Iron in PDB 7zkv: F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans

Enzymatic activity of F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans

All present enzymatic activity of F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans:
1.2.7.4; 2.3.1.169;

Protein crystallography data

The structure of F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans, PDB code: 7zkv was solved by J.Ruickoldt, J.-H.Jeoung, Y.Basak, L.Domnik, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.38 / 2.07
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 142.64, 142.64, 291.31, 90, 90, 120
R / Rfree (%) 17.3 / 21.4

Other elements in 7zkv:

The structure of F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans also contains other interesting chemical elements:

Nickel (Ni) 3 atoms
Sodium (Na) 1 atom

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Iron atom in the F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans (pdb code 7zkv). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 14 binding sites of Iron where determined in the F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans, PDB code: 7zkv:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 14 in 7zkv

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Iron binding site 1 out of 14 in the F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:37.0
occ:0.43
 FE1 A:RQM701 0.0 37.0 0.4
S3 A:RQM701 2.3 48.0 0.8
SG A:CYS354 2.3 48.6 1.0
S4 A:RQM701 2.4 46.8 0.7
S2 A:RQM701 2.4 63.9 1.0
FE3 A:RQM701 2.6 31.8 0.5
FE4 A:RQM701 2.8 47.5 0.8
CB A:CYS354 3.2 47.7 1.0
NI A:RQM701 3.4 41.7 0.4
FE2 A:RQM701 3.6 38.4 0.9
S1 A:RQM701 3.8 50.0 0.8
NZ A:LYS583 3.8 53.9 1.0
CE1 A:HIS282 4.1 38.0 1.0
NE2 A:HIS282 4.3 46.5 1.0
CE A:LYS583 4.4 47.1 1.0
SG A:CYS467 4.5 47.5 1.0
CE A:MET580 4.6 44.1 1.0
CA A:CYS354 4.6 43.5 1.0
OG A:SER581 4.7 27.4 1.0
O A:OH705 4.8 43.4 1.0
SG A:CYS497 4.9 48.0 1.0
O A:OH704 5.0 45.3 1.0

Iron binding site 2 out of 14 in 7zkv

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Iron binding site 2 out of 14 in the F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:38.4
occ:0.86
 FE2 A:RQM701 0.0 38.4 0.9
O A:OH705 1.9 43.4 1.0
NE2 A:HIS282 2.2 46.5 1.0
SG A:CYS316 2.3 37.8 1.0
S3 A:RQM701 2.4 48.0 0.8
NI A:RQM701 2.8 41.7 0.4
SG A:CYS546 3.0 43.7 0.5
CE1 A:HIS282 3.1 38.0 1.0
CD2 A:HIS282 3.1 41.2 1.0
CB A:CYS316 3.3 33.5 1.0
CB A:CYS546 3.4 41.1 0.5
CB A:CYS546 3.5 41.0 0.5
NZ A:LYS583 3.5 53.9 1.0
FE1 A:RQM701 3.6 37.0 0.4
S4 A:RQM701 3.7 46.8 0.7
SG A:CYS546 3.8 48.5 0.5
ND1 A:HIS282 4.2 40.1 1.0
FE4 A:RQM701 4.2 47.5 0.8
S1 A:RQM701 4.2 50.0 0.8
CG A:HIS282 4.2 42.5 1.0
O A:HOH1042 4.3 36.3 1.0
N A:CYS546 4.5 32.3 0.5
N A:CYS546 4.5 32.2 0.5
CA A:CYS316 4.5 34.6 1.0
CA A:CYS546 4.6 34.3 0.5
CA A:CYS546 4.6 34.4 0.5
CE A:LYS583 4.7 47.1 1.0
N A:CYS316 4.7 38.5 1.0
FE3 A:RQM701 4.7 31.8 0.5
O A:OH704 4.9 45.3 1.0

Iron binding site 3 out of 14 in 7zkv

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Iron binding site 3 out of 14 in the F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:31.8
occ:0.50
 FE3 A:RQM701 0.0 31.8 0.5
SG A:CYS467 2.2 47.5 1.0
S4 A:RQM701 2.3 46.8 0.7
S1 A:RQM701 2.3 50.0 0.8
S2 A:RQM701 2.3 63.9 1.0
FE1 A:RQM701 2.6 37.0 0.4
NI A:RQM701 2.7 41.7 0.4
FE4 A:RQM701 2.8 47.5 0.8
CB A:CYS467 3.0 60.9 1.0
O A:OH704 3.4 45.3 1.0
CA A:CYS467 3.4 57.0 1.0
N A:CYS467 3.7 52.7 1.0
S3 A:RQM701 3.9 48.0 0.8
OG A:SER581 4.0 27.4 1.0
C A:GLY466 4.0 44.3 1.0
SG A:CYS354 4.4 48.6 1.0
CA A:GLY466 4.4 38.5 1.0
O A:GLY466 4.5 37.7 1.0
CE A:MET580 4.5 44.1 1.0
SG A:CYS546 4.6 43.7 0.5
SG A:CYS497 4.7 48.0 1.0
FE2 A:RQM701 4.7 38.4 0.9
CB A:SER581 4.7 25.8 1.0
C A:CYS467 4.8 54.1 1.0

