Iron in PDB 9fpn: Ni,Fe-Codh : Eu(II)-Reduced pH 6.0
Enzymatic activity of Ni,Fe-Codh : Eu(II)-Reduced pH 6.0
All present enzymatic activity of Ni,Fe-Codh : Eu(II)-Reduced pH 6.0:
1.2.7.4;
Protein crystallography data
The structure of Ni,Fe-Codh : Eu(II)-Reduced pH 6.0, PDB code: 9fpn
was solved by
Y.Basak,
J.-H.Jeoung,
H.Dobbek,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
33.11 /
1.16
|
|
Space group
|
C 1 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
112.328,
75.123,
71.08,
90,
111.37,
90
|
|
R / Rfree (%)
|
13.4 /
16.5
|
Other elements in 9fpn:
The structure of Ni,Fe-Codh : Eu(II)-Reduced pH 6.0 also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Ni,Fe-Codh : Eu(II)-Reduced pH 6.0
(pdb code 9fpn). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the
Ni,Fe-Codh : Eu(II)-Reduced pH 6.0, PDB code: 9fpn:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 10 in 9fpn
Go back to
Iron Binding Sites List in 9fpn
Iron binding site 1 out
of 10 in the Ni,Fe-Codh : Eu(II)-Reduced pH 6.0
 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 : Eu(II)-Reduced pH 6.0 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Fe1001
b:9.3
occ:1.00
|
FE1
|
X:SF41001
|
0.0
|
9.3
|
1.0
|
|
S3
|
X:SF41001
|
2.2
|
9.5
|
1.0
|
|
S4
|
X:SF41001
|
2.3
|
9.5
|
1.0
|
|
S2
|
X:SF41001
|
2.3
|
9.8
|
1.0
|
|
SG
|
X:CYS56
|
2.3
|
9.5
|
1.0
|
|
FE3
|
X:SF41001
|
2.6
|
9.4
|
1.0
|
|
FE2
|
X:SF41001
|
2.7
|
9.1
|
1.0
|
|
FE4
|
X:SF41001
|
2.7
|
9.1
|
1.0
|
|
HB2
|
X:CYS56
|
2.9
|
10.9
|
1.0
|
|
CB
|
X:CYS56
|
3.2
|
9.1
|
1.0
|
|
H
|
X:ILE69
|
3.3
|
11.4
|
1.0
|
|
HB
|
X:ILE69
|
3.5
|
12.1
|
1.0
|
|
HB3
|
X:CYS56
|
3.7
|
10.9
|
1.0
|
|
S1
|
X:SF41001
|
3.8
|
9.3
|
1.0
|
|
H
|
X:CYS70
|
3.9
|
11.6
|
1.0
|
|
HB3
|
X:CYS48
|
4.0
|
11.0
|
1.0
|
|
N
|
X:ILE69
|
4.0
|
9.5
|
1.0
|
|
HA2
|
X:GLY54
|
4.1
|
10.7
|
1.0
|
|
HA3
|
X:GLY54
|
4.1
|
10.7
|
1.0
|
|
H
|
X:CYS56
|
4.2
|
10.7
|
1.0
|
|
HA3
|
X:GLY68
|
4.3
|
12.4
|
1.0
|
|
HD12
|
X:ILE69
|
4.4
|
15.4
|
1.0
|
|
CB
|
X:ILE69
|
4.4
|
10.1
|
1.0
|
|
CA
|
X:GLY54
|
4.4
|
8.9
|
1.0
|
|
CA
|
X:CYS56
|
4.4
|
9.0
|
1.0
|
|
HB2
|
X:GLN53
|
4.5
|
11.3
|
1.0
|
|
N
|
X:CYS56
|
4.5
|
8.9
|
1.0
|
|
N
|
X:GLY54
|
4.5
|
9.6
|
1.0
|
|
H
|
X:GLY54
|
4.5
|
11.6
|
1.0
|
|
O
|
X:CYS48
|
4.6
|
9.6
|
1.0
|
|
HA2
|
X:GLY68
|
4.6
|
12.4
|
1.0
|
|
SG
|
X:CYS48
|
4.6
|
9.2
|
1.0
|
|
SG
|
X:CYS51
|
4.6
|
9.4
|
1.0
|
|
HG13
|
X:ILE69
|
4.7
|
13.4
|
1.0
|
|
CA
|
X:ILE69
|
4.7
|
10.4
|
1.0
|
|
N
|
X:CYS70
|
4.7
|
9.6
|
1.0
|
|
CB
|
X:CYS48
|
4.8
|
9.2
|
1.0
|
|
SG
|
X:CYS70
|
4.8
|
9.7
|
1.0
