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Iron in PDB 3i39: Ni,Fe-Codh-320 Mv+Cn State

Enzymatic activity of Ni,Fe-Codh-320 Mv+Cn State

All present enzymatic activity of Ni,Fe-Codh-320 Mv+Cn State:
1.2.99.2;

Protein crystallography data

The structure of Ni,Fe-Codh-320 Mv+Cn State, PDB code: 3i39 was solved by J.-H.Jeoung, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.60 / 1.36
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 111.279, 75.834, 71.099, 90.00, 111.33, 90.00
R / Rfree (%) 15.4 / 19

Other elements in 3i39:

The structure of Ni,Fe-Codh-320 Mv+Cn State 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 Ni,Fe-Codh-320 Mv+Cn State (pdb code 3i39). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 11 binding sites of Iron where determined in the Ni,Fe-Codh-320 Mv+Cn State, PDB code: 3i39:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 11 in 3i39

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Iron binding site 1 out of 11 in the Ni,Fe-Codh-320 Mv+Cn State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ni,Fe-Codh-320 Mv+Cn State within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Fe5000

b:7.7
occ:1.00
 FE1 X:SF45000 0.0 7.7 1.0
S3 X:SF45000 2.2 7.7 1.0
S4 X:SF45000 2.3 7.8 1.0
S2 X:SF45000 2.3 7.7 1.0
SG X:CYS56 2.3 7.7 1.0
FE3 X:SF45000 2.6 7.1 1.0
FE2 X:SF45000 2.7 7.2 1.0
FE4 X:SF45000 2.7 7.4 1.0
CB X:CYS56 3.2 8.3 1.0
S1 X:SF45000 3.8 7.6 1.0
N X:ILE69 4.0 6.8 1.0
CA X:GLY54 4.4 8.5 1.0
CA X:CYS56 4.4 6.1 1.0
CB X:ILE69 4.4 8.5 1.0
N X:GLY54 4.5 7.8 1.0
N X:CYS56 4.5 6.4 1.0
SG X:CYS51 4.6 7.5 1.0
O X:CYS48 4.6 7.9 1.0
SG X:CYS48 4.7 6.9 1.0
N X:CYS70 4.7 7.0 1.0
CA X:ILE69 4.7 8.4 1.0
CA X:GLY68 4.8 7.1 1.0
CB X:CYS48 4.8 7.7 1.0
SG X:CYS70 4.8 7.7 1.0
C X:GLY68 4.8 7.6 1.0
CG1 X:ILE69 4.9 8.8 1.0
C X:GLN53 5.0 8.2 1.0

Iron binding site 2 out of 11 in 3i39

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Iron binding site 2 out of 11 in the Ni,Fe-Codh-320 Mv+Cn State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ni,Fe-Codh-320 Mv+Cn State within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Fe5000

b:7.2
occ:1.00
 FE2 X:SF45000 0.0 7.2 1.0
S4 X:SF45000 2.2 7.8 1.0
S1 X:SF45000 2.3 7.6 1.0
SG X:CYS51 2.3 7.5 1.0
S3 X:SF45000 2.3 7.7 1.0
FE3 X:SF45000 2.6 7.1 1.0
FE1 X:SF45000 2.7 7.7 1.0
FE4 X:SF45000 2.7 7.4 1.0
CB X:CYS51 3.3 5.4 1.0
N X:CYS51 3.6 5.8 1.0
S2 X:SF45000 3.8 7.7 1.0
CA X:CYS51 3.8 7.7 1.0
O X:HOH663 4.0 18.0 1.0
C X:CYS51 4.3 6.2 1.0
O X:CYS51 4.3 7.2 1.0
C X:HIS50 4.3 7.2 1.0
N X:GLY54 4.4 7.8 1.0
CG X:MET199 4.5 8.6 1.0
CB X:GLN53 4.6 7.8 1.0
N X:HIS50 4.8 7.0 1.0
SG X:CYS48 4.8 6.9 1.0
SG X:CYS56 4.8 7.7 1.0
SG X:CYS70 4.8 7.7 1.0
N X:GLN53 4.8 7.8 1.0
CB X:MET199 4.9 7.1 1.0
CA X:HIS50 5.0 9.4 1.0
CA X:GLY54 5.0 8.5 1.0

