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Iron in PDB 8x9d: Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration

Enzymatic activity of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration

All present enzymatic activity of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration:
1.2.7.4;

Protein crystallography data

The structure of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration, PDB code: 8x9d was solved by H.H.Lee, Y.Heo, H.J.Yoon, S.M.Kim, S.Y.Kong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.02 / 2.11
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 112.045, 74.552, 71.309, 90, 111.53, 90
R / Rfree (%) 16.5 / 21.9

Other elements in 8x9d:

The structure of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration also contains other interesting chemical elements:

Nickel (Ni) 1 atom

Iron Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration (pdb code 8x9d). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 11 binding sites of Iron where determined in the Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration, PDB code: 8x9d:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 11 in 8x9d

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Iron binding site 1 out of 11 in the Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:17.4
occ:1.00
 FE1 A:SF4701 0.0 17.4 1.0
S4 A:SF4701 2.2 19.4 1.0
S2 A:SF4701 2.3 19.1 1.0
S3 A:SF4701 2.3 19.8 1.0
SG A:CYS70 2.4 19.1 1.0
FE2 A:SF4701 2.7 16.8 1.0
FE3 A:SF4701 2.7 18.1 1.0
FE4 A:SF4701 2.7 18.5 1.0
CB A:CYS70 3.5 20.5 1.0
N A:CYS70 3.8 20.5 1.0
S1 A:SF4701 3.9 20.1 1.0
O A:HOH947 4.1 19.8 1.0
NH2 A:ARG80 4.2 18.2 1.0
CA A:CYS70 4.3 20.5 1.0
CB A:ALA72 4.3 20.4 1.0
N A:ILE69 4.6 21.0 1.0
CG A:MET199 4.6 20.7 1.0
SG A:CYS51 4.7 19.4 1.0
SG A:CYS48 4.8 17.7 1.0
SG A:CYS56 4.9 20.7 1.0
C A:ILE69 5.0 21.2 1.0
C A:GLY68 5.0 21.4 1.0

Iron binding site 2 out of 11 in 8x9d

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Iron binding site 2 out of 11 in the Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:16.8
occ:1.00
 FE2 A:SF4701 0.0 16.8 1.0
S1 A:SF4701 2.2 20.1 1.0
S3 A:SF4701 2.3 19.8 1.0
S4 A:SF4701 2.3 19.4 1.0
SG A:CYS48 2.4 17.7 1.0
FE4 A:SF4701 2.6 18.5 1.0
FE3 A:SF4701 2.7 18.1 1.0
FE1 A:SF4701 2.7 17.4 1.0
CB A:CYS48 3.2 20.0 1.0
NH2 A:ARG80 3.7 18.2 1.0
S2 A:SF4701 3.8 19.1 1.0
N A:HIS50 4.1 19.2 1.0
C A:CYS48 4.2 20.5 1.0
O A:CYS48 4.2 21.3 1.0
CA A:CYS48 4.3 21.0 1.0
CB A:HIS50 4.4 19.7 1.0
N A:CYS51 4.5 20.1 1.0
N A:ARG49 4.6 20.3 1.0
CA A:HIS50 4.6 19.8 1.0
SG A:CYS56 4.8 20.7 1.0
C A:HIS50 4.8 20.2 1.0
CB A:CYS56 4.8 21.9 1.0
CZ A:ARG80 4.8 19.6 1.0
SG A:CYS51 4.9 19.4 1.0
SG A:CYS70 5.0 19.1 1.0
O A:HOH983 5.0 18.8 1.0

