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Iron in PDB 1su8: Carbon Monoxide Induced Decomposition of the Active Site [Ni-4FE-5S] Cluster of Co Dehydrogenase

Enzymatic activity of Carbon Monoxide Induced Decomposition of the Active Site [Ni-4FE-5S] Cluster of Co Dehydrogenase

All present enzymatic activity of Carbon Monoxide Induced Decomposition of the Active Site [Ni-4FE-5S] Cluster of Co Dehydrogenase:
1.2.99.2;

Protein crystallography data

The structure of Carbon Monoxide Induced Decomposition of the Active Site [Ni-4FE-5S] Cluster of Co Dehydrogenase, PDB code: 1su8 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 / 1.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 111.792, 74.740, 70.930, 90.00, 111.16, 90.00
R / Rfree (%) 14.6 / 18.5

Other elements in 1su8:

The structure of Carbon Monoxide Induced Decomposition of the Active Site [Ni-4FE-5S] Cluster of Co Dehydrogenase also contains other interesting chemical elements:

Nickel (Ni) 1 atom

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Carbon Monoxide Induced Decomposition of the Active Site [Ni-4FE-5S] Cluster of Co Dehydrogenase (pdb code 1su8). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Carbon Monoxide Induced Decomposition of the Active Site [Ni-4FE-5S] Cluster of Co Dehydrogenase, PDB code: 1su8:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 1su8

Go back to Iron Binding Sites List in 1su8
Iron binding site 1 out of 12 in the Carbon Monoxide Induced Decomposition of the Active Site [Ni-4FE-5S] Cluster of Co Dehydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Carbon Monoxide Induced Decomposition of the Active Site [Ni-4FE-5S] Cluster of Co Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe637

b:6.3
occ:1.00
 FE1 A:SF4637 0.0 6.3 1.0
S4 A:SF4637 2.3 7.6 1.0
SG A:CYS70 2.3 7.4 1.0
S3 A:SF4637 2.3 7.4 1.0
S2 A:SF4637 2.3 7.5 1.0
FE2 A:SF4637 2.7 6.2 1.0
FE3 A:SF4637 2.7 6.4 1.0
FE4 A:SF4637 2.8 6.2 1.0
CB A:CYS70 3.3 7.4 1.0
N A:CYS70 3.8 7.6 1.0
S1 A:SF4637 4.0 7.3 1.0
O A:HOH642 4.1 7.3 1.0
NH2 A:ARG80 4.1 7.5 1.0
CA A:CYS70 4.2 7.4 1.0
CB A:ALA72 4.4 8.7 1.0
CG A:MET199 4.6 7.7 1.0
N A:ILE69 4.6 7.5 1.0
SG A:CYS51 4.7 7.3 1.0
SG A:CYS48 4.8 7.2 1.0
SG A:CYS56 4.8 7.7 1.0
C A:ILE69 5.0 7.1 1.0

Iron binding site 2 out of 12 in 1su8

Go back to Iron Binding Sites List in 1su8
Iron binding site 2 out of 12 in the Carbon Monoxide Induced Decomposition of the Active Site [Ni-4FE-5S] Cluster of Co Dehydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Carbon Monoxide Induced Decomposition of the Active Site [Ni-4FE-5S] Cluster of Co Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe637

b:6.2
occ:1.00
 FE2 A:SF4637 0.0 6.2 1.0
S3 A:SF4637 2.2 7.4 1.0
SG A:CYS48 2.3 7.2 1.0
S1 A:SF4637 2.3 7.3 1.0
S4 A:SF4637 2.3 7.6 1.0
FE3 A:SF4637 2.7 6.4 1.0
FE4 A:SF4637 2.7 6.2 1.0
FE1 A:SF4637 2.7 6.3 1.0
CB A:CYS48 3.2 7.4 1.0
NH2 A:ARG80 3.6 7.5 1.0
S2 A:SF4637 3.8 7.5 1.0
N A:HIS50 4.0 7.4 1.0
C A:CYS48 4.2 6.7 1.0
O A:CYS48 4.2 8.1 1.0
CB A:HIS50 4.3 7.5 1.0
CA A:CYS48 4.3 7.0 1.0
N A:CYS51 4.5 7.6 1.0
CA A:HIS50 4.5 7.3 1.0
N A:ARG49 4.6 7.3 1.0
SG A:CYS56 4.7 7.7 1.0
CB A:CYS56 4.7 8.2 1.0
C A:HIS50 4.8 7.6 1.0
CZ A:ARG80 4.8 7.3 1.0
SG A:CYS70 4.9 7.4 1.0
SG A:CYS51 4.9 7.3 1.0
C A:ARG49 4.9 8.0 1.0