|
|
CA
|
X:GLY68
|
4.8
|
10.3
|
1.0
|
|
C
|
X:GLY68
|
4.8
|
9.2
|
1.0
|
|
HA
|
X:CYS56
|
4.9
|
10.8
|
1.0
|
|
CG1
|
X:ILE69
|
5.0
|
11.2
|
1.0
|
|
HE21
|
X:GLN53
|
5.0
|
18.2
|
1.0
|
|
C
|
X:GLN53
|
5.0
|
9.7
|
1.0
|
|
Iron binding site 2 out
of 10 in 9fpn
Go back to
Iron Binding Sites List in 9fpn
Iron binding site 2 out
of 10 in the Ni,Fe-Codh : Eu(II)-Reduced pH 6.0
 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 : Eu(II)-Reduced pH 6.0 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Fe1001
b:9.1
occ:1.00
|
FE2
|
X:SF41001
|
0.0
|
9.1
|
1.0
|
|
S4
|
X:SF41001
|
2.2
|
9.5
|
1.0
|
|
S1
|
X:SF41001
|
2.3
|
9.3
|
1.0
|
|
S3
|
X:SF41001
|
2.3
|
9.5
|
1.0
|
|
SG
|
X:CYS51
|
2.3
|
9.4
|
1.0
|
|
FE1
|
X:SF41001
|
2.7
|
9.3
|
1.0
|
|
FE3
|
X:SF41001
|
2.7
|
9.4
|
1.0
|
|
FE4
|
X:SF41001
|
2.8
|
9.1
|
1.0
|
|
H
|
X:CYS51
|
3.2
|
10.4
|
1.0
|
|
HB3
|
X:CYS51
|
3.3
|
11.4
|
1.0
|
|
CB
|
X:CYS51
|
3.3
|
9.5
|
1.0
|
|
N
|
X:CYS51
|
3.6
|
8.7
|
1.0
|
|
HB2
|
X:GLN53
|
3.7
|
11.3
|
1.0
|
|
HG3
|
X:MET199
|
3.7
|
10.6
|
0.4
|
|
HG3
|
X:MET199
|
3.7
|
12.6
|
0.6
|
|
CA
|
X:CYS51
|
3.9
|
9.7
|
1.0
|
|
S2
|
X:SF41001
|
3.9
|
9.8
|
1.0
|
|
H
|
X:GLY54
|
4.0
|
11.6
|
1.0
|
|
O
|
X:HOH1274
|
4.0
|
9.5
|
0.4
|
|
HB2
|
X:CYS51
|
4.2
|
11.4
|
1.0
|
|
HB2
|
X:MET199
|
4.2
|
11.9
|
0.6
|
|
H
|
X:GLN53
|
4.2
|
12.2
|
1.0
|
|
HG2
|
X:MET199
|
4.2
|
10.6
|
0.4
|
|
O
|
X:CYS51
|
4.2
|
9.7
|
1.0
|
|
HE21
|
X:GLN53
|
4.3
|
18.2
|
1.0
|
|
C
|
X:CYS51
|
4.3
|
8.8
|
1.0
|
|
HB2
|
X:MET199
|
4.3
|
10.6
|
0.4
|
|
C
|
X:HIS50
|
4.3
|
8.7
|
1.0
|
|
CG
|
X:MET199
|
4.4
|
8.9
|
0.4
|
|
N
|
X:GLY54
|
4.4
|
9.6
|
1.0
|
|
HG2
|
X:MET199
|
4.4
|
12.6
|
0.6
|
|
H
|
X:HIS50
|
4.4
|
9.9
|
1.0
|
|
CG
|
X:MET199
|
4.5
|
10.5
|
0.6
|
|
HB2
|
X:HIS50
|
4.5
|
11.5
|
1.0
|
|
HB3
|
X:CYS70
|
4.6
|
11.5
|
1.0
|
|
HA3
|
X:GLY54
|
4.6
|
10.7
|
1.0
|
|
CB
|
X:GLN53
|
4.6
|
9.4
|
1.0
|
|
HA
|
X:CYS51
|
4.8
|
11.7
|
1.0
|
|
SG
|
X:CYS48
|
4.8
|
9.2
|
1.0
|
|
N
|
X:HIS50
|
4.8
|
8.3
|
1.0
|
|
SG
|
X:CYS56
|
4.8
|
9.5
|
1.0
|
|
N
|
X:GLN53
|
4.8
|
10.2
|
1.0
|
|
SG
|
X:CYS70
|
4.8
|
9.7
|
1.0
|
|
CB
|
X:MET199
|
4.9
|
9.9
|
0.6
|
|
H
|
X:CYS70
|
4.9
|
11.6
|
1.0
|
|
CB
|
X:MET199
|
4.9
|
8.8
|
0.4
|
|
CA
|
X:HIS50
|
4.9
|
9.0
|
1.0
|
|
HB
|
X:ILE69
|
4.9
|
12.1
|
1.0
|
|
CA
|
X:GLY54
|
5.0
|
8.9
|
1.0
|
|
O
|
X:HIS50
|
5.0
|
10.2
|
1.0
|
|
C
|
X:GLN53
|
5.0
|
9.7
|
1.0
|
|
Iron binding site 3 out
of 10 in 9fpn
Go back to
Iron Binding Sites List in 9fpn
Iron binding site 3 out
of 10 in the Ni,Fe-Codh : Eu(II)-Reduced pH 6.0
