Iron in PDB 4udy: Nco- Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True- Atomic Resolution
Enzymatic activity of Nco- Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True- Atomic Resolution
All present enzymatic activity of Nco- Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True- Atomic Resolution:
1.2.99.2;
Protein crystallography data
The structure of Nco- Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True- Atomic Resolution, PDB code: 4udy
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)
|
33.16 /
1.09
|
|
Space group
|
C 1 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
112.183,
75.008,
71.149,
90.00,
111.22,
90.00
|
|
R / Rfree (%)
|
13.63 /
16.48
|
Other elements in 4udy:
The structure of Nco- 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 Nco- Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True- Atomic Resolution
(pdb code 4udy). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 11 binding sites of Iron where determined in the
Nco- Bound to Cluster C of Ni,Fe-Co Dehydrogenase at True- Atomic Resolution, PDB code: 4udy:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 11 in 4udy
Go back to
Iron Binding Sites List in 4udy
Iron binding site 1 out
of 11 in the Nco- 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 Nco- 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
|
|
S3
|
X:SF41001
|
2.3
|
6.4
|
1.0
|
|
SG
|
X:CYS56
|
2.3
|
6.5
|
1.0
|
|
S4
|
X:SF41001
|
2.3
|
6.2
|
1.0
|
|
S2
|
X:SF41001
|
2.3
|
6.3
|
1.0
|
|
FE3
|
X:SF41001
|
2.7
|
5.9
|
1.0
|
|
FE2
|
X:SF41001
|
2.7
|
6.0
|
1.0
|
|
FE4
|
X:SF41001
|
2.7
|
6.1
|
1.0
|
|
HB2
|
X:CYS56
|
3.0
|
8.3
|
1.0
|
|
CB
|
X:CYS56
|
3.2
|
6.9
|
1.0
|
|
H
|
X:ILE69
|
3.3
|
7.7
|
1.0
|
|
HB
|
X:ILE69
|
3.5
|
8.0
|
1.0
|
|
HB3
|
X:CYS56
|
3.8
|
8.3
|
1.0
|
|
S1
|
X:SF41001
|
3.9
|
6.1
|
1.0
|
|
H
|
X:CYS70
|
3.9
|
7.7
|
1.0
|
|
HB3
|
X:CYS48
|
4.0
|
6.7
|
1.0
|
|
HA2
|
X:GLY54
|
4.0
|
8.6
|
1.0
|
|
N
|
X:ILE69
|
4.0
|
6.4
|
1.0
|
|
HA3
|
X:GLY54
|
4.2
|
8.6
|
1.0
|
|
H
|
X:CYS56