Iron binding site 4 out of 14 in 7zkv

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Iron binding site 4 out of 14 in the F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:47.5
occ:0.81
 FE4 A:RQM701 0.0 47.5 0.8
SG A:CYS497 2.2 48.0 1.0
S2 A:RQM701 2.3 63.9 1.0
S1 A:RQM701 2.3 50.0 0.8
S3 A:RQM701 2.4 48.0 0.8
FE1 A:RQM701 2.8 37.0 0.4
FE3 A:RQM701 2.8 31.8 0.5
CB A:CYS497 3.3 39.4 1.0
NI A:RQM701 3.7 41.7 0.4
N A:CYS497 4.0 35.0 1.0
S4 A:RQM701 4.1 46.8 0.7
FE2 A:RQM701 4.2 38.4 0.9
CA A:CYS497 4.2 33.8 1.0
CB A:PHE333 4.3 41.8 1.0
SG A:CYS315 4.4 46.4 0.6
CA A:CYS467 4.4 57.0 1.0
CB A:CYS315 4.6 50.9 0.4
SG A:CYS546 4.6 43.7 0.5
CB A:CYS467 4.7 60.9 1.0
O A:GLY466 4.7 37.7 1.0
SG A:CYS316 4.8 37.8 1.0
CB A:CYS315 4.8 51.2 0.6
SG A:CYS467 4.9 47.5 1.0
C A:GLY496 4.9 32.9 1.0
C A:GLY466 5.0 44.3 1.0

Iron binding site 5 out of 14 in 7zkv

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Iron binding site 5 out of 14 in the F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:31.0
occ:1.00
 FE2 A:SF4702 0.0 31.0 1.0
S1 A:SF4702 2.2 30.5 1.0
SG A:CYS67 2.3 33.2 1.0
S4 A:SF4702 2.3 29.2 1.0
FE3 A:SF4702 2.6 31.6 1.0
CB A:CYS67 3.1 27.5 1.0
CA A:CYS67 4.6 25.1 1.0
SG A:CYS59 4.7 36.4 1.0
CD A:ARG69 4.9 27.5 1.0
N A:GLY62 5.0 30.0 1.0
CB A:PHE61 5.0 33.2 1.0

Iron binding site 6 out of 14 in 7zkv

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Iron binding site 6 out of 14 in the F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:31.6
occ:1.00
 FE3 A:SF4702 0.0 31.6 1.0
S4 A:SF4702 2.2 29.2 1.0
S1 A:SF4702 2.3 30.5 1.0
SG A:CYS59 2.3 36.4 1.0
FE2 A:SF4702 2.6 31.0 1.0
CB A:CYS59 3.3 31.4 1.0
O A:HOH862 3.8 45.3 1.0
N A:GLY62 4.2 30.0 1.0
CB A:PHE61 4.4 33.2 1.0
CA A:CYS59 4.7 30.3 1.0
SG A:CYS67 4.7 33.2 1.0
CA A:GLY62 4.8 26.4 1.0
CB A:CYS67 4.9 27.5 1.0

Iron binding site 7 out of 14 in 7zkv

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Iron binding site 7 out of 14 in the F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:29.9
occ:1.00
 FE1 A:SF4703 0.0 29.9 1.0
S2 A:SF4703 2.2 29.7 1.0
S3 A:SF4703 2.3 26.8 1.0
S4 A:SF4703 2.3 27.8 1.0
SG A:CYS71 2.3 33.8 1.0
FE3 A:SF4703 2.7 30.8 1.0
FE4 A:SF4703 2.7 29.9 1.0
FE2 A:SF4703 2.8 29.4 1.0
CB A:CYS71 3.3 31.1 1.0
N A:CYS71 3.5 31.5 1.0
CD1 A:ILE220 3.9 45.0 1.0
CA A:CYS71 3.9 28.4 1.0
S1 A:SF4703 3.9 28.8 1.0
O A:CYS71 4.2 32.1 1.0
C A:CYS71 4.3 29.8 1.0
C A:PHE70 4.3 27.1 1.0
N A:GLY74 4.6 29.8 1.0
N A:PHE70 4.7 28.2 1.0
CB A:GLN73 4.7 40.0 1.0
SG A:CYS89 4.7 34.8 1.0
CG1 A:ILE220 4.7 33.7 1.0
SG A:CYS68 4.8 26.5 1.0
SG A:CYS76 4.9 33.0 1.0
N A:GLN73 4.9 32.0 1.0
CA A:PHE70 4.9 24.7 1.0
CB A:ILE220 5.0 31.2 1.0

