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Iron in PDB 3b53: Ni,Fe-Codh-320 Mv State

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

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

Protein crystallography data

The structure of Ni,Fe-Codh-320 Mv State, PDB code: 3b53 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) 26.66 / 1.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 111.830, 74.520, 70.740, 90.00, 111.40, 90.00
R / Rfree (%) 14.5 / 17.8

Other elements in 3b53:

The structure of Ni,Fe-Codh-320 Mv 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 State (pdb code 3b53). 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 State, PDB code: 3b53:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 11 in 3b53

Go back to Iron Binding Sites List in 3b53
Iron binding site 1 out of 11 in the Ni,Fe-Codh-320 Mv 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 State within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Fe1004

b:12.5
occ:0.30
 FE X:FE21004 0.0 12.5 0.3
FE X:FE21004 1.2 12.6 0.6
S1 X:WCC1003 2.0 11.8 0.8
SG X:CYS295 2.2 13.2 0.7
SG X:CYS295 2.3 9.8 0.3
NI X:WCC1003 2.4 13.6 0.6
SG X:CYS526 2.7 11.4 1.0
O X:HOH1888 2.7 10.3 0.6
NE2 X:HIS261 3.0 16.8 1.0
FE4 X:WCC1003 3.1 13.0 0.8
S2 X:WCC1003 3.2 12.6 0.8
FE1 X:WCC1003 3.2 11.7 0.8
CB X:CYS295 3.3 10.8 0.3
CB X:CYS295 3.5 11.2 0.7
O X:HOH1268 3.5 16.8 1.0
CB X:CYS526 3.6 9.9 1.0
S3 X:WCC1003 3.7 13.1 0.8
CD2 X:HIS261 3.8 15.9 1.0
CE1 X:HIS261 3.9 15.2 1.0
FE3 X:WCC1003 4.1 12.6 0.8
N X:CYS295 4.1 11.4 0.7
N X:CYS295 4.2 11.3 0.3
CA X:CYS295 4.2 11.2 0.7
CA X:CYS295 4.3 10.8 0.3
N X:CYS526 4.5 8.8 1.0
NZ X:LYS563 4.5 9.7 1.0
CA X:GLY475 4.5 10.0 1.0
SG X:CYS476 4.6 17.0 1.0
CA X:CYS526 4.7 9.3 1.0
O X:HOH1762 4.7 20.2 1.0
S4 X:WCC1003 4.8 11.5 0.8
O X:HOH1103 4.8 10.3 1.0
N X:CYS476 4.9 11.7 1.0
SG X:CYS333 4.9 11.6 1.0
CG X:HIS261 5.0 13.0 1.0

Iron binding site 2 out of 11 in 3b53

Go back to Iron Binding Sites List in 3b53
Iron binding site 2 out of 11 in the Ni,Fe-Codh-320 Mv 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 State within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Fe1004

b:12.6
occ:0.60
 FE X:FE21004 0.0 12.6 0.6
FE X:FE21004 1.2 12.5 0.3
NE2 X:HIS261 1.8 16.8 1.0
O X:HOH1888 2.0 10.3 0.6
S1 X:WCC1003 2.2 11.8 0.8
SG X:CYS295 2.3 13.2 0.7
CD2 X:HIS261 2.7 15.9 1.0
NI X:WCC1003 2.9 13.6 0.6
CE1 X:HIS261 2.9 15.2 1.0
SG X:CYS295 2.9 9.8 0.3
FE1 X:WCC1003 3.2 11.7 0.8
CB X:CYS295 3.3 10.8 0.3
CB X:CYS295 3.3 11.2 0.7
SG X:CYS526 3.4 11.4 1.0
NZ X:LYS563 3.5 9.7 1.0
S3 X:WCC1003 3.6 13.1 0.8
CB X:CYS526 3.8 9.9 1.0
CG X:HIS261 3.9 13.0 1.0
ND1 X:HIS261 3.9 14.9 1.0
FE4 X:WCC1003 3.9 13.0 0.8
O X:HOH1762 3.9 20.2 1.0
S2 X:WCC1003 4.1 12.6 0.8
N X:CYS295 4.3 11.4 0.7
N X:CYS295 4.3 11.3 0.3
CA X:CYS295 4.3 11.2 0.7
O X:HOH1103 4.4 10.3 1.0
SG X:CYS333 4.4 11.6 1.0
CA X:CYS295 4.4 10.8 0.3
O X:HOH1268 4.5 16.8 1.0
FE3 X:WCC1003 4.6 12.6 0.8
CE X:LYS563 4.8 8.2 1.0
N X:CYS526 4.8 8.8 1.0
CA X:CYS526 5.0 9.3 1.0