|
4.3
|
7.3
|
1.0
|
|
HA3
|
X:GLY68
|
4.3
|
8.6
|
1.0
|
|
HD13
|
X:ILE69
|
4.3
|
12.9
|
1.0
|
|
HB2
|
X:GLN53
|
4.4
|
8.3
|
1.0
|
|
CB
|
X:ILE69
|
4.4
|
6.6
|
1.0
|
|
CA
|
X:CYS56
|
4.4
|
6.1
|
1.0
|
|
CA
|
X:GLY54
|
4.4
|
7.2
|
1.0
|
|
N
|
X:CYS56
|
4.5
|
6.1
|
1.0
|
|
N
|
X:GLY54
|
4.5
|
7.2
|
1.0
|
|
H
|
X:GLY54
|
4.5
|
8.6
|
1.0
|
|
HA2
|
X:GLY68
|
4.6
|
8.6
|
1.0
|
|
O
|
X:CYS48
|
4.6
|
6.2
|
1.0
|
|
SG
|
X:CYS51
|
4.6
|
6.2
|
1.0
|
|
HG13
|
X:ILE69
|
4.7
|
8.7
|
1.0
|
|
SG
|
X:CYS48
|
4.7
|
6.0
|
1.0
|
|
N
|
X:CYS70
|
4.7
|
6.4
|
1.0
|
|
CA
|
X:ILE69
|
4.7
|
6.7
|
1.0
|
|
CB
|
X:CYS48
|
4.8
|
5.5
|
1.0
|
|
CA
|
X:GLY68
|
4.8
|
7.2
|
1.0
|
|
SG
|
X:CYS70
|
4.8
|
6.3
|
1.0
|
|
C
|
X:GLY68
|
4.8
|
6.3
|
1.0
|
|
HA
|
X:CYS56
|
4.9
|
7.4
|
1.0
|
|
CG1
|
X:ILE69
|
4.9
|
7.2
|
1.0
|
|
C
|
X:GLN53
|
5.0
|
6.7
|
1.0
|
|
HB3
|
X:CYS70
|
5.0
|
7.5
|
1.0
|
|
Iron binding site 2 out
of 11 in 4udy
Go back to
Iron Binding Sites List in 4udy
Iron binding site 2 out
of 11 in the Nco- 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 Nco- 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:5.9
occ:1.00
|
FE3
|
X:SF41001
|
0.0
|
5.9
|
1.0
|
|
S1
|
X:SF41001
|
2.3
|
6.1
|
1.0
|
|
SG
|
X:CYS48
|
2.3
|
6.0
|
1.0
|
|
S4
|
X:SF41001
|
2.3
|
6.2
|
1.0
|
|
S2
|
X:SF41001
|
2.3
|
6.3
|
1.0
|
|
FE1
|
X:SF41001
|
2.7
|
6.1
|
1.0
|
|
FE2
|
X:SF41001
|
2.7
|
6.0
|
1.0
|
|
FE4
|
X:SF41001
|
2.7
|
6.1
|
1.0
|
|
HB3
|
X:CYS48
|
3.0
|
6.7
|
1.0
|
|
HH22
|
X:ARG80
|
3.2
|
8.3
|
1.0
|
|
CB
|
X:CYS48
|
3.2
|
5.5
|
1.0
|
|
H
|
X:HIS50
|
3.3
|
6.7
|
1.0
|
|
HB2
|
X:HIS50
|
3.4
|
7.1
|
1.0
|
|
HH21
|
X:ARG80
|
3.6
|
8.3
|
1.0
|
|
NH2
|
X:ARG80
|
3.6
|
7.0
|
1.0
|
|
HB2
|
X:CYS48
|
3.9
|
6.7
|
1.0
|
|
S3
|
X:SF41001
|
3.9
|
6.4
|
1.0
|
|
HB2
|
X:CYS56
|
4.0
|
8.3
|
1.0
|
|
N
|
X:HIS50
|
4.0
|
5.6
|
1.0
|
|
H
|
X:CYS51
|
4.0
|
7.2
|
1.0
|
|
C
|
X:CYS48
|
4.2
|
5.4
|
1.0
|
|
O
|
X:CYS48
|
4.2
|
6.2
|
1.0
|
|
CB
|
X:HIS50
|
4.3
|
5.9
|
1.0
|
|
CA
|
X:CYS48
|
4.3
|
5.5
|
1.0
|
|
CA
|
X:HIS50
|
4.5
|
5.7
|
1.0
|
|
N
|
