Iron in PDB 8omx: Ni,Fe-Codh -600MV State : 1 Min Dioxygen Exposure
Enzymatic activity of Ni,Fe-Codh -600MV State : 1 Min Dioxygen Exposure
All present enzymatic activity of Ni,Fe-Codh -600MV State : 1 Min Dioxygen Exposure:
1.2.7.4;
Protein crystallography data
The structure of Ni,Fe-Codh -600MV State : 1 Min Dioxygen Exposure, PDB code: 8omx
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)
|
40.82 /
1.50
|
|
Space group
|
C 1 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
112.74,
75.501,
71.503,
90,
111.77,
90
|
|
R / Rfree (%)
|
15.5 /
19.3
|
Other elements in 8omx:
The structure of Ni,Fe-Codh -600MV State : 1 Min Dioxygen Exposure also contains other interesting chemical elements:
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 -600MV State : 1 Min Dioxygen Exposure
(pdb code 8omx). 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 -600MV State : 1 Min Dioxygen Exposure, PDB code: 8omx:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 11 in 8omx
Go back to
Iron Binding Sites List in 8omx
Iron binding site 1 out
of 11 in the Ni,Fe-Codh -600MV State : 1 Min Dioxygen Exposure
 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 -600MV State : 1 Min Dioxygen Exposure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Fe1001
b:13.3
occ:1.00
|
FE1
|
X:SF41001
|
0.0
|
13.3
|
1.0
|
|
S4
|
X:SF41001
|
2.2
|
12.2
|
1.0
|
|
S3
|
X:SF41001
|
2.2
|
13.5
|
1.0
|
|
S2
|
X:SF41001
|
2.3
|
13.1
|
1.0
|
|
SG
|
X:CYS56
|
2.4
|
13.5
|
1.0
|
|
FE3
|
X:SF41001
|
2.6
|
12.2
|
1.0
|
|
FE2
|
X:SF41001
|
2.7
|
13.3
|
1.0
|
|
FE4
|
X:SF41001
|
2.7
|
13.4
|
1.0
|
|
HB2
|
X:CYS56
|
2.9
|
18.5
|
1.0
|
|
CB
|
X:CYS56
|
3.3
|
14.8
|
1.0
|
|
H
|
X:ILE69
|
3.3
|
15.0
|
1.0
|
|
HB
|
X:ILE69
|
3.6
|
18.9
|
1.0
|
|
HB3
|
X:CYS56
|
3.8
|
18.5
|
1.0
|
|
S1
|
X:SF41001
|
3.8
|
12.9
|
1.0
|
|
H
|
X:CYS70
|
3.9
|
14.7
|
1.0
|
|
HB3
|
X:CYS48
|
4.0
|
16.2
|
1.0
|
|
N
|
X:ILE69
|
4.0
|
11.9
|
1.0
|
|
HA2
|
X:GLY54
|
4.0
|
19.2
|
1.0
|
|
HA3
|
X:GLY54
|
4.1
|
19.2
|
1.0
|
|
H
|
X:CYS56
|
4.1
|
14.7
|
1.0
|
|
HA3
|
X:GLY68
|
4.3
|
17.3
|
1.0
|
|
CA
|
X:GLY54
|
4.4
|
15.2
|
1.0
|
|
N
|
X:CYS56
|
4.4
|
11.4
|
1.0
|
|
HB2
|
X:GLN53
|
4.4
|
21.2
|
1.0
|
|
CA
|
X:CYS56
|
4.4
|
12.8
|
1.0
|
|
HD12
|
X:ILE69
|
4.4
|
22.4
|
1.0
|
|
CB
|
X:ILE69
|
4.5
|
14.9
|
1.0
|
|
N
|
X:GLY54
|
4.5
|
14.6
|
1.0
|
|
O
|
X:CYS48
|
4.5
|
12.8
|
1.0
|
|
H
|
X:GLY54
|
4.5
|
18.6
|
1.0
|
|
HG13
|
X:ILE69
|
4.6
|
17.7
|
1.0
|
|
HA2
|
X:GLY68
|
4.6
|
17.3
|
1.0
|
|
SG
|
X:CYS51
|
4.6
|
13.9
|
1.0
|
|
SG
|