Iron binding site 3 out of 11 in 8x9d

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Iron binding site 3 out of 11 in the Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:18.1
occ:1.00
 FE3 A:SF4701 0.0 18.1 1.0
S2 A:SF4701 2.2 19.1 1.0
S4 A:SF4701 2.3 19.4 1.0
S1 A:SF4701 2.3 20.1 1.0
SG A:CYS56 2.4 20.7 1.0
FE2 A:SF4701 2.7 16.8 1.0
FE4 A:SF4701 2.7 18.5 1.0
FE1 A:SF4701 2.7 17.4 1.0
CB A:CYS56 3.3 21.9 1.0
S3 A:SF4701 3.9 19.8 1.0
N A:ILE69 3.9 21.0 1.0
CB A:ILE69 4.3 21.1 1.0
CA A:GLY54 4.4 23.1 1.0
N A:GLY54 4.4 22.7 1.0
CA A:CYS56 4.5 22.8 1.0
N A:CYS56 4.6 22.3 1.0
O A:CYS48 4.6 21.3 1.0
CA A:ILE69 4.6 20.9 1.0
SG A:CYS51 4.7 19.4 1.0
CA A:GLY68 4.7 21.4 1.0
N A:CYS70 4.7 20.5 1.0
SG A:CYS48 4.7 17.7 1.0
C A:GLY68 4.7 21.4 1.0
CB A:CYS48 4.8 20.0 1.0
CG1 A:ILE69 4.8 21.4 1.0
SG A:CYS70 4.8 19.1 1.0
CD1 A:ILE69 4.9 21.9 1.0
C A:GLN53 5.0 22.7 1.0

Iron binding site 4 out of 11 in 8x9d

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Iron binding site 4 out of 11 in the Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:18.5
occ:1.00
 FE4 A:SF4701 0.0 18.5 1.0
S1 A:SF4701 2.2 20.1 1.0
S3 A:SF4701 2.3 19.8 1.0
S2 A:SF4701 2.3 19.1 1.0
SG A:CYS51 2.3 19.4 1.0
FE2 A:SF4701 2.6 16.8 1.0
FE3 A:SF4701 2.7 18.1 1.0
FE1 A:SF4701 2.7 17.4 1.0
CB A:CYS51 3.3 20.2 1.0
N A:CYS51 3.7 20.1 1.0
S4 A:SF4701 3.9 19.4 1.0
CA A:CYS51 3.9 20.4 1.0
O A:CYS51 4.2 21.3 1.0
C A:CYS51 4.3 22.1 1.0
CG A:MET199 4.4 20.7 1.0
C A:HIS50 4.4 20.2 1.0
N A:GLY54 4.4 22.7 1.0
CB A:GLN53 4.6 21.7 1.0
CB A:MET199 4.8 19.6 1.0
N A:GLN53 4.8 22.5 1.0
SG A:CYS48 4.8 17.7 1.0
SG A:CYS70 4.9 19.1 1.0
N A:HIS50 4.9 19.2 1.0
NE2 A:GLN53 4.9 20.9 1.0
SG A:CYS56 4.9 20.7 1.0
CA A:GLY54 5.0 23.1 1.0

Iron binding site 5 out of 11 in 8x9d

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Iron binding site 5 out of 11 in the Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:17.8
occ:1.00
 FE1 A:FES702 0.0 17.8 1.0
S2 A:FES702 2.2 23.0 1.0
S1 A:FES702 2.2 25.7 1.0
SG A:CYS47 2.4 22.1 1.0
FE2 A:FES702 2.7 25.1 1.0
CB A:CYS47 3.2 22.2 1.0
CA A:CYS47 4.6 22.0 1.0
CB A:PHE41 4.8 27.8 1.0
SG A:CYS39 4.8 30.6 1.0
CB A:PRO55 4.9 24.2 1.0
CD A:ARG49 5.0 23.4 1.0

Iron binding site 6 out of 11 in 8x9d

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Iron binding site 6 out of 11 in the Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:25.1
occ:1.00
 FE2 A:FES702 0.0 25.1 1.0
S2 A:FES702 2.2 23.0 1.0
S1 A:FES702 2.2 25.7 1.0
SG A:CYS39 2.4 30.6 1.0
FE1 A:FES702 2.7 17.8 1.0
CB A:CYS39 3.2 34.0 1.0
OH7 A:1PE705 4.0 50.0 0.5
N A:GLY42 4.2 26.6 1.0
CB A:PHE41 4.2 27.8 1.0
CD2 A:PHE41 4.6 33.4 1.0
CA A:CYS39 4.7 35.0 1.0
CA A:GLY42 4.8 26.1 1.0
C16 A:1PE705 4.8 49.1 1.0
SG A:CYS47 4.9 22.1 1.0
CG A:PHE41 4.9 29.6 1.0
CB A:CYS47 5.0 22.2 1.0