Iron binding site 3 out of 12 in 1su8

Go back to Iron Binding Sites List in 1su8
Iron binding site 3 out of 12 in the Carbon Monoxide Induced Decomposition of the Active Site [Ni-4FE-5S] Cluster of Co Dehydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Carbon Monoxide Induced Decomposition of the Active Site [Ni-4FE-5S] Cluster of Co Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe637

b:6.4
occ:1.00
 FE3 A:SF4637 0.0 6.4 1.0
S2 A:SF4637 2.2 7.5 1.0
SG A:CYS56 2.3 7.7 1.0
S1 A:SF4637 2.3 7.3 1.0
S4 A:SF4637 2.3 7.6 1.0
FE2 A:SF4637 2.7 6.2 1.0
FE4 A:SF4637 2.7 6.2 1.0
FE1 A:SF4637 2.7 6.3 1.0
CB A:CYS56 3.2 8.2 1.0
S3 A:SF4637 3.9 7.4 1.0
N A:ILE69 4.0 7.5 1.0
CA A:CYS56 4.4 7.7 1.0
CB A:ILE69 4.4 7.5 1.0
CA A:GLY54 4.4 9.3 1.0
N A:CYS56 4.4 7.2 1.0
N A:GLY54 4.5 8.8 1.0
O A:CYS48 4.6 8.1 1.0
SG A:CYS51 4.6 7.3 1.0
SG A:CYS48 4.6 7.2 1.0
N A:CYS70 4.7 7.6 1.0
CA A:GLY68 4.7 8.7 1.0
CB A:CYS48 4.7 7.4 1.0
CA A:ILE69 4.8 7.6 1.0
SG A:CYS70 4.8 7.4 1.0
C A:GLY68 4.8 7.2 1.0
CG1 A:ILE69 4.9 8.1 1.0
C A:GLN53 5.0 8.0 1.0

Iron binding site 4 out of 12 in 1su8

Go back to Iron Binding Sites List in 1su8
Iron binding site 4 out of 12 in the Carbon Monoxide Induced Decomposition of the Active Site [Ni-4FE-5S] Cluster of Co Dehydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Carbon Monoxide Induced Decomposition of the Active Site [Ni-4FE-5S] Cluster of Co Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe637

b:6.2
occ:1.00
 FE4 A:SF4637 0.0 6.2 1.0
SG A:CYS51 2.3 7.3 1.0
S1 A:SF4637 2.3 7.3 1.0
S3 A:SF4637 2.3 7.4 1.0
S2 A:SF4637 2.3 7.5 1.0
FE2 A:SF4637 2.7 6.2 1.0
FE3 A:SF4637 2.7 6.4 1.0
FE1 A:SF4637 2.8 6.3 1.0
CB A:CYS51 3.3 7.5 1.0
N A:CYS51 3.5 7.6 1.0
CA A:CYS51 3.9 7.7 1.0
S4 A:SF4637 3.9 7.6 1.0
O A:CYS51 4.2 8.2 1.0
C A:CYS51 4.3 7.1 1.0
C A:HIS50 4.3 7.6 1.0
CG A:MET199 4.4 7.7 1.0
N A:GLY54 4.4 8.8 1.0
CB A:GLN53 4.6 7.9 1.0
CB A:MET199 4.7 7.5 1.0
N A:HIS50 4.8 7.4 1.0
SG A:CYS48 4.8 7.2 1.0
NE2 A:GLN53 4.8 9.3 1.0
SG A:CYS70 4.8 7.4 1.0
N A:GLN53 4.8 7.8 1.0
SG A:CYS56 4.8 7.7 1.0
CA A:HIS50 4.9 7.3 1.0
CA A:GLY54 4.9 9.3 1.0
C A:GLN53 5.0 8.0 1.0

Iron binding site 5 out of 12 in 1su8

Go back to Iron Binding Sites List in 1su8
Iron binding site 5 out of 12 in the Carbon Monoxide Induced Decomposition of the Active Site [Ni-4FE-5S] Cluster of Co Dehydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Carbon Monoxide Induced Decomposition of the Active Site [Ni-4FE-5S] Cluster of Co Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe638

b:7.3
occ:1.00
 FE1 A:FES638 0.0 7.3 1.0
SG A:CYS47 2.3 8.2 1.0
S1 A:FES638 2.3 8.6 1.0
S2 A:FES638 2.3 8.8 1.0
FE2 A:FES638 2.7 7.5 1.0
CB A:CYS47 3.2 8.1 1.0
O A:HOH715 3.6 12.5 1.0
CA A:CYS47 4.6 7.6 1.0
SG A:CYS39 4.7 9.6 1.0
CB A:PHE41 4.9 8.4 1.0
N A:GLY42 4.9 9.6 1.0
CD A:ARG49 4.9 15.4 1.0