X:CYS48
|
4.6
|
12.8
|
1.0
|
|
N
|
X:CYS70
|
4.7
|
11.7
|
1.0
|
|
CB
|
X:CYS48
|
4.7
|
12.8
|
1.0
|
|
SG
|
X:CYS70
|
4.8
|
13.5
|
1.0
|
|
CA
|
X:GLY68
|
4.8
|
13.3
|
1.0
|
|
CA
|
X:ILE69
|
4.8
|
14.0
|
1.0
|
|
C
|
X:GLY68
|
4.9
|
14.9
|
1.0
|
|
HA
|
X:CYS56
|
4.9
|
16.0
|
1.0
|
|
CG1
|
X:ILE69
|
4.9
|
14.1
|
1.0
|
|
HB3
|
X:CYS70
|
5.0
|
19.7
|
1.0
|
|
C
|
X:GLN53
|
5.0
|
15.5
|
1.0
|
|
HE21
|
X:GLN53
|
5.0
|
21.0
|
1.0
|
|
Iron binding site 2 out
of 11 in 8omx
Go back to
Iron Binding Sites List in 8omx
Iron binding site 2 out
of 11 in the Ni,Fe-Codh -600MV State : 1 Min Dioxygen Exposure
 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 -600MV State : 1 Min Dioxygen Exposure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Fe1001
b:13.3
occ:1.00
|
FE2
|
X:SF41001
|
0.0
|
13.3
|
1.0
|
|
S4
|
X:SF41001
|
2.2
|
12.2
|
1.0
|
|
S3
|
X:SF41001
|
2.2
|
13.5
|
1.0
|
|
S1
|
X:SF41001
|
2.3
|
12.9
|
1.0
|
|
SG
|
X:CYS51
|
2.3
|
13.9
|
1.0
|
|
FE3
|
X:SF41001
|
2.7
|
12.2
|
1.0
|
|
FE1
|
X:SF41001
|
2.7
|
13.3
|
1.0
|
|
FE4
|
X:SF41001
|
2.8
|
13.4
|
1.0
|
|
HB3
|
X:CYS51
|
3.2
|
17.3
|
1.0
|
|
H
|
X:CYS51
|
3.2
|
16.3
|
1.0
|
|
CB
|
X:CYS51
|
3.3
|
13.4
|
1.0
|
|
N
|
X:CYS51
|
3.6
|
12.5
|
1.0
|
|
HB2
|
X:GLN53
|
3.6
|
21.2
|
1.0
|
|
HG3
|
X:MET199
|
3.7
|
17.5
|
1.0
|
|
CA
|
X:CYS51
|
3.9
|
12.5
|
1.0
|
|
S2
|
X:SF41001
|
3.9
|
13.1
|
1.0
|
|
HE21
|
X:GLN53
|
4.0
|
21.0
|
1.0
|
|
H
|
X:GLY54
|
4.0
|
18.6
|
1.0
|
|
HB2
|
X:CYS51
|
4.1
|
17.3
|
1.0
|
|
HG2
|
X:MET199
|
4.2
|
17.5
|
1.0
|
|
O
|
X:CYS51
|
4.2
|
13.6
|
1.0
|
|
H
|
X:GLN53
|
4.2
|
19.4
|
1.0
|
|
HB2
|
X:MET199
|
4.2
|
16.6
|
1.0
|
|
C
|
X:CYS51
|
4.3
|
13.0
|
1.0
|
|
CG
|
X:MET199
|
4.3
|
14.5
|
1.0
|
|
C
|
X:HIS50
|
4.4
|
12.4
|
1.0
|
|
H
|
X:HIS50
|
4.4
|
15.5
|
1.0
|
|
N
|
X:GLY54
|
4.5
|
14.6
|
1.0
|
|
HB3
|
X:CYS70
|
4.5
|
19.7
|
1.0
|
|
HB2
|
X:HIS50
|
4.5
|
18.0
|
1.0
|
|
CB
|
X:GLN53
|
4.6
|
17.2
|
1.0
|
|
HA3
|
X:GLY54
|
4.6
|
19.2
|
1.0
|
|
N
|
X:HIS50
|
4.8
|
12.2
|
1.0
|
|
HA
|
X:CYS51
|
4.8
|
16.3
|
1.0
|
|
SG
|
X:CYS70
|
4.8
|
13.5
|
1.0
|
|
SG
|
X:CYS48
|
4.8
|
12.8
|
1.0
|
|
CB
|
X:MET199
|
4.8
|
13.6
|
1.0
|
|
N
|
X:GLN53
|
4.9
|
15.3
|
1.0
|
|
H
|
X:CYS70
|
4.9
|
14.7
|
1.0
|
|
NE2
|
X:GLN53
|
4.9
|
17.1
|
1.0
|
|
SG
|
X:CYS56
|
4.9
|
13.5
|
1.0
|
|
HB
|
X:ILE69
|
5.0
|
18.9
|
1.0
|
|
HB3
|
X:GLN53
|
5.0
|
21.2
|
1.0
|
|
Iron binding site 3 out
of 11 in 8omx
Go back to
Iron Binding Sites List in 8omx
Iron binding site 3 out
of 11 in the Ni,Fe-Codh -600MV State : 1 Min Dioxygen Exposure
