Iron in PDB 7xdm: CHCODH2 A559W Mutant in Anaerobic Condition

Enzymatic activity of CHCODH2 A559W Mutant in Anaerobic Condition

All present enzymatic activity of CHCODH2 A559W Mutant in Anaerobic Condition:
1.2.7.4;

Protein crystallography data

The structure of CHCODH2 A559W Mutant in Anaerobic Condition, PDB code: 7xdm was solved by Y.Y.Heo, S.M.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.83 / 1.74
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 111.483, 75.803, 71.384, 90, 111.48, 90
R / Rfree (%) 16.4 / 19.2

Other elements in 7xdm:

The structure of CHCODH2 A559W Mutant in Anaerobic Condition also contains other interesting chemical elements:

Nickel (Ni) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the CHCODH2 A559W Mutant in Anaerobic Condition (pdb code 7xdm). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the CHCODH2 A559W Mutant in Anaerobic Condition, PDB code: 7xdm:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 7xdm

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Iron binding site 1 out of 10 in the CHCODH2 A559W Mutant in Anaerobic Condition


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of CHCODH2 A559W Mutant in Anaerobic Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:18.3
occ:1.00
 FE1 A:SF4701 0.0 18.3 1.0
S4 A:SF4701 2.2 18.1 1.0
S3 A:SF4701 2.3 17.1 1.0
S2 A:SF4701 2.3 17.6 1.0
SG A:CYS70 2.4 18.2 1.0
FE2 A:SF4701 2.7 16.1 1.0
FE3 A:SF4701 2.7 16.8 1.0
FE4 A:SF4701 2.7 16.9 1.0
CB A:CYS70 3.4 16.8 1.0
N A:CYS70 3.8 15.4 1.0
S1 A:SF4701 3.9 16.8 1.0
O A:HOH1028 4.2 17.5 1.0
NH2 A:ARG80 4.2 15.9 1.0
CA A:CYS70 4.2 14.4 1.0
CB A:ALA72 4.4 18.5 1.0
N A:ILE69 4.6 15.4 1.0
CG A:MET199 4.7 17.6 1.0
SG A:CYS48 4.7 16.0 1.0
SG A:CYS51 4.7 17.6 1.0
SG A:CYS56 4.8 16.7 1.0
C A:ILE69 5.0 18.1 1.0

Iron binding site 2 out of 10 in 7xdm

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Iron binding site 2 out of 10 in the CHCODH2 A559W Mutant in Anaerobic Condition


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of CHCODH2 A559W Mutant in Anaerobic Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:16.1
occ:1.00
 FE2 A:SF4701 0.0 16.1 1.0
S3 A:SF4701 2.2 17.1 1.0
S1 A:SF4701 2.3 16.8 1.0
SG A:CYS48 2.3 16.0 1.0
S4 A:SF4701 2.3 18.1 1.0
FE3 A:SF4701 2.7 16.8 1.0
FE4 A:SF4701 2.7 16.9 1.0
FE1 A:SF4701 2.7 18.3 1.0
CB A:CYS48 3.2 14.9 1.0
NH2 A:ARG80 3.7 15.9 1.0
S2 A:SF4701 3.8 17.6 1.0
N A:HIS50 4.0 17.4 1.0
C A:CYS48 4.2 16.7 1.0
O A:CYS48 4.3 17.4 1.0
CB A:HIS50 4.3 16.0 1.0
CA A:CYS48 4.3 15.8 1.0
N A:CYS51 4.5 15.7 1.0
CA A:HIS50 4.6 16.4 1.0
N A:ARG49 4.6 16.9 1.0
SG A:CYS56 4.7 16.7 1.0
CB A:CYS56 4.7 14.5 1.0
C A:HIS50 4.8 13.5 1.0
CZ A:ARG80 4.9 17.0 1.0
SG A:CYS70 4.9 18.2 1.0
SG A:CYS51 4.9 17.6 1.0
C A:ARG49 5.0 18.8 1.0

Iron binding site 3 out of 10 in 7xdm

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Iron binding site 3 out of 10 in the CHCODH2 A559W Mutant in Anaerobic Condition