X:CYS51
|
4.5
|
6.0
|
1.0
|
|
N
|
X:ARG49
|
4.6
|
5.4
|
1.0
|
|
SG
|
X:CYS56
|
4.7
|
6.5
|
1.0
|
|
HG12
|
X:ILE77
|
4.7
|
9.1
|
1.0
|
|
C
|
X:HIS50
|
4.7
|
5.8
|
1.0
|
|
CB
|
X:CYS56
|
4.7
|
6.9
|
1.0
|
|
CZ
|
X:ARG80
|
4.8
|
6.2
|
1.0
|
|
HA
|
X:CYS48
|
4.8
|
6.6
|
1.0
|
|
HA
|
X:ARG49
|
4.9
|
7.2
|
1.0
|
|
SG
|
X:CYS70
|
4.9
|
6.3
|
1.0
|
|
HB1
|
X:ALA72
|
4.9
|
10.9
|
1.0
|
|
H
|
X:ARG49
|
4.9
|
6.5
|
1.0
|
|
SG
|
X:CYS51
|
4.9
|
6.2
|
1.0
|
|
HB3
|
X:HIS50
|
4.9
|
7.1
|
1.0
|
|
C
|
X:ARG49
|
4.9
|
5.3
|
1.0
|
|
Iron binding site 3 out
of 11 in 4udy
Go back to
Iron Binding Sites List in 4udy
Iron binding site 3 out
of 11 in the Nco- 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 Nco- 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
|
|
SG
|
X:CYS51
|
2.3
|
6.2
|
1.0
|
|
S4
|
X:SF41001
|
2.3
|
6.2
|
1.0
|
|
S1
|
X:SF41001
|
2.3
|
6.1
|
1.0
|
|
S3
|
X:SF41001
|
2.3
|
6.4
|
1.0
|
|
FE1
|
X:SF41001
|
2.7
|
6.1
|
1.0
|
|
FE3
|
X:SF41001
|
2.7
|
5.9
|
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
|
7.1
|
1.0
|
|
CB
|
X:CYS51
|
3.3
|
6.0
|
1.0
|
|
N
|
X:CYS51
|
3.6
|
6.0
|
1.0
|
|
HB2
|
X:GLN53
|
3.7
|
8.3
|
1.0
|
|
HG3
|
X:MET199
|
3.7
|
7.6
|
1.0
|
|
CA
|
X:CYS51
|
3.9
|
5.8
|
1.0
|
|
S2
|
X:SF41001
|
3.9
|
6.3
|
1.0
|
|
H
|
X:GLY54
|
4.0
|
8.6
|
1.0
|
|
O
|
X:HOH2161
|
4.0
|
18.0
|
1.0
|
|
HB2
|
X:MET199
|
4.2
|
7.5
|
1.0
|
|
HB2
|
X:CYS51
|
4.2
|
7.1
|
1.0
|
|
O
|
X:CYS51
|
4.2
|
6.5
|
1.0
|
|
H
|
X:GLN53
|
4.2
|
7.7
|
1.0
|
|
C
|
X:CYS51
|
4.3
|
6.0
|
1.0
|
|
C
|
X:HIS50
|
4.3
|
5.8
|
1.0
|
|
HG2
|
X:MET199
|
4.4
|
7.6
|
1.0
|
|
N
|
X:GLY54
|
4.4
|
7.2
|
1.0
|
|
CG
|
X:MET199
|
4.4
|
6.4
|
1.0
|
|
HB3
|
X:CYS70
|
4.5
|
7.5
|
1.0
|
|
H
|
X:HIS50
|
4.5
|
6.7
|
1.0
|
|
HB2
|
X:HIS50
|
4.5
|
7.1
|
1.0
|
|
HA3
|
X:GLY54
|
4.6
|
8.6
|
1.0
|
|
CB
|
X:GLN53
|
4.6
|
7.0
|
1.0
|
|
HA
|
X:CYS51
|
4.8
|
6.9
|
1.0
|
|
N
|
X:HIS50
|
4.8
|
5.6
|
1.0
|
|
SG
|
X:CYS48
|
4.8
|
6.0
|
1.0
|
|
CB
|
X:MET199
|
4.8
|
6.3
|
1.0
|
|
SG
|
X:CYS70
|
4.8
|
6.3
|
1.0
|
|
SG
|
X:CYS56
|
4.8
|
6.5