 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 -600MV State : 1 Min Dioxygen Exposure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Fe1001
b:12.2
occ:1.00
|
FE3
|
X:SF41001
|
0.0
|
12.2
|
1.0
|
|
S4
|
X:SF41001
|
2.2
|
12.2
|
1.0
|
|
S1
|
X:SF41001
|
2.2
|
12.9
|
1.0
|
|
S2
|
X:SF41001
|
2.3
|
13.1
|
1.0
|
|
SG
|
X:CYS48
|
2.4
|
12.8
|
1.0
|
|
FE1
|
X:SF41001
|
2.6
|
13.3
|
1.0
|
|
FE2
|
X:SF41001
|
2.7
|
13.3
|
1.0
|
|
FE4
|
X:SF41001
|
2.7
|
13.4
|
1.0
|
|
HB3
|
X:CYS48
|
3.0
|
16.2
|
1.0
|
|
H
|
X:HIS50
|
3.2
|
15.5
|
1.0
|
|
HH22
|
X:ARG80
|
3.3
|
17.9
|
1.0
|
|
CB
|
X:CYS48
|
3.3
|
12.8
|
1.0
|
|
HB2
|
X:HIS50
|
3.5
|
18.0
|
1.0
|
|
HH21
|
X:ARG80
|
3.6
|
17.9
|
1.0
|
|
NH2
|
X:ARG80
|
3.7
|
15.5
|
1.0
|
|
S3
|
X:SF41001
|
3.7
|
13.5
|
1.0
|
|
HB2
|
X:CYS48
|
3.9
|
16.2
|
1.0
|
|
N
|
X:HIS50
|
4.0
|
12.2
|
1.0
|
|
HB2
|
X:CYS56
|
4.0
|
18.5
|
1.0
|
|
H
|
X:CYS51
|
4.0
|
16.3
|
1.0
|
|
O
|
X:CYS48
|
4.2
|
12.8
|
1.0
|
|
C
|
X:CYS48
|
4.2
|
13.0
|
1.0
|
|
CA
|
X:CYS48
|
4.4
|
12.0
|
1.0
|
|
CB
|
X:HIS50
|
4.4
|
14.2
|
1.0
|
|
N
|
X:CYS51
|
4.5
|
12.5
|
1.0
|
|
CA
|
X:HIS50
|
4.6
|
14.2
|
1.0
|
|
N
|
X:ARG49
|
4.7
|
13.9
|
1.0
|
|
SG
|
X:CYS56
|
4.7
|
13.5
|
1.0
|
|
HG12
|
X:ILE77
|
4.7
|
18.3
|
1.0
|
|
CB
|
X:CYS56
|
4.8
|
14.8
|
1.0
|
|
C
|
X:HIS50
|
4.8
|
12.4
|
1.0
|
|
CZ
|
X:ARG80
|
4.8
|
16.0
|
1.0
|
|
SG
|
X:CYS70
|
4.9
|
13.5
|
1.0
|
|
HA
|
X:CYS48
|
4.9
|
15.4
|
1.0
|
|
HA
|
X:ARG49
|
4.9
|
18.5
|
1.0
|
|
SG
|
X:CYS51
|
4.9
|
13.9
|
1.0
|
|
H
|
X:CYS56
|
4.9
|
14.7
|
1.0
|
|
C
|
X:ARG49
|
4.9
|
13.6
|
1.0
|
|
HB3
|
X:ALA72
|
4.9
|
17.7
|
1.0
|
|
Iron binding site 4 out
of 11 in 8omx
Go back to
Iron Binding Sites List in 8omx
Iron binding site 4 out
of 11 in the Ni,Fe-Codh -600MV State : 1 Min Dioxygen Exposure
 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 -600MV State : 1 Min Dioxygen Exposure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Fe1001
b:13.4
occ:1.00
|
FE4
|
X:SF41001
|
0.0
|
13.4
|
1.0
|
|
S3
|
X:SF41001
|
2.3
|
13.5
|
1.0
|
|
S2
|
X:SF41001
|
2.3
|
13.1
|
1.0
|
|
SG
|
X:CYS70
|
2.3
|
13.5
|
1.0
|
|
S1
|
X:SF41001
|
2.3
|
12.9
|
1.0
|
|
FE3
|
X:SF41001
|
2.7
|
12.2
|
1.0
|
|
FE1
|
X:SF41001
|
2.7
|
13.3
|
1.0
|
|
FE2
|
X:SF41001
|
2.8
|
13.3
|
1.0
|
|
H
|
X:CYS70
|
3.0
|
14.7
|
1.0
|
|
HB3
|
X:CYS70
|
3.1
|
19.7
|
1.0
|
|
CB
|
X:CYS70
|
3.3
|
15.4
|
1.0
|
|
HH22
|
X:ARG80
|
3.4
|
17.9
|
1.0
|
|
N
|
X:CYS70
|
3.8
|
11.7
|
1.0
|
|
HB2
|
X:ALA72
|
3.9
|
17.7
|
1.0
|
|
S4
|
X:SF41001
|
3.9
|
12.2
|
1.0
|
|
HG2
|
X:MET199
|
