Iron in PDB 4udx: CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution
Enzymatic activity of CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution
All present enzymatic activity of CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution:
1.2.99.2;
Protein crystallography data
The structure of CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution, PDB code: 4udx
was solved by
J.Fesseler,
J.-H.Jeoung,
H.Dobbek,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
50.00 /
1.03
|
|
Space group
|
C 1 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
112.516,
74.870,
71.075,
90.00,
111.26,
90.00
|
|
R / Rfree (%)
|
13.2 /
15.65
|
Other elements in 4udx:
The structure of CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution 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 CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution
(pdb code 4udx). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 11 binding sites of Iron where determined in the
CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution, PDB code: 4udx:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 11 in 4udx
Go back to
Iron Binding Sites List in 4udx
Iron binding site 1 out
of 11 in the CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Fe1001
b:6.1
occ:1.00
|
FE1
|
X:SF41001
|
0.0
|
6.1
|
1.0
|
|
SG
|
X:CYS51
|
2.3
|
6.3
|
1.0
|
|
S2
|
X:SF41001
|
2.3
|
6.1
|
1.0
|
|
S1
|
X:SF41001
|
2.3
|
6.1
|
1.0
|
|
S4
|
X:SF41001
|
2.4
|
6.5
|
1.0
|
|
FE3
|
X:SF41001
|
2.7
|
6.2
|
1.0
|
|
FE2
|
X:SF41001
|
2.7
|
6.0
|
1.0
|
|
FE4
|
X:SF41001
|
2.8
|
6.1
|
1.0
|
|
H
|
X:CYS51
|
3.3
|
7.2
|
1.0
|
|
HB3
|
X:CYS51
|
3.3
|
7.3
|
1.0
|
|
CB
|
X:CYS51
|
3.3
|
6.1
|
1.0
|
|
N
|
X:CYS51
|
3.6
|
6.0
|
1.0
|
|
HB2
|
X:GLN53
|
3.7
|
7.8
|
1.0
|
|
HG3
|
X:MET199
|
3.7
|
8.0
|
1.0
|
|
CA
|
X:CYS51
|
3.9
|
6.2
|
1.0
|
|
S3
|
X:SF41001
|
4.0
|
6.4
|
1.0
|
|
H
|
X:GLY54
|
4.0
|
8.0
|
1.0
|
|
O
|
X:HOH2151
|
4.0
|
18.4
|
1.0
|
|
HB2
|
X:MET199
|
4.1
|
7.1
|
1.0
|
|
HB2
|
X:CYS51
|
4.2
|
7.3
|
1.0
|
|
H
|
X:GLN53
|
4.2
|
7.7
|
1.0
|
|
O
|
X:CYS51
|
4.3
|
6.6
|
1.0
|
|
C
|
X:CYS51
|
4.3
|
5.9
|
1.0
|
|
C
|
X:HIS50
|
4.3
|
6.0
|
1.0
|
|
HG2
|
X:MET199
|
4.4
|
8.0
|
1.0
|
|
N
|
X:GLY54
|
4.4
|
6.7
|
1.0
|
|
CG
|
X:MET199
|
4.4
|
6.6
|
1.0
|
|
H
|
X:HIS50
|
4.5
|
7.1
|
1.0
|
|
HB2