|
1.0
|
|
N
|
X:GLN53
|
4.8
|
6.4
|
1.0
|
|
H
|
X:CYS70
|
4.9
|
7.7
|
1.0
|
|
CA
|
X:HIS50
|
4.9
|
5.7
|
1.0
|
|
CA
|
X:GLY54
|
5.0
|
7.2
|
1.0
|
|
O
|
X:HIS50
|
5.0
|
7.3
|
1.0
|
|
HB
|
X:ILE69
|
5.0
|
8.0
|
1.0
|
|
C
|
X:GLN53
|
5.0
|
6.7
|
1.0
|
|
HH22
|
X:ARG80
|
5.0
|
8.3
|
1.0
|
|
Iron binding site 4 out
of 11 in 4udy
Go back to
Iron Binding Sites List in 4udy
Iron binding site 4 out
of 11 in the Nco- 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 Nco- 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
|
|
S2
|
X:SF41001
|
2.3
|
6.3
|
1.0
|
|
SG
|
X:CYS70
|
2.3
|
6.3
|
1.0
|
|
S1
|
X:SF41001
|
2.3
|
6.1
|
1.0
|
|
S3
|
X:SF41001
|
2.3
|
6.4
|
1.0
|
|
FE3
|
X:SF41001
|
2.7
|
5.9
|
1.0
|
|
FE1
|
X:SF41001
|
2.7
|
6.1
|
1.0
|
|
FE2
|
X:SF41001
|
2.8
|
6.0
|
1.0
|
|
H
|
X:CYS70
|
3.1
|
7.7
|
1.0
|
|
HB3
|
X:CYS70
|
3.1
|
7.5
|
1.0
|
|
HH22
|
X:ARG80
|
3.3
|
8.3
|
1.0
|
|
CB
|
X:CYS70
|
3.3
|
6.2
|
1.0
|
|
N
|
X:CYS70
|
3.8
|
6.4
|
1.0
|
|
HB1
|
X:ALA72
|
3.9
|
10.9
|
1.0
|
|
HB3
|
X:ALA72
|
3.9
|
10.9
|
1.0
|
|
S4
|
X:SF41001
|
4.0
|
6.2
|
1.0
|
|
HG2
|
X:MET199
|
4.0
|
7.6
|
1.0
|
|
HB2
|
X:CYS70
|
4.1
|
7.5
|
1.0
|
|
NH2
|
X:ARG80
|
4.2
|
7.0
|
1.0
|
|
O
|
X:HOH2212
|
4.2
|
6.7
|
1.0
|
|
CA
|
X:CYS70
|
4.2
|
6.4
|
1.0
|
|
HG3
|
X:MET199
|
4.3
|
7.6
|
1.0
|
|
H
|
X:ALA72
|
4.3
|
8.4
|
1.0
|
|
H
|
X:ILE69
|
4.3
|
7.7
|
1.0
|
|
HA3
|
X:GLY68
|
4.4
|
8.6
|
1.0
|
|
CB
|
X:ALA72
|
4.4
|
7.3
|
1.0
|
|
HH21
|
X:ARG80
|
4.5
|
8.3
|
1.0
|
|
O
|
X:HOH2161
|
4.5
|
18.0
|
1.0
|
|
HH12
|
X:ARG80
|
4.5
|
8.4
|
1.0
|
|
CG
|
X:MET199
|
4.6
|
6.4
|
1.0
|
|
HB
|
X:ILE69
|
4.6
|
8.0
|
1.0
|
|
N
|
X:ILE69
|
4.6
|
6.4
|
1.0
|
|
SG
|
X:CYS51
|
4.7
|
6.2
|
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
|
7.7
|
1.0
|
|
C
|
X:ILE69
|
5.0
|
6.7
|
1.0
|
|
Iron binding site 5 out
of 11 in 4udy
Go back to
Iron Binding Sites List in 4udy
Iron binding site 5 out
of 11 in the Nco- 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 Nco- 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:7.0