Iron binding site 7 out of 11 in 8x9d

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Iron binding site 7 out of 11 in the Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:25.5
occ:0.64
 FE1 A:XCC703 0.0 25.5 0.6
FE A:FE704 1.9 27.4 0.4
S4 A:XCC703 2.3 25.7 0.7
S3 A:XCC703 2.3 27.4 0.7
S2 A:XCC703 2.3 26.2 0.7
SG A:CYS476 2.3 27.4 1.0
FE4 A:XCC703 2.6 26.2 0.7
FE3 A:XCC703 2.8 25.6 0.7
CB A:CYS476 3.3 23.9 1.0
FE2 A:XCC703 3.5 28.8 0.7
SG A:CYS294 3.6 29.0 0.4
O A:HOH993 3.7 25.9 1.0
N A:CYS476 3.9 23.4 1.0
NI A:XCC703 4.0 28.1 0.7
S1 A:XCC703 4.1 26.2 0.7
CA A:CYS446 4.2 23.0 1.0
CA A:CYS476 4.2 23.3 1.0
CB A:CYS446 4.3 23.4 1.0
SG A:CYS294 4.3 27.5 0.6
O A:GLY445 4.5 24.0 1.0
SG A:CYS526 4.5 25.2 0.5
CB A:SER312 4.6 25.2 1.0
OG A:SER312 4.6 24.5 1.0
SG A:CYS333 4.7 26.3 1.0
N A:CYS446 4.8 22.7 1.0
C A:GLY445 4.8 23.5 1.0
SG A:CYS446 4.8 24.4 1.0
SG A:CYS295 4.8 25.7 1.0
C A:GLY475 4.8 23.6 1.0
CE1 A:HIS261 4.9 26.9 1.0
CB A:CYS294 5.0 29.6 0.4

Iron binding site 8 out of 11 in 8x9d

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Iron binding site 8 out of 11 in the Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:28.8
occ:0.70
 FE2 A:XCC703 0.0 28.8 0.7
NE2 A:HIS261 1.9 27.1 1.0
S3 A:XCC703 2.3 27.4 0.7
CE1 A:HIS261 2.6 26.9 1.0
SG A:CYS295 2.6 25.7 1.0
SG A:CYS526 2.8 25.2 0.5
NI A:XCC703 2.8 28.1 0.7
CD2 A:HIS261 3.0 26.7 1.0
FE4 A:XCC703 3.2 26.2 0.7
O A:HOH829 3.2 37.9 1.0
S4 A:XCC703 3.5 25.7 0.7
S1 A:XCC703 3.5 26.2 0.7
CB A:CYS295 3.5 26.6 1.0
CB A:CYS526 3.5 24.7 0.5
FE1 A:XCC703 3.5 25.5 0.6
CB A:CYS526 3.6 24.5 0.5
SG A:CYS526 3.7 27.7 0.5
ND1 A:HIS261 3.8 26.4 1.0
NZ A:LYS563 3.8 25.9 1.0
SG A:CYS294 4.0 29.0 0.4
CG A:HIS261 4.0 26.3 1.0
FE A:FE704 4.1 27.4 0.4
O A:HOH993 4.2 25.9 1.0
FE3 A:XCC703 4.2 25.6 0.7
SG A:CYS333 4.5 26.3 1.0
N A:CYS295 4.5 27.3 1.0
CA A:CYS295 4.6 27.0 1.0
N A:CYS526 4.6 23.3 1.0
O A:HOH973 4.6 24.4 1.0
CA A:CYS526 4.6 23.6 0.5
CA A:CYS526 4.7 22.8 0.5
S2 A:XCC703 5.0 26.2 0.7