|
X:HIS50
|
4.5
|
7.9
|
1.0
|
|
HB3
|
X:CYS70
|
4.5
|
8.1
|
1.0
|
|
HA3
|
X:GLY54
|
4.6
|
8.8
|
1.0
|
|
CB
|
X:GLN53
|
4.6
|
6.5
|
1.0
|
|
HA
|
X:CYS51
|
4.8
|
7.4
|
1.0
|
|
N
|
X:HIS50
|
4.8
|
5.9
|
1.0
|
|
CB
|
X:MET199
|
4.8
|
5.9
|
1.0
|
|
SG
|
X:CYS48
|
4.8
|
6.0
|
1.0
|
|
SG
|
X:CYS70
|
4.8
|
6.5
|
1.0
|
|
N
|
X:GLN53
|
4.8
|
6.4
|
1.0
|
|
SG
|
X:CYS56
|
4.9
|
6.5
|
1.0
|
|
H
|
X:CYS70
|
4.9
|
7.9
|
1.0
|
|
CA
|
X:HIS50
|
4.9
|
5.9
|
1.0
|
|
CA
|
X:GLY54
|
5.0
|
7.4
|
1.0
|
|
HH22
|
X:ARG80
|
5.0
|
8.0
|
1.0
|
|
O
|
X:HIS50
|
5.0
|
7.1
|
1.0
|
|
HB
|
X:ILE69
|
5.0
|
8.4
|
1.0
|
|
Iron binding site 2 out
of 11 in 4udx
Go back to
Iron Binding Sites List in 4udx
Iron binding site 2 out
of 11 in the CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Fe1001
b:6.0
occ:1.00
|
FE2
|
X:SF41001
|
0.0
|
6.0
|
1.0
|
|
S1
|
X:SF41001
|
2.3
|
6.1
|
1.0
|
|
SG
|
X:CYS48
|
2.3
|
6.0
|
1.0
|
|
S2
|
X:SF41001
|
2.3
|
6.1
|
1.0
|
|
S3
|
X:SF41001
|
2.3
|
6.4
|
1.0
|
|
FE3
|
X:SF41001
|
2.7
|
6.2
|
1.0
|
|
FE1
|
X:SF41001
|
2.7
|
6.1
|
1.0
|
|
FE4
|
X:SF41001
|
2.7
|
6.1
|
1.0
|
|
HB3
|
X:CYS48
|
3.0
|
7.1
|
1.0
|
|
HH22
|
X:ARG80
|
3.2
|
8.0
|
1.0
|
|
CB
|
X:CYS48
|
3.2
|
5.9
|
1.0
|
|
H
|
X:HIS50
|
3.3
|
7.1
|
1.0
|
|
HB2
|
X:HIS50
|
3.4
|
7.9
|
1.0
|
|
HH21
|
X:ARG80
|
3.5
|
8.0
|
1.0
|
|
NH2
|
X:ARG80
|
3.6
|
6.7
|
1.0
|
|
HB2
|
X:CYS48
|
3.9
|
7.1
|
1.0
|
|
S4
|
X:SF41001
|
3.9
|
6.5
|
1.0
|
|
HB2
|
X:CYS56
|
3.9
|
8.0
|
1.0
|
|
N
|
X:HIS50
|
4.0
|
5.9
|
1.0
|
|
H
|
X:CYS51
|
4.0
|
7.2
|
1.0
|
|
C
|
X:CYS48
|
4.2
|
5.5
|
1.0
|
|
O
|
X:CYS48
|
4.2
|
6.4
|
1.0
|
|
CB
|
X:HIS50
|
4.3
|
6.6
|
1.0
|
|
CA
|
X:CYS48
|
4.3
|
5.7
|
1.0
|
|
CA
|
X:HIS50
|
4.5
|
5.9
|
1.0
|
|
N
|
X:CYS51
|
4.5
|
6.0
|
1.0
|
|
N
|
X:ARG49
|
4.6
|
5.7
|
1.0
|
|
HG12
|
X:ILE77
|
4.7
|
9.4
|
1.0
|
|
SG
|
X:CYS56
|
4.7
|
6.5
|
1.0
|
|
CB
|
X:CYS56
|
4.7
|
6.7
|
1.0
|
|
C
|
X:HIS50
|
4.7
|
6.0
|
1.0
|
|
CZ
|
X:ARG80
|
4.8
|
6.3
|
1.0
|
|
HA
|
X:CYS48
|
4.8
|
6.8
|
1.0
|
|
HA
|
X:ARG49
|
4.8
|
7.3
|
1.0
|
|
SG
|
X:CYS70
|
4.9
|
6.5
|
1.0
|
|
HB1
|
X:ALA72
|
4.9
|
11.1
|
1.0
|
|
H
|
X:ARG49
|
4.9
|
6.8
|
1.0
|
|
SG
|
X:CYS51
|
4.9
|
6.3
|
1.0
|
|
HB3
|
X:HIS50
|
4.9
|
7.9
|
1.0
|
|
C
|
X:ARG49
|
4.9
|
5.6
|
1.0
|
|
H
|
X:CYS56
|
5.0
|
7.3
|
1.0
|
|
Iron binding site 3 out
of 11 in 4udx
Go back to