3.9
|
17.5
|
1.0
|
|
HB3
|
X:ALA72
|
4.0
|
17.7
|
1.0
|
|
HB2
|
X:CYS70
|
4.0
|
19.7
|
1.0
|
|
O
|
X:HOH1388
|
4.1
|
14.2
|
1.0
|
|
CA
|
X:CYS70
|
4.2
|
15.4
|
1.0
|
|
NH2
|
X:ARG80
|
4.2
|
15.5
|
1.0
|
|
H
|
X:ALA72
|
4.3
|
18.9
|
1.0
|
|
H
|
X:ILE69
|
4.3
|
15.0
|
1.0
|
|
HA3
|
X:GLY68
|
4.4
|
17.3
|
1.0
|
|
CB
|
X:ALA72
|
4.4
|
13.6
|
1.0
|
|
HG3
|
X:MET199
|
4.5
|
17.5
|
1.0
|
|
HH12
|
X:ARG80
|
4.5
|
18.2
|
1.0
|
|
HH21
|
X:ARG80
|
4.6
|
17.9
|
1.0
|
|
CG
|
X:MET199
|
4.6
|
14.5
|
1.0
|
|
N
|
X:ILE69
|
4.6
|
11.9
|
1.0
|
|
HB
|
X:ILE69
|
4.6
|
18.9
|
1.0
|
|
SG
|
X:CYS51
|
4.7
|
13.9
|
1.0
|
|
SG
|
X:CYS56
|
4.8
|
13.5
|
1.0
|
|
SG
|
X:CYS48
|
4.8
|
12.8
|
1.0
|
|
HE21
|
X:GLN53
|
4.9
|
21.0
|
1.0
|
|
HA
|
X:CYS70
|
4.9
|
19.3
|
1.0
|
|
C
|
X:ILE69
|
5.0
|
15.3
|
1.0
|
|
Iron binding site 5 out
of 11 in 8omx
Go back to
Iron Binding Sites List in 8omx
Iron binding site 5 out
of 11 in the Ni,Fe-Codh -600MV State : 1 Min Dioxygen Exposure
 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 -600MV State : 1 Min Dioxygen Exposure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Fe1002
b:15.0
occ:1.00
|
FE1
|
X:FES1002
|
0.0
|
15.0
|
1.0
|
|
S1
|
X:FES1002
|
2.2
|
14.6
|
1.0
|
|
S2
|
X:FES1002
|
2.3
|
14.3
|
1.0
|
|
SG
|
X:CYS47
|
2.3
|
15.1
|
1.0
|
|
FE2
|
X:FES1002
|
2.7
|
14.4
|
1.0
|
|
HB2
|
X:CYS47
|
3.1
|
19.9
|
1.0
|
|
CB
|
X:CYS47
|
3.2
|
15.4
|
1.0
|
|
O
|
X:HOH1519
|
3.5
|
25.9
|
1.0
|
|
HB3
|
X:CYS47
|
3.5
|
19.9
|
1.0
|
|
HG2
|
X:ARG57
|
4.2
|
22.1
|
0.3
|
|
HD2
|
X:ARG49
|
4.2
|
24.1
|
1.0
|
|
HB2
|
X:PHE41
|
4.2
|
18.2
|
1.0
|
|
HB3
|
X:PRO55
|
4.4
|
20.5
|
1.0
|
|
CA
|
X:CYS47
|
4.6
|
13.4
|
1.0
|
|
H
|
X:GLY42
|
4.6
|
20.4
|
1.0
|
|
SG
|
X:CYS39
|
4.7
|
16.0
|
1.0
|
|
HA
|
X:CYS47
|
4.7
|
17.4
|
1.0
|
|
HG3
|
X:ARG49
|
4.7
|
20.1
|
1.0
|
|
HB2
|
X:PRO55
|
4.8
|
20.5
|
1.0
|
|
HD3
|
X:ARG57
|
4.8
|
24.1
|
0.3
|
|
HB3
|
X:ARG57
|
4.8
|
20.0
|
0.7
|
|
HB3
|
X:PHE41
|
4.8
|
18.2
|
1.0
|
|
HG3
|
X:ARG57
|
4.9
|
22.1
|
0.3
|
|
N
|
X:GLY42
|
4.9
|
16.6
|
1.0
|
|
CG
|
X:ARG57
|
4.9
|
17.9
|
0.3
|
|
HA2
|
X:GLY42
|
4.9
|
24.3
|
1.0
|
|
HA3
|
X:GLY42
|
5.0
|
24.3
|
1.0
|
|
CD
|
X:ARG49
|
5.0
|
19.5
|
1.0
|
|
CB
|
X:PHE41
|
5.0
|
14.9
|
1.0
|
|
Iron binding site 6 out
of 11 in 8omx
Go back to
Iron Binding Sites List in 8omx
Iron binding site 6 out
of 11 in the Ni,Fe-Codh -600MV State : 1 Min Dioxygen Exposure
 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 -600MV State : 1 Min Dioxygen Exposure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Fe1002
