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Iron in PDB 1suf: Carbon Monoxide Dehydrogenase From Carboxydothermus Hydrogenoformans- Inactive State

Enzymatic activity of Carbon Monoxide Dehydrogenase From Carboxydothermus Hydrogenoformans- Inactive State

All present enzymatic activity of Carbon Monoxide Dehydrogenase From Carboxydothermus Hydrogenoformans- Inactive State:
1.2.99.2;

Protein crystallography data

The structure of Carbon Monoxide Dehydrogenase From Carboxydothermus Hydrogenoformans- Inactive State, PDB code: 1suf was solved by H.Dobbek, V.Svetlitchnyi, J.Liss, O.Meyer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.15
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 112.614, 75.004, 71.374, 90.00, 110.97, 90.00
R / Rfree (%) 15.2 / 19

Other elements in 1suf:

The structure of Carbon Monoxide Dehydrogenase From Carboxydothermus Hydrogenoformans- Inactive State also contains other interesting chemical elements:

Nickel (Ni) 1 atom

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Iron atom in the Carbon Monoxide Dehydrogenase From Carboxydothermus Hydrogenoformans- Inactive State (pdb code 1suf). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 11 binding sites of Iron where determined in the Carbon Monoxide Dehydrogenase From Carboxydothermus Hydrogenoformans- Inactive State, PDB code: 1suf:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 11 in 1suf

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Iron binding site 1 out of 11 in the Carbon Monoxide Dehydrogenase From Carboxydothermus Hydrogenoformans- Inactive State


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 Carboxydothermus Hydrogenoformans- Inactive State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe637

b:-0.3
occ:1.00
 FE1 A:SF4637 0.0 -0.3 1.0
S4 A:SF4637 2.2 8.4 1.0
SG A:CYS70 2.3 8.3 1.0
S3 A:SF4637 2.3 8.0 1.0
S2 A:SF4637 2.3 8.5 1.0
FE2 A:SF4637 2.7 -0.5 1.0
FE3 A:SF4637 2.7 -0.4 1.0
FE4 A:SF4637 2.8 -0.3 1.0
CB A:CYS70 3.4 8.8 1.0
N A:CYS70 3.8 8.8 1.0
S1 A:SF4637 3.9 8.0 1.0
NH2 A:ARG80 4.1 9.1 1.0
O A:HOH642 4.2 9.1 1.0
CA A:CYS70 4.2 8.2 1.0
CB A:ALA72 4.4 9.9 1.0
O A:HOH1421 4.5 16.5 1.0
CG A:MET199 4.6 9.0 1.0
N A:ILE69 4.6 8.9 1.0
SG A:CYS51 4.7 8.5 1.0
SG A:CYS48 4.8 8.6 1.0
SG A:CYS56 4.8 8.2 1.0
C A:ILE69 5.0 8.2 1.0

Iron binding site 2 out of 11 in 1suf

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Iron binding site 2 out of 11 in the Carbon Monoxide Dehydrogenase From Carboxydothermus Hydrogenoformans- Inactive State


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 Carboxydothermus Hydrogenoformans- Inactive State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe637

b:-0.5
occ:1.00
 FE2 A:SF4637 0.0 -0.5 1.0
S3 A:SF4637 2.3 8.0 1.0
S4 A:SF4637 2.3 8.4 1.0
SG A:CYS48 2.3 8.6 1.0
S1 A:SF4637 2.3 8.0 1.0
FE3 A:SF4637 2.7 -0.4 1.0
FE4 A:SF4637 2.7 -0.3 1.0
FE1 A:SF4637 2.7 -0.3 1.0
CB A:CYS48 3.3 9.2 1.0
NH2 A:ARG80 3.6 9.1 1.0
S2 A:SF4637 3.9 8.5 1.0
N A:HIS50 4.0 8.6 1.0
C A:CYS48 4.2 7.5 1.0
O A:CYS48 4.2 8.7 1.0
CB A:HIS50 4.3 8.9 1.0
CA A:CYS48 4.3 8.4 1.0
N A:CYS51 4.5 8.1 1.0
CA A:HIS50 4.5 8.8 1.0
N A:ARG49 4.6 8.5 1.0
SG A:CYS56 4.7 8.2 1.0
CB A:CYS56 4.7 8.5 1.0
C A:HIS50 4.8 8.8 1.0
CZ A:ARG80 4.8 8.7 1.0
SG A:CYS70 4.9 8.3 1.0
SG A:CYS51 4.9 8.5 1.0
C A:ARG49 5.0 8.6 1.0