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of CHCODH2 A559W Mutant in Anaerobic Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:16.8
occ:1.00
 FE3 A:SF4701 0.0 16.8 1.0
S2 A:SF4701 2.2 17.6 1.0
S1 A:SF4701 2.3 16.8 1.0
S4 A:SF4701 2.3 18.1 1.0
SG A:CYS56 2.4 16.7 1.0
FE2 A:SF4701 2.7 16.1 1.0
FE4 A:SF4701 2.7 16.9 1.0
FE1 A:SF4701 2.7 18.3 1.0
CB A:CYS56 3.2 14.5 1.0
S3 A:SF4701 3.9 17.1 1.0
N A:ILE69 4.0 15.4 1.0
CA A:CYS56 4.4 14.6 1.0
N A:CYS56 4.4 16.5 1.0
CB A:ILE69 4.4 14.2 1.0
CA A:GLY54 4.4 18.2 1.0
N A:GLY54 4.5 17.4 1.0
SG A:CYS48 4.6 16.0 1.0
O A:CYS48 4.7 17.4 1.0
SG A:CYS51 4.7 17.6 1.0
N A:CYS70 4.7 15.4 1.0
CA A:GLY68 4.7 19.1 1.0
CB A:CYS48 4.8 14.9 1.0
CA A:ILE69 4.8 17.6 1.0
C A:GLY68 4.8 17.1 1.0
SG A:CYS70 4.8 18.2 1.0
CG1 A:ILE69 4.9 17.1 1.0

Iron binding site 4 out of 10 in 7xdm

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Iron binding site 4 out of 10 in the CHCODH2 A559W Mutant in Anaerobic Condition


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of CHCODH2 A559W Mutant in Anaerobic Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:16.9
occ:1.00
 FE4 A:SF4701 0.0 16.9 1.0
S1 A:SF4701 2.3 16.8 1.0
S3 A:SF4701 2.3 17.1 1.0
S2 A:SF4701 2.3 17.6 1.0
SG A:CYS51 2.4 17.6 1.0
FE2 A:SF4701 2.7 16.1 1.0
FE3 A:SF4701 2.7 16.8 1.0
FE1 A:SF4701 2.7 18.3 1.0
CB A:CYS51 3.4 15.8 1.0
N A:CYS51 3.6 15.7 1.0
S4 A:SF4701 3.9 18.1 1.0
CA A:CYS51 3.9 16.2 1.0
O A:CYS51 4.2 17.8 1.0
C A:CYS51 4.3 15.7 1.0
CG A:MET199 4.4 17.6 1.0
C A:HIS50 4.4 13.5 1.0
N A:GLY54 4.4 17.4 1.0
CB A:GLN53 4.6 15.9 1.0
SG A:CYS48 4.8 16.0 1.0
N A:HIS50 4.8 17.4 1.0
CB A:MET199 4.9 18.2 1.0
SG A:CYS56 4.9 16.7 1.0
SG A:CYS70 4.9 18.2 1.0
OE1 A:GLN53 4.9 23.0 1.0
N A:GLN53 4.9 17.3 1.0
CA A:GLY54 5.0 18.2 1.0

Iron binding site 5 out of 10 in 7xdm

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Iron binding site 5 out of 10 in the CHCODH2 A559W Mutant in Anaerobic Condition


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of CHCODH2 A559W Mutant in Anaerobic Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:18.4
occ:1.00
 FE1 A:FES702 0.0 18.4 1.0
S1 A:FES702 2.2 18.4 1.0
S2 A:FES702 2.3 17.6 1.0
SG A:CYS47 2.3 18.4 1.0
FE2 A:FES702 2.6 17.1 1.0
CB A:CYS47 3.2 19.3 1.0
O A:HOH1085 3.7 18.9 1.0
CA A:CYS47 4.6 15.8 1.0
SG A:CYS39 4.8 18.3 1.0
CB A:PHE41 4.8 16.3 1.0
N A:GLY42 4.9 20.1 1.0
CD A:ARG49 5.0 25.9 1.0