occ:1.00
|
FE1
|
X:FES1002
|
0.0
|
7.0
|
1.0
|
|
S2
|
X:FES1002
|
2.3
|
7.0
|
1.0
|
|
SG
|
X:CYS39
|
2.3
|
7.9
|
1.0
|
|
S1
|
X:FES1002
|
2.3
|
7.3
|
1.0
|
|
FE2
|
X:FES1002
|
2.7
|
6.7
|
1.0
|
|
CB
|
X:CYS39
|
3.2
|
7.8
|
1.0
|
|
HB3
|
X:CYS39
|
3.2
|
9.3
|
1.0
|
|
HB2
|
X:CYS39
|
3.2
|
9.3
|
1.0
|
|
HB2
|
X:PHE41
|
3.4
|
8.7
|
1.0
|
|
H
|
X:GLY42
|
3.5
|
9.7
|
1.0
|
|
HD2
|
X:PHE41
|
4.0
|
10.8
|
1.0
|
|
N
|
X:GLY42
|
4.1
|
8.1
|
1.0
|
|
CB
|
X:PHE41
|
4.3
|
7.3
|
1.0
|
|
HA3
|
X:GLY42
|
4.4
|
9.9
|
1.0
|
|
HB2
|
X:CYS47
|
4.4
|
7.8
|
1.0
|
|
H
|
X:PHE41
|
4.6
|
9.1
|
1.0
|
|
CA
|
X:CYS39
|
4.6
|
7.9
|
1.0
|
|
HB3
|
X:PHE41
|
4.7
|
8.7
|
1.0
|
|
CA
|
X:GLY42
|
4.8
|
8.2
|
1.0
|
|
CD2
|
X:PHE41
|
4.8
|
9.0
|
1.0
|
|
SG
|
X:CYS47
|
4.8
|
6.9
|
1.0
|
|
HA
|
X:CYS39
|
4.9
|
9.5
|
1.0
|
|
HA2
|
X:GLY42
|
5.0
|
9.9
|
1.0
|
|
C
|
X:PHE41
|
5.0
|
7.0
|
1.0
|
|
Iron binding site 6 out
of 11 in 4udy
Go back to
Iron Binding Sites List in 4udy
Iron binding site 6 out
of 11 in the Nco- 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 Nco- 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
|
6.9
|
1.0
|
|
S1
|
X:FES1002
|
2.3
|
7.3
|
1.0
|
|
S2
|
X:FES1002
|
2.3
|
7.0
|
1.0
|
|
FE1
|
X:FES1002
|
2.7
|
7.0
|
1.0
|
|
HB2
|
X:CYS47
|
3.0
|
7.8
|
1.0
|
|
CB
|
X:CYS47
|
3.2
|
6.5
|
1.0
|
|
HB3
|
X:CYS47
|
3.4
|
7.8
|
1.0
|
|
O
|
X:HOH2145
|
3.6
|
8.5
|
1.0
|
|
HB2
|
X:PHE41
|
4.1
|
8.7
|
1.0
|
|
HD2
|
X:ARG49
|
4.2
|
13.6
|
1.0
|
|
HB2
|
X:PRO55
|
4.5
|
9.4
|
1.0
|
|
CA
|
X:CYS47
|
4.6
|
5.9
|
1.0
|
|
HA
|
X:CYS47
|
4.7
|
7.1
|
1.0
|
|
HB3
|
X:PHE41
|
4.7
|
8.7
|
1.0
|
|
SG
|
X:CYS39
|
4.7
|
7.9
|
1.0
|
|
H
|
X:GLY42
|
4.7
|
9.7
|
1.0
|
|
HG3
|
X:ARG49
|
4.8
|
9.6
|
1.0
|
|
HB3
|
X:ARG57
|
4.9
|
10.0
|
1.0
|
|
CB
|
X:PHE41
|
4.9
|
7.3
|
1.0
|
|
Iron binding site 7 out
of 11 in 4udy
Go back to
Iron Binding Sites List in 4udy
Iron binding site 7 out
of 11 in the Nco- 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 Nco- 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:7.2
occ:0.68
|
FE4