Iron binding site 3 out of 11 in 3b53

Go back to Iron Binding Sites List in 3b53
Iron binding site 3 out of 11 in the Ni,Fe-Codh-320 Mv 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 State within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Fe1001

b:9.7
occ:1.00
 FE1 X:SF41001 0.0 9.7 1.0
S3 X:SF41001 2.3 8.6 1.0
SG X:CYS56 2.3 8.0 1.0
S4 X:SF41001 2.3 8.7 1.0
S2 X:SF41001 2.3 9.6 1.0
FE3 X:SF41001 2.7 8.8 1.0
FE2 X:SF41001 2.7 8.4 1.0
FE4 X:SF41001 2.7 9.2 1.0
CB X:CYS56 3.1 9.0 1.0
S1 X:SF41001 3.9 9.0 1.0
N X:ILE69 4.0 8.8 1.0
CB X:ILE69 4.3 9.2 1.0
CA X:CYS56 4.3 8.4 1.0
CA X:GLY54 4.4 9.4 1.0
N X:CYS56 4.4 8.3 1.0
N X:GLY54 4.4 10.1 1.0
O X:CYS48 4.6 6.4 1.0
SG X:CYS51 4.6 9.2 1.0
SG X:CYS48 4.6 8.3 1.0
N X:CYS70 4.7 9.2 1.0
CA X:ILE69 4.7 9.1 1.0
CA X:GLY68 4.7 9.0 1.0
CB X:CYS48 4.7 8.3 1.0
SG X:CYS70 4.8 8.4 1.0
C X:GLY68 4.8 8.6 1.0
CG1 X:ILE69 4.8 10.2 1.0
C X:GLN53 4.9 10.0 1.0

Iron binding site 4 out of 11 in 3b53

Go back to Iron Binding Sites List in 3b53
Iron binding site 4 out of 11 in the Ni,Fe-Codh-320 Mv 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 State within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Fe1001

b:8.4
occ:1.00
 FE2 X:SF41001 0.0 8.4 1.0
S4 X:SF41001 2.3 8.7 1.0
SG X:CYS51 2.3 9.2 1.0
S1 X:SF41001 2.3 9.0 1.0
S3 X:SF41001 2.3 8.6 1.0
FE3 X:SF41001 2.7 8.8 1.0
FE1 X:SF41001 2.7 9.7 1.0
FE4 X:SF41001 2.8 9.2 1.0
CB X:CYS51 3.3 8.2 1.0
N X:CYS51 3.6 8.0 1.0
CA X:CYS51 3.9 8.0 1.0
S2 X:SF41001 3.9 9.6 1.0
O X:HOH1759 4.1 22.5 1.0
O X:CYS51 4.2 7.4 1.0
C X:CYS51 4.3 7.9 1.0
C X:HIS50 4.3 8.5 1.0
N X:GLY54 4.4 10.1 1.0
CG X:MET199 4.4 7.8 1.0
CB X:GLN53 4.6 9.7 1.0
N X:HIS50 4.8 8.6 1.0
SG X:CYS48 4.8 8.3 1.0
CB X:MET199 4.8 7.9 1.0
SG X:CYS56 4.8 8.0 1.0
N X:GLN53 4.8 8.6 1.0
SG X:CYS70 4.8 8.4 1.0
CA X:GLY54 4.9 9.4 1.0
O X:HIS50 4.9 8.6 1.0
C X:GLN53 4.9 10.0 1.0
NE2 X:GLN53 4.9 12.4 1.0
CA X:HIS50 4.9 8.3 1.0

