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Iron in PDB 9iym: CHCODH2 A559W_V610H Mutant

Enzymatic activity of CHCODH2 A559W_V610H Mutant

All present enzymatic activity of CHCODH2 A559W_V610H Mutant:
1.2.7.4;

Protein crystallography data

The structure of CHCODH2 A559W_V610H Mutant, PDB code: 9iym was solved by S.Y.Kong, H.J.Yoon, S.M.Kim, H.H.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.87 / 1.82
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 111.738, 75.745, 71.428, 90, 111.3, 90
R / Rfree (%) 16.7 / 20.8

Other elements in 9iym:

The structure of CHCODH2 A559W_V610H Mutant 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 CHCODH2 A559W_V610H Mutant (pdb code 9iym). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 11 binding sites of Iron where determined in the CHCODH2 A559W_V610H Mutant, PDB code: 9iym:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 11 in 9iym

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Iron binding site 1 out of 11 in the CHCODH2 A559W_V610H Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of CHCODH2 A559W_V610H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:18.8
occ:1.00
 FE1 A:SF4701 0.0 18.8 1.0
S4 A:SF4701 2.3 18.5 1.0
S2 A:SF4701 2.3 19.4 1.0
S3 A:SF4701 2.3 17.4 1.0
SG A:CYS70 2.4 19.4 1.0
FE3 A:SF4701 2.7 17.9 1.0
FE2 A:SF4701 2.7 17.5 1.0
FE4 A:SF4701 2.7 17.5 1.0
CB A:CYS70 3.4 15.7 1.0
N A:CYS70 3.8 17.3 1.0
S1 A:SF4701 3.9 17.6 1.0
O A:HOH989 4.1 18.2 1.0
CA A:CYS70 4.2 15.4 1.0
NH2 A:ARG80 4.2 16.1 1.0
CB A:ALA72 4.4 17.3 1.0
CG A:MET199 4.6 18.5 1.0
N A:ILE69 4.6 16.4 1.0
SG A:CYS51 4.7 18.2 1.0
SG A:CYS48 4.8 16.9 1.0
SG A:CYS56 4.8 17.1 1.0
C A:ILE69 5.0 20.0 1.0

Iron binding site 2 out of 11 in 9iym

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Iron binding site 2 out of 11 in the CHCODH2 A559W_V610H Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of CHCODH2 A559W_V610H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:17.5
occ:1.00
 FE2 A:SF4701 0.0 17.5 1.0
S3 A:SF4701 2.2 17.4 1.0
S1 A:SF4701 2.3 17.6 1.0
S4 A:SF4701 2.3 18.5 1.0
SG A:CYS48 2.3 16.9 1.0
FE3 A:SF4701 2.7 17.9 1.0
FE4 A:SF4701 2.7 17.5 1.0
FE1 A:SF4701 2.7 18.8 1.0
CB A:CYS48 3.3 13.1 1.0
NH2 A:ARG80 3.7 16.1 1.0
S2 A:SF4701 3.8 19.4 1.0
N A:HIS50 4.0 19.9 1.0
C A:CYS48 4.1 16.7 1.0
O A:CYS48 4.1 18.6 1.0
CB A:HIS50 4.4 17.0 1.0
CA A:CYS48 4.4 16.5 1.0
N A:CYS51 4.5 16.8 1.0
N A:ARG49 4.5 17.0 1.0
CA A:HIS50 4.6 16.3 1.0
SG A:CYS56 4.7 17.1 1.0
CB A:CYS56 4.8 16.6 1.0
C A:HIS50 4.8 14.9 1.0
CZ A:ARG80 4.9 20.5 1.0
C A:ARG49 4.9 20.2 1.0
SG A:CYS51 4.9 18.2 1.0
SG A:CYS70 5.0 19.4 1.0

