Iron in PDB 7xdp: Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S Mutant in Anaerobic Condition)

Enzymatic activity of Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S Mutant in Anaerobic Condition)

All present enzymatic activity of Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S Mutant in Anaerobic Condition):
1.2.7.4;

Protein crystallography data

The structure of Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S Mutant in Anaerobic Condition), PDB code: 7xdp 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) 33.23 / 1.84
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 111.934, 74.969, 71.323, 90, 111.29, 90
R / Rfree (%) 14.8 / 19.3

Other elements in 7xdp:

The structure of Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S 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 Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S Mutant in Anaerobic Condition) (pdb code 7xdp). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S Mutant in Anaerobic Condition), PDB code: 7xdp:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 7xdp

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Iron binding site 1 out of 10 in the Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S 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 Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S Mutant in Anaerobic Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:12.5
occ:1.00
 FE1 A:SF4701 0.0 12.5 1.0
S4 A:SF4701 2.3 12.3 1.0
S2 A:SF4701 2.3 11.7 1.0
S3 A:SF4701 2.3 12.1 1.0
SG A:CYS70 2.4 13.3 1.0
FE2 A:SF4701 2.7 11.9 1.0
FE3 A:SF4701 2.7 12.3 1.0
FE4 A:SF4701 2.8 12.0 1.0
CB A:CYS70 3.4 12.6 1.0
N A:CYS70 3.9 11.6 1.0
S1 A:SF4701 3.9 11.9 1.0
NH2 A:ARG80 4.1 11.2 1.0
O A:HOH1065 4.2 12.2 1.0
CA A:CYS70 4.2 11.4 1.0
CB A:ALA72 4.4 12.3 1.0
CG A:MET199 4.6 10.9 1.0
N A:ILE69 4.6 11.7 1.0
SG A:CYS51 4.7 12.7 1.0
SG A:CYS48 4.8 12.2 1.0
SG A:CYS56 4.8 13.2 1.0
C A:ILE69 5.0 12.5 1.0

Iron binding site 2 out of 10 in 7xdp

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Iron binding site 2 out of 10 in the Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S 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 Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S Mutant in Anaerobic Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:11.9
occ:1.00
 FE2 A:SF4701 0.0 11.9 1.0
S3 A:SF4701 2.3 12.1 1.0
S1 A:SF4701 2.3 11.9 1.0
S4 A:SF4701 2.3 12.3 1.0
SG A:CYS48 2.3 12.2 1.0
FE3 A:SF4701 2.7 12.3 1.0
FE4 A:SF4701 2.7 12.0 1.0
FE1 A:SF4701 2.7 12.5 1.0
CB A:CYS48 3.2 9.9 1.0
NH2 A:ARG80 3.6 11.2 1.0
S2 A:SF4701 3.8 11.7 1.0
N A:HIS50 4.0 12.8 1.0
C A:CYS48 4.2 13.4 1.0
O A:CYS48 4.2 11.7 1.0
CA A:CYS48 4.3 10.3 1.0
CB A:HIS50 4.3 11.0 1.0
N A:CYS51 4.5 11.7 1.0
CA A:HIS50 4.6 12.9 1.0
N A:ARG49 4.6 12.0 1.0
SG A:CYS56 4.7 13.2 1.0
CB A:CYS56 4.8 14.5 1.0
CZ A:ARG80 4.8 12.5 1.0
C A:HIS50 4.8 11.3 1.0
C A:ARG49 4.9 15.8 1.0
SG A:CYS51 4.9 12.7 1.0
SG A:CYS70 5.0 13.3 1.0

Iron binding site 3 out of 10 in 7xdp

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Iron binding site 3 out of 10 in the Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S 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 Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S Mutant in Anaerobic Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:12.3
occ:1.00
 FE3 A:SF4701 0.0 12.3 1.0
S2 A:SF4701 2.2 11.7 1.0
S4 A:SF4701 2.3 12.3 1.0
S1 A:SF4701 2.3 11.9 1.0
SG A:CYS56 2.4 13.2 1.0
FE2 A:SF4701 2.7 11.9 1.0
FE4 A:SF4701 2.7 12.0 1.0
FE1 A:SF4701 2.7 12.5 1.0
CB A:CYS56 3.2 14.5 1.0
S3 A:SF4701 3.9 12.1 1.0
N A:ILE69 4.0 11.7 1.0
N A:CYS56 4.4 11.9 1.0
CB A:ILE69 4.4 11.4 1.0
CA A:CYS56 4.4 14.0 1.0
CA A:GLY54 4.4 12.4 1.0
N A:GLY54 4.6 14.3 1.0
O A:CYS48 4.6 11.7 1.0
SG A:CYS51 4.7 12.7 1.0
SG A:CYS48 4.7 12.2 1.0
N A:CYS70 4.7 11.6 1.0
CA A:GLY68 4.7 13.7 1.0
CB A:CYS48 4.8 9.9 1.0
CA A:ILE69 4.8 11.5 1.0
C A:GLY68 4.8 12.3 1.0
SG A:CYS70 4.9 13.3 1.0
CG1 A:ILE69 4.9 11.8 1.0