Iron binding site 5 out of 11 in 3b53

Go back to Iron Binding Sites List in 3b53
Iron binding site 5 out of 11 in the Ni,Fe-Codh-320 Mv 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 State within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Fe1001

b:8.8
occ:1.00
 FE3 X:SF41001 0.0 8.8 1.0
S4 X:SF41001 2.3 8.7 1.0
SG X:CYS48 2.3 8.3 1.0
S1 X:SF41001 2.3 9.0 1.0
S2 X:SF41001 2.3 9.6 1.0
FE1 X:SF41001 2.7 9.7 1.0
FE2 X:SF41001 2.7 8.4 1.0
FE4 X:SF41001 2.7 9.2 1.0
CB X:CYS48 3.2 8.3 1.0
NH2 X:ARG80 3.6 9.8 1.0
S3 X:SF41001 3.9 8.6 1.0
N X:HIS50 4.0 8.6 1.0
O X:CYS48 4.1 6.4 1.0
C X:CYS48 4.2 7.7 1.0
CB X:HIS50 4.3 9.3 1.0
CA X:CYS48 4.3 7.8 1.0
CA X:HIS50 4.5 8.3 1.0
N X:CYS51 4.5 8.0 1.0
CB X:CYS56 4.6 9.0 1.0
N X:ARG49 4.6 7.6 1.0
SG X:CYS56 4.6 8.0 1.0
C X:HIS50 4.7 8.5 1.0
CZ X:ARG80 4.8 9.9 1.0
SG X:CYS70 4.9 8.4 1.0
SG X:CYS51 4.9 9.2 1.0
C X:ARG49 4.9 8.1 1.0
CG X:HIS50 5.0 9.0 1.0

Iron binding site 6 out of 11 in 3b53

Go back to Iron Binding Sites List in 3b53
Iron binding site 6 out of 11 in the Ni,Fe-Codh-320 Mv 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 State within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Fe1001

b:9.2
occ:1.00
 FE4 X:SF41001 0.0 9.2 1.0
S2 X:SF41001 2.3 9.6 1.0
S3 X:SF41001 2.3 8.6 1.0
S1 X:SF41001 2.3 9.0 1.0
SG X:CYS70 2.3 8.4 1.0
FE3 X:SF41001 2.7 8.8 1.0
FE1 X:SF41001 2.7 9.7 1.0
FE2 X:SF41001 2.8 8.4 1.0
CB X:CYS70 3.3 8.9 1.0
N X:CYS70 3.8 9.2 1.0
S4 X:SF41001 3.9 8.7 1.0
O X:HOH1007 4.1 8.2 1.0
NH2 X:ARG80 4.2 9.8 1.0
CA X:CYS70 4.2 9.0 1.0
CB X:ALA72 4.4 9.6 1.0
O X:HOH1759 4.5 22.5 1.0
N X:ILE69 4.6 8.8 1.0
CG X:MET199 4.6 7.8 1.0
SG X:CYS51 4.7 9.2 1.0
SG X:CYS56 4.8 8.0 1.0
SG X:CYS48 4.8 8.3 1.0
C X:ILE69 4.9 9.0 1.0
C X:GLY68 5.0 8.6 1.0

Iron binding site 7 out of 11 in 3b53

Go back to Iron Binding Sites List in 3b53
Iron binding site 7 out of 11 in the Ni,Fe-Codh-320 Mv 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 State within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Fe1002

b:10.1
occ:1.00
 FE1 X:FES1002 0.0 10.1 1.0
S1 X:FES1002 2.3 8.5 1.0
S2 X:FES1002 2.3 9.6 1.0
SG X:CYS47 2.3 9.7 1.0
FE2 X:FES1002 2.6 9.5 1.0
CB X:CYS47 3.2 10.0 1.0
O X:HOH1080 3.6 9.9 1.0
CA X:CYS47 4.6 9.1 1.0
SG X:CYS39 4.6 9.5 1.0
CB X:PHE41 4.8 10.5 1.0
N X:GLY42 4.9 10.2 1.0
CD X:ARG49 5.0 9.7 1.0
O X:HOH1019 5.0 9.6 1.0