Iron Binding Sites List in 4udx
Iron binding site 3 out
of 11 in the CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Fe1001
b:6.2
occ:1.00
|
FE3
|
X:SF41001
|
0.0
|
6.2
|
1.0
|
|
S4
|
X:SF41001
|
2.3
|
6.5
|
1.0
|
|
SG
|
X:CYS56
|
2.3
|
6.5
|
1.0
|
|
S2
|
X:SF41001
|
2.3
|
6.1
|
1.0
|
|
S3
|
X:SF41001
|
2.3
|
6.4
|
1.0
|
|
FE2
|
X:SF41001
|
2.7
|
6.0
|
1.0
|
|
FE1
|
X:SF41001
|
2.7
|
6.1
|
1.0
|
|
FE4
|
X:SF41001
|
2.7
|
6.1
|
1.0
|
|
HB2
|
X:CYS56
|
3.0
|
8.0
|
1.0
|
|
CB
|
X:CYS56
|
3.2
|
6.7
|
1.0
|
|
H
|
X:ILE69
|
3.3
|
8.2
|
1.0
|
|
HB
|
X:ILE69
|
3.5
|
8.4
|
1.0
|
|
HB3
|
X:CYS56
|
3.8
|
8.0
|
1.0
|
|
S1
|
X:SF41001
|
3.9
|
6.1
|
1.0
|
|
H
|
X:CYS70
|
3.9
|
7.9
|
1.0
|
|
HB3
|
X:CYS48
|
4.0
|
7.1
|
1.0
|
|
HA2
|
X:GLY54
|
4.0
|
8.8
|
1.0
|
|
N
|
X:ILE69
|
4.0
|
6.9
|
1.0
|
|
HA3
|
X:GLY54
|
4.1
|
8.8
|
1.0
|
|
H
|
X:CYS56
|
4.2
|
7.3
|
1.0
|
|
HA3
|
X:GLY68
|
4.3
|
8.6
|
1.0
|
|
HD13
|
X:ILE69
|
4.3
|
12.3
|
1.0
|
|
HB2
|
X:GLN53
|
4.4
|
7.8
|
1.0
|
|
CA
|
X:GLY54
|
4.4
|
7.4
|
1.0
|
|
CA
|
X:CYS56
|
4.4
|
6.1
|
1.0
|
|
CB
|
X:ILE69
|
4.4
|
7.0
|
1.0
|
|
N
|
X:CYS56
|
4.5
|
6.1
|
1.0
|
|
N
|
X:GLY54
|
4.5
|
6.7
|
1.0
|
|
H
|
X:GLY54
|
4.5
|
8.0
|
1.0
|
|
HA2
|
X:GLY68
|
4.6
|
8.6
|
1.0
|
|
O
|
X:CYS48
|
4.6
|
6.4
|
1.0
|
|
HG13
|
X:ILE69
|
4.6
|
8.8
|
1.0
|
|
SG
|
X:CYS51
|
4.6
|
6.3
|
1.0
|
|
SG
|
X:CYS48
|
4.7
|
6.0
|
1.0
|
|
N
|
X:CYS70
|
4.7
|
6.6
|
1.0
|
|
CB
|
X:CYS48
|
4.8
|
5.9
|
1.0
|
|
CA
|
X:GLY68
|
4.8
|
7.1
|
1.0
|
|
CA
|
X:ILE69
|
4.8
|
7.0
|
1.0
|
|
SG
|
X:CYS70
|
4.8
|
6.5
|
1.0
|
|
HA
|
X:CYS56
|
4.8
|
7.3
|
1.0
|
|
C
|
X:GLY68
|
4.9
|
6.4
|
1.0
|
|
CG1
|
X:ILE69
|
4.9
|
7.3
|
1.0
|
|
C
|
X:GLN53
|
5.0
|
7.0
|
1.0
|
|
Iron binding site 4 out
of 11 in 4udx
Go back to
Iron Binding Sites List in 4udx
Iron binding site 4 out
of 11 in the CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Fe1001
b:6.1
occ:1.00
|
FE4
|
X:SF41001
|
0.0
|
6.1
|
1.0
|
|
S3
|
X:SF41001
|
2.3
|
6.4
|
1.0
|
|
SG
|
X:CYS70
|
2.3
|
6.5
|
1.0
|
|
S1
|
X:SF41001
|
2.3
|
6.1
|
1.0
|
|
S4
|
X:SF41001
|
2.4
|
6.5
|
1.0
|
|
FE2
|
X:SF41001
|
2.7
|
6.0
|
1.0
|
|
FE3
|
X:SF41001
|
2.7
|
6.2
|
1.0
|
|
FE1
|
X:SF41001
|
2.8
|
6.1
|
1.0
|
|
H
|
X:CYS70
|
3.1
|
7.9
|
1.0
|
|
HB3
|
X:CYS70
|
3.2
|
8.1
|
1.0
|
|
HH22
|
X:ARG80
|
3.3
|
8.0
|
1.0
|
|
CB
|
X:CYS70
|
3.4
|
6.7
