Iron in PDB 7zkk: A216H Variant of the Codh/Acs Complex of C. Hydrogenoformans

Enzymatic activity of A216H Variant of the Codh/Acs Complex of C. Hydrogenoformans

All present enzymatic activity of A216H Variant of the Codh/Acs Complex of C. Hydrogenoformans:
1.2.7.4; 2.3.1.169;

Protein crystallography data

The structure of A216H Variant of the Codh/Acs Complex of C. Hydrogenoformans, PDB code: 7zkk 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) 45.12 / 1.97
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 142.63, 142.63, 291.34, 90, 90, 120
R / Rfree (%) 15.8 / 19.2

Other elements in 7zkk:

The structure of A216H Variant of the Codh/Acs Complex of C. Hydrogenoformans also contains other interesting chemical elements:

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

Iron Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iron atom in the A216H Variant of the Codh/Acs Complex of C. Hydrogenoformans (pdb code 7zkk). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 14 binding sites of Iron where determined in the A216H Variant of the Codh/Acs Complex of C. Hydrogenoformans, PDB code: 7zkk:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 14 in 7zkk

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Iron binding site 1 out of 14 in the A216H 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 A216H Variant of the Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:38.0
occ:0.61
 FE1 A:RQM701 0.0 38.0 0.6
S3 A:RQM701 2.3 46.8 0.8
SG A:CYS354 2.3 46.8 1.0
S4 A:RQM701 2.4 43.8 0.7
S2 A:RQM701 2.4 53.1 0.9
FE3 A:RQM701 2.6 37.9 0.6
FE4 A:RQM701 3.0 42.1 0.9
CB A:CYS354 3.2 37.8 1.0
FE2 A:RQM701 3.3 53.9 0.9
NI A:RQM701 3.4 62.1 0.3
S1 A:RQM701 3.8 41.9 0.8
NZ A:LYS583 3.8 50.5 1.0
NE2 A:HIS282 4.1 51.1 1.0
CE1 A:HIS282 4.1 50.9 1.0
O A:OH705 4.5 56.8 1.0
CE A:MET580 4.6 39.7 1.0
CE A:LYS583 4.6 48.8 1.0
CA A:CYS354 4.6 38.5 1.0
OG A:SER581 4.7 34.5 1.0
CB A:CYS467 4.8 44.2 1.0
SG A:CYS467 4.8 35.5 1.0

Iron binding site 2 out of 14 in 7zkk

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Iron binding site 2 out of 14 in the A216H 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 A216H Variant of the Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:53.9
occ:0.93
 FE2 A:RQM701 0.0 53.9 0.9
O A:OH705 1.9 56.8 1.0
NE2 A:HIS282 2.2 51.1 1.0
S3 A:RQM701 2.3 46.8 0.8
SG A:CYS316 2.4 41.6 1.0
NI A:RQM701 2.8 62.1 0.3
SG A:CYS546 3.1 55.5 0.7
CD2 A:HIS282 3.2 51.3 1.0
CE1 A:HIS282 3.2 50.9 1.0
FE1 A:RQM701 3.3 38.0 0.6
CB A:CYS316 3.3 43.7 1.0
NZ A:LYS583 3.5 50.5 1.0
S4 A:RQM701 3.6 43.8 0.7
CB A:CYS546 3.7 44.4 0.3
CB A:CYS546 3.8 43.9 0.7
S1 A:RQM701 4.1 41.9 0.8
FE4 A:RQM701 4.1 42.1 0.9
CG A:HIS282 4.3 51.4 1.0
ND1 A:HIS282 4.3 50.4 1.0
SG A:CYS546 4.4 51.0 0.3
CA A:CYS316 4.5 41.0 1.0
N A:CYS316 4.5 41.6 1.0
FE3 A:RQM701 4.5 37.9 0.6
O A:HOH1052 4.7 35.0 1.0
N A:CYS546 4.7 32.9 0.7
N A:CYS546 4.7 33.4 0.3
SG A:CYS354 4.8 46.8 1.0
CE A:LYS583 4.8 48.8 1.0
O A:OH704 4.9 55.5 1.0
CA A:CYS546 4.9 36.2 0.3
CA A:CYS546 4.9 36.0 0.7

Iron binding site 3 out of 14 in 7zkk

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Iron binding site 3 out of 14 in the A216H 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 A216H Variant of the Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:37.9
occ:0.58
 FE3 A:RQM701 0.0 37.9 0.6
S4 A:RQM701 2.3 43.8 0.7
S1 A:RQM701 2.3 41.9 0.8
S2 A:RQM701 2.3 53.1 0.9
SG A:CYS467 2.5 35.5 1.0
FE1 A:RQM701 2.6 38.0 0.6
NI A:RQM701 2.7 62.1 0.3
CB A:CYS467 2.7 44.2 1.0
FE4 A:RQM701 3.0 42.1 0.9
CA A:CYS467 3.4 36.4 1.0
O A:OH704 3.6 55.5 1.0
N A:CYS467 3.6 35.6 1.0
OG A:SER581 3.9 34.5 1.0
S3 A:RQM701 4.0 46.8 0.8
C A:GLY466 4.1 36.6 1.0
CA A:GLY466 4.5 32.8 1.0
FE2 A:RQM701 4.5 53.9 0.9
SG A:CYS354 4.5 46.8 1.0
CE A:MET580 4.6 39.7 1.0
SG A:CYS546 4.6 55.5 0.7
O A:GLY466 4.6 29.9 1.0
CB A:SER581 4.7 26.7 1.0
C A:CYS467 4.9 34.5 1.0
SG A:CYS497 4.9 45.1 1.0

