N A:CYS101 3.7 25.5 1.0
O B:HOH1925 3.7 25.9 1.0
CA A:CYS101 3.9 25.6 1.0
N A:GLY102 4.0 25.6 1.0
N A:CYS138 4.1 24.8 1.0
N A:PHE103 4.2 24.7 1.0
C A:CYS101 4.3 26.0 1.0
SG A:CYS136 4.3 23.7 1.0
CA A:CYS138 4.4 25.5 1.0
CB A:PHE103 4.7 23.5 1.0
N A:ARG137 4.7 24.4 1.0
SG A:CYS104 4.7 25.3 1.0
N A:CYS104 4.8 24.0 1.0
C A:GLN100 4.8 25.3 1.0
C A:ARG137 4.9 24.8 1.0
CA A:GLY102 4.9 25.1 1.0
CA A:PHE103 4.9 24.1 1.0

Iron binding site 2 out of 8 in 1ffu

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Iron binding site 2 out of 8 in the Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor


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 Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1907

b:26.1
occ:1.00
FE2 A:FES1907 0.0 26.1 1.0
S1 A:FES1907 2.2 25.0 1.0
S2 A:FES1907 2.2 25.1 1.0
SG A:CYS104 2.3 25.3 1.0
SG A:CYS136 2.3 23.7 1.0
FE1 A:FES1907 2.7 24.1 1.0
CB A:CYS104 3.4 24.5 1.0
CB A:CYS136 3.5 24.3 1.0
CA A:CYS136 3.8 24.3 1.0
N A:CYS104 4.0 24.0 1.0
N A:ARG137 4.1 24.4 1.0
CA A:CYS104 4.3 23.9 1.0
N A:CYS138 4.3 24.8 1.0
O A:HOH1919 4.3 18.5 1.0
C A:CYS136 4.4 24.3 1.0
SG A:CYS138 4.5 25.8 1.0
CB A:CYS138 4.6 25.4 1.0
SG A:CYS101 4.7 25.2 1.0
CG2 A:THR139 4.8 24.3 1.0
C A:CYS104 4.9 23.9 1.0
N A:THR105 4.9 24.0 1.0
O A:LEU135 4.9 24.9 1.0
N A:PHE103 4.9 24.7 1.0
N A:THR139 5.0 25.5 1.0
CA A:CYS138 5.0 25.5 1.0

Iron binding site 3 out of 8 in 1ffu

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Iron binding site 3 out of 8 in the Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor


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 Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor 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 24.6 1.0
S2 A:FES1908 2.2 25.7 1.0
SG A:CYS47 2.3 26.1 1.0
SG A:CYS42 2.3 25.1 1.0
FE2 A:FES1908 2.7 26.3 1.0
N A:CYS42 3.5 24.6 1.0
CB A:CYS47 3.5 24.9 1.0
CB A:CYS42 3.6 25.0 1.0
N A:CYS47 3.6 24.8 1.0
N A:GLY48 3.7 23.8 1.0
O A:CYS42 3.9 25.1 1.0
CA A:CYS47 3.9 24.7 1.0
CA A:CYS42 3.9 24.7 1.0
O A:HOH1923 3.9 33.3 1.0
C A:CYS42 4.1 25.0 1.0
N A:GLY41 4.1 23.7 1.0
C A:GLY41 4.3 24.5 1.0
C A:CYS47 4.3 24.2 1.0
N A:HIS46 4.3 24.8 1.0
SG A:CYS62 4.3 25.0 1.0
CA A:GLY41 4.5 24.0 1.0
CA A:SER45 4.5 25.0 1.0
C A:HIS46 4.6 25.2 1.0
C A:SER45 4.6 25.1 1.0
N A:ALA49 4.6 24.1 1.0
N A:SER45 4.6 25.0 1.0
SG A:CYS50 4.6 23.4 1.0
CA A:GLY48 4.7 23.4 1.0
CA A:HIS46 5.0 24.9 1.0

Iron binding site 4 out of 8 in 1ffu

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Iron binding site 4 out of 8 in the Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor


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 Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1908

b:26.3
occ:1.00
FE2 A:FES1908 0.0 26.3 1.0
S1 A:FES1908 2.2 24.6 1.0
S2 A:FES1908 2.2 25.7 1.0
SG A:CYS50 2.3 23.4 1.0
SG A:CYS62 2.3 25.0 1.0
FE1 A:FES1908 2.7 26.1 1.0
CB A:CYS62 3.2 25.0 1.0
CB A:CYS50 3.4 24.5 1.0
O A:HOH1923 3.7 33.3 1.0
N A:CYS62 4.3 25.1 1.0
CB A:LYS60 4.3 24.2 1.0
N A:CYS50 4.4 24.3 1.0
CA A:CYS62 4.4 24.7 1.0
SG A:CYS47 4.4 26.1 1.0
N A:GLY48 4.4 23.8 1.0
CA A:CYS50 4.5 24.0 1.0
SG A:CYS42 4.6 25.1 1.0
CA A:GLY48 4.7 23.4 1.0
CA A:SER45 4.7 25.0 1.0
N A:ALA49 4.8 24.1 1.0
CG A:LYS60 4.9 24.3 1.0
CD A:LYS60 4.9 24.6 1.0
O A:CYS42 4.9 25.1 1.0

Iron binding site 5 out of 8 in 1ffu

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Iron binding site 5 out of 8 in the Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor


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 Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1909

b:26.1
occ:1.00
FE1 D:FES1909 0.0 26.1 1.0
S1 D:FES1909 2.2 25.6 1.0
S2 D:FES1909 2.2 25.3 1.0
SG D:CYS101 2.3 26.0 1.0
SG D:CYS138 2.4 27.5 1.0
FE2 D:FES1909 2.7 27.0 1.0
CB D:CYS138 3.4 27.7 1.0
CB D:CYS101 3.4 25.3 1.0
N D:CYS101 3.8 25.0 1.0
O E:HOH1929 3.9 31.7 1.0
N D:GLY102 3.9 24.9 1.0
N D:CYS138 4.0 28.0 1.0
CA D:CYS101 4.0 24.9 1.0
N D:PHE103 4.2 24.4 1.0
CA D:CYS138 4.3 27.9 1.0
C D:CYS101 4.3 24.6 1.0
SG D:CYS136 4.4 25.3 1.0
N D:ARG137 4.7 26.7 1.0
CB D:PHE103 4.7 23.7 1.0
N D:CYS104 4.8 24.7 1.0
SG D:CYS104 4.8 25.0 1.0
CA D:GLY102 4.9 24.5 1.0
C D:ARG137 4.9 27.9 1.0
C D:GLN100 4.9 25.6 1.0
CA D:PHE103 4.9 24.5 1.0

Iron binding site 6 out of 8 in 1ffu

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Iron binding site 6 out of 8 in the Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor


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 Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1909

b:27.0
occ:1.00
FE2 D:FES1909 0.0 27.0 1.0
S2 D:FES1909 2.2 25.3 1.0
S1 D:FES1909 2.2 25.6 1.0
SG D:CYS104 2.3 25.0 1.0
SG D:CYS136 2.3 25.3 1.0
FE1 D:FES1909 2.7 26.1 1.0
CB D:CYS104 3.3 24.6 1.0
CB D:CYS136 3.5 25.8 1.0
CA D:CYS136 3.9 25.7 1.0
N D:CYS104 3.9 24.7 1.0
N D:ARG137 4.2 26.7 1.0
CA D:CYS104 4.2 25.1 1.0
N D:CYS138 4.3 28.0 1.0
O D:HOH1961 4.4 23.8 1.0
C D:CYS136 4.5 26.3 1.0
SG D:CYS138 4.5 27.5 1.0
CB D:CYS138 4.5 27.7 1.0
CG2 D:THR139 4.7 27.0 1.0
SG D:CYS101 4.7 26.0 1.0
N D:THR105 4.8 25.3 1.0
N D:PHE103 4.8 24.4 1.0
C D:CYS104 4.8 25.4 1.0
N D:THR139 4.9 28.0 1.0
CA D:CYS138 5.0 27.9 1.0
OG1 D:THR105 5.0 23.5 1.0

Iron binding site 7 out of 8 in 1ffu

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Iron binding site 7 out of 8 in the Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor


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 Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1910

b:27.4
occ:1.00
FE1 D:FES1910 0.0 27.4 1.0
S2 D:FES1910 2.3 26.2 1.0
S1 D:FES1910 2.3 25.8 1.0
SG D:CYS47 2.3 26.1 1.0
SG D:CYS42 2.3 24.2 1.0
FE2 D:FES1910 2.7 26.3 1.0
CB D:CYS47 3.5 25.8 1.0
N D:CYS47 3.5 25.9 1.0
N D:CYS42 3.5 25.8 1.0
CB D:CYS42 3.6 25.5 1.0
N D:GLY48 3.7 25.8 1.0
CA D:CYS47 3.8 25.7 1.0
O D:CYS42 3.9 26.9 1.0
CA D:CYS42 4.0 25.8 1.0
C D:CYS42 4.2 25.9 1.0
N D:GLY41 4.2 25.2 1.0
O F:HOH1938 4.2 27.7 1.0
C D:GLY41 4.2 25.8 1.0
N D:HIS46 4.2 26.2 1.0
C D:CYS47 4.2 25.7 1.0
SG D:CYS62 4.3 26.1 1.0
CA D:GLY41 4.5 25.3 1.0
C D:HIS46 4.6 26.5 1.0
CA D:SER45 4.6 26.4 1.0
N D:ALA49 4.6 25.5 1.0
C D:SER45 4.7 26.6 1.0
SG D:CYS50 4.7 25.4 1.0
N D:SER45 4.7 26.7 1.0
CA D:GLY48 4.8 25.2 1.0
CA D:HIS46 5.0 26.1 1.0

Iron binding site 8 out of 8 in 1ffu

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Iron binding site 8 out of 8 in the Carbon Monoxide Dehydrogenase From Hydrogenophaga Pseudoflava Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor


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 Which Lacks the Mo-Pyranopterin Moiety of the Molybdenum Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1910

b:26.3
occ:1.00
FE2 D:FES1910 0.0 26.3 1.0
S1 D:FES1910 2.2 25.8 1.0
S2 D:FES1910 2.3 26.2 1.0
SG D:CYS50 2.3 25.4 1.0
SG D:CYS62 2.3 26.1 1.0
FE1 D:FES1910 2.7 27.4 1.0
CB D:CYS62 3.3 24.9 1.0
CB D:CYS50 3.4 25.5 1.0
O F:HOH1938 4.0 27.7 1.0
CB D:LYS60 4.3 24.7 1.0
N D:CYS50 4.3 25.0 1.0
N D:CYS62 4.3 25.0 1.0
SG D:CYS47 4.4 26.1 1.0
CA D:CYS62 4.4 24.9 1.0
N D:GLY48 4.4 25.8 1.0
CA D:CYS50 4.5 24.9 1.0
SG D:CYS42 4.6 24.2 1.0
CA D:GLY48 4.7 25.2 1.0
CD D:LYS60 4.7 24.6 1.0
CA D:SER45 4.8 26.4 1.0
CG D:LYS60 4.8 24.4 1.0
N D:ALA49 4.8 25.5 1.0
CA D:LYS60 5.0 25.3 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: Sat Aug 3 04:59:29 2024

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