b:14.4
occ:1.00
|
FE2
|
X:FES1002
|
0.0
|
14.4
|
1.0
|
|
S2
|
X:FES1002
|
2.2
|
14.3
|
1.0
|
|
S1
|
X:FES1002
|
2.3
|
14.6
|
1.0
|
|
SG
|
X:CYS39
|
2.3
|
16.0
|
1.0
|
|
FE1
|
X:FES1002
|
2.7
|
15.0
|
1.0
|
|
CB
|
X:CYS39
|
3.2
|
15.0
|
1.0
|
|
HB3
|
X:CYS39
|
3.2
|
18.6
|
1.0
|
|
HB2
|
X:CYS39
|
3.2
|
18.6
|
1.0
|
|
H
|
X:GLY42
|
3.5
|
20.4
|
1.0
|
|
HB2
|
X:PHE41
|
3.5
|
18.2
|
1.0
|
|
HD2
|
X:PHE41
|
4.1
|
22.2
|
1.0
|
|
N
|
X:GLY42
|
4.2
|
16.6
|
1.0
|
|
HA3
|
X:GLY42
|
4.3
|
24.3
|
1.0
|
|
CB
|
X:PHE41
|
4.5
|
14.9
|
1.0
|
|
HB2
|
X:CYS47
|
4.5
|
19.9
|
1.0
|
|
HD3
|
X:ARG57
|
4.6
|
24.1
|
0.3
|
|
CA
|
X:CYS39
|
4.6
|
13.9
|
1.0
|
|
H
|
X:PHE41
|
4.7
|
21.2
|
1.0
|
|
CA
|
X:GLY42
|
4.8
|
19.6
|
1.0
|
|
SG
|
X:CYS47
|
4.8
|
15.1
|
1.0
|
|
HB3
|
X:PHE41
|
4.9
|
18.2
|
1.0
|
|
CD2
|
X:PHE41
|
4.9
|
18.8
|
1.0
|
|
HA
|
X:CYS39
|
4.9
|
16.9
|
1.0
|
|
HH11
|
X:ARG57
|
5.0
|
26.0
|
0.3
|
|
Iron binding site 7 out
of 11 in 8omx
Go back to
Iron Binding Sites List in 8omx
Iron binding site 7 out
of 11 in the Ni,Fe-Codh -600MV State : 1 Min Dioxygen Exposure
 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 -600MV State : 1 Min Dioxygen Exposure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Fe1003
b:20.3
occ:0.63
|
FE2
|
X:NFS1003
|
0.0
|
20.3
|
0.6
|
|
S5
|
X:NFS1003
|
2.2
|
21.7
|
0.7
|
|
SG
|
X:CYS333
|
2.2
|
21.1
|
1.0
|
|
S4
|
X:NFS1003
|
2.3
|
21.3
|
0.7
|
|
S1
|
X:NFS1003
|
2.3
|
21.9
|
0.8
|
|
FE3
|
X:NFS1003
|
2.6
|
20.9
|
0.7
|
|
FE4
|
X:NFS1003
|
2.7
|
20.9
|
0.6
|
|
HB3
|
X:CYS333
|
3.0
|
23.0
|
1.0
|
|
CB
|
X:CYS333
|
3.1
|
19.5
|
1.0
|
|
HE1
|
X:HIS261
|
3.1
|
28.1
|
1.0
|
|
S
|
X:H2S1005
|
3.1
|
21.4
|
0.2
|
|
HB2
|
X:CYS333
|
3.3
|
23.0
|
1.0
|
|
NI1
|
X:NFS1003
|
3.3
|
23.1
|
0.6
|
|
FE
|
X:FE21004
|
3.4
|
21.9
|
0.6
|
|
HZ1
|
X:LYS563
|
3.4
|
25.9
|
1.0
|
|
FE
|
X:FE21004
|
3.5
|
23.1
|
0.3
|
|
S3
|
X:NFS1003
|
3.6
|
22.4
|
0.7
|
|
CE1
|
X:HIS261
|
3.7
|
23.4
|
1.0
|
|
NE2
|
X:HIS261
|
3.8
|
26.0
|
1.0
|
|
HZ2
|
X:LYS563
|
3.9
|
25.9
|
1.0
|
|
O
|
X:HOH1568
|
3.9
|
23.6
|
0.3
|
|
NZ
|
X:LYS563
|
4.0
|
21.5
|
1.0
|
|
S2
|
X:NFS1003
|
4.1
|
25.5
|
0.6
|
|
HB2
|
X:HIS561
|
4.1
|
18.2
|
1.0
|
|
HG
|
X:CYS294
|
4.2
|
27.9
|
1.0
|
|
HE3
|
X:LYS563
|
4.3
|
27.1
|
1.0
|
|
HE1
|
X:MET560
|
4.3
|
23.8
|
1.0
|
|
HE3
|
X:MET560
|
4.4
|
23.8
|
1.0
|
|
CA
|
X:CYS333
|
4.5
|
17.1
|
1.0
|
|
HA
|
X:CYS333
|
4.6
|
20.2
|
1.0
|
|
SG
|
X:CYS446
|
4.6
|
18.2
|
1.0
|
|
HB3
|
X:CYS446
|
4.6
|
19.1
|
1.0
|
|
HD2
|
X:HIS561
|
4.7
|
16.5
|
1.0
|
|
O
|
X:HOH1314
|
4.7
|