 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 : Eu(II)-Reduced pH 6.0 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Fe1001
b:9.4
occ:1.00
|
FE3
|
X:SF41001
|
0.0
|
9.4
|
1.0
|
|
S1
|
X:SF41001
|
2.2
|
9.3
|
1.0
|
|
S4
|
X:SF41001
|
2.2
|
9.5
|
1.0
|
|
S2
|
X:SF41001
|
2.3
|
9.8
|
1.0
|
|
SG
|
X:CYS48
|
2.3
|
9.2
|
1.0
|
|
FE1
|
X:SF41001
|
2.6
|
9.3
|
1.0
|
|
FE2
|
X:SF41001
|
2.7
|
9.1
|
1.0
|
|
FE4
|
X:SF41001
|
2.7
|
9.1
|
1.0
|
|
HB3
|
X:CYS48
|
3.0
|
11.0
|
1.0
|
|
HH22
|
X:ARG80
|
3.2
|
11.8
|
1.0
|
|
H
|
X:HIS50
|
3.3
|
9.9
|
1.0
|
|
CB
|
X:CYS48
|
3.3
|
9.2
|
1.0
|
|
HB2
|
X:HIS50
|
3.4
|
11.5
|
1.0
|
|
HH21
|
X:ARG80
|
3.6
|
11.8
|
1.0
|
|
NH2
|
X:ARG80
|
3.7
|
9.8
|
1.0
|
|
S3
|
X:SF41001
|
3.8
|
9.5
|
1.0
|
|
HB2
|
X:CYS56
|
3.9
|
10.9
|
1.0
|
|
HB2
|
X:CYS48
|
3.9
|
11.0
|
1.0
|
|
N
|
X:HIS50
|
4.0
|
8.3
|
1.0
|
|
H
|
X:CYS51
|
4.0
|
10.4
|
1.0
|
|
C
|
X:CYS48
|
4.2
|
9.3
|
1.0
|
|
O
|
X:CYS48
|
4.2
|
9.6
|
1.0
|
|
CB
|
X:HIS50
|
4.3
|
9.6
|
1.0
|
|
CA
|
X:CYS48
|
4.4
|
8.6
|
1.0
|
|
N
|
X:CYS51
|
4.5
|
8.7
|
1.0
|
|
CA
|
X:HIS50
|
4.5
|
9.0
|
1.0
|
|
SG
|
X:CYS56
|
4.6
|
9.5
|
1.0
|
|
N
|
X:ARG49
|
4.6
|
9.7
|
1.0
|
|
HG12
|
X:ILE77
|
4.7
|
13.7
|
1.0
|
|
CB
|
X:CYS56
|
4.7
|
9.1
|
1.0
|
|
C
|
X:HIS50
|
4.8
|
8.7
|
1.0
|
|
CZ
|
X:ARG80
|
4.8
|
10.5
|
1.0
|
|
HA
|
X:CYS48
|
4.9
|
10.4
|
1.0
|
|
SG
|
X:CYS70
|
4.9
|
9.7
|
1.0
|
|
HA
|
X:ARG49
|
4.9
|
12.3
|
1.0
|
|
SG
|
X:CYS51
|
4.9
|
9.4
|
1.0
|
|
HB3
|
X:HIS50
|
4.9
|
11.5
|
1.0
|
|
HB3
|
X:ALA72
|
5.0
|
13.9
|
1.0
|
|
H
|
X:CYS56
|
5.0
|
10.7
|
1.0
|
|
H
|
X:ARG49
|
5.0
|
11.7
|
1.0
|
|
Iron binding site 4 out
of 10 in 9fpn
Go back to
Iron Binding Sites List in 9fpn
Iron binding site 4 out
of 10 in the Ni,Fe-Codh : Eu(II)-Reduced pH 6.0
 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 : Eu(II)-Reduced pH 6.0 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Fe1001
b:9.1
occ:1.00
|
FE4
|
X:SF41001
|
0.0
|
9.1
|
1.0
|
|
S2
|
X:SF41001
|
2.2
|
9.8
|
1.0
|
|
S1
|
X:SF41001
|
2.3
|
9.3
|
1.0
|
|
S3
|
X:SF41001
|
2.3
|
9.5
|
1.0
|
|
SG
|
X:CYS70
|
2.4
|
9.7
|
1.0
|
|
FE3
|
X:SF41001
|
2.7
|
9.4
|
1.0
|
|
FE1
|
X:SF41001
|
2.7
|
9.3
|
1.0
|
|
FE2
|
X:SF41001
|
2.8
|
9.1
|
1.0
|
|
H
|
X:CYS70
|
3.1
|
11.6
|
1.0
|
|
HB3
|
X:CYS70
|
3.2
|
11.5
|
1.0
|
|
HH22
|
X:ARG80
|
3.3
|
11.8
|
1.0
|
|
CB
|
X:CYS70
|
3.4
|
9.6
|
1.0
|
|
N
|
X:CYS70
|
3.9
|
9.6
|
1.0
|
|
S4
|
X:SF41001
|
3.9
|
9.5
|
1.0
|
|
HB2
|
X:ALA72
|
3.9
|
13.9
|
1.0
|
|
HG2
|
X:MET199
|
3.9
|
10.6
|
0.4
|
|
HB3
|
X:ALA72
|
4.0
|
13.9
|
1.0
|
|
HG2
|
X:MET199
|
4.0
|
12.6
|
0.6
|