Iron binding site 3 out of 11 in 3i39

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Iron binding site 3 out of 11 in the Ni,Fe-Codh-320 Mv+Cn State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ni,Fe-Codh-320 Mv+Cn State within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Fe5000

b:7.1
occ:1.00
 FE3 X:SF45000 0.0 7.1 1.0
S1 X:SF45000 2.2 7.6 1.0
S4 X:SF45000 2.2 7.8 1.0
S2 X:SF45000 2.3 7.7 1.0
SG X:CYS48 2.3 6.9 1.0
FE1 X:SF45000 2.6 7.7 1.0
FE2 X:SF45000 2.6 7.2 1.0
FE4 X:SF45000 2.7 7.4 1.0
CB X:CYS48 3.3 7.7 1.0
NH2 X:ARG80 3.6 8.1 1.0
S3 X:SF45000 3.8 7.7 1.0
N X:HIS50 4.0 7.0 1.0
C X:CYS48 4.2 7.3 1.0
O X:CYS48 4.2 7.9 1.0
CB X:HIS50 4.3 7.9 1.0
CA X:CYS48 4.4 6.1 1.0
N X:CYS51 4.5 5.8 1.0
CA X:HIS50 4.5 9.4 1.0
N X:ARG49 4.6 7.4 1.0
SG X:CYS56 4.7 7.7 1.0
CB X:CYS56 4.7 8.3 1.0
C X:HIS50 4.7 7.2 1.0
CZ X:ARG80 4.8 7.7 1.0
SG X:CYS51 4.8 7.5 1.0
SG X:CYS70 4.9 7.7 1.0
C X:ARG49 5.0 9.4 1.0

Iron binding site 4 out of 11 in 3i39

Go back to Iron Binding Sites List in 3i39
Iron binding site 4 out of 11 in the Ni,Fe-Codh-320 Mv+Cn State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Ni,Fe-Codh-320 Mv+Cn State within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Fe5000

b:7.4
occ:1.00
 FE4 X:SF45000 0.0 7.4 1.0
S2 X:SF45000 2.2 7.7 1.0
S1 X:SF45000 2.3 7.6 1.0
S3 X:SF45000 2.3 7.7 1.0
SG X:CYS70 2.3 7.7 1.0
FE3 X:SF45000 2.7 7.1 1.0
FE1 X:SF45000 2.7 7.7 1.0
FE2 X:SF45000 2.7 7.2 1.0
CB X:CYS70 3.4 8.9 1.0
N X:CYS70 3.8 7.0 1.0
S4 X:SF45000 3.9 7.8 1.0
NH2 X:ARG80 4.1 8.1 1.0
O X:HOH639 4.2 7.7 1.0
CA X:CYS70 4.2 8.2 1.0
CB X:ALA72 4.4 8.9 1.0
O X:HOH663 4.5 18.0 1.0
N X:ILE69 4.6 6.8 1.0
CG X:MET199 4.6 8.6 1.0
SG X:CYS51 4.6 7.5 1.0
SG X:CYS48 4.8 6.9 1.0
SG X:CYS56 4.8 7.7 1.0
C X:ILE69 5.0 7.5 1.0

Iron binding site 5 out of 11 in 3i39

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Iron binding site 5 out of 11 in the Ni,Fe-Codh-320 Mv+Cn State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Ni,Fe-Codh-320 Mv+Cn State within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Fe5001

b:7.5
occ:1.00
 FE1 X:FES5001 0.0 7.5 1.0
SG X:CYS47 2.3 7.9 1.0
S1 X:FES5001 2.3 7.7 1.0
S2 X:FES5001 2.3 7.5 1.0
FE2 X:FES5001 2.7 8.2 1.0
CB X:CYS47 3.2 8.1 1.0
O X:HOH1208 3.7 8.0 1.0
O X:HOH651 4.3 10.0 1.0
CA X:CYS47 4.6 7.6 1.0
SG X:CYS39 4.7 9.2 1.0
CB X:PHE41 4.8 8.5 1.0
N X:GLY42 5.0 8.9 1.0
CD X:ARG49 5.0 13.3 1.0