|
X:WCC1003
|
0.0
|
7.2
|
0.7
|
|
S1
|
X:WCC1003
|
2.3
|
8.2
|
0.8
|
|
S2
|
X:WCC1003
|
2.3
|
7.2
|
0.7
|
|
SG
|
X:CYS476
|
2.3
|
11.4
|
1.0
|
|
S3
|
X:WCC1003
|
2.3
|
9.2
|
0.8
|
|
FE1
|
X:WCC1003
|
2.7
|
7.0
|
0.7
|
|
FE3
|
X:WCC1003
|
2.7
|
6.8
|
0.7
|
|
HB2
|
X:CYS476
|
3.0
|
12.6
|
1.0
|
|
FE
|
X:FE21004
|
3.2
|
21.2
|
0.3
|
|
CB
|
X:CYS476
|
3.3
|
10.5
|
1.0
|
|
H
|
X:CYS476
|
3.5
|
9.6
|
1.0
|
|
SG
|
X:CYS294
|
3.5
|
14.0
|
0.2
|
|
HA
|
X:CYS446
|
3.5
|
9.5
|
1.0
|
|
NI
|
X:WCC1003
|
3.6
|
8.0
|
0.6
|
|
HB2
|
X:SER312
|
3.7
|
11.1
|
1.0
|
|
FE
|
X:FE21004
|
3.9
|
8.5
|
0.7
|
|
O
|
X:HOH2495
|
3.9
|
13.5
|
1.0
|
|
S4
|
X:WCC1003
|
4.0
|
8.4
|
0.7
|
|
HB3
|
X:CYS476
|
4.0
|
12.6
|
1.0
|
|
N
|
X:CYS476
|
4.0
|
8.0
|
1.0
|
|
CA
|
X:CYS476
|
4.3
|
8.6
|
1.0
|
|
HA
|
X:CYS294
|
4.3
|
10.2
|
0.8
|
|
SG
|
X:CYS294
|
4.4
|
9.0
|
0.8
|
|
HA
|
X:CYS294
|
4.4
|
10.7
|
0.2
|
|
CA
|
X:CYS446
|
4.4
|
7.9
|
1.0
|
|
CB
|
X:SER312
|
4.5
|
9.3
|
1.0
|
|
HB3
|
X:CYS446
|
4.5
|
10.9
|
1.0
|
|
HB3
|
X:CYS333
|
4.5
|
10.7
|
1.0
|
|
HB3
|
X:CYS294
|
4.5
|
12.4
|
0.8
|
|
HA
|
X:SER312
|
4.6
|
9.7
|
1.0
|
|
OG
|
X:SER312
|
4.6
|
10.3
|
1.0
|
|
HG
|
X:SER312
|
4.6
|
15.4
|
1.0
|
|
SG
|
X:CYS526
|
4.6
|
10.5
|
1.0
|
|
HA
|
X:CYS476
|
4.7
|
10.3
|
1.0
|
|
H
|
X:SER312
|
4.8
|
10.5
|
1.0
|
|
CB
|
X:CYS446
|
4.8
|
9.1
|
1.0
|
|
SG
|
X:CYS446
|
4.8
|
9.8
|
1.0
|
|
SG
|
X:CYS333
|
4.8
|
10.0
|
1.0
|
|
H
|
X:CYS295
|
4.9
|
8.9
|
0.7
|
|
CB
|
X:CYS294
|
4.9
|
10.4
|
0.8
|
|
HA3
|
X:GLY475
|
4.9
|
9.0
|
1.0
|
|
O
|
X:GLY445
|
4.9
|
10.0
|
1.0
|
|
SG
|
X:CYS295
|
4.9
|
9.1
|
0.7
|
|
N
|
X:CYS446
|
4.9
|
8.0
|
1.0
|
|
SG
|
X:CYS295
|
4.9
|
12.1
|
0.3
|
|
C
|
X:GLY445
|
5.0
|
7.8
|
1.0
|
|
C
|
X:0NM1005
|
5.0
|
8.4
|
0.6
|
|
C
|
X:GLY475
|
5.0
|
6.9
|
1.0
|
|
Iron binding site 8 out
of 11 in 4udy
Go back to
Iron Binding Sites List in 4udy
Iron binding site 8 out
of 11 in the Nco- 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 Nco- 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
|
FE3
|
X:WCC1003
|
0.0
|