|
HB2
|
X:CYS70
|
4.1
|
11.5
|
1.0
|
|
NH2
|
X:ARG80
|
4.2
|
9.8
|
1.0
|
|
O
|
X:HOH1433
|
4.2
|
9.5
|
1.0
|
|
CA
|
X:CYS70
|
4.3
|
9.6
|
1.0
|
|
HG3
|
X:MET199
|
4.3
|
12.6
|
0.6
|
|
H
|
X:ILE69
|
4.3
|
11.4
|
1.0
|
|
H
|
X:ALA72
|
4.3
|
12.3
|
1.0
|
|
HA3
|
X:GLY68
|
4.4
|
12.4
|
1.0
|
|
HG3
|
X:MET199
|
4.4
|
10.6
|
0.4
|
|
CB
|
X:ALA72
|
4.4
|
11.6
|
1.0
|
|
O
|
X:HOH1274
|
4.5
|
9.5
|
0.4
|
|
HH21
|
X:ARG80
|
4.5
|
11.8
|
1.0
|
|
HH12
|
X:ARG80
|
4.6
|
13.4
|
1.0
|
|
HB
|
X:ILE69
|
4.6
|
12.1
|
1.0
|
|
N
|
X:ILE69
|
4.6
|
9.5
|
1.0
|
|
CG
|
X:MET199
|
4.6
|
8.9
|
0.4
|
|
CG
|
X:MET199
|
4.6
|
10.5
|
0.6
|
|
SG
|
X:CYS51
|
4.7
|
9.4
|
1.0
|
|
SG
|
X:CYS48
|
4.7
|
9.2
|
1.0
|
|
SG
|
X:CYS56
|
4.8
|
9.5
|
1.0
|
|
HE21
|
X:GLN53
|
5.0
|
18.2
|
1.0
|
|
C
|
X:ILE69
|
5.0
|
10.1
|
1.0
|
|
HA
|
X:CYS70
|
5.0
|
11.5
|
1.0
|
|
Iron binding site 5 out
of 10 in 9fpn
Go back to
Iron Binding Sites List in 9fpn
Iron binding site 5 out
of 10 in the Ni,Fe-Codh : Eu(II)-Reduced pH 6.0
 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 : Eu(II)-Reduced pH 6.0 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Fe1002
b:9.6
occ:1.00
|
FE1
|
X:FES1002
|
0.0
|
9.6
|
1.0
|
|
SG
|
X:CYS47
|
2.3
|
9.6
|
1.0
|
|
S1
|
X:FES1002
|
2.3
|
10.4
|
1.0
|
|
S2
|
X:FES1002
|
2.3
|
10.2
|
1.0
|
|
FE2
|
X:FES1002
|
2.7
|
10.0
|
1.0
|
|
HB2
|
X:CYS47
|
3.0
|
11.0
|
1.0
|
|
CB
|
X:CYS47
|
3.2
|
9.2
|
1.0
|
|
HB3
|
X:CYS47
|
3.4
|
11.0
|
1.0
|
|
O
|
X:HOH1560
|
3.7
|
10.4
|
1.0
|
|
HB2
|
X:PHE41
|
4.1
|
12.4
|
1.0
|
|
HD2
|
X:ARG49
|
4.2
|
15.5
|
1.0
|
|
HB2
|
X:PRO55
|
4.5
|
13.1
|
1.0
|
|
CA
|
X:CYS47
|
4.5
|
8.8
|
1.0
|
|
HA
|
X:CYS47
|
4.6
|
10.6
|
1.0
|
|
H
|
X:GLY42
|
4.6
|
12.8
|
1.0
|
|
HB3
|
X:PHE41
|
4.7
|
12.4
|
1.0
|
|
SG
|
X:CYS39
|
4.7
|
10.9
|
1.0
|
|
HG3
|
X:ARG49
|
4.7
|
13.6
|
1.0
|
|
CB
|
X:PHE41
|
4.9
|
10.4
|
1.0
|
|
HB3
|
X:ARG57
|
4.9
|
13.7
|
1.0
|
|
N
|
X:GLY42
|
5.0
|
10.6
|
1.0
|
|
HB3
|
X:PRO55
|
5.0
|
13.1
|
1.0
|
|
Iron binding site 6 out
of 10 in 9fpn
Go back to
Iron Binding Sites List in 9fpn
Iron binding site 6 out
of 10 in the Ni,Fe-Codh : Eu(II)-Reduced pH 6.0
 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 : Eu(II)-Reduced pH 6.0 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Fe1002
b:10.0
occ:1.00
|
FE2
|
X:FES1002
|
0.0
|
10.0
|
1.0
|
|
S2
|
X:FES1002
|
2.2
|
10.2
|
1.0
|
|
SG
|
X:CYS39
|
2.3
|
10.9
|
1.0
|
|
S1
|
X:FES1002
|
2.3
|
10.4
|
1.0
|
|
FE1
|
X:FES1002
|
2.7
|
9.6
|
1.0
|
|
CB
|
X:CYS39
|
3.2
|
10.8
|
1.0
|
|
HB3
|
X:CYS39
|
3.2
|
12.9
|
1.0
|
|
HB2
|
X:CYS39
|
3.3
|