Iron binding site 3 out of 11 in 9iym

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Iron binding site 3 out of 11 in the CHCODH2 A559W_V610H Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of CHCODH2 A559W_V610H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:17.9
occ:1.00
 FE3 A:SF4701 0.0 17.9 1.0
S2 A:SF4701 2.2 19.4 1.0
S1 A:SF4701 2.3 17.6 1.0
S4 A:SF4701 2.3 18.5 1.0
SG A:CYS56 2.4 17.1 1.0
FE2 A:SF4701 2.7 17.5 1.0
FE4 A:SF4701 2.7 17.5 1.0
FE1 A:SF4701 2.7 18.8 1.0
CB A:CYS56 3.3 16.6 1.0
S3 A:SF4701 3.9 17.4 1.0
N A:ILE69 4.0 16.4 1.0
CB A:ILE69 4.4 16.4 1.0
N A:CYS56 4.4 17.4 1.0
CA A:CYS56 4.4 19.3 1.0
CA A:GLY54 4.4 19.1 1.0
N A:GLY54 4.5 19.1 1.0
O A:CYS48 4.6 18.6 1.0
SG A:CYS51 4.7 18.2 1.0
SG A:CYS48 4.7 16.9 1.0
N A:CYS70 4.7 17.3 1.0
CA A:ILE69 4.8 17.7 1.0
CA A:GLY68 4.8 17.6 1.0
C A:GLY68 4.8 17.9 1.0
SG A:CYS70 4.8 19.4 1.0
CG1 A:ILE69 4.9 17.1 1.0
CB A:CYS48 4.9 13.1 1.0

Iron binding site 4 out of 11 in 9iym

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Iron binding site 4 out of 11 in the CHCODH2 A559W_V610H Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of CHCODH2 A559W_V610H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:17.5
occ:1.00
 FE4 A:SF4701 0.0 17.5 1.0
S1 A:SF4701 2.2 17.6 1.0
S2 A:SF4701 2.3 19.4 1.0
S3 A:SF4701 2.3 17.4 1.0
SG A:CYS51 2.3 18.2 1.0
FE3 A:SF4701 2.7 17.9 1.0
FE2 A:SF4701 2.7 17.5 1.0
FE1 A:SF4701 2.7 18.8 1.0
CB A:CYS51 3.3 16.8 1.0
N A:CYS51 3.6 16.8 1.0
CA A:CYS51 3.9 20.4 1.0
S4 A:SF4701 3.9 18.5 1.0
O A:CYS51 4.2 16.3 1.0
C A:CYS51 4.2 17.7 1.0
C A:HIS50 4.4 14.9 1.0
CG A:MET199 4.4 18.5 1.0
N A:GLY54 4.4 19.1 1.0
CB A:MET199 4.6 20.7 1.0
CB A:GLN53 4.7 18.9 1.0
N A:HIS50 4.8 19.9 1.0
SG A:CYS48 4.8 16.9 1.0
SG A:CYS56 4.9 17.1 1.0
SG A:CYS70 4.9 19.4 1.0
OE1 A:GLN53 4.9 22.6 1.0
N A:GLN53 4.9 16.2 1.0
CA A:GLY54 5.0 19.1 1.0

Iron binding site 5 out of 11 in 9iym

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Iron binding site 5 out of 11 in the CHCODH2 A559W_V610H Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of CHCODH2 A559W_V610H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:19.3
occ:1.00
 FE1 A:FES702 0.0 19.3 1.0
S1 A:FES702 2.2 20.7 1.0
S2 A:FES702 2.2 19.8 1.0
SG A:CYS47 2.4 19.2 1.0
FE2 A:FES702 2.6 18.7 1.0
CB A:CYS47 3.2 21.0 1.0
O A:HOH1054 3.6 19.7 1.0
CA A:CYS47 4.7 17.4 1.0
SG A:CYS39 4.7 19.2 1.0
CB A:PHE41 4.9 18.7 1.0
N A:GLY42 5.0 21.0 1.0