Iron binding site 6 out of 11 in 3i39

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Iron binding site 6 out of 11 in the Ni,Fe-Codh-320 Mv+Cn State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Ni,Fe-Codh-320 Mv+Cn State within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Fe5001

b:8.2
occ:1.00
 FE2 X:FES5001 0.0 8.2 1.0
S2 X:FES5001 2.3 7.5 1.0
SG X:CYS39 2.3 9.2 1.0
S1 X:FES5001 2.3 7.7 1.0
FE1 X:FES5001 2.7 7.5 1.0
CB X:CYS39 3.2 5.9 1.0
N X:GLY42 4.1 8.9 1.0
CB X:PHE41 4.3 8.5 1.0
O X:HOH1363 4.6 34.6 1.0
CA X:CYS39 4.6 7.4 1.0
CA X:GLY42 4.7 10.6 1.0
CD2 X:PHE41 4.7 10.0 1.0
SG X:CYS47 4.8 7.9 1.0

Iron binding site 7 out of 11 in 3i39

Go back to Iron Binding Sites List in 3i39
Iron binding site 7 out of 11 in the Ni,Fe-Codh-320 Mv+Cn State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Ni,Fe-Codh-320 Mv+Cn State within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Fe5002

b:10.9
occ:0.80
 FE1 X:WCC5002 0.0 10.9 0.8
S2 X:WCC5002 2.2 11.4 0.8
SG X:CYS333 2.3 11.1 1.0
S4 X:WCC5002 2.3 13.2 0.8
S3 X:WCC5002 2.3 13.2 0.8
FE4 X:WCC5002 2.5 11.3 0.8
FE3 X:WCC5002 2.6 13.1 0.8
FE X:FE25004 3.0 25.4 0.1
CB X:CYS333 3.1 12.9 1.0
FE X:FE25003 3.4 16.8 0.7
NI X:WCC5002 3.4 13.8 0.7
S1 X:WCC5002 3.5 11.6 0.8
CE1 X:HIS261 3.6 12.7 1.0
NE2 X:HIS261 3.8 17.4 1.0
NZ X:LYS563 4.1 11.3 1.0
C X:CYN5005 4.1 14.2 0.7
CA X:CYS333 4.5 11.0 1.0
O X:HOH1131 4.5 14.1 1.0
SG X:CYS446 4.5 11.1 1.0
CE X:MET560 4.7 11.1 1.0
SG X:CYS476 4.8 12.0 0.7
SG X:CYS476 4.8 6.9 0.3
ND1 X:HIS261 4.9 14.7 1.0
CE X:LYS563 4.9 10.0 1.0
CB X:HIS561 4.9 7.0 1.0

Iron binding site 8 out of 11 in 3i39

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Iron binding site 8 out of 11 in the Ni,Fe-Codh-320 Mv+Cn State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Ni,Fe-Codh-320 Mv+Cn State within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Fe5002

b:13.1
occ:0.80
 FE3 X:WCC5002 0.0 13.1 0.8
S1 X:WCC5002 2.2 11.6 0.8
S2 X:WCC5002 2.2 11.4 0.8
S4 X:WCC5002 2.2 13.2 0.8
SG X:CYS476 2.4 6.9 0.3
SG X:CYS476 2.4 12.0 0.7
FE1 X:WCC5002 2.6 10.9 0.8
FE4 X:WCC5002 2.6 11.3 0.8
CB X:CYS476 3.3 11.4 0.7
FE X:FE25003 3.4 16.8 0.7
CB X:CYS476 3.4 5.9 0.3
NI X:WCC5002 3.7 13.8 0.7
FE X:FE25004 3.8 25.4 0.1
S3 X:WCC5002 3.8 13.2 0.8
O X:HOH856 3.9 21.0 1.0
N X:CYS476 4.0 8.7 1.0
CA X:CYS446 4.2 7.8 1.0
CA X:CYS476 4.2 13.4 0.3
CA X:CYS476 4.3 10.8 0.7
CB X:SER312 4.4 15.0 1.0
OG X:SER312 4.5 11.9 1.0
SG X:CYS294 4.6 12.3 1.0
CB X:CYS446 4.6 9.0 1.0
SG X:CYS526 4.6 12.4 1.0
SG X:CYS446 4.7 11.1 1.0
O X:GLY445 4.7 11.7 1.0
SG X:CYS333 4.8 11.1 1.0
N X:CYS446 4.8 9.3 1.0
C X:GLY445 4.8 9.8 1.0
SG X:CYS295 4.9 12.3 0.7
C X:GLY475 4.9 8.4 1.0
NE2 X:HIS261 5.0 17.4 1.0