24.3
|
1.0
|
|
O
|
X:HOH1524
|
4.7
|
22.1
|
0.3
|
|
CE
|
X:LYS563
|
4.7
|
22.3
|
1.0
|
|
HZ3
|
X:LYS563
|
4.7
|
25.9
|
1.0
|
|
HB3
|
X:HIS561
|
4.7
|
18.2
|
1.0
|
|
CB
|
X:HIS561
|
4.8
|
14.7
|
1.0
|
|
CE
|
X:MET560
|
4.8
|
19.7
|
1.0
|
|
SG
|
X:CYS476
|
4.9
|
27.6
|
1.0
|
|
CD2
|
X:HIS561
|
5.0
|
13.4
|
1.0
|
|
HB3
|
X:CYS294
|
5.0
|
24.4
|
1.0
|
|
Iron binding site 8 out
of 11 in 8omx
Go back to
Iron Binding Sites List in 8omx
Iron binding site 8 out
of 11 in the Ni,Fe-Codh -600MV State : 1 Min Dioxygen Exposure
 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 -600MV State : 1 Min Dioxygen Exposure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Fe1003
b:20.9
occ:0.67
|
FE3
|
X:NFS1003
|
0.0
|
20.9
|
0.7
|
|
S5
|
X:NFS1003
|
2.2
|
21.7
|
0.7
|
|
S3
|
X:NFS1003
|
2.3
|
22.4
|
0.7
|
|
S4
|
X:NFS1003
|
2.3
|
21.3
|
0.7
|
|
SG
|
X:CYS446
|
2.4
|
18.2
|
1.0
|
|
O
|
X:HOH1568
|
2.5
|
23.6
|
0.3
|
|
FE2
|
X:NFS1003
|
2.6
|
20.3
|
0.6
|
|
FE4
|
X:NFS1003
|
2.7
|
20.9
|
0.6
|
|
NI1
|
X:NFS1003
|
2.9
|
23.1
|
0.6
|
|
HB3
|
X:CYS446
|
2.9
|
19.1
|
1.0
|
|
CB
|
X:CYS446
|
3.0
|
15.5
|
1.0
|
|
HA
|
X:CYS446
|
3.0
|
25.1
|
1.0
|
|
CA
|
X:CYS446
|
3.3
|
20.4
|
1.0
|
|
N
|
X:CYS446
|
3.5
|
18.4
|
1.0
|
|
H
|
X:CYS446
|
3.8
|
22.8
|
1.0
|
|
HB2
|
X:HIS561
|
3.8
|
18.2
|
1.0
|
|
HE3
|
X:MET560
|
3.9
|
23.8
|
1.0
|
|
HA2
|
X:GLY445
|
3.9
|
18.0
|
1.0
|
|
HB2
|
X:CYS446
|
3.9
|
19.1
|
1.0
|
|
S1
|
X:NFS1003
|
4.0
|
21.9
|
0.8
|
|
C
|
X:GLY445
|
4.0
|
18.2
|
1.0
|
|
HB3
|
X:HIS561
|
4.1
|
18.2
|
1.0
|
|
FE
|
X:FE21004
|
4.2
|
23.1
|
0.3
|
|
HB2
|
X:ALA564
|
4.2
|
22.0
|
1.0
|
|
O
|
X:HOH1524
|
4.3
|
22.1
|
0.3
|
|
H
|
X:HIS561
|
4.3
|
16.9
|
1.0
|
|
HB2
|
X:CYS476
|
4.3
|
23.1
|
1.0
|
|
S
|
X:H2S1005
|
4.3
|
21.4
|
0.2
|
|
CB
|
X:HIS561
|
4.4
|
14.7
|
1.0
|
|
SG
|
X:CYS333
|
4.4
|
21.1
|
1.0
|
|
CA
|
X:GLY445
|
4.5
|
15.2
|
1.0
|
|
O
|
X:GLY445
|
4.5
|
21.1
|
1.0
|
|
HB3
|
X:MET560
|
4.6
|
17.8
|
1.0
|
|
HG
|
X:SER312
|
4.7
|
23.2
|
1.0
|
|
FE
|
X:FE21004
|
4.7
|
21.9
|
0.6
|
|
CE
|
X:MET560
|
4.7
|
19.7
|
1.0
|
|
S2
|
X:NFS1003
|
4.7
|
25.5
|
0.6
|
|
HE1
|
X:MET560
|
4.7
|
23.8
|
1.0
|
|
H
|
X:CYS476
|
4.7
|
21.8
|
1.0
|
|
SG
|
X:CYS476
|
4.7
|
27.6
|
1.0
|
|
SG
|
X:CYS526
|
4.7
|
18.9
|
0.7
|
|
C
|
X:CYS446
|
4.8
|
18.2
|
1.0
|
|
HA3
|
X:GLY445
|
4.9
|
18.0
|
1.0
|
|
H
|
X:MET560
|
5.0
|
18.1
|
1.0
|
|
CB
|
X:CYS476
|
5.0
|
19.4
|
1.0
|
|
Iron binding site 9 out
of 11 in 8omx
Go back to
Iron Binding Sites List in 8omx
Iron binding site 9 out
of 11 in the Ni,Fe-Codh -600MV State : 1 Min Dioxygen Exposure