Iron binding site 4 out of 14 in 7zkk

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Iron binding site 4 out of 14 in the A216H 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 A216H Variant of the Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:42.1
occ:0.90
 FE4 A:RQM701 0.0 42.1 0.9
SG A:CYS497 2.2 45.1 1.0
S2 A:RQM701 2.3 53.1 0.9
S1 A:RQM701 2.4 41.9 0.8
S3 A:RQM701 2.4 46.8 0.8
FE3 A:RQM701 3.0 37.9 0.6
FE1 A:RQM701 3.0 38.0 0.6
CB A:CYS497 3.3 38.1 1.0
NI A:RQM701 3.8 62.1 0.3
N A:CYS497 3.9 30.3 1.0
FE2 A:RQM701 4.1 53.9 0.9
CB A:PHE333 4.1 46.4 1.0
CA A:CYS497 4.2 29.1 1.0
CA A:CYS467 4.2 36.4 1.0
CB A:CYS467 4.3 44.2 1.0
S4 A:RQM701 4.4 43.8 0.7
SG A:CYS315 4.5 48.8 0.6
CB A:CYS315 4.7 49.8 0.4
O A:GLY466 4.8 29.9 1.0
C A:GLY496 4.9 31.3 1.0
CB A:CYS315 4.9 49.2 0.6
N A:CYS467 4.9 35.6 1.0
SG A:CYS546 4.9 55.5 0.7
CG A:PHE333 4.9 37.8 1.0
C A:GLY466 5.0 36.6 1.0

Iron binding site 5 out of 14 in 7zkk

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Iron binding site 5 out of 14 in the A216H 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 A216H Variant of the Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:26.9
occ:1.00
 FE2 A:SF4702 0.0 26.9 1.0
S1 A:SF4702 2.2 27.0 1.0
SG A:CYS67 2.3 30.6 1.0
S4 A:SF4702 2.3 28.4 1.0
FE3 A:SF4702 2.7 26.8 1.0
CB A:CYS67 3.1 24.0 1.0
CA A:CYS67 4.6 22.9 1.0
SG A:CYS59 4.8 29.1 1.0
N A:GLY62 4.9 26.6 1.0
CD A:ARG69 4.9 27.7 1.0
CB A:PHE61 5.0 26.4 1.0

Iron binding site 6 out of 14 in 7zkk

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Iron binding site 6 out of 14 in the A216H 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 A216H Variant of the Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:26.8
occ:1.00
 FE3 A:SF4702 0.0 26.8 1.0
S4 A:SF4702 2.2 28.4 1.0
SG A:CYS59 2.3 29.1 1.0
S1 A:SF4702 2.3 27.0 1.0
FE2 A:SF4702 2.7 26.9 1.0
CB A:CYS59 3.3 28.5 1.0
N A:GLY62 4.2 26.6 1.0
CB A:PHE61 4.4 26.4 1.0
CA A:CYS59 4.7 28.9 1.0
SG A:CYS67 4.8 30.6 1.0
CA A:GLY62 4.8 26.9 1.0
CB A:CYS67 4.9 24.0 1.0
CD1 A:PHE61 5.0 31.8 1.0

Iron binding site 7 out of 14 in 7zkk

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Iron binding site 7 out of 14 in the A216H 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 A216H Variant of the Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:24.7
occ:1.00
 FE1 A:SF4703 0.0 24.7 1.0
S2 A:SF4703 2.2 25.4 1.0
SG A:CYS71 2.3 28.9 1.0
S4 A:SF4703 2.3 26.4 1.0
S3 A:SF4703 2.3 27.3 1.0
FE3 A:SF4703 2.7 27.2 1.0
FE4 A:SF4703 2.7 25.5 1.0
FE2 A:SF4703 2.8 25.6 1.0
CB A:CYS71 3.2 21.7 1.0
N A:CYS71 3.5 25.0 1.0
CA A:CYS71 3.8 24.4 1.0
S1 A:SF4703 3.9 26.8 1.0
O A:CYS71 4.1 29.5 1.0
C A:CYS71 4.2 27.0 1.0
CG1 A:ILE220 4.3 41.8 1.0
C A:PHE70 4.3 26.2 1.0
N A:GLY74 4.5 27.7 1.0
CB A:GLN73 4.6 32.7 1.0
N A:PHE70 4.7 26.6 1.0
SG A:CYS89 4.8 30.7 1.0
SG A:CYS68 4.8 26.4 1.0
N A:GLN73 4.9 31.1 1.0
SG A:CYS76 4.9 29.9 1.0
CB A:ILE220 4.9 40.5 1.0
CA A:PHE70 5.0 26.3 1.0
CA A:GLY74 5.0 29.8 1.0