Iron binding site 3 out of 11 in 1suf

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Iron binding site 3 out of 11 in the Carbon Monoxide Dehydrogenase From Carboxydothermus Hydrogenoformans- Inactive State


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 Carboxydothermus Hydrogenoformans- Inactive State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe637

b:-0.4
occ:1.00
 FE3 A:SF4637 0.0 -0.4 1.0
S2 A:SF4637 2.2 8.5 1.0
S1 A:SF4637 2.3 8.0 1.0
S4 A:SF4637 2.3 8.4 1.0
SG A:CYS56 2.3 8.2 1.0
FE2 A:SF4637 2.7 -0.5 1.0
FE4 A:SF4637 2.7 -0.3 1.0
FE1 A:SF4637 2.7 -0.3 1.0
CB A:CYS56 3.2 8.5 1.0
S3 A:SF4637 3.9 8.0 1.0
N A:ILE69 4.0 8.9 1.0
CB A:ILE69 4.4 9.2 1.0
CA A:CYS56 4.4 8.5 1.0
CA A:GLY54 4.4 9.8 1.0
N A:CYS56 4.5 8.4 1.0
N A:GLY54 4.5 9.6 1.0
O A:CYS48 4.6 8.7 1.0
SG A:CYS51 4.6 8.5 1.0
SG A:CYS48 4.7 8.6 1.0
N A:CYS70 4.7 8.8 1.0
CA A:GLY68 4.8 9.1 1.0
CA A:ILE69 4.8 9.3 1.0
SG A:CYS70 4.8 8.3 1.0
CB A:CYS48 4.8 9.2 1.0
C A:GLY68 4.9 8.4 1.0
CG1 A:ILE69 4.9 10.0 1.0

Iron binding site 4 out of 11 in 1suf

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Iron binding site 4 out of 11 in the Carbon Monoxide Dehydrogenase From Carboxydothermus Hydrogenoformans- Inactive State


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 Carboxydothermus Hydrogenoformans- Inactive State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe637

b:-0.3
occ:1.00
 FE4 A:SF4637 0.0 -0.3 1.0
S1 A:SF4637 2.2 8.0 1.0
SG A:CYS51 2.3 8.5 1.0
S2 A:SF4637 2.3 8.5 1.0
S3 A:SF4637 2.3 8.0 1.0
FE3 A:SF4637 2.7 -0.4 1.0
FE2 A:SF4637 2.7 -0.5 1.0
FE1 A:SF4637 2.8 -0.3 1.0
CB A:CYS51 3.4 8.6 1.0
N A:CYS51 3.5 8.1 1.0
CA A:CYS51 3.9 9.1 1.0
S4 A:SF4637 3.9 8.4 1.0
O A:HOH1421 4.1 16.5 1.0
O A:CYS51 4.3 9.4 1.0
C A:CYS51 4.3 8.3 1.0
C A:HIS50 4.3 8.8 1.0
N A:GLY54 4.4 9.6 1.0
CG A:MET199 4.5 9.0 1.0
CB A:GLN53 4.7 8.8 1.0
N A:HIS50 4.8 8.6 1.0
SG A:CYS48 4.8 8.6 1.0
SG A:CYS56 4.8 8.2 1.0
SG A:CYS70 4.8 8.3 1.0
N A:GLN53 4.8 9.2 1.0
CB A:MET199 4.9 8.6 1.0
CA A:GLY54 4.9 9.8 1.0
CA A:HIS50 5.0 8.8 1.0

Iron binding site 5 out of 11 in 1suf

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Iron binding site 5 out of 11 in the Carbon Monoxide Dehydrogenase From Carboxydothermus Hydrogenoformans- Inactive State


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 Carboxydothermus Hydrogenoformans- Inactive State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe638

b:-0.4
occ:1.00
 FE1 A:FES638 0.0 -0.4 1.0
SG A:CYS47 2.3 9.2 1.0
S1 A:FES638 2.3 8.9 1.0
S2 A:FES638 2.3 9.0 1.0
FE2 A:FES638 2.7 -0.4 1.0
CB A:CYS47 3.2 10.0 1.0
O A:HOH715 3.7 10.7 1.0
CA A:CYS47 4.6 8.3 1.0
SG A:CYS39 4.7 10.1 1.0
CB A:PHE41 4.8 9.8 1.0
N A:GLY42 5.0 9.8 1.0