 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 -600MV State : 1 Min Dioxygen Exposure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Fe1003
b:20.9
occ:0.64
|
FE4
|
X:NFS1003
|
0.0
|
20.9
|
0.6
|
|
S
|
X:H2S1005
|
2.0
|
21.4
|
0.2
|
|
S3
|
X:NFS1003
|
2.1
|
22.4
|
0.7
|
|
S1
|
X:NFS1003
|
2.2
|
21.9
|
0.8
|
|
S4
|
X:NFS1003
|
2.2
|
21.3
|
0.7
|
|
SG
|
X:CYS476
|
2.4
|
27.6
|
1.0
|
|
FE2
|
X:NFS1003
|
2.7
|
20.3
|
0.6
|
|
FE3
|
X:NFS1003
|
2.7
|
20.9
|
0.7
|
|
FE
|
X:FE21004
|
3.1
|
23.1
|
0.3
|
|
HB2
|
X:CYS476
|
3.2
|
23.1
|
1.0
|
|
HG
|
X:CYS294
|
3.3
|
27.9
|
1.0
|
|
CB
|
X:CYS476
|
3.4
|
19.4
|
1.0
|
|
HA
|
X:CYS446
|
3.5
|
25.1
|
1.0
|
|
H
|
X:CYS476
|
3.5
|
21.8
|
1.0
|
|
NI1
|
X:NFS1003
|
3.6
|
23.1
|
0.6
|
|
HB2
|
X:SER312
|
3.7
|
25.0
|
1.0
|
|
O
|
X:HOH1428
|
3.8
|
28.8
|
1.0
|
|
S5
|
X:NFS1003
|
3.9
|
21.7
|
0.7
|
|
FE
|
X:FE21004
|
3.9
|
21.9
|
0.6
|
|
N
|
X:CYS476
|
4.0
|
18.1
|
1.0
|
|
HB3
|
X:CYS476
|
4.1
|
23.1
|
1.0
|
|
HG
|
X:SER312
|
4.2
|
23.2
|
1.0
|
|
HB3
|
X:CYS446
|
4.2
|
19.1
|
1.0
|
|
CA
|
X:CYS446
|
4.3
|
20.4
|
1.0
|
|
CA
|
X:CYS476
|
4.4
|
17.1
|
1.0
|
|
SG
|
X:CYS294
|
4.5
|
24.3
|
1.0
|
|
HB3
|
X:CYS333
|
4.5
|
23.0
|
1.0
|
|
HA
|
X:CYS294
|
4.5
|
24.1
|
1.0
|
|
CB
|
X:SER312
|
4.5
|
21.7
|
1.0
|
|
HB3
|
X:CYS294
|
4.6
|
24.4
|
1.0
|
|
OG
|
X:SER312
|
4.6
|
20.0
|
1.0
|
|
CB
|
X:CYS446
|
4.6
|
15.5
|
1.0
|
|
SG
|
X:CYS526
|
4.7
|
18.9
|
0.7
|
|
HA
|
X:SER312
|
4.7
|
25.9
|
1.0
|
|
O
|
X:GLY445
|
4.7
|
21.1
|
1.0
|
|
O
|
X:HOH1568
|
4.7
|
23.6
|
0.3
|
|
SG
|
X:CYS295
|
4.7
|
19.4
|
0.4
|
|
HE1
|
X:HIS261
|
4.7
|
28.1
|
1.0
|
|
HA
|
X:CYS476
|
4.7
|
20.3
|
1.0
|
|
SG
|
X:CYS333
|
4.8
|
21.1
|
1.0
|
|
SG
|
X:CYS446
|
4.8
|
18.2
|
1.0
|
|
H
|
X:SER312
|
4.9
|
22.2
|
1.0
|
|
N
|
X:CYS446
|
4.9
|
18.4
|
1.0
|
|
C
|
X:GLY445
|
4.9
|
18.2
|
1.0
|
|
HA3
|
X:GLY475
|
4.9
|
21.1
|
1.0
|
|
C
|
X:GLY475
|
5.0
|
18.9
|
1.0
|
|
CB
|
X:CYS333
|
5.0
|
19.5
|
1.0
|
|
CB
|
X:CYS294
|
5.0
|
21.7
|
1.0
|
|
H
|
X:ASN447
|
5.0
|
17.9
|
1.0
|
|
Iron binding site 10 out
of 11 in 8omx
Go back to
Iron Binding Sites List in 8omx
Iron binding site 10 out
of 11 in the Ni,Fe-Codh -600MV State : 1 Min Dioxygen Exposure
 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 -600MV State : 1 Min Dioxygen Exposure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Fe1004
b:21.9
occ:0.55
|
FE
|
X:FE21004
|
0.0
|
21.9
|
0.6
|
|
FE
|
X:FE21004
|
1.4
|
23.1
|
0.3
|
|
NE2
|
X:HIS261
|
1.7
|
26.0
|
1.0
|
|
S2
|
X:NFS1003
|
2.4
|
25.5