|
1.0
|
|
N
|
X:CYS70
|
3.9
|
6.6
|
1.0
|
|
HB3
|
X:ALA72
|
3.9
|
11.1
|
1.0
|
|
HB1
|
X:ALA72
|
3.9
|
11.1
|
1.0
|
|
S2
|
X:SF41001
|
4.0
|
6.1
|
1.0
|
|
HG2
|
X:MET199
|
4.0
|
8.0
|
1.0
|
|
HB2
|
X:CYS70
|
4.1
|
8.1
|
1.0
|
|
NH2
|
X:ARG80
|
4.2
|
6.7
|
1.0
|
|
O
|
X:HOH2203
|
4.2
|
6.9
|
1.0
|
|
CA
|
X:CYS70
|
4.2
|
6.5
|
1.0
|
|
HG3
|
X:MET199
|
4.3
|
8.0
|
1.0
|
|
H
|
X:ALA72
|
4.3
|
8.7
|
1.0
|
|
H
|
X:ILE69
|
4.3
|
8.2
|
1.0
|
|
HA3
|
X:GLY68
|
4.4
|
8.6
|
1.0
|
|
CB
|
X:ALA72
|
4.4
|
7.4
|
1.0
|
|
HH21
|
X:ARG80
|
4.5
|
8.0
|
1.0
|
|
O
|
X:HOH2151
|
4.5
|
18.4
|
1.0
|
|
HH12
|
X:ARG80
|
4.5
|
8.2
|
1.0
|
|
CG
|
X:MET199
|
4.6
|
6.6
|
1.0
|
|
HB
|
X:ILE69
|
4.7
|
8.4
|
1.0
|
|
N
|
X:ILE69
|
4.7
|
6.9
|
1.0
|
|
SG
|
X:CYS51
|
4.7
|
6.3
|
1.0
|
|
SG
|
X:CYS48
|
4.8
|
6.0
|
1.0
|
|
SG
|
X:CYS56
|
4.8
|
6.5
|
1.0
|
|
HA
|
X:CYS70
|
5.0
|
7.8
|
1.0
|
|
HB2
|
X:MET199
|
5.0
|
7.1
|
1.0
|
|
HB2
|
X:ALA72
|
5.0
|
11.1
|
1.0
|
|
C
|
X:ILE69
|
5.0
|
6.4
|
1.0
|
|
Iron binding site 5 out
of 11 in 4udx
Go back to
Iron Binding Sites List in 4udx
Iron binding site 5 out
of 11 in the CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Fe1002
b:6.9
occ:1.00
|
FE1
|
X:FES1002
|
0.0
|
6.9
|
1.0
|
|
S2
|
X:FES1002
|
2.3
|
7.0
|
1.0
|
|
SG
|
X:CYS39
|
2.3
|
7.7
|
1.0
|
|
S1
|
X:FES1002
|
2.3
|
7.2
|
1.0
|
|
FE2
|
X:FES1002
|
2.7
|
6.7
|
1.0
|
|
CB
|
X:CYS39
|
3.2
|
7.7
|
1.0
|
|
HB3
|
X:CYS39
|
3.2
|
9.2
|
1.0
|
|
HB2
|
X:CYS39
|
3.3
|
9.2
|
1.0
|
|
HB2
|
X:PHE41
|
3.4
|
8.6
|
1.0
|
|
H
|
X:GLY42
|
3.5
|
9.7
|
1.0
|
|
HD2
|
X:PHE41
|
4.0
|
10.6
|
1.0
|
|
N
|
X:GLY42
|
4.1
|
8.1
|
1.0
|
|
CB
|
X:PHE41
|
4.3
|
7.2
|
1.0
|
|
HA3
|
X:GLY42
|
4.4
|
10.1
|
1.0
|
|
HB2
|
X:CYS47
|
4.4
|
7.9
|
1.0
|
|
H
|
X:PHE41
|
4.6
|
8.8
|
1.0
|
|
CA
|
X:CYS39
|
4.6
|
7.8
|
1.0
|
|
HB3
|
X:PHE41
|
4.7
|
8.6
|
1.0
|
|
CA
|
X:GLY42
|
4.8
|
8.4
|
1.0
|
|
SG
|
X:CYS47
|
4.8
|
6.7
|
1.0
|
|
CD2
|
X:PHE41
|
4.8
|
8.8
|
1.0
|
|
HA
|
X:CYS39
|
4.9
|
9.4
|
1.0
|
|
HA2
|
X:GLY42
|
5.0
|
10.1
|
1.0
|
|
Iron binding site 6 out
of 11 in 4udx
Go back to
Iron Binding Sites List in 4udx
Iron binding site 6 out
of 11 in the CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Fe1002
b:6.7
occ:1.00
|
FE2
|
X:FES1002
|
0.0
|
6.7
|
1.0
|
|
SG
|
X:CYS47
|
2.3
|
6.7
|
1.0
|
|
S1
|
X:FES1002
|
2.3
|
7.2
|
1.0
|