6.8
|
0.7
|
|
S4
|
X:WCC1003
|
2.3
|
8.4
|
0.7
|
|
S1
|
X:WCC1003
|
2.3
|
8.2
|
0.8
|
|
SG
|
X:CYS446
|
2.4
|
9.8
|
1.0
|
|
S2
|
X:WCC1003
|
2.4
|
7.2
|
0.7
|
|
FE1
|
X:WCC1003
|
2.6
|
7.0
|
0.7
|
|
FE4
|
X:WCC1003
|
2.7
|
7.2
|
0.7
|
|
NI
|
X:WCC1003
|
2.8
|
8.0
|
0.6
|
|
HA
|
X:CYS446
|
3.1
|
9.5
|
1.0
|
|
CB
|
X:CYS446
|
3.1
|
9.1
|
1.0
|
|
HB3
|
X:CYS446
|
3.2
|
10.9
|
1.0
|
|
CA
|
X:CYS446
|
3.4
|
7.9
|
1.0
|
|
N
|
X:CYS446
|
3.6
|
8.0
|
1.0
|
|
H
|
X:CYS446
|
3.8
|
9.6
|
1.0
|
|
HE1
|
X:MET560
|
3.8
|
13.3
|
1.0
|
|
HA2
|
X:GLY445
|
3.9
|
9.1
|
1.0
|
|
HB2
|
X:HIS561
|
3.9
|
7.3
|
1.0
|
|
S3
|
X:WCC1003
|
4.0
|
9.2
|
0.8
|
|
FE
|
X:FE21004
|
4.0
|
21.2
|
0.3
|
|
HB2
|
X:CYS446
|
4.1
|
10.9
|
1.0
|
|
C
|
X:GLY445
|
4.1
|
7.8
|
1.0
|
|
O
|
X:HOH2677
|
4.1
|
15.4
|
0.3
|
|
HB2
|
X:CYS476
|
4.2
|
12.6
|
1.0
|
|
C
|
X:0NM1005
|
4.2
|
8.4
|
0.6
|
|
HB3
|
X:HIS561
|
4.2
|
7.3
|
1.0
|
|
H
|
X:HIS561
|
4.3
|
8.0
|
1.0
|
|
HB3
|
X:ALA564
|
4.4
|
14.5
|
1.0
|
|
SG
|
X:CYS333
|
4.4
|
10.0
|
1.0
|
|
CA
|
X:GLY445
|
4.5
|
7.5
|
1.0
|
|
CB
|
X:HIS561
|
4.5
|
6.0
|
1.0
|
|
HE2
|
X:MET560
|
4.6
|
13.3
|
1.0
|
|
FE
|
X:FE21004
|
4.6
|
8.5
|
0.7
|
|
HB3
|
X:MET560
|
4.6
|
8.9
|
1.0
|
|
CE
|
X:MET560
|
4.6
|
8.8
|
1.0
|
|
O
|
X:GLY445
|
4.6
|
10.0
|
1.0
|
|
SG
|
X:CYS526
|
4.7
|
10.5
|
1.0
|
|
H
|
X:CYS476
|
4.7
|
9.6
|
1.0
|
|
SG
|
X:CYS476
|
4.8
|
11.4
|
1.0
|
|
HG
|
X:SER312
|
4.9
|
15.4
|
1.0
|
|
C
|
X:CYS446
|
4.9
|
7.3
|
1.0
|
|
HA3
|
X:GLY445
|
4.9
|
9.1
|
1.0
|
|
CB
|
X:CYS476
|
4.9
|
10.5
|
1.0
|
|
O
|
X:0NM1005
|
5.0
|
7.7
|
0.6
|
|
Iron binding site 9 out
of 11 in 4udy
Go back to
Iron Binding Sites List in 4udy
Iron binding site 9 out
of 11 in the Nco- 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 Nco- 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:0.70
|
FE1
|
X:WCC1003
|
0.0
|
7.0
|
0.7
|
|
SG
|
X:CYS333
|
2.2
|
10.0
|
1.0
|
|
S3
|
X:WCC1003
|
2.3
|
9.2
|
0.8
|
|
S2
|
X:WCC1003
|
2.4
|
7.2
|
0.7
|
|
S4
|
X:WCC1003
|
2.4
|
8.4
|
0.7
|
|
FE3
|
X:WCC1003
|
2.6
|
6.8
|
0.7
|