Iron binding site 6 out of 11 in 9iym

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Iron binding site 6 out of 11 in the CHCODH2 A559W_V610H Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of CHCODH2 A559W_V610H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:18.7
occ:1.00
 FE2 A:FES702 0.0 18.7 1.0
S2 A:FES702 2.2 19.8 1.0
S1 A:FES702 2.2 20.7 1.0
SG A:CYS39 2.3 19.2 1.0
FE1 A:FES702 2.6 19.3 1.0
CB A:CYS39 3.2 16.8 1.0
N A:GLY42 4.1 21.0 1.0
CB A:PHE41 4.4 18.7 1.0
CA A:CYS39 4.6 19.5 1.0
CA A:GLY42 4.7 22.3 1.0
CD2 A:PHE41 4.8 21.6 1.0
SG A:CYS47 4.8 19.2 1.0
C A:PHE41 5.0 23.0 1.0

Iron binding site 7 out of 11 in 9iym

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Iron binding site 7 out of 11 in the CHCODH2 A559W_V610H Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of CHCODH2 A559W_V610H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:39.8
occ:0.65
 FE1 A:XCC703 0.0 39.8 0.7
FE A:FE704 1.9 54.3 1.0
S3 A:XCC703 2.3 43.5 0.7
S4 A:XCC703 2.3 35.0 0.7
S2 A:XCC703 2.3 37.7 0.7
SG A:CYS476 2.5 34.5 1.0
FE4 A:XCC703 2.6 43.2 0.7
FE3 A:XCC703 3.0 30.3 0.7
O A:HOH1052 3.1 40.7 1.0
FE2 A:XCC703 3.5 39.5 0.7
CB A:CYS476 3.5 26.0 1.0
SG A:CYS294 3.6 30.1 0.4
NI A:XCC703 4.1 36.1 0.7
N A:CYS476 4.2 24.1 1.0
S1 A:XCC703 4.2 40.1 0.7
SG A:CYS294 4.3 35.2 0.6
CA A:CYS446 4.4 26.2 1.0
CA A:CYS476 4.5 23.9 1.0
OG A:SER312 4.5 27.0 1.0
CB A:SER312 4.5 29.1 1.0
SG A:CYS333 4.6 33.0 1.0
CB A:CYS446 4.7 23.9 1.0
SG A:CYS295 4.8 30.3 1.0
SG A:CYS526 4.8 27.7 0.5
O A:GLY445 4.9 22.7 1.0
CB A:CYS333 4.9 29.2 1.0
NE2 A:HIS261 4.9 33.1 1.0
CB A:CYS294 4.9 27.5 0.4
SG A:CYS446 4.9 22.2 1.0
CB A:CYS294 4.9 27.5 0.6
CA A:SER312 5.0 27.8 1.0

Iron binding site 8 out of 11 in 9iym

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Iron binding site 8 out of 11 in the CHCODH2 A559W_V610H Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of CHCODH2 A559W_V610H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:39.5
occ:0.65
 FE2 A:XCC703 0.0 39.5 0.7
O A:HOH801 2.1 33.6 0.9
S3 A:XCC703 2.2 43.5 0.7
NE2 A:HIS261 2.3 33.1 1.0
SG A:CYS295 2.6 30.3 1.0
NI A:XCC703 2.8 36.1 0.7
CD2 A:HIS261 2.9 26.6 1.0
FE4 A:XCC703 3.1 43.2 0.7
SG A:CYS526 3.1 27.7 0.5
CB A:CYS295 3.4 28.6 1.0
S4 A:XCC703 3.4 35.0 0.7
FE1 A:XCC703 3.5 39.8 0.7
S1 A:XCC703 3.5 40.1 0.7
CE1 A:HIS261 3.5 30.4 1.0
NZ A:LYS563 3.5 30.4 1.0
CB A:CYS526 3.5 23.6 0.5
CB A:CYS526 3.7 23.7 0.5
SG A:CYS294 3.9 30.1 0.4
SG A:CYS526 3.9 35.0 0.5
O A:HOH1052 4.0 40.7 1.0
CG A:HIS261 4.2 25.2 1.0
FE A:FE704 4.2 54.3 1.0
FE3 A:XCC703 4.2 30.3 0.7
ND1 A:HIS261 4.4 32.0 1.0
SG A:CYS333 4.4 33.0 1.0
N A:CYS295 4.5 25.2 1.0
CA A:CYS295 4.5 22.9 1.0
O A:HOH1023 4.5 24.2 1.0
N A:CYS526 4.8 17.7 1.0
CA A:CYS526 4.8 21.4 0.5
CA A:CYS526 4.8 21.4 0.5
S2 A:XCC703 4.9 37.7 0.7
CE A:LYS563 5.0 28.4 1.0