|
S2
|
X:FES1002
|
2.3
|
7.0
|
1.0
|
|
FE1
|
X:FES1002
|
2.7
|
6.9
|
1.0
|
|
HB2
|
X:CYS47
|
3.0
|
7.9
|
1.0
|
|
CB
|
X:CYS47
|
3.2
|
6.6
|
1.0
|
|
HB3
|
X:CYS47
|
3.5
|
7.9
|
1.0
|
|
O
|
X:HOH2136
|
3.7
|
7.9
|
1.0
|
|
HB2
|
X:PHE41
|
4.1
|
8.6
|
1.0
|
|
HD2
|
X:ARG49
|
4.2
|
15.5
|
1.0
|
|
HB2
|
X:PRO55
|
4.5
|
9.2
|
1.0
|
|
CA
|
X:CYS47
|
4.6
|
6.2
|
1.0
|
|
HA
|
X:CYS47
|
4.7
|
7.4
|
1.0
|
|
HB3
|
X:PHE41
|
4.7
|
8.6
|
1.0
|
|
H
|
X:GLY42
|
4.7
|
9.7
|
1.0
|
|
SG
|
X:CYS39
|
4.7
|
7.7
|
1.0
|
|
HG3
|
X:ARG49
|
4.8
|
9.1
|
1.0
|
|
HB3
|
X:ARG57
|
4.8
|
9.2
|
1.0
|
|
CB
|
X:PHE41
|
4.9
|
7.2
|
1.0
|
|
HA2
|
X:GLY42
|
5.0
|
10.1
|
1.0
|
|
N
|
X:GLY42
|
5.0
|
8.1
|
1.0
|
|
Iron binding site 7 out
of 11 in 4udx
Go back to
Iron Binding Sites List in 4udx
Iron binding site 7 out
of 11 in the CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Fe1003
b:6.8
occ:0.69
|
FE1
|
X:WCC1003
|
0.0
|
6.8
|
0.7
|
|
SG
|
X:CYS333
|
2.2
|
9.3
|
1.0
|
|
S3
|
X:WCC1003
|
2.3
|
9.1
|
0.8
|
|
S4
|
X:WCC1003
|
2.4
|
7.8
|
0.7
|
|
S2
|
X:WCC1003
|
2.4
|
7.6
|
0.7
|
|
FE3
|
X:WCC1003
|
2.6
|
7.0
|
0.7
|
|
FE4
|
X:WCC1003
|
2.7
|
7.5
|
0.7
|
|
HB3
|
X:CYS333
|
2.9
|
10.7
|
1.0
|
|
CB
|
X:CYS333
|
3.1
|
8.9
|
1.0
|
|
FE
|
X:FE21004
|
3.2
|
8.8
|
0.6
|
|
HB2
|
X:CYS333
|
3.3
|
10.7
|
1.0
|
|
NI
|
X:WCC1003
|
3.3
|
8.5
|
0.6
|
|
FE
|
X:FE21004
|
3.4
|
19.0
|
0.4
|
|
HE1
|
X:HIS261
|
3.6
|
12.8
|
1.0
|
|
S1
|
X:WCC1003
|
3.7
|
7.7
|
0.7
|
|
NZ
|
X:LYS563
|
4.0
|
10.2
|
1.0
|
|
O2
|
X:CO21005
|
4.1
|
8.4
|
0.6
|
|
C
|
X:CO21005
|
4.1
|
8.4
|
0.6
|
|
NE2
|
X:HIS261
|
4.2
|
14.1
|
1.0
|
|
CE1
|
X:HIS261
|
4.2
|
10.6
|
1.0
|
|
HB2
|
X:HIS561
|
4.2
|
7.6
|
1.0
|
|
HE2
|
X:MET560
|
4.3
|
13.4
|
1.0
|
|
HE3
|
X:LYS563
|
4.3
|
10.3
|
1.0
|
|
HE1
|
X:MET560
|
4.4
|
13.4
|
1.0
|
|
CA
|
X:CYS333
|
4.5
|
8.3
|
1.0
|
|
HA
|
X:CYS333
|
4.6
|
10.0
|
1.0
|
|
SG
|
X:CYS446
|
4.6
|
8.9
|
1.0
|
|
O
|
X:HOH2517
|
4.6
|
11.0
|
1.0
|
|
SG
|
X:CYS476
|
4.7
|
11.2
|
0.1
|
|
CE
|
X:LYS563
|
4.7
|
8.6
|
1.0
|
|
HB3
|
X:CYS294
|
4.8
|
11.7
|
1.0
|
|
CE
|
X:MET560
|
4.8
|
9.0
|
1.0
|
|
HB3
|
X:HIS561
|
4.8
|
7.6
|
1.0
|
|
HD2
|
X:HIS561
|
4.8
|
8.4
|
1.0
|
|
SG
|
X:CYS476
|
4.9
|
10.2
|
0.9
|
|
CB
|
X:HIS561
|
4.9
|
6.4
|
1.0
|
|
SG
|
X:CYS294
|
5.0
|
10.6
|
1.0
|
|
HB3
|
X:CYS446
|
5.0
|
9.5
|
1.0
|
|