Iron binding site 9 out of 11 in 8x9d

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Iron binding site 9 out of 11 in the Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:25.6
occ:0.70
 FE3 A:XCC703 0.0 25.6 0.7
S1 A:XCC703 2.3 26.2 0.7
S4 A:XCC703 2.3 25.7 0.7
SG A:CYS446 2.3 24.4 1.0
S2 A:XCC703 2.4 26.2 0.7
FE4 A:XCC703 2.4 26.2 0.7
FE1 A:XCC703 2.8 25.5 0.6
CB A:CYS446 2.8 23.4 1.0
NI A:XCC703 2.9 28.1 0.7
CA A:CYS446 3.3 23.0 1.0
N A:CYS446 3.5 22.7 1.0
C A:GLY445 3.9 23.5 1.0
S3 A:XCC703 4.0 27.4 0.7
FE2 A:XCC703 4.2 28.8 0.7
SG A:CYS333 4.2 26.3 1.0
FE A:FE704 4.3 27.4 0.4
CB A:HIS561 4.4 21.4 1.0
O A:GLY445 4.4 24.0 1.0
CA A:GLY445 4.5 22.3 1.0
SG A:CYS526 4.5 25.2 0.5
CE A:MET560 4.5 23.3 1.0
O A:HOH829 4.7 37.9 1.0
SG A:CYS476 4.8 27.4 1.0
C A:CYS446 4.8 22.8 1.0
SG A:CYS526 4.9 27.7 0.5
CB A:CYS476 5.0 23.9 1.0
N A:HIS561 5.0 20.5 1.0

Iron binding site 10 out of 11 in 8x9d

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Iron binding site 10 out of 11 in the Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Co Dehydrogenase Mutant with Increased Affinity For Electron Mediators in High Peg Concentration within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:26.2
occ:0.70
 FE4 A:XCC703 0.0 26.2 0.7
SG A:CYS333 2.2 26.3 1.0
S3 A:XCC703 2.3 27.4 0.7
S2 A:XCC703 2.3 26.2 0.7
S1 A:XCC703 2.3 26.2 0.7
FE3 A:XCC703 2.4 25.6 0.7
FE1 A:XCC703 2.6 25.5 0.6
FE A:FE704 3.2 27.4 0.4
FE2 A:XCC703 3.2 28.8 0.7
CB A:CYS333 3.2 24.4 1.0
S4 A:XCC703 3.5 25.7 0.7
CE1 A:HIS261 3.5 26.9 1.0
NI A:XCC703 3.6 28.1 0.7
SG A:CYS294 3.9 29.0 0.4
NE2 A:HIS261 3.9 27.1 1.0
NZ A:LYS563 4.0 25.9 1.0
O A:HOH829 4.4 37.9 1.0
SG A:CYS446 4.5 24.4 1.0
O A:HOH961 4.6 29.4 1.0
CA A:CYS333 4.6 22.4 1.0
CE A:MET560 4.7 23.3 1.0
CB A:CYS446 4.7 23.4 1.0
ND1 A:HIS261 4.8 26.4 1.0
CB A:HIS561 4.8 21.4 1.0
CE A:LYS563 4.8 24.1 1.0
SG A:CYS526 4.9 25.2 0.5
SG A:CYS476 4.9 27.4 1.0
SG A:CYS294 5.0 27.5 0.6

Reference:

S.M.Kim, S.H.Kang, J.Lee, Y.Heo, E.G.Poloniataki, J.Kang, H.J.Yoon, S.Y.Kong, Y.Yun, H.Kim, J.Ryu, H.H.Lee, Y.H.Kim. Identifying A Key Spot For Electron Mediator-Interaction to Tailor Co Dehydrogenase'S Affinity Nat Commun V. 15 2732 2024.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-024-46909-1
Page generated: Fri Aug 8 00:46:43 2025

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