Iron binding site 6 out of 11 in 1suf

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Iron binding site 6 out of 11 in the Carbon Monoxide Dehydrogenase From Carboxydothermus Hydrogenoformans- Inactive State


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 Carboxydothermus Hydrogenoformans- Inactive State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe638

b:-0.4
occ:1.00
 FE2 A:FES638 0.0 -0.4 1.0
S2 A:FES638 2.3 9.0 1.0
S1 A:FES638 2.3 8.9 1.0
SG A:CYS39 2.3 10.1 1.0
FE1 A:FES638 2.7 -0.4 1.0
CB A:CYS39 3.2 10.9 1.0
N A:GLY42 4.1 9.8 1.0
CB A:PHE41 4.4 9.8 1.0
O A:HOH1438 4.4 35.2 1.0
CA A:CYS39 4.7 10.2 1.0
CA A:GLY42 4.8 10.3 1.0
SG A:CYS47 4.8 9.2 1.0
CD2 A:PHE41 4.8 10.9 1.0

Iron binding site 7 out of 11 in 1suf

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Iron binding site 7 out of 11 in the Carbon Monoxide Dehydrogenase From Carboxydothermus Hydrogenoformans- Inactive State


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 Carboxydothermus Hydrogenoformans- Inactive State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe639

b:4.3
occ:0.60
 FE1 A:NFS639 0.0 4.3 0.6
FE1 A:NFS639 1.6 7.6 0.3
O A:HOH1636 2.1 21.4 1.0
NE2 A:HIS261 2.3 14.9 1.0
S1 A:NFS639 2.3 11.9 1.0
SG A:CYS295 2.3 13.8 1.0
NI1 A:NFS639 3.1 1.6 0.6
CD2 A:HIS261 3.1 14.7 1.0
FE4 A:NFS639 3.2 0.1 1.0
SG A:CYS526 3.3 10.9 1.0
CE1 A:HIS261 3.3 13.3 1.0
CB A:CYS295 3.3 12.8 1.0
S3 A:NFS639 3.4 13.3 1.0
NZ A:LYS563 3.7 11.3 1.0
CB A:CYS526 3.8 11.0 1.0
FE2 A:NFS639 3.9 0.5 1.0
O A:HOH1420 4.0 18.8 1.0
O A:HOH1433 4.1 27.7 1.0
S5 A:NFS639 4.2 11.2 1.0
N A:CYS295 4.3 9.9 1.0
O A:HOH738 4.3 11.5 1.0
CG A:HIS261 4.3 12.6 1.0
CA A:CYS295 4.4 10.4 1.0
O A:HOH903 4.4 14.0 1.0
ND1 A:HIS261 4.4 12.7 1.0
SG A:CYS333 4.4 10.1 1.0
FE3 A:NFS639 4.5 0.3 1.0
N A:CYS526 4.8 8.8 1.0
CE A:LYS563 4.9 9.9 1.0
CA A:CYS526 5.0 9.7 1.0

Iron binding site 8 out of 11 in 1suf

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Iron binding site 8 out of 11 in the Carbon Monoxide Dehydrogenase From Carboxydothermus Hydrogenoformans- Inactive State


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 Carboxydothermus Hydrogenoformans- Inactive State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe639

b:7.6
occ:0.30
 FE1 A:NFS639 0.0 7.6 0.3
FE1 A:NFS639 1.6 4.3 0.6
NI1 A:NFS639 2.0 1.6 0.6
SG A:CYS526 2.3 10.9 1.0
S1 A:NFS639 2.4 11.9 1.0
S5 A:NFS639 2.6 11.2 1.0
O A:HOH1636 2.8 21.4 1.0
SG A:CYS295 2.8 13.8 1.0
FE2 A:NFS639 2.9 0.5 1.0
S3 A:NFS639 3.0 13.3 1.0
FE4 A:NFS639 3.0 0.1 1.0
FE3 A:NFS639 3.4 0.3 1.0
CB A:CYS526 3.6 11.0 1.0
NE2 A:HIS261 3.8 14.9 1.0
O A:HOH903 3.9 14.0 1.0
O A:HOH1433 4.0 27.7 1.0
CB A:CYS295 4.3 12.8 1.0
S4 A:NFS639 4.4 10.8 1.0
CA A:GLY475 4.6 8.9 1.0
SG A:CYS476 4.6 11.8 1.0
NZ A:LYS563 4.6 11.3 1.0
CA A:CYS526 4.7 9.7 1.0
N A:CYS526 4.7 8.8 1.0
CE1 A:HIS261 4.7 13.3 1.0
CD2 A:HIS261 4.7 14.7 1.0
N A:CYS476 4.7 8.9 1.0
O A:HOH1423 4.8 25.3 1.0
SG A:CYS333 4.9 10.1 1.0
N A:CYS295 4.9 9.9 1.0
O A:HOH1420 5.0 18.8 1.0