12.9
|
1.0
|
|
HB2
|
X:PHE41
|
3.4
|
12.4
|
1.0
|
|
H
|
X:GLY42
|
3.4
|
12.8
|
1.0
|
|
H22
|
X:PEG1005
|
3.9
|
38.9
|
0.7
|
|
HD2
|
X:PHE41
|
4.1
|
13.8
|
1.0
|
|
N
|
X:GLY42
|
4.1
|
10.6
|
1.0
|
|
H21
|
X:PEG1005
|
4.2
|
38.9
|
0.7
|
|
H12
|
X:PEG1005
|
4.2
|
40.1
|
0.7
|
|
HA3
|
X:GLY42
|
4.4
|
14.6
|
1.0
|
|
CB
|
X:PHE41
|
4.4
|
10.4
|
1.0
|
|
HB2
|
X:CYS47
|
4.4
|
11.0
|
1.0
|
|
C2
|
X:PEG1005
|
4.4
|
32.4
|
0.7
|
|
H
|
X:PHE41
|
4.5
|
12.6
|
1.0
|
|
CA
|
X:CYS39
|
4.6
|
10.8
|
1.0
|
|
C1
|
X:PEG1005
|
4.7
|
33.4
|
0.7
|
|
HB3
|
X:PHE41
|
4.8
|
12.4
|
1.0
|
|
CA
|
X:GLY42
|
4.8
|
12.2
|
1.0
|
|
SG
|
X:CYS47
|
4.8
|
9.6
|
1.0
|
|
CD2
|
X:PHE41
|
4.8
|
11.5
|
1.0
|
|
HA
|
X:CYS39
|
4.9
|
13.0
|
1.0
|
|
O1
|
X:PEG1005
|
4.9
|
34.9
|
0.7
|
|
Iron binding site 7 out
of 10 in 9fpn
Go back to
Iron Binding Sites List in 9fpn
Iron binding site 7 out
of 10 in the Ni,Fe-Codh : Eu(II)-Reduced pH 6.0
 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 : Eu(II)-Reduced pH 6.0 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Fe1003
b:11.1
occ:0.81
|
FE1
|
X:WCC1003
|
0.0
|
11.1
|
0.8
|
|
SG
|
X:CYS333
|
2.3
|
11.8
|
1.0
|
|
S3
|
X:WCC1003
|
2.3
|
13.4
|
0.8
|
|
S2
|
X:WCC1003
|
2.3
|
12.4
|
0.8
|
|
S4
|
X:WCC1003
|
2.4
|
11.8
|
0.8
|
|
FE3
|
X:WCC1003
|
2.5
|
11.4
|
0.8
|
|
FE4
|
X:WCC1003
|
2.7
|
12.6
|
0.8
|
|
HE1
|
X:HIS261
|
2.8
|
17.8
|
1.0
|
|
NI
|
X:WCC1003
|
3.0
|
12.4
|
0.8
|
|
HB3
|
X:CYS333
|
3.0
|
14.1
|
1.0
|
|
CB
|
X:CYS333
|
3.1
|
11.8
|
1.0
|
|
FE
|
X:FE1004
|
3.3
|
13.0
|
0.8
|
|
HB2
|
X:CYS333
|
3.4
|
14.1
|
1.0
|
|
HZ1
|
X:LYS563
|
3.4
|
15.2
|
1.0
|
|
CE1
|
X:HIS261
|
3.4
|
14.8
|
1.0
|
|
S1
|
X:WCC1003
|
3.6
|
12.7
|
0.9
|
|
NE2
|
X:HIS261
|
3.6
|
13.6
|
1.0
|
|
HZ2
|
X:LYS563
|
3.6
|
15.2
|
1.0
|
|
SG
|
X:CYS294
|
3.8
|
16.1
|
0.2
|
|
NZ
|
X:LYS563
|
3.9
|
12.7
|
1.0
|
|
HB2
|
X:HIS561
|
4.2
|
11.9
|
1.0
|
|
HE3
|
X:LYS563
|
4.3
|
14.6
|
1.0
|
|
HB3
|
X:SER312
|
4.4
|
18.1
|
1.0
|
|
HE1
|
X:MET560
|
4.4
|
14.3
|
1.0
|
|
HE3
|
X:MET560
|
4.5
|
14.3
|
1.0
|
|
CA
|
X:CYS333
|
4.5
|
10.1
|
1.0
|
|
HG
|
X:CYS294
|
4.6
|
14.4
|
0.8
|
|
HB3
|
X:CYS446
|
4.6
|
13.1
|
1.0
|
|
HZ3
|
X:LYS563
|
4.6
|
15.2
|
1.0
|
|
HA
|
X:CYS333
|
4.6
|
12.2
|
1.0
|
|
SG
|
X:CYS446
|
4.6
|
12.0
|
1.0
|
|
ND1
|
X:HIS261
|
4.7
|
14.6
|
1.0
|
|
SG
|
X:CYS526
|
4.7
|
11.3
|
0.9
|
|
CE
|
X:LYS563
|
4.7
|
12.2
|
1.0
|
|
O
|
X:HOH1284
|
4.7
|
15.2
|
1.0
|
|
HD2
|
X:HIS561
|
4.8
|
11.4
|
1.0
|
|
HB3
|
X:CYS294
|
4.8
|
13.6
|
0.8
|
|
HB3
|
X:HIS561
|
4.8
|
11.9
|
1.0
|
|
SG
|
X:CYS476
|
4.9
|
14.6
|
0.4
|
|
CB
|