Iron binding site 8 out of 14 in 7zkv

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Iron binding site 8 out of 14 in the F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:29.4
occ:1.00
 FE2 A:SF4703 0.0 29.4 1.0
S1 A:SF4703 2.2 28.8 1.0
SG A:CYS89 2.3 34.8 1.0
S3 A:SF4703 2.3 26.8 1.0
S4 A:SF4703 2.3 27.8 1.0
FE4 A:SF4703 2.7 29.9 1.0
FE3 A:SF4703 2.8 30.8 1.0
FE1 A:SF4703 2.8 29.9 1.0
CB A:CYS89 3.4 38.6 1.0
N A:CYS89 3.9 27.8 1.0
S2 A:SF4703 3.9 29.7 1.0
O A:HOH1013 4.1 28.6 1.0
CD1 A:ILE220 4.2 45.0 1.0
CB A:ALA91 4.2 36.1 1.0
CA A:CYS89 4.2 36.4 1.0
N A:ILE88 4.5 29.9 1.0
NH1 A:ARG99 4.5 32.3 1.0
CG1 A:ILE220 4.6 33.7 1.0
SG A:CYS71 4.7 33.8 1.0
SG A:CYS68 4.7 26.5 1.0
SG A:CYS76 4.8 33.0 1.0
C A:GLY87 4.9 32.0 1.0
CA A:GLY87 4.9 28.1 1.0
N A:ALA91 4.9 27.6 1.0

Iron binding site 9 out of 14 in 7zkv

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Iron binding site 9 out of 14 in the F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:30.8
occ:1.00
 FE3 A:SF4703 0.0 30.8 1.0
S4 A:SF4703 2.2 27.8 1.0
S2 A:SF4703 2.3 29.7 1.0
S1 A:SF4703 2.3 28.8 1.0
SG A:CYS76 2.3 33.0 1.0
FE1 A:SF4703 2.7 29.9 1.0
FE4 A:SF4703 2.7 29.9 1.0
FE2 A:SF4703 2.8 29.4 1.0
CB A:CYS76 3.1 27.7 1.0
S3 A:SF4703 3.9 26.8 1.0
N A:ILE88 3.9 29.9 1.0
CA A:CYS76 4.4 28.1 1.0
N A:CYS76 4.4 27.1 1.0
CA A:GLY74 4.5 33.7 1.0
CA A:GLY87 4.5 28.1 1.0
CB A:ILE88 4.6 37.1 1.0
O A:CYS68 4.6 26.8 1.0
SG A:CYS68 4.6 26.5 1.0
N A:GLY74 4.7 29.8 1.0
C A:GLY87 4.7 32.0 1.0
SG A:CYS71 4.7 33.8 1.0
N A:CYS89 4.8 27.8 1.0
SG A:CYS89 4.8 34.8 1.0
CB A:CYS68 4.8 30.1 1.0
CA A:ILE88 4.8 36.6 1.0
CD1 A:ILE88 4.9 43.8 1.0

Iron binding site 10 out of 14 in 7zkv

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Iron binding site 10 out of 14 in the F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:29.9
occ:1.00
 FE4 A:SF4703 0.0 29.9 1.0
SG A:CYS68 2.2 26.5 1.0
S3 A:SF4703 2.2 26.8 1.0
S1 A:SF4703 2.3 28.8 1.0
S2 A:SF4703 2.3 29.7 1.0
FE2 A:SF4703 2.7 29.4 1.0
FE3 A:SF4703 2.7 30.8 1.0
FE1 A:SF4703 2.7 29.9 1.0
CB A:CYS68 3.2 30.1 1.0
NH1 A:ARG99 3.8 32.3 1.0
S4 A:SF4703 3.8 27.8 1.0
N A:PHE70 3.9 28.2 1.0
C A:CYS68 4.1 28.7 1.0
O A:CYS68 4.2 26.8 1.0
CA A:CYS68 4.3 29.5 1.0
CB A:PHE70 4.4 26.4 1.0
N A:ARG69 4.5 26.9 1.0
CA A:PHE70 4.5 24.7 1.0
N A:CYS71 4.5 31.5 1.0
CB A:CYS76 4.8 27.7 1.0
C A:PHE70 4.8 27.1 1.0
C A:ARG69 4.8 31.1 1.0
SG A:CYS76 4.8 33.0 1.0
SG A:CYS89 4.8 34.8 1.0
CZ A:ARG99 4.9 35.7 1.0
CA A:ARG69 4.9 25.5 1.0
SG A:CYS71 5.0 33.8 1.0

Reference:

J.Ruickoldt, Y.Basak, L.Domnik, J.H.Jeoung, H.Dobbek. On the Kinetics of CO2 Reduction By Ni, Fe-Co Dehydrogenases Acs Catal. 2022.
DOI: 10.1021/ACSCATAL.2C02221
Page generated: Wed Apr 5 07:33:50 2023

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