Iron binding site 4 out of 10 in 7xdp

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Iron binding site 4 out of 10 in the Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S 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 Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S Mutant in Anaerobic Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:12.0
occ:1.00
 FE4 A:SF4701 0.0 12.0 1.0
S1 A:SF4701 2.2 11.9 1.0
S2 A:SF4701 2.3 11.7 1.0
S3 A:SF4701 2.3 12.1 1.0
SG A:CYS51 2.3 12.7 1.0
FE3 A:SF4701 2.7 12.3 1.0
FE2 A:SF4701 2.7 11.9 1.0
FE1 A:SF4701 2.8 12.5 1.0
CB A:CYS51 3.3 12.5 1.0
N A:CYS51 3.6 11.7 1.0
S4 A:SF4701 3.9 12.3 1.0
CA A:CYS51 3.9 12.5 1.0
O A:CYS51 4.2 13.9 1.0
C A:CYS51 4.3 14.3 1.0
C A:HIS50 4.4 11.3 1.0
CG A:MET199 4.4 10.9 1.0
N A:GLY54 4.5 14.3 1.0
CB A:GLN53 4.6 12.0 1.0
CB A:MET199 4.7 13.7 1.0
N A:HIS50 4.8 12.8 1.0
SG A:CYS48 4.8 12.2 1.0
N A:GLN53 4.9 12.0 1.0
NE2 A:GLN53 4.9 12.4 1.0
SG A:CYS56 4.9 13.2 1.0
SG A:CYS70 4.9 13.3 1.0
CA A:GLY54 4.9 12.4 1.0

Iron binding site 5 out of 10 in 7xdp

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Iron binding site 5 out of 10 in the Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S 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 Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S Mutant in Anaerobic Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:15.2
occ:1.00
 FE1 A:FES702 0.0 15.2 1.0
S2 A:FES702 2.2 14.9 1.0
S1 A:FES702 2.2 14.7 1.0
SG A:CYS47 2.4 16.1 1.0
FE2 A:FES702 2.7 14.3 1.0
CB A:CYS47 3.2 14.6 1.0
O A:HOH1193 3.6 17.3 1.0
CA A:CYS47 4.6 11.1 1.0
SG A:CYS39 4.8 14.8 1.0
CB A:PHE41 4.9 12.9 1.0
N A:GLY42 4.9 14.4 1.0

Iron binding site 6 out of 10 in 7xdp

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Iron binding site 6 out of 10 in the Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S 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 Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S Mutant in Anaerobic Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:14.3
occ:1.00
 FE2 A:FES702 0.0 14.3 1.0
S2 A:FES702 2.2 14.9 1.0
S1 A:FES702 2.2 14.7 1.0
SG A:CYS39 2.4 14.8 1.0
FE1 A:FES702 2.7 15.2 1.0
CB A:CYS39 3.2 13.5 1.0
N A:GLY42 4.1 14.4 1.0
CB A:PHE41 4.4 12.9 1.0
CA A:CYS39 4.6 15.0 1.0
CA A:GLY42 4.7 16.3 1.0
CD2 A:PHE41 4.7 15.9 1.0
SG A:CYS47 4.9 16.1 1.0
CB A:CYS47 5.0 14.6 1.0

Iron binding site 7 out of 10 in 7xdp

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Iron binding site 7 out of 10 in the Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S 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 Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S Mutant in Anaerobic Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:50.2
occ:1.00
 FE1 A:NFS703 0.0 50.2 1.0
NE2 A:HIS261 2.0 28.1 1.0
S2 A:NFS703 2.4 56.0 1.0
SG A:CYS295 2.6 24.5 1.0
S1 A:NFS703 2.6 58.3 1.0
NI1 A:NFS703 2.8 63.1 1.0
CD2 A:HIS261 2.8 23.3 1.0
CE1 A:HIS261 3.1 23.1 1.0
SG A:CYS526 3.2 50.3 1.0
S5 A:NFS703 3.2 46.5 1.0
CB A:CYS295 3.3 18.8 1.0
FE4 A:NFS703 3.5 56.7 1.0
FE2 A:NFS703 3.6 57.1 1.0
CB A:CYS526 3.7 25.2 1.0
NZ A:LYS563 3.8 26.6 1.0
S3 A:NFS703 3.9 54.4 1.0
CG A:HIS261 4.0 20.5 1.0
ND1 A:HIS261 4.1 22.5 1.0
O A:HOH1188 4.2 32.4 1.0
FE3 A:NFS703 4.4 72.5 1.0
N A:CYS295 4.4 16.9 1.0
CA A:CYS295 4.4 16.8 1.0
SG A:CYS333 4.4 28.4 1.0
O A:HOH1103 4.6 15.8 1.0
N A:CYS526 4.7 15.5 1.0
CA A:CYS526 4.9 17.3 1.0
CE A:LYS563 5.0 24.6 1.0