Iron binding site 6 out of 12 in 1su8

Go back to Iron Binding Sites List in 1su8
Iron binding site 6 out of 12 in the Carbon Monoxide Induced Decomposition of the Active Site [Ni-4FE-5S] Cluster of Co Dehydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Carbon Monoxide Induced Decomposition of the Active Site [Ni-4FE-5S] Cluster of Co Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe638

b:7.5
occ:1.00
 FE2 A:FES638 0.0 7.5 1.0
S2 A:FES638 2.2 8.8 1.0
SG A:CYS39 2.3 9.6 1.0
S1 A:FES638 2.3 8.6 1.0
FE1 A:FES638 2.7 7.3 1.0
CB A:CYS39 3.2 9.3 1.0
N A:GLY42 4.1 9.6 1.0
CB A:PHE41 4.4 8.4 1.0
CA A:CYS39 4.6 9.7 1.0
CD2 A:PHE41 4.7 10.4 1.0
CA A:GLY42 4.7 9.8 1.0
SG A:CYS47 4.8 8.2 1.0
C A:PHE41 5.0 8.6 1.0
CB A:CYS47 5.0 8.1 1.0

Iron binding site 7 out of 12 in 1su8

Go back to Iron Binding Sites List in 1su8
Iron binding site 7 out of 12 in the Carbon Monoxide Induced Decomposition of the Active Site [Ni-4FE-5S] Cluster of Co Dehydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Carbon Monoxide Induced Decomposition of the Active Site [Ni-4FE-5S] Cluster of Co Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe639

b:11.1
occ:0.80
 FE1 A:NFS639 0.0 11.1 0.8
FE1 A:NFS639 1.2 9.0 0.1
NE2 A:HIS261 2.1 12.3 1.0
S2 A:NFS639 2.3 14.3 0.8
S1 A:NFS639 2.3 14.1 1.0
SG A:CYS295 2.3 12.0 1.0
NI1 A:NFS639 2.8 11.3 0.9
CD2 A:HIS261 3.0 12.2 1.0
CE1 A:HIS261 3.1 11.0 1.0
FE4 A:NFS639 3.3 10.1 0.9
CB A:CYS295 3.4 9.8 1.0
SG A:CYS526 3.4 12.2 1.0
NZ A:LYS563 3.7 12.4 1.0
S3 A:NFS639 3.8 12.0 0.9
CB A:CYS526 3.9 10.3 1.0
FE2 A:NFS639 3.9 10.4 0.8
O A:HOH1475 4.0 34.4 1.0
FE2 A:NFS639 4.1 10.1 0.1
S5 A:NFS639 4.1 12.0 1.0
CG A:HIS261 4.2 11.8 1.0
ND1 A:HIS261 4.2 11.2 1.0
O A:HOH738 4.3 10.2 1.0
O A:HOH904 4.4 12.6 1.0
N A:CYS295 4.4 8.4 1.0
CA A:CYS295 4.4 8.9 1.0
SG A:CYS333 4.5 10.5 1.0
FE3 A:NFS639 4.7 9.6 1.0
O A:HOH1440 4.7 49.3 1.0
O A:HOH1524 4.8 0.7 1.0
N A:CYS526 4.8 8.2 1.0
CE A:LYS563 4.9 10.7 1.0

Iron binding site 8 out of 12 in 1su8

Go back to Iron Binding Sites List in 1su8
Iron binding site 8 out of 12 in the Carbon Monoxide Induced Decomposition of the Active Site [Ni-4FE-5S] Cluster of Co Dehydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Carbon Monoxide Induced Decomposition of the Active Site [Ni-4FE-5S] Cluster of Co Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe639

b:9.0
occ:0.10
 FE1 A:NFS639 0.0 9.0 0.1
FE1 A:NFS639 1.2 11.1 0.8
S1 A:NFS639 2.1 14.1 1.0
SG A:CYS295 2.1 12.0 1.0
NI1 A:NFS639 2.6 11.3 0.9
SG A:CYS526 2.8 12.2 1.0
S2 A:NFS639 3.0 14.3 0.8
FE2 A:NFS639 3.1 10.4 0.8
NE2 A:HIS261 3.2 12.3 1.0
FE2 A:NFS639 3.2 10.1 0.1
S5 A:NFS639 3.2 12.0 1.0
O A:HOH904 3.3 12.6 1.0
FE4 A:NFS639 3.4 10.1 0.9
CB A:CYS295 3.4 9.8 1.0
CB A:CYS526 3.8 10.3 1.0
S3 A:NFS639 4.0 12.0 0.9
CE1 A:HIS261 4.1 11.0 1.0
N A:CYS295 4.1 8.4 1.0
CD2 A:HIS261 4.1 12.2 1.0
CA A:CYS295 4.2 8.9 1.0
FE3 A:NFS639 4.3 9.6 1.0
SG A:CYS476 4.5 12.6 1.0
N A:CYS526 4.5 8.2 1.0
CA A:GLY475 4.6 8.7 1.0
O A:HOH1440 4.7 49.3 1.0
NZ A:LYS563 4.8 12.4 1.0
O A:HOH738 4.8 10.2 1.0
CA A:CYS526 4.8 8.9 1.0
S4 A:NFS639 4.8 11.6 1.0
N A:CYS476 4.9 8.9 1.0
O A:HOH1475 4.9 34.4 1.0