Iron binding site 9 out of 11 in 3i39

Go back to Iron Binding Sites List in 3i39
Iron binding site 9 out of 11 in the Ni,Fe-Codh-320 Mv+Cn State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Ni,Fe-Codh-320 Mv+Cn State within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Fe5002

b:11.3
occ:0.80
 FE4 X:WCC5002 0.0 11.3 0.8
S3 X:WCC5002 2.2 13.2 0.8
S1 X:WCC5002 2.2 11.6 0.8
S2 X:WCC5002 2.3 11.4 0.8
SG X:CYS446 2.4 11.1 1.0
FE1 X:WCC5002 2.5 10.9 0.8
FE3 X:WCC5002 2.6 13.1 0.8
NI X:WCC5002 2.8 13.8 0.7
CB X:CYS446 3.2 9.0 1.0
CA X:CYS446 3.4 7.8 1.0
N X:CYS446 3.6 9.3 1.0
S4 X:WCC5002 3.9 13.2 0.8
C X:GLY445 4.0 9.8 1.0
C X:CYN5005 4.1 14.2 0.7
FE X:FE25003 4.2 16.8 0.7
SG X:CYS333 4.4 11.1 1.0
SG X:CYS476 4.4 6.9 0.3
FE X:FE25004 4.4 25.4 0.1
CA X:GLY445 4.5 10.0 1.0
CB X:HIS561 4.5 7.0 1.0
O X:GLY445 4.6 11.7 1.0
CE X:MET560 4.6 11.1 1.0
SG X:CYS526 4.6 12.4 1.0
CB X:CYS476 4.8 5.9 0.3
C X:CYS446 4.9 8.4 1.0
SG X:CYS476 4.9 12.0 0.7

Iron binding site 10 out of 11 in 3i39

Go back to Iron Binding Sites List in 3i39
Iron binding site 10 out of 11 in the Ni,Fe-Codh-320 Mv+Cn State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Ni,Fe-Codh-320 Mv+Cn State within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Fe5003

b:16.8
occ:0.70
 FE X:FE25004 1.2 25.4 0.1
SG X:CYS295 2.0 8.5 0.3
S4 X:WCC5002 2.2 13.2 0.8
SG X:CYS295 2.4 12.3 0.7
NE2 X:HIS261 2.4 17.4 1.0
SG X:CYS526 2.5 12.4 1.0
NI X:WCC5002 2.6 13.8 0.7
C X:CYN5005 3.2 14.2 0.7
S1 X:WCC5002 3.3 11.6 0.8
CE1 X:HIS261 3.3 12.7 1.0
CB X:CYS295 3.3 9.4 0.7
CB X:CYS295 3.4 22.1 0.3
FE3 X:WCC5002 3.4 13.1 0.8
FE1 X:WCC5002 3.4 10.9 0.8
CD2 X:HIS261 3.4 16.5 1.0
CB X:CYS526 3.5 10.7 1.0
S3 X:WCC5002 3.7 13.2 0.8
O X:HOH856 3.9 21.0 1.0
N X:CYN5005 4.0 13.4 0.7
FE4 X:WCC5002 4.2 11.3 0.8
CA X:CYS295 4.3 15.5 0.3
N X:CYS526 4.3 9.1 1.0
N X:CYS295 4.3 11.1 1.0
CA X:CYS295 4.4 8.9 0.7
ND1 X:HIS261 4.4 14.7 1.0
CG X:HIS261 4.5 15.6 1.0
NZ X:LYS563 4.5 11.3 1.0
CA X:GLY475 4.5 8.3 1.0
CA X:CYS526 4.5 9.7 1.0
O X:HOH726 4.8 12.7 1.0
SG X:CYS476 4.8 12.0 0.7
SG X:CYS333 4.9 11.1 1.0
S2 X:WCC5002 5.0 11.4 0.8

Reference:

J.H.Jeoung, H.Dobbek. Structural Basis of Cyanide Inhibition of Ni, Fe-Containing Carbon Monoxide Dehydrogenase J.Am.Chem.Soc. V. 131 9922 2009.
ISSN: ISSN 0002-7863
PubMed: 19583208
DOI: 10.1021/JA9046476
Page generated: Sun Dec 13 15:08:17 2020

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