X:HIS561
|
4.9
|
9.9
|
1.0
|
|
SG
|
X:CYS476
|
4.9
|
11.7
|
0.6
|
|
CD2
|
X:HIS261
|
4.9
|
13.9
|
1.0
|
|
CE
|
X:MET560
|
4.9
|
11.9
|
1.0
|
|
HA
|
X:CYS446
|
5.0
|
12.7
|
1.0
|
|
Iron binding site 8 out
of 10 in 9fpn
Go back to
Iron Binding Sites List in 9fpn
Iron binding site 8 out
of 10 in the Ni,Fe-Codh : Eu(II)-Reduced pH 6.0
 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 : Eu(II)-Reduced pH 6.0 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Fe1003
b:11.4
occ:0.80
|
FE3
|
X:WCC1003
|
0.0
|
11.4
|
0.8
|
|
S4
|
X:WCC1003
|
2.2
|
11.8
|
0.8
|
|
S1
|
X:WCC1003
|
2.3
|
12.7
|
0.9
|
|
S2
|
X:WCC1003
|
2.3
|
12.4
|
0.8
|
|
SG
|
X:CYS446
|
2.4
|
12.0
|
1.0
|
|
FE1
|
X:WCC1003
|
2.5
|
11.1
|
0.8
|
|
NI
|
X:WCC1003
|
2.6
|
12.4
|
0.8
|
|
FE4
|
X:WCC1003
|
2.7
|
12.6
|
0.8
|
|
HB3
|
X:CYS446
|
2.9
|
13.1
|
1.0
|
|
CB
|
X:CYS446
|
3.0
|
10.9
|
1.0
|
|
HA
|
X:CYS446
|
3.2
|
12.7
|
1.0
|
|
CA
|
X:CYS446
|
3.4
|
10.5
|
1.0
|
|
N
|
X:CYS446
|
3.4
|
10.7
|
1.0
|
|
H
|
X:CYS446
|
3.4
|
12.8
|
1.0
|
|
HB2
|
X:HIS561
|
3.7
|
11.9
|
1.0
|
|
HA2
|
X:GLY445
|
3.8
|
13.2
|
1.0
|
|
HE3
|
X:MET560
|
3.9
|
14.3
|
1.0
|
|
HB2
|
X:CYS446
|
3.9
|
13.1
|
1.0
|
|
S3
|
X:WCC1003
|
4.0
|
13.4
|
0.8
|
|
HB3
|
X:HIS561
|
4.1
|
11.9
|
1.0
|
|
C
|
X:GLY445
|
4.1
|
11.7
|
1.0
|
|
H
|
X:HIS561
|
4.1
|
10.6
|
1.0
|
|
HB2
|
X:ALA564
|
4.2
|
14.1
|
1.0
|
|
CB
|
X:HIS561
|
4.3
|
9.9
|
1.0
|
|
SG
|
X:CYS333
|
4.3
|
11.8
|
1.0
|
|
CA
|
X:GLY445
|
4.4
|
11.0
|
1.0
|
|
FE
|
X:FE1004
|
4.5
|
13.0
|
0.8
|
|
HB2
|
X:CYS476
|
4.5
|
15.2
|
0.6
|
|
HB2
|
X:CYS476
|
4.6
|
17.0
|
0.4
|
|
SG
|
X:CYS526
|
4.6
|
11.3
|
0.9
|
|
SG
|
X:CYS476
|
4.6
|
11.7
|
0.6
|
|
HB3
|
X:MET560
|
4.6
|
11.6
|
1.0
|
|
HE1
|
X:MET560
|
4.7
|
14.3
|
1.0
|
|
O
|
X:GLY445
|
4.7
|
13.0
|
1.0
|
|
CE
|
X:MET560
|
4.7
|
11.9
|
1.0
|
|
H
|
X:CYS476
|
4.7
|
13.6
|
0.6
|
|
HB3
|
X:SER312
|
4.8
|
18.1
|
1.0
|
|
H
|
X:CYS476
|
4.8
|
14.5
|
0.4
|
|
HA3
|
X:GLY445
|
4.8
|
13.2
|
1.0
|
|
C
|
X:CYS446
|
4.9
|
9.5
|
1.0
|
|
N
|
X:HIS561
|
4.9
|
8.8
|
1.0
|
|
SG
|
X:CYS476
|
4.9
|
14.6
|
0.4
|
|
H
|
X:MET560
|
5.0
|
10.9
|
1.0
|
|
HZ2
|
X:LYS563
|
5.0
|
15.2
|
1.0
|
|
Iron binding site 9 out
of 10 in 9fpn
Go back to
Iron Binding Sites List in 9fpn
Iron binding site 9 out
of 10 in the Ni,Fe-Codh : Eu(II)-Reduced pH 6.0
 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 : Eu(II)-Reduced pH 6.0 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Fe1003
b:12.6
occ:0.80
|
FE4
|
X:WCC1003
|
0.0
|
12.6
|
0.8
|
|
S1
|
X:WCC1003
|
2.3
|
12.7
|
0.9
|
|
S3
|
X:WCC1003
|
2.3
|
13.4