Iron binding site 6 out of 10 in 7xdm

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Iron binding site 6 out of 10 in the CHCODH2 A559W Mutant in Anaerobic Condition


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of CHCODH2 A559W Mutant in Anaerobic Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:17.1
occ:1.00
 FE2 A:FES702 0.0 17.1 1.0
S2 A:FES702 2.2 17.6 1.0
S1 A:FES702 2.2 18.4 1.0
SG A:CYS39 2.4 18.3 1.0
FE1 A:FES702 2.6 18.4 1.0
CB A:CYS39 3.2 18.1 1.0
N A:GLY42 4.1 20.1 1.0
CB A:PHE41 4.3 16.3 1.0
CA A:CYS39 4.6 18.7 1.0
CA A:GLY42 4.7 20.2 1.0
O A:HOH1217 4.7 36.3 0.5
CD2 A:PHE41 4.8 19.1 1.0
SG A:CYS47 4.8 18.4 1.0
C A:PHE41 5.0 19.6 1.0

Iron binding site 7 out of 10 in 7xdm

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Iron binding site 7 out of 10 in the CHCODH2 A559W Mutant in Anaerobic Condition


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of CHCODH2 A559W Mutant in Anaerobic Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:46.8
occ:1.00
 FE1 A:NFS703 0.0 46.8 1.0
NE2 A:HIS261 1.9 30.6 1.0
S2 A:NFS703 2.4 49.1 1.0
S1 A:NFS703 2.5 41.6 1.0
SG A:CYS295 2.6 30.4 1.0
CD2 A:HIS261 2.6 25.1 1.0
NI1 A:NFS703 2.8 39.8 1.0
SG A:CYS526 2.9 33.2 1.0
CE1 A:HIS261 3.1 27.5 1.0
CB A:CYS295 3.3 27.3 1.0
FE4 A:NFS703 3.4 36.5 1.0
CB A:CYS526 3.5 24.8 1.0
NZ A:LYS563 3.7 27.6 1.0
FE2 A:NFS703 3.8 35.0 1.0
S5 A:NFS703 3.8 30.4 1.0
S3 A:NFS703 3.8 31.6 1.0
CG A:HIS261 3.8 22.4 1.0
ND1 A:HIS261 4.0 26.5 1.0
O A:HOH1061 4.3 21.8 1.0
FE3 A:NFS703 4.5 30.4 1.0
CA A:CYS295 4.5 21.4 1.0
N A:CYS295 4.5 23.4 1.0
O A:HOH1040 4.6 32.9 1.0
N A:CYS526 4.6 17.9 1.0
SG A:CYS333 4.6 25.7 1.0
CA A:CYS526 4.7 21.0 1.0

Iron binding site 8 out of 10 in 7xdm

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Iron binding site 8 out of 10 in the CHCODH2 A559W Mutant in Anaerobic Condition


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of CHCODH2 A559W Mutant in Anaerobic Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:35.0
occ:1.00
 FE2 A:NFS703 0.0 35.0 1.0
S1 A:NFS703 2.1 41.6 1.0
S4 A:NFS703 2.3 30.7 1.0
S5 A:NFS703 2.3 30.4 1.0
SG A:CYS476 2.3 29.3 1.0
FE4 A:NFS703 2.7 36.5 1.0
FE3 A:NFS703 2.8 30.4 1.0
CB A:CYS476 3.5 25.4 1.0
FE1 A:NFS703 3.8 46.8 1.0
O A:HOH1040 3.8 32.9 1.0
NI1 A:NFS703 3.8 39.8 1.0
N A:CYS476 4.0 21.1 1.0
S3 A:NFS703 4.1 31.6 1.0
CA A:CYS446 4.3 22.9 1.0
CA A:CYS476 4.4 21.1 1.0
OG A:SER312 4.4 24.6 1.0
CB A:CYS446 4.4 20.8 1.0
CB A:SER312 4.4 26.5 1.0
SG A:CYS294 4.6 39.8 1.0
SG A:CYS526 4.6 33.2 1.0
SG A:CYS333 4.7 25.7 1.0
O A:GLY445 4.7 21.8 1.0
SG A:CYS446 4.8 20.3 1.0
SG A:CYS295 4.9 30.4 1.0
NE2 A:HIS261 4.9 30.6 1.0
CA A:SER312 4.9 25.7 1.0
N A:CYS446 4.9 19.0 1.0
C A:GLY445 5.0 22.6 1.0