Iron binding site 8 out of 10 in 7xdp

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Iron binding site 8 out of 10 in the Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S 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 Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S Mutant in Anaerobic Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:57.1
occ:1.00
 FE2 A:NFS703 0.0 57.1 1.0
S1 A:NFS703 2.0 58.3 1.0
S4 A:NFS703 2.3 47.6 1.0
SG A:CYS476 2.3 28.7 1.0
S5 A:NFS703 2.5 46.5 1.0
FE4 A:NFS703 2.7 56.7 1.0
FE3 A:NFS703 2.8 72.5 1.0
CB A:CYS476 3.4 25.1 1.0
FE1 A:NFS703 3.6 50.2 1.0
SG A:CYS294 3.8 38.7 1.0
NI1 A:NFS703 4.1 63.1 1.0
S3 A:NFS703 4.1 54.4 1.0
N A:CYS476 4.3 17.5 1.0
CB A:SER312 4.3 22.7 1.0
CA A:CYS446 4.4 24.8 1.0
CB A:CYS446 4.4 20.5 1.0
CA A:CYS476 4.4 16.8 1.0
OG A:SER312 4.5 22.1 1.0
SG A:CYS333 4.6 28.4 1.0
CB A:CYS333 4.7 22.6 1.0
CA A:SER312 4.7 21.4 1.0
CB A:CYS294 4.7 24.8 1.0
NE2 A:HIS261 4.9 28.1 1.0
N A:SER312 4.9 20.4 1.0
O A:GLY445 4.9 17.9 1.0
SG A:CYS295 4.9 24.5 1.0
O A:HOH869 4.9 23.9 1.0
CA A:CYS294 5.0 17.6 1.0

Iron binding site 9 out of 10 in 7xdp

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Iron binding site 9 out of 10 in the Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S 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 Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S Mutant in Anaerobic Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:72.5
occ:1.00
 FE3 A:NFS703 0.0 72.5 1.0
S3 A:NFS703 2.2 54.4 1.0
S5 A:NFS703 2.3 46.5 1.0
SG A:CYS446 2.4 24.4 1.0
CB A:CYS446 2.5 20.5 1.0
FE4 A:NFS703 2.6 56.7 1.0
S4 A:NFS703 2.7 47.6 1.0
FE2 A:NFS703 2.8 57.1 1.0
NI1 A:NFS703 2.9 63.1 1.0
CA A:CYS446 2.9 24.8 1.0
N A:CYS446 3.2 24.5 1.0
C A:GLY445 3.6 20.0 1.0
O A:HOH1198 3.8 33.9 1.0
O A:GLY445 3.9 17.9 1.0
S1 A:NFS703 3.9 58.3 1.0
CA A:GLY445 4.3 19.4 1.0
C A:CYS446 4.4 17.6 1.0
FE1 A:NFS703 4.4 50.2 1.0
SG A:CYS476 4.5 28.7 1.0
CB A:CYS476 4.5 25.1 1.0
SG A:CYS526 4.6 50.3 1.0
SG A:CYS333 4.6 28.4 1.0
S2 A:NFS703 4.8 56.0 1.0
CB A:HIS561 4.9 16.3 1.0
N A:ASN447 4.9 14.7 1.0

Iron binding site 10 out of 10 in 7xdp

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Iron binding site 10 out of 10 in the Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S 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 Tunnel-Redesigned O2-Tolerant Co Dehydrogenase For Removal of Co in Real Flue Gas (CHCODH2 A559S Mutant in Anaerobic Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:56.7
occ:1.00
 FE4 A:NFS703 0.0 56.7 1.0
S4 A:NFS703 2.2 47.6 1.0
SG A:CYS333 2.2 28.4 1.0
S1 A:NFS703 2.3 58.3 1.0
S3 A:NFS703 2.4 54.4 1.0
FE3 A:NFS703 2.6 72.5 1.0
FE2 A:NFS703 2.7 57.1 1.0
CB A:CYS333 3.0 22.6 1.0
FE1 A:NFS703 3.5 50.2 1.0
NI1 A:NFS703 3.6 63.1 1.0
S5 A:NFS703 3.6 46.5 1.0
NE2 A:HIS261 4.0 28.1 1.0
CE1 A:HIS261 4.0 23.1 1.0
NZ A:LYS563 4.2 26.6 1.0
SG A:CYS446 4.2 24.4 1.0
S2 A:NFS703 4.3 56.0 1.0
CA A:CYS333 4.4 18.7 1.0
O A:HOH869 4.4 23.9 1.0
CB A:CYS446 4.4 20.5 1.0
CB A:HIS561 4.6 16.3 1.0
CE A:LYS563 4.8 24.6 1.0
CD2 A:HIS561 4.8 16.0 1.0
CG A:HIS561 4.9 12.3 1.0
SG A:CYS294 4.9 38.7 1.0
SG A:CYS476 5.0 28.7 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: Fri Aug 9 11:02:42 2024

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