Iron binding site 8 out
of 11 in 4udx
Go back to
Iron Binding Sites List in 4udx
Iron binding site 8 out
of 11 in the CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Fe1003
b:7.0
occ:0.71
|
FE3
|
X:WCC1003
|
0.0
|
7.0
|
0.7
|
|
S4
|
X:WCC1003
|
2.3
|
7.8
|
0.7
|
|
S1
|
X:WCC1003
|
2.3
|
7.7
|
0.7
|
|
SG
|
X:CYS446
|
2.4
|
8.9
|
1.0
|
|
S2
|
X:WCC1003
|
2.4
|
7.6
|
0.7
|
|
FE1
|
X:WCC1003
|
2.6
|
6.8
|
0.7
|
|
FE4
|
X:WCC1003
|
2.7
|
7.5
|
0.7
|
|
NI
|
X:WCC1003
|
2.8
|
8.5
|
0.6
|
|
HA
|
X:CYS446
|
3.0
|
9.6
|
1.0
|
|
CB
|
X:CYS446
|
3.2
|
7.9
|
1.0
|
|
HB3
|
X:CYS446
|
3.2
|
9.5
|
1.0
|
|
CA
|
X:CYS446
|
3.4
|
8.0
|
1.0
|
|
N
|
X:CYS446
|
3.6
|
8.1
|
1.0
|
|
H
|
X:CYS446
|
3.8
|
9.7
|
1.0
|
|
HA2
|
X:GLY445
|
3.8
|
9.3
|
1.0
|
|
HE1
|
X:MET560
|
3.9
|
13.4
|
1.0
|
|
HB2
|
X:HIS561
|
3.9
|
7.6
|
1.0
|
|
FE
|
X:FE21004
|
4.0
|
19.0
|
0.4
|
|
SG
|
X:CYS476
|
4.0
|
11.2
|
0.1
|
|
S3
|
X:WCC1003
|
4.0
|
9.1
|
0.8
|
|
O
|
X:HOH2702
|
4.0
|
27.3
|
1.0
|
|
HB2
|
X:CYS446
|
4.1
|
9.5
|
1.0
|
|
C
|
X:GLY445
|
4.1
|
7.8
|
1.0
|
|
HB2
|
X:CYS476
|
4.2
|
11.6
|
0.9
|
|
C
|
X:CO21005
|
4.2
|
8.4
|
0.6
|
|
HB3
|
X:HIS561
|
4.2
|
7.6
|
1.0
|
|
H
|
X:HIS561
|
4.3
|
8.3
|
1.0
|
|
HB2
|
X:CYS476
|
4.3
|
10.5
|
0.1
|
|
SG
|
X:CYS333
|
4.4
|
9.3
|
1.0
|
|
HB3
|
X:ALA564
|
4.4
|
13.5
|
1.0
|
|
CA
|
X:GLY445
|
4.5
|
7.7
|
1.0
|
|
CB
|
X:HIS561
|
4.6
|
6.4
|
1.0
|
|
FE
|
X:FE21004
|
4.6
|
8.8
|
0.6
|
|
HE2
|
X:MET560
|
4.6
|
13.4
|
1.0
|
|
HB3
|
X:MET560
|
4.6
|
9.2
|
1.0
|
|
O
|
X:GLY445
|
4.6
|
9.9
|
1.0
|
|
SG
|
X:CYS526
|
4.7
|
9.3
|
0.9
|
|
CE
|
X:MET560
|
4.7
|
9.0
|
1.0
|
|
H
|
X:CYS476
|
4.7
|
10.0
|
1.0
|
|
CB
|
X:CYS476
|
4.7
|
8.8
|
0.1
|
|
SG
|
X:CYS476
|
4.8
|
10.2
|
0.9
|
|
HG
|
X:SER312
|
4.8
|
14.5
|
1.0
|
|
C
|
X:CYS446
|
4.9
|
7.5
|
1.0
|
|
HA3
|
X:GLY445
|
4.9
|
9.3
|
1.0
|
|
O2
|
X:CO21005
|
4.9
|
8.4
|
0.6
|
|
CB
|
X:CYS476
|
5.0
|
9.7
|
0.9
|
|
O1
|
X:CO21005
|
5.0
|
9.8
|
0.6
|
|
H
|
X:ASN447
|
5.0
|
8.4
|
1.0
|
|
Iron binding site 9 out
of 11 in 4udx
Go back to
Iron Binding Sites List in 4udx
Iron binding site 9 out
of 11 in the CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 9 of CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Fe1003
b:7.5
occ:0.70
|
FE4
|
X:WCC1003
|
0.0
|
7.5
|
0.7
|
|
SG
|
X:CYS476
|
2.1
|
11.2
|
0.1
|
|
S3
|
X:WCC1003
|
2.3
|