Iron binding site 9 out of 11 in 1suf

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Iron binding site 9 out of 11 in the Carbon Monoxide Dehydrogenase From Carboxydothermus Hydrogenoformans- Inactive State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Carbon Monoxide Dehydrogenase From Carboxydothermus Hydrogenoformans- Inactive State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe639

b:0.5
occ:1.00
 FE2 A:NFS639 0.0 0.5 1.0
S5 A:NFS639 2.3 11.2 1.0
S1 A:NFS639 2.3 11.9 1.0
SG A:CYS476 2.3 11.8 1.0
S4 A:NFS639 2.3 10.8 1.0
FE4 A:NFS639 2.7 0.1 1.0
FE3 A:NFS639 2.7 0.3 1.0
FE1 A:NFS639 2.9 7.6 0.3
CB A:CYS476 3.3 10.3 1.0
NI1 A:NFS639 3.8 1.6 0.6
FE1 A:NFS639 3.9 4.3 0.6
O A:HOH903 3.9 14.0 1.0
S3 A:NFS639 4.0 13.3 1.0
N A:CYS476 4.0 8.9 1.0
CA A:CYS476 4.3 9.5 1.0
SG A:CYS294 4.3 11.5 1.0
CB A:SER312 4.4 11.1 1.0
CA A:CYS446 4.4 9.6 1.0
OG A:SER312 4.5 10.5 1.0
SG A:CYS526 4.7 10.9 1.0
CB A:CYS446 4.8 10.3 1.0
SG A:CYS446 4.8 10.4 1.0
CB A:CYS294 4.8 10.7 1.0
SG A:CYS333 4.9 10.1 1.0
SG A:CYS295 4.9 13.8 1.0
CA A:SER312 4.9 8.8 1.0
N A:CYS446 5.0 8.4 1.0
O A:GLY445 5.0 11.0 1.0

Iron binding site 10 out of 11 in 1suf

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Iron binding site 10 out of 11 in the Carbon Monoxide Dehydrogenase From Carboxydothermus Hydrogenoformans- Inactive State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Carbon Monoxide Dehydrogenase From Carboxydothermus Hydrogenoformans- Inactive State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe639

b:0.3
occ:1.00
 FE3 A:NFS639 0.0 0.3 1.0
S3 A:NFS639 2.3 13.3 1.0
S5 A:NFS639 2.3 11.2 1.0
S4 A:NFS639 2.4 10.8 1.0
SG A:CYS446 2.4 10.4 1.0
FE4 A:NFS639 2.5 0.1 1.0
FE2 A:NFS639 2.7 0.5 1.0
NI1 A:NFS639 2.8 1.6 0.6
CB A:CYS446 3.2 10.3 1.0
FE1 A:NFS639 3.4 7.6 0.3
CA A:CYS446 3.5 9.6 1.0
N A:CYS446 3.6 8.4 1.0
S1 A:NFS639 3.9 11.9 1.0
C A:GLY445 4.2 8.9 1.0
O A:HOH1423 4.3 25.3 1.0
SG A:CYS333 4.4 10.1 1.0
FE1 A:NFS639 4.5 4.3 0.6
CB A:HIS561 4.5 8.8 1.0
CA A:GLY445 4.5 9.1 1.0
SG A:CYS526 4.6 10.9 1.0
CE A:MET560 4.7 11.4 1.0
O A:GLY445 4.8 11.0 1.0
SG A:CYS476 4.8 11.8 1.0
C A:CYS446 4.9 8.7 1.0
O A:HOH1636 5.0 21.4 1.0

Reference:

H.Dobbek, V.Svetlitchnyi, J.Liss, O.Meyer. Carbon Monoxide Induced Decomposition of the Active Site [Ni-4FE-5S] Cluster of Co Dehydrogenase J.Am.Chem.Soc. V. 126 5382 2004.
ISSN: ISSN 0002-7863
PubMed: 15113209
DOI: 10.1021/JA037776V
Page generated: Sat Aug 3 15:03:15 2024

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