|
0.8
|
|
S2
|
X:WCC1003
|
2.3
|
12.4
|
0.8
|
|
SG
|
X:CYS476
|
2.3
|
11.7
|
0.6
|
|
SG
|
X:CYS476
|
2.4
|
14.6
|
0.4
|
|
FE1
|
X:WCC1003
|
2.7
|
11.1
|
0.8
|
|
FE3
|
X:WCC1003
|
2.7
|
11.4
|
0.8
|
|
HB2
|
X:CYS476
|
3.0
|
17.0
|
0.4
|
|
HA
|
X:CYS446
|
3.1
|
12.7
|
1.0
|
|
HB3
|
X:SER312
|
3.1
|
18.1
|
1.0
|
|
CB
|
X:CYS476
|
3.3
|
14.2
|
0.4
|
|
HB2
|
X:CYS476
|
3.3
|
15.2
|
0.6
|
|
H
|
X:CYS476
|
3.4
|
14.5
|
0.4
|
|
H
|
X:CYS476
|
3.4
|
13.6
|
0.6
|
|
NI
|
X:WCC1003
|
3.4
|
12.4
|
0.8
|
|
CB
|
X:CYS476
|
3.5
|
12.7
|
0.6
|
|
FE
|
X:FE1004
|
3.6
|
13.0
|
0.8
|
|
SG
|
X:CYS294
|
3.7
|
16.1
|
0.2
|
|
HB3
|
X:CYS446
|
3.8
|
13.1
|
1.0
|
|
O
|
X:HOH1236
|
3.9
|
10.5
|
0.6
|
|
N
|
X:CYS476
|
3.9
|
11.3
|
0.6
|
|
N
|
X:CYS476
|
4.0
|
12.1
|
0.4
|
|
CA
|
X:CYS446
|
4.0
|
10.5
|
1.0
|
|
HB3
|
X:CYS476
|
4.0
|
17.0
|
0.4
|
|
CB
|
X:SER312
|
4.0
|
15.1
|
1.0
|
|
O
|
X:HOH1236
|
4.1
|
15.3
|
0.4
|
|
S4
|
X:WCC1003
|
4.1
|
11.8
|
0.8
|
|
HB3
|
X:CYS476
|
4.2
|
15.2
|
0.6
|
|
CB
|
X:CYS446
|
4.2
|
10.9
|
1.0
|
|
OG
|
X:SER312
|
4.3
|
14.6
|
1.0
|
|
CA
|
X:CYS476
|
4.3
|
11.4
|
0.6
|
|
CA
|
X:CYS476
|
4.3
|
13.2
|
0.4
|
|
H
|
X:SER312
|
4.4
|
15.4
|
1.0
|
|
HG
|
X:SER312
|
4.5
|
17.5
|
1.0
|
|
HG
|
X:CYS294
|
4.5
|
14.4
|
0.8
|
|
HB3
|
X:CYS333
|
4.5
|
14.1
|
1.0
|
|
HB2
|
X:SER312
|
4.5
|
18.1
|
1.0
|
|
N
|
X:CYS446
|
4.5
|
10.7
|
1.0
|
|
HE1
|
X:HIS261
|
4.5
|
17.8
|
1.0
|
|
HA
|
X:CYS476
|
4.5
|
13.7
|
0.6
|
|
H
|
X:ASN447
|
4.6
|
11.6
|
1.0
|
|
SG
|
X:CYS526
|
4.6
|
11.3
|
0.9
|
|
O
|
X:GLY445
|
4.7
|
13.0
|
1.0
|
|
HB3
|
X:CYS294
|
4.7
|
13.6
|
0.8
|
|
SG
|
X:CYS446
|
4.7
|
12.0
|
1.0
|
|
HA3
|
X:GLY475
|
4.7
|
13.4
|
0.6
|
|
HA3
|
X:GLY475
|
4.7
|
13.7
|
0.4
|
|
SG
|
X:CYS294
|
4.8
|
12.0
|
0.8
|
|
C
|
X:GLY445
|
4.8
|
11.7
|
1.0
|
|
HA
|
X:CYS476
|
4.8
|
15.8
|
0.4
|
|
SG
|
X:CYS333
|
4.8
|
11.8
|
1.0
|
|
HA
|
X:CYS294
|
4.8
|
15.2
|
0.2
|
|
C
|
X:GLY475
|
4.9
|
10.6
|
0.6
|
|
HA
|
X:CYS294
|
4.9
|
13.9
|
0.8
|
|
C
|
X:GLY475
|
4.9
|
11.1
|
0.4
|
|
NE2
|
X:HIS261
|
5.0
|
13.6
|
1.0
|
|
HA2
|
X:GLY475
|
5.0
|
13.4
|
0.6
|
|
Iron binding site 10 out
of 10 in 9fpn
Go back to
Iron Binding Sites List in 9fpn
Iron binding site 10 out
of 10 in the Ni,Fe-Codh : Eu(II)-Reduced pH 6.0
 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 : Eu(II)-Reduced pH 6.0 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Fe1004
b:13.0
occ:0.78
|
NE2
|
X:HIS261
|
2.0
|
13.6
|
1.0
|
|
SG
|
X:CYS295
|
2.1
|
15.8
|
0.4
|
|
S3
|
X:WCC1003
|
2.3
|
13.4
|
0.8
|
|
SG
|
X:CYS295
|
2.4
|
11.6
|
0.6
|
|
SG
|
X:CYS526
|
2.5
|