9.1
|
0.8
|
|
S1
|
X:WCC1003
|
2.3
|
7.7
|
0.7
|
|
S2
|
X:WCC1003
|
2.3
|
7.6
|
0.7
|
|
SG
|
X:CYS476
|
2.3
|
10.2
|
0.9
|
|
FE1
|
X:WCC1003
|
2.7
|
6.8
|
0.7
|
|
FE3
|
X:WCC1003
|
2.7
|
7.0
|
0.7
|
|
HB2
|
X:CYS476
|
3.0
|
11.6
|
0.9
|
|
FE
|
X:FE21004
|
3.1
|
19.0
|
0.4
|
|
CB
|
X:CYS476
|
3.3
|
9.7
|
0.9
|
|
H
|
X:CYS476
|
3.4
|
10.0
|
1.0
|
|
HA
|
X:CYS446
|
3.5
|
9.6
|
1.0
|
|
CB
|
X:CYS476
|
3.6
|
8.8
|
0.1
|
|
NI
|
X:WCC1003
|
3.6
|
8.5
|
0.6
|
|
HB2
|
X:SER312
|
3.6
|
10.5
|
1.0
|
|
HB2
|
X:CYS476
|
3.7
|
10.5
|
0.1
|
|
O
|
X:HOH2504
|
3.9
|
14.3
|
1.0
|
|
FE
|
X:FE21004
|
3.9
|
8.8
|
0.6
|
|
HB3
|
X:CYS476
|
4.0
|
11.6
|
0.9
|
|
N
|
X:CYS476
|
4.0
|
8.3
|
1.0
|
|
S4
|
X:WCC1003
|
4.0
|
7.8
|
0.7
|
|
CA
|
X:CYS476
|
4.2
|
8.3
|
0.1
|
|
HB3
|
X:CYS476
|
4.3
|
10.5
|
0.1
|
|
CA
|
X:CYS476
|
4.3
|
9.0
|
0.9
|
|
HA
|
X:CYS294
|
4.3
|
11.0
|
1.0
|
|
SG
|
X:CYS294
|
4.4
|
10.6
|
1.0
|
|
HA
|
X:CYS476
|
4.4
|
10.0
|
0.1
|
|
CB
|
X:SER312
|
4.4
|
8.7
|
1.0
|
|
CA
|
X:CYS446
|
4.4
|
8.0
|
1.0
|
|
HB3
|
X:CYS333
|
4.5
|
10.7
|
1.0
|
|
HB3
|
X:CYS294
|
4.5
|
11.7
|
1.0
|
|
HB3
|
X:CYS446
|
4.5
|
9.5
|
1.0
|
|
OG
|
X:SER312
|
4.6
|
9.7
|
1.0
|
|
HA
|
X:SER312
|
4.6
|
9.9
|
1.0
|
|
HG
|
X:SER312
|
4.6
|
14.5
|
1.0
|
|
SG
|
X:CYS526
|
4.6
|
9.3
|
0.9
|
|
H
|
X:SER312
|
4.7
|
10.4
|
1.0
|
|
HA
|
X:CYS476
|
4.7
|
10.8
|
0.9
|
|
CB
|
X:CYS446
|
4.8
|
7.9
|
1.0
|
|
SG
|
X:CYS333
|
4.8
|
9.3
|
1.0
|
|
SG
|
X:CYS446
|
4.8
|
8.9
|
1.0
|
|
CB
|
X:CYS294
|
4.8
|
9.7
|
1.0
|
|
H
|
X:CYS295
|
4.8
|
9.6
|
0.7
|
|
SG
|
X:CYS295
|
4.9
|
11.9
|
0.3
|
|
HA3
|
X:GLY475
|
4.9
|
9.0
|
1.0
|
|
O
|
X:GLY445
|
4.9
|
9.9
|
1.0
|
|
SG
|
X:CYS295
|
4.9
|
9.4
|
0.7
|
|
N
|
X:CYS446
|
4.9
|
8.1
|
1.0
|
|
C
|
X:GLY475
|
5.0
|
7.1
|
1.0
|
|
H
|
X:CYS295
|
5.0
|
10.8
|
0.3
|
|
CA
|
X:SER312
|
5.0
|
8.3
|
1.0
|
|
Iron binding site 10 out
of 11 in 4udx
Go back to
Iron Binding Sites List in 4udx
Iron binding site 10 out
of 11 in the CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 10 of CO2 Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True-Atomic Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Fe1004
b:19.0
occ:0.36
|
FE
|
X:FE21004
|
0.0
|
19.0
|
0.4
|
|
FE
|
X:FE21004
|
1.4
|
8.8
|
0.6
|
|
NI
|
X:WCC1003
|
2.1
|
8.5
|
0.6
|
|
SG
|
X:CYS295
|
2.3
|
9.4
|
0.7
|
|
SG
|
X:CYS526
|