|
0.6
|
|
SG
|
X:CYS295
|
2.4
|
18.5
|
0.6
|
|
S1
|
X:NFS1003
|
2.5
|
21.9
|
0.8
|
|
CD2
|
X:HIS261
|
2.6
|
22.9
|
1.0
|
|
CE1
|
X:HIS261
|
2.8
|
23.4
|
1.0
|
|
NI1
|
X:NFS1003
|
2.8
|
23.1
|
0.6
|
|
HB2
|
X:CYS295
|
2.8
|
22.5
|
0.4
|
|
HD2
|
X:HIS261
|
2.8
|
27.4
|
1.0
|
|
HB2
|
X:CYS526
|
2.9
|
21.2
|
0.3
|
|
HZ2
|
X:LYS563
|
3.0
|
25.9
|
1.0
|
|
HE1
|
X:HIS261
|
3.0
|
28.1
|
1.0
|
|
HB2
|
X:CYS295
|
3.1
|
21.2
|
0.6
|
|
SG
|
X:CYS295
|
3.1
|
19.4
|
0.4
|
|
HB2
|
X:CYS526
|
3.1
|
20.9
|
0.7
|
|
SG
|
X:CYS526
|
3.3
|
18.9
|
0.7
|
|
FE2
|
X:NFS1003
|
3.4
|
20.3
|
0.6
|
|
CB
|
X:CYS295
|
3.4
|
18.6
|
0.6
|
|
CB
|
X:CYS295
|
3.4
|
19.7
|
0.4
|
|
HZ1
|
X:LYS563
|
3.5
|
25.9
|
1.0
|
|
HB3
|
X:CYS526
|
3.5
|
21.2
|
0.3
|
|
CB
|
X:CYS526
|
3.6
|
17.3
|
0.3
|
|
NZ
|
X:LYS563
|
3.6
|
21.5
|
1.0
|
|
S5
|
X:NFS1003
|
3.6
|
21.7
|
0.7
|
|
CB
|
X:CYS526
|
3.7
|
17.0
|
0.7
|
|
CG
|
X:HIS261
|
3.8
|
24.6
|
1.0
|
|
ND1
|
X:HIS261
|
3.8
|
22.6
|
1.0
|
|
HZ3
|
X:LYS563
|
3.9
|
25.9
|
1.0
|
|
HB3
|
X:CYS295
|
3.9
|
22.5
|
0.4
|
|
O
|
X:HOH1524
|
3.9
|
22.1
|
0.3
|
|
FE4
|
X:NFS1003
|
3.9
|
20.9
|
0.6
|
|
S3
|
X:NFS1003
|
4.0
|
22.4
|
0.7
|
|
HB3
|
X:CYS295
|
4.0
|
21.2
|
0.6
|
|
H
|
X:CYS526
|
4.0
|
18.2
|
0.7
|
|
H
|
X:CYS526
|
4.0
|
18.2
|
0.3
|
|
H
|
X:CYS295
|
4.1
|
23.3
|
0.6
|
|
H
|
X:CYS295
|
4.1
|
23.3
|
0.4
|
|
HB3
|
X:CYS526
|
4.2
|
20.9
|
0.7
|
|
O
|
X:HOH1455
|
4.2
|
19.7
|
1.0
|
|
SG
|
X:CYS526
|
4.4
|
23.1
|
0.3
|
|
CA
|
X:CYS295
|
4.5
|
21.1
|
0.6
|
|
S
|
X:H2S1005
|
4.5
|
21.4
|
0.2
|
|
N
|
X:CYS295
|
4.5
|
20.3
|
0.6
|
|
SG
|
X:CYS333
|
4.5
|
21.1
|
1.0
|
|
N
|
X:CYS295
|
4.6
|
20.3
|
0.4
|
|
HD1
|
X:HIS261
|
4.6
|
26.7
|
1.0
|
|
CA
|
X:CYS295
|
4.6
|
21.0
|
0.4
|
|
FE3
|
X:NFS1003
|
4.7
|
20.9
|
0.7
|
|
HA
|
X:CYS295
|
4.7
|
24.1
|
0.6
|
|
O
|
X:HOH1568
|
4.7
|
23.6
|
0.3
|
|
N
|
X:CYS526
|
4.7
|
15.3
|
1.0
|
|
HB3
|
X:CYS294
|
4.8
|
24.4
|
1.0
|
|
CA
|
X:CYS526
|
4.8
|
16.9
|
0.3
|
|
CA
|
X:CYS526
|
4.8
|
16.9
|
0.7
|
|
O
|
X:HOH1428
|
4.9
|
28.8
|
1.0
|
|
HB2
|
X:CYS333
|
4.9
|
23.0
|
1.0
|
|
CE
|
X:LYS563
|
4.9
|
22.3
|
1.0
|
|
HE3
|
X:LYS563
|
4.9
|
27.1
|
1.0
|
|
HD2
|
X:LYS563
|
4.9
|
21.4
|
1.0
|
|
HE2
|
X:HIS93
|
5.0
|
23.3
|
1.0
|
|
Reference:
Y.Basak,
J.H.Jeoung,
L.Domnik,
H.Dobbek.
Stepwise O 2 -Induced Rearrangement and Disassembly of the [Nife 4 (Oh)( Mu 3 -S) 4 ] Active Site Cluster of Co Dehydrogenase. Angew.Chem.Int.Ed.Engl. V. 62 05341 2023.
ISSN: ESSN 1521-3773
PubMed: 37279092
DOI: 10.1002/ANIE.202305341
Page generated: Sat Aug 10 07:59:01 2024
|