Iron binding site 9 out of 10 in 7xdm

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Iron binding site 9 out of 10 in the CHCODH2 A559W Mutant in Anaerobic Condition


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of CHCODH2 A559W Mutant in Anaerobic Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:30.4
occ:1.00
 FE3 A:NFS703 0.0 30.4 1.0
S3 A:NFS703 2.2 31.6 1.0
S5 A:NFS703 2.3 30.4 1.0
SG A:CYS446 2.4 20.3 1.0
S4 A:NFS703 2.5 30.7 1.0
FE4 A:NFS703 2.5 36.5 1.0
FE2 A:NFS703 2.8 35.0 1.0
NI1 A:NFS703 2.8 39.8 1.0
CB A:CYS446 2.9 20.8 1.0
CA A:CYS446 3.4 22.9 1.0
N A:CYS446 3.6 19.0 1.0
S1 A:NFS703 4.0 41.6 1.0
C A:GLY445 4.0 22.6 1.0
CB A:HIS561 4.4 16.9 1.0
SG A:CYS333 4.4 25.7 1.0
FE1 A:NFS703 4.5 46.8 1.0
O A:GLY445 4.5 21.8 1.0
CE A:MET560 4.5 26.6 1.0
SG A:CYS526 4.5 33.2 1.0
CA A:GLY445 4.5 17.4 1.0
S2 A:NFS703 4.6 49.1 1.0
SG A:CYS476 4.7 29.3 1.0
C A:CYS446 4.8 21.9 1.0

Iron binding site 10 out of 10 in 7xdm

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Iron binding site 10 out of 10 in the CHCODH2 A559W Mutant in Anaerobic Condition


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of CHCODH2 A559W Mutant in Anaerobic Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:36.5
occ:1.00
 FE4 A:NFS703 0.0 36.5 1.0
SG A:CYS333 2.2 25.7 1.0
S4 A:NFS703 2.2 30.7 1.0
S1 A:NFS703 2.3 41.6 1.0
S3 A:NFS703 2.5 31.6 1.0
FE3 A:NFS703 2.5 30.4 1.0
FE2 A:NFS703 2.7 35.0 1.0
CB A:CYS333 3.1 25.6 1.0
FE1 A:NFS703 3.4 46.8 1.0
NI1 A:NFS703 3.5 39.8 1.0
S5 A:NFS703 3.6 30.4 1.0
NE2 A:HIS261 3.7 30.6 1.0
CE1 A:HIS261 3.8 27.5 1.0
NZ A:LYS563 4.0 27.6 1.0
S2 A:NFS703 4.1 49.1 1.0
CA A:CYS333 4.5 20.6 1.0
SG A:CYS446 4.6 20.3 1.0
CE A:MET560 4.6 26.6 1.0
O A:HOH977 4.7 27.8 1.0
CB A:HIS561 4.8 16.9 1.0
CE A:LYS563 4.8 23.1 1.0
CD2 A:HIS561 4.9 18.5 1.0
SG A:CYS476 4.9 29.3 1.0
CB A:CYS446 5.0 20.8 1.0
CG A:HIS561 5.0 15.9 1.0

Reference:

S.M.Kim, J.H.Lee, S.H.Kang, Y.Y.Heo, H.J.Yoon, J.S.Hahn, H.H.Lee, Y.H.Kim. O2-Tolerant Co Dehydrogenase Via Tunnel Redesign For the Removal of Co From Industrial Flue Gas Nat Catal V. 5 807 2022.
ISSN: ESSN 2520-1158
DOI: 10.1038/S41929-022-00834-Y
Page generated: Wed Apr 5 07:04:00 2023

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