11.3
|
0.9
|
|
HB2
|
X:CYS526
|
2.5
|
16.1
|
0.1
|
|
NI
|
X:WCC1003
|
2.6
|
12.4
|
0.8
|
|
CE1
|
X:HIS261
|
3.0
|
14.8
|
1.0
|
|
CD2
|
X:HIS261
|
3.1
|
13.9
|
1.0
|
|
HB2
|
X:CYS295
|
3.1
|
13.1
|
0.6
|
|
HB2
|
X:CYS295
|
3.1
|
17.6
|
0.4
|
|
HE1
|
X:HIS261
|
3.2
|
17.8
|
1.0
|
|
HB2
|
X:CYS526
|
3.3
|
13.4
|
0.9
|
|
CB
|
X:CYS295
|
3.3
|
14.7
|
0.4
|
|
HD2
|
X:HIS261
|
3.3
|
16.7
|
1.0
|
|
O
|
X:HOH1236
|
3.3
|
15.3
|
0.4
|
|
CB
|
X:CYS295
|
3.3
|
10.9
|
0.6
|
|
FE1
|
X:WCC1003
|
3.3
|
11.1
|
0.8
|
|
CB
|
X:CYS526
|
3.5
|
13.4
|
0.1
|
|
CB
|
X:CYS526
|
3.5
|
11.2
|
0.9
|
|
S1
|
X:WCC1003
|
3.6
|
12.7
|
0.9
|
|
FE4
|
X:WCC1003
|
3.6
|
12.6
|
0.8
|
|
H
|
X:CYS526
|
3.6
|
13.6
|
0.9
|
|
HZ2
|
X:LYS563
|
3.8
|
15.2
|
1.0
|
|
HB3
|
X:CYS526
|
3.8
|
16.1
|
0.1
|
|
H
|
X:CYS526
|
3.8
|
13.2
|
0.1
|
|
HA2
|
X:GLY475
|
3.9
|
13.7
|
0.4
|
|
SG
|
X:CYS294
|
3.9
|
16.1
|
0.2
|
|
HB3
|
X:CYS295
|
4.0
|
13.1
|
0.6
|
|
HB3
|
X:CYS295
|
4.0
|
17.6
|
0.4
|
|
S4
|
X:WCC1003
|
4.0
|
11.8
|
0.8
|
|
HA2
|
X:GLY475
|
4.0
|
13.4
|
0.6
|
|
H
|
X:CYS295
|
4.0
|
14.9
|
0.4
|
|
ND1
|
X:HIS261
|
4.1
|
14.6
|
1.0
|
|
H
|
X:CYS295
|
4.1
|
12.3
|
0.6
|
|
CG
|
X:HIS261
|
4.1
|
14.0
|
1.0
|
|
O
|
X:HOH1236
|
4.1
|
10.5
|
0.6
|
|
HB3
|
X:CYS526
|
4.2
|
13.4
|
0.9
|
|
CA
|
X:CYS295
|
4.2
|
13.7
|
0.4
|
|
HA3
|
X:GLY475
|
4.2
|
13.4
|
0.6
|
|
SG
|
X:CYS526
|
4.2
|
15.0
|
0.1
|
|
HA3
|
X:GLY475
|
4.2
|
13.7
|
0.4
|
|
N
|
X:CYS526
|
4.3
|
11.4
|
0.9
|
|
HA
|
X:CYS295
|
4.3
|
16.4
|
0.4
|
|
N
|
X:CYS295
|
4.3
|
12.4
|
0.4
|
|
N
|
X:CYS526
|
4.3
|
11.0
|
0.1
|
|
N
|
X:CYS295
|
4.4
|
10.3
|
0.6
|
|
CA
|
X:CYS295
|
4.4
|
11.0
|
0.6
|
|
HZ1
|
X:LYS563
|
4.4
|
15.2
|
1.0
|
|
NZ
|
X:LYS563
|
4.5
|
12.7
|
1.0
|
|
FE3
|
X:WCC1003
|
4.5
|
11.4
|
0.8
|
|
CA
|
X:CYS526
|
4.5
|
11.6
|
0.1
|
|
HB3
|
X:CYS294
|
4.5
|
13.6
|
0.8
|
|
CA
|
X:CYS526
|
4.5
|
11.9
|
0.9
|
|
O
|
X:HOH1550
|
4.5
|
8.0
|
0.2
|
|
CA
|
X:GLY475
|
4.5
|
11.4
|
0.4
|
|
CA
|
X:GLY475
|
4.6
|
11.2
|
0.6
|
|
HA
|
X:CYS295
|
4.6
|
13.2
|
0.6
|
|
H
|
X:CYS476
|
4.7
|
14.5
|
0.4
|
|
HZ3
|
X:LYS563
|
4.7
|
15.2
|
1.0
|
|
HA
|
X:CYS526
|
4.7
|
13.9
|
0.1
|
|
H
|
X:CYS476
|
4.7
|
13.6
|
0.6
|
|
O
|
X:HOH1465
|
4.7
|
13.1
|
1.0
|
|
HD1
|
X:HIS261
|
4.9
|
17.5
|
1.0
|
|
HA
|
X:CYS526
|
4.9
|
14.2
|
0.9
|
|
HD21
|
X:ASN298
|
4.9
|
13.9
|
1.0
|
|
SG
|
X:CYS333
|
4.9
|
11.8
|
1.0
|
|
SG
|
X:CYS476
|
4.9
|
14.6
|
0.4
|
|
Reference:
Y.Basak,
J.-H.Jeoung,
H.Dobbek.
Ni,Fe-Codh : Ti(III)-Reduced pH 8.0 Nature Catalysis 2025.
DOI: 10.1038/S41929-025-01388-5
Page generated: Fri Aug 8 05:49:23 2025
|