2.3
|
9.3
|
0.9
|
|
S3
|
X:WCC1003
|
2.4
|
9.1
|
0.8
|
|
HB2
|
X:CYS526
|
2.5
|
11.5
|
0.1
|
|
SG
|
X:CYS295
|
2.6
|
11.9
|
0.3
|
|
O2
|
X:CO21005
|
2.7
|
8.4
|
0.6
|
|
C
|
X:CO21005
|
2.8
|
8.4
|
0.6
|
|
S1
|
X:WCC1003
|
3.0
|
7.7
|
0.7
|
|
FE4
|
X:WCC1003
|
3.1
|
7.5
|
0.7
|
|
HB2
|
X:CYS526
|
3.3
|
9.6
|
0.9
|
|
CB
|
X:CYS526
|
3.4
|
9.6
|
0.1
|
|
FE1
|
X:WCC1003
|
3.4
|
6.8
|
0.7
|
|
CB
|
X:CYS526
|
3.4
|
8.0
|
0.9
|
|
HB2
|
X:CYS295
|
3.5
|
12.1
|
0.3
|
|
NE2
|
X:HIS261
|
3.6
|
14.1
|
1.0
|
|
S4
|
X:WCC1003
|
3.6
|
7.8
|
0.7
|
|
O
|
X:HOH2504
|
3.7
|
14.3
|
1.0
|
|
CB
|
X:CYS295
|
3.7
|
10.1
|
0.3
|
|
H
|
X:CYS526
|
3.7
|
8.6
|
1.0
|
|
CB
|
X:CYS295
|
3.8
|
10.3
|
0.7
|
|
HB3
|
X:CYS526
|
3.9
|
11.5
|
0.1
|
|
HB2
|
X:CYS295
|
3.9
|
12.4
|
0.7
|
|
SG
|
X:CYS526
|
3.9
|
9.5
|
0.1
|
|
HA2
|
X:GLY475
|
3.9
|
9.0
|
1.0
|
|
FE3
|
X:WCC1003
|
4.0
|
7.0
|
0.7
|
|
HA3
|
X:GLY475
|
4.0
|
9.0
|
1.0
|
|
O1
|
X:CO21005
|
4.0
|
9.8
|
0.6
|
|
HB3
|
X:CYS526
|
4.0
|
9.6
|
0.9
|
|
H
|
X:CYS476
|
4.1
|
10.0
|
1.0
|
|
H
|
X:CYS295
|
4.2
|
9.6
|
0.7
|
|
H
|
X:CYS295
|
4.3
|
10.8
|
0.3
|
|
HB3
|
X:CYS295
|
4.3
|
12.1
|
0.3
|
|
N
|
X:CYS526
|
4.3
|
7.2
|
1.0
|
|
HD2
|
X:HIS261
|
4.3
|
17.9
|
1.0
|
|
CA
|
X:CYS526
|
4.4
|
7.8
|
0.1
|
|
CD2
|
X:HIS261
|
4.4
|
14.9
|
1.0
|
|
CA
|
X:GLY475
|
4.4
|
7.5
|
1.0
|
|
HB3
|
X:CYS295
|
4.5
|
12.4
|
0.7
|
|
CA
|
X:CYS526
|
4.5
|
7.9
|
0.9
|
|
CE1
|
X:HIS261
|
4.5
|
10.6
|
1.0
|
|
N
|
X:CYS295
|
4.5
|
8.0
|
0.7
|
|
HA
|
X:CYS526
|
4.5
|
9.4
|
0.1
|
|
HE1
|
X:HIS261
|
4.5
|
12.8
|
1.0
|
|
CA
|
X:CYS295
|
4.6
|
7.7
|
0.7
|
|
HA
|
X:CYS295
|
4.6
|
9.2
|
0.7
|
|
N
|
X:CYS295
|
4.6
|
9.0
|
0.3
|
|
CA
|
X:CYS295
|
4.7
|
8.5
|
0.3
|
|
SG
|
X:CYS476
|
4.7
|
10.2
|
0.9
|
|
NZ
|
X:LYS563
|
4.7
|
10.2
|
1.0
|
|
N
|
X:CYS476
|
4.8
|
8.3
|
1.0
|
|
HA
|
X:CYS295
|
4.8
|
10.2
|
0.3
|
|
O
|
X:HOH2230
|
4.8
|
9.3
|
0.3
|
|
HA
|
X:CYS526
|
4.8
|
9.5
|
0.9
|
|
O
|
X:HOH2505
|
4.9
|
10.7
|
1.0
|
|
SG
|
X:CYS476
|
4.9
|
11.2
|
0.1
|
|
S2
|
X:WCC1003
|
4.9
|
7.6
|
0.7
|
|
HB3
|
X:CYS294
|
5.0
|
11.7
|
1.0
|
|
Reference:
J.Fesseler,
J.H.Jeoung,
H.Dobbek.
How the [NIFE4 S4 ] Cluster of Co Dehydrogenase Activates CO2 and Nco(.) Angew.Chem.Int.Ed.Engl. 2015.
ISSN: ESSN 1521-3773
PubMed: 25926100
DOI: 10.1002/ANIE.201501778
Page generated: Mon Aug 5 12:37:02 2024
|