Iron binding site 9 out of 12 in 1su8

Go back to Iron Binding Sites List in 1su8
Iron binding site 9 out of 12 in the Carbon Monoxide Induced Decomposition of the Active Site [Ni-4FE-5S] Cluster of Co Dehydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Carbon Monoxide Induced Decomposition of the Active Site [Ni-4FE-5S] Cluster of Co Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe639

b:10.4
occ:0.85
 FE2 A:NFS639 0.0 10.4 0.8
FE2 A:NFS639 0.5 10.1 0.1
SG A:CYS476 2.3 12.6 1.0
S4 A:NFS639 2.3 11.6 1.0
S1 A:NFS639 2.3 14.1 1.0
S5 A:NFS639 2.4 12.0 1.0
FE4 A:NFS639 2.7 10.1 0.9
FE3 A:NFS639 2.7 9.6 1.0
FE1 A:NFS639 3.1 9.0 0.1
CB A:CYS476 3.3 11.6 1.0
NI1 A:NFS639 3.6 11.3 0.9
FE1 A:NFS639 3.9 11.1 0.8
O A:HOH904 3.9 12.6 1.0
S3 A:NFS639 4.0 12.0 0.9
N A:CYS476 4.1 8.9 1.0
CA A:CYS476 4.3 10.1 1.0
SG A:CYS294 4.4 13.9 1.0
CA A:CYS446 4.5 8.5 1.0
CB A:SER312 4.5 10.4 1.0
OG A:SER312 4.6 10.5 1.0
SG A:CYS526 4.6 12.2 1.0
SG A:CYS333 4.8 10.5 1.0
SG A:CYS446 4.8 9.4 1.0
CB A:CYS446 4.8 8.4 1.0
CB A:CYS294 4.9 12.0 1.0
SG A:CYS295 4.9 12.0 1.0
O A:GLY445 4.9 10.3 1.0
N A:CYS446 5.0 8.2 1.0
CA A:SER312 5.0 9.0 1.0

Iron binding site 10 out of 12 in 1su8

Go back to Iron Binding Sites List in 1su8
Iron binding site 10 out of 12 in the Carbon Monoxide Induced Decomposition of the Active Site [Ni-4FE-5S] Cluster of Co Dehydrogenase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Carbon Monoxide Induced Decomposition of the Active Site [Ni-4FE-5S] Cluster of Co Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe639

b:10.1
occ:0.10
 FE2 A:NFS639 0.0 10.1 0.1
FE2 A:NFS639 0.5 10.4 0.8
S5 A:NFS639 2.0 12.0 1.0
S4 A:NFS639 2.3 11.6 1.0
SG A:CYS476 2.4 12.6 1.0
FE3 A:NFS639 2.4 9.6 1.0
S1 A:NFS639 2.7 14.1 1.0
FE4 A:NFS639 2.9 10.1 0.9
CB A:CYS476 3.1 11.6 1.0
FE1 A:NFS639 3.2 9.0 0.1
NI1 A:NFS639 3.5 11.3 0.9
N A:CYS476 3.8 8.9 1.0
S3 A:NFS639 3.9 12.0 0.9
CA A:CYS446 4.0 8.5 1.0
CA A:CYS476 4.1 10.1 1.0
O A:HOH904 4.1 12.6 1.0
FE1 A:NFS639 4.1 11.1 0.8
O A:GLY445 4.4 10.3 1.0
SG A:CYS446 4.5 9.4 1.0
CB A:CYS446 4.5 8.4 1.0
SG A:CYS526 4.5 12.2 1.0
N A:CYS446 4.5 8.2 1.0
OG A:SER312 4.5 10.5 1.0
C A:GLY445 4.5 8.0 1.0
CB A:SER312 4.5 10.4 1.0
C A:GLY475 4.9 8.1 1.0
SG A:CYS294 4.9 13.9 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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