Iron binding site 8 out of 14 in 7zkk

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Iron binding site 8 out of 14 in the A216H 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 A216H Variant of the Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:25.6
occ:1.00
 FE2 A:SF4703 0.0 25.6 1.0
S1 A:SF4703 2.3 26.8 1.0
SG A:CYS89 2.3 30.7 1.0
S3 A:SF4703 2.3 27.3 1.0
S4 A:SF4703 2.3 26.4 1.0
FE4 A:SF4703 2.7 25.5 1.0
FE3 A:SF4703 2.8 27.2 1.0
FE1 A:SF4703 2.8 24.7 1.0
CB A:CYS89 3.4 29.1 1.0
S2 A:SF4703 3.9 25.4 1.0
N A:CYS89 3.9 28.4 1.0
O A:HOH994 4.2 30.5 1.0
CA A:CYS89 4.2 27.5 1.0
NH1 A:ARG99 4.3 42.2 1.0
CB A:ALA91 4.3 31.4 1.0
CG1 A:ILE220 4.5 41.8 1.0
N A:ILE88 4.6 30.2 1.0
SG A:CYS71 4.7 28.9 1.0
SG A:CYS68 4.7 26.4 1.0
SG A:CYS76 4.8 29.9 1.0
CA A:GLY87 4.9 26.2 1.0
C A:GLY87 4.9 31.1 1.0
N A:ALA91 4.9 27.3 1.0

Iron binding site 9 out of 14 in 7zkk

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Iron binding site 9 out of 14 in the A216H 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 A216H Variant of the Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:27.2
occ:1.00
 FE3 A:SF4703 0.0 27.2 1.0
S4 A:SF4703 2.2 26.4 1.0
SG A:CYS76 2.3 29.9 1.0
S2 A:SF4703 2.3 25.4 1.0
S1 A:SF4703 2.4 26.8 1.0
FE1 A:SF4703 2.7 24.7 1.0
FE4 A:SF4703 2.7 25.5 1.0
FE2 A:SF4703 2.8 25.6 1.0
CB A:CYS76 3.2 27.7 1.0
S3 A:SF4703 3.9 27.3 1.0
N A:ILE88 4.0 30.2 1.0
N A:CYS76 4.3 29.3 1.0
CA A:CYS76 4.3 28.9 1.0
CA A:GLY74 4.5 29.8 1.0
CB A:ILE88 4.5 34.3 1.0
CA A:GLY87 4.6 26.2 1.0
N A:GLY74 4.6 27.7 1.0
O A:CYS68 4.7 23.6 1.0
SG A:CYS68 4.7 26.4 1.0
SG A:CYS71 4.7 28.9 1.0
C A:GLY87 4.7 31.1 1.0
N A:CYS89 4.7 28.4 1.0
CA A:ILE88 4.8 37.7 1.0
SG A:CYS89 4.8 30.7 1.0
CB A:CYS68 4.8 25.5 1.0
CG1 A:ILE88 4.9 31.8 1.0
CD1 A:ILE88 4.9 30.2 1.0

Iron binding site 10 out of 14 in 7zkk

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Iron binding site 10 out of 14 in the A216H 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 A216H Variant of the Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:25.5
occ:1.00
 FE4 A:SF4703 0.0 25.5 1.0
S3 A:SF4703 2.2 27.3 1.0
SG A:CYS68 2.3 26.4 1.0
S1 A:SF4703 2.3 26.8 1.0
S2 A:SF4703 2.3 25.4 1.0
FE2 A:SF4703 2.7 25.6 1.0
FE1 A:SF4703 2.7 24.7 1.0
FE3 A:SF4703 2.7 27.2 1.0
CB A:CYS68 3.3 25.5 1.0
NH1 A:ARG99 3.6 42.2 1.0
N A:PHE70 3.8 26.6 1.0
S4 A:SF4703 3.8 26.4 1.0
C A:CYS68 4.1 25.4 1.0
O A:CYS68 4.2 23.6 1.0
CB A:PHE70 4.3 26.4 1.0
CA A:CYS68 4.3 23.6 1.0
CA A:PHE70 4.5 26.3 1.0
N A:CYS71 4.5 25.0 1.0
N A:ARG69 4.5 22.9 1.0
C A:PHE70 4.7 26.2 1.0
SG A:CYS76 4.7 29.9 1.0
CB A:CYS76 4.8 27.7 1.0
C A:ARG69 4.8 29.1 1.0
CZ A:ARG99 4.8 37.3 1.0
SG A:CYS89 4.8 30.7 1.0
CA A:ARG69 5.0 24.9 1.0
SG A:CYS71 5.0 28.9 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 Catalysis 2022.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.2C02221
Page generated: Wed Apr 5 07:33:55 2023

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