Iron binding site 8 out of 11 in 3b53

Go back to Iron Binding Sites List in 3b53
Iron binding site 8 out of 11 in the Ni,Fe-Codh-320 Mv 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 State within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Fe1002

b:9.5
occ:1.00
 FE2 X:FES1002 0.0 9.5 1.0
S2 X:FES1002 2.3 9.6 1.0
SG X:CYS39 2.3 9.5 1.0
S1 X:FES1002 2.3 8.5 1.0
FE1 X:FES1002 2.6 10.1 1.0
CB X:CYS39 3.1 9.6 1.0
N X:GLY42 4.1 10.2 1.0
CB X:PHE41 4.3 10.5 1.0
O X:HOH1700 4.6 38.5 1.0
CA X:CYS39 4.6 9.8 1.0
CA X:GLY42 4.7 10.7 1.0
SG X:CYS47 4.8 9.7 1.0
CD2 X:PHE41 4.8 11.2 1.0
C X:PHE41 5.0 10.4 1.0
CB X:CYS47 5.0 10.0 1.0
CA X:PHE41 5.0 10.6 1.0

Iron binding site 9 out of 11 in 3b53

Go back to Iron Binding Sites List in 3b53
Iron binding site 9 out of 11 in the Ni,Fe-Codh-320 Mv 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 State within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Fe1003

b:11.7
occ:0.80
 FE1 X:WCC1003 0.0 11.7 0.8
S1 X:WCC1003 2.2 11.8 0.8
S3 X:WCC1003 2.3 13.1 0.8
S4 X:WCC1003 2.3 11.5 0.8
SG X:CYS333 2.3 11.6 1.0
FE3 X:WCC1003 2.4 12.6 0.8
FE4 X:WCC1003 2.5 13.0 0.8
NI X:WCC1003 3.1 13.6 0.6
CB X:CYS333 3.1 10.8 1.0
FE X:FE21004 3.2 12.6 0.6
FE X:FE21004 3.2 12.5 0.3
S2 X:WCC1003 3.5 12.6 0.8
NE2 X:HIS261 3.9 16.8 1.0
O X:HOH1888 3.9 10.3 0.6
NZ X:LYS563 4.0 9.7 1.0
CE1 X:HIS261 4.0 15.2 1.0
CA X:CYS333 4.5 10.6 1.0
SG X:CYS446 4.6 10.6 1.0
O X:HOH1121 4.6 13.9 1.0
CE X:LYS563 4.7 8.2 1.0
CE X:MET560 4.7 10.1 1.0
SG X:CYS476 4.8 17.0 1.0
CB X:HIS561 4.8 7.7 1.0
SG X:CYS526 5.0 11.4 1.0

Iron binding site 10 out of 11 in 3b53

Go back to Iron Binding Sites List in 3b53
Iron binding site 10 out of 11 in the Ni,Fe-Codh-320 Mv 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 State within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Fe1003

b:12.6
occ:0.80
 FE3 X:WCC1003 0.0 12.6 0.8
S2 X:WCC1003 2.2 12.6 0.8
S3 X:WCC1003 2.2 13.1 0.8
S4 X:WCC1003 2.3 11.5 0.8
SG X:CYS446 2.4 10.6 1.0
FE1 X:WCC1003 2.4 11.7 0.8
FE4 X:WCC1003 2.6 13.0 0.8
NI X:WCC1003 2.6 13.6 0.6
CB X:CYS446 3.1 10.2 1.0
CA X:CYS446 3.4 9.9 1.0
N X:CYS446 3.6 9.7 1.0
S1 X:WCC1003 3.9 11.8 0.8
C X:GLY445 4.0 9.6 1.0
FE X:FE21004 4.1 12.5 0.3
SG X:CYS333 4.3 11.6 1.0
CB X:HIS561 4.4 7.7 1.0
CA X:GLY445 4.5 9.2 1.0
O X:GLY445 4.6 10.4 1.0
FE X:FE21004 4.6 12.6 0.6
CE X:MET560 4.6 10.1 1.0
SG X:CYS526 4.6 11.4 1.0
SG X:CYS476 4.7 17.0 1.0
O X:HOH1888 4.8 10.3 0.6
C X:CYS446 4.9 9.7 1.0
CB X:CYS476 4.9 13.0 1.0
N X:HIS561 5.0 8.6 1.0

Reference:

J.H.Jeoung, H.Dobbek. Carbon Dioxide Activation at the Ni,Fe-Cluster of Anaerobic Carbon Monoxide Dehydrogenase. Science V. 318 1461 2007.
ISSN: ISSN 0036-8075
PubMed: 18048691
DOI: 10.1126/SCIENCE.1148481
Page generated: Sun Aug 4 07:39:20 2024

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