Iron binding site 9 out of 11 in 9iym

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Iron binding site 9 out of 11 in the CHCODH2 A559W_V610H Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of CHCODH2 A559W_V610H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:30.3
occ:0.65
 FE3 A:XCC703 0.0 30.3 0.7
S1 A:XCC703 2.2 40.1 0.7
S4 A:XCC703 2.3 35.0 0.7
SG A:CYS446 2.3 22.2 1.0
FE4 A:XCC703 2.4 43.2 0.7
S2 A:XCC703 2.4 37.7 0.7
NI A:XCC703 3.0 36.1 0.7
FE1 A:XCC703 3.0 39.8 0.7
CB A:CYS446 3.1 23.9 1.0
CA A:CYS446 3.5 26.2 1.0
N A:CYS446 3.7 24.0 1.0
S3 A:XCC703 4.1 43.5 0.7
C A:GLY445 4.1 24.4 1.0
SG A:CYS333 4.2 33.0 1.0
FE2 A:XCC703 4.2 39.5 0.7
CB A:HIS561 4.2 17.2 1.0
SG A:CYS526 4.6 27.7 0.5
O A:GLY445 4.6 22.7 1.0
FE A:FE704 4.6 54.3 1.0
O A:HOH801 4.6 33.6 0.9
CA A:GLY445 4.7 25.2 1.0
SG A:CYS526 4.8 35.0 0.5
N A:HIS561 5.0 18.4 1.0
NZ A:LYS563 5.0 30.4 1.0
SG A:CYS476 5.0 34.5 1.0
C A:CYS446 5.0 21.8 1.0

Iron binding site 10 out of 11 in 9iym

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Iron binding site 10 out of 11 in the CHCODH2 A559W_V610H Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of CHCODH2 A559W_V610H Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe703

b:43.2
occ:0.65
 FE4 A:XCC703 0.0 43.2 0.7
SG A:CYS333 2.2 33.0 1.0
S2 A:XCC703 2.3 37.7 0.7
S3 A:XCC703 2.3 43.5 0.7
S1 A:XCC703 2.4 40.1 0.7
FE3 A:XCC703 2.4 30.3 0.7
FE1 A:XCC703 2.6 39.8 0.7
FE2 A:XCC703 3.1 39.5 0.7
CB A:CYS333 3.2 29.2 1.0
FE A:FE704 3.3 54.3 1.0
S4 A:XCC703 3.4 35.0 0.7
NI A:XCC703 3.5 36.1 0.7
NE2 A:HIS261 3.6 33.1 1.0
NZ A:LYS563 3.7 30.4 1.0
O A:HOH801 3.8 33.6 0.9
CE1 A:HIS261 4.0 30.4 1.0
SG A:CYS294 4.0 30.1 0.4
SG A:CYS446 4.5 22.2 1.0
CA A:CYS333 4.6 23.9 1.0
CE A:LYS563 4.6 28.4 1.0
CB A:HIS561 4.7 17.2 1.0
O A:HOH999 4.8 31.7 1.0
CD2 A:HIS261 4.9 26.6 1.0
CD2 A:HIS561 5.0 18.0 1.0
CG A:HIS561 5.0 18.2 1.0
CB A:CYS446 5.0 23.9 1.0

Reference:

S.Y.Kong, H.J.Yoon, S.M.Kim, H.H.Lee. Air-Viable, Rapid Co Dehydrogenase with A Selectively Sealed Tunnel To Be Published.
Page generated: Sat Aug 23 03:20:13 2025

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