|
FE4
|
X:WCC1003
|
2.7
|
7.2
|
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
|
8.5
|
0.7
|
|
HB2
|
X:CYS333
|
3.3
|
10.7
|
1.0
|
|
NI
|
X:WCC1003
|
3.4
|
8.0
|
0.6
|
|
HZ2
|
X:LYS563
|
3.4
|
16.3
|
1.0
|
|
FE
|
X:FE21004
|
3.5
|
21.2
|
0.3
|
|
HE1
|
X:HIS261
|
3.7
|
11.6
|
1.0
|
|
S1
|
X:WCC1003
|
3.7
|
8.2
|
0.8
|
|
SG
|
X:CYS294
|
3.8
|
14.0
|
0.2
|
|
C
|
X:0NM1005
|
4.0
|
8.4
|
0.6
|
|
HZ3
|
X:LYS563
|
4.0
|
16.3
|
1.0
|
|
O
|
X:0NM1005
|
4.0
|
7.7
|
0.6
|
|
NZ
|
X:LYS563
|
4.1
|
10.8
|
1.0
|
|
NE2
|
X:HIS261
|
4.1
|
12.5
|
1.0
|
|
HB2
|
X:HIS561
|
4.2
|
7.3
|
1.0
|
|
CE1
|
X:HIS261
|
4.2
|
9.7
|
1.0
|
|
HE2
|
X:MET560
|
4.2
|
13.3
|
1.0
|
|
HE3
|
X:LYS563
|
4.3
|
10.6
|
1.0
|
|
HE1
|
X:MET560
|
4.4
|
13.3
|
1.0
|
|
CA
|
X:CYS333
|
4.5
|
7.8
|
1.0
|
|
HA
|
X:CYS333
|
4.5
|
9.4
|
1.0
|
|
SG
|
X:CYS446
|
4.6
|
9.8
|
1.0
|
|
O
|
X:HOH2505
|
4.6
|
11.4
|
1.0
|
|
CE
|
X:LYS563
|
4.8
|
8.8
|
1.0
|
|
CE
|
X:MET560
|
4.8
|
8.8
|
1.0
|
|
HB3
|
X:CYS294
|
4.8
|
12.4
|
0.8
|
|
HB3
|
X:HIS561
|
4.8
|
7.3
|
1.0
|
|
HZ1
|
X:LYS563
|
4.8
|
16.3
|
1.0
|
|
HD2
|
X:HIS561
|
4.8
|
8.3
|
1.0
|
|
SG
|
X:CYS476
|
4.9
|
11.4
|
1.0
|
|
CB
|
X:HIS561
|
4.9
|
6.0
|
1.0
|
|
HB3
|
X:CYS446
|
4.9
|
10.9
|
1.0
|
|
SG
|
X:CYS294
|
4.9
|
9.0
|
0.8
|
|
Iron binding site 10 out
of 11 in 4udy
Go back to
Iron Binding Sites List in 4udy
Iron binding site 10 out
of 11 in the Nco- 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 Nco- 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:21.2
occ:0.35
|
FE
|
X:FE21004
|
0.0
|
21.2
|
0.3
|
|
FE
|
X:FE21004
|
1.5
|
8.5
|
0.7
|
|
NI
|
X:WCC1003
|
2.1
|
8.0
|
0.6
|
|
SG
|
X:CYS295
|
2.2
|
9.1
|
0.7
|
|
SG
|
X:CYS526
|
2.3
|
10.5
|
1.0
|
|
SG
|
X:CYS295
|
2.5
|
12.1
|
0.3
|
|
S3
|
X:WCC1003
|
2.5
|
9.2
|
0.8
|
|
O
|
X:0NM1005
|
2.7
|
7.7
|
0.6
|
|
C
|
X:0NM1005
|
2.7
|
8.4
|
0.6
|
|
S1
|
X:WCC1003
|
3.0
|
8.2
|
0.8
|
|
HB2
|
X:CYS526
|
3.2
|
11.0
|
1.0
|
|
FE4
|
X:WCC1003
|
3.2
|
7.2
|
0.7
|
|
CB
|
X:CYS526
|
3.4
|
9.1
|
1.0
|
|
HB2
|
X:CYS295
|
3.4
|
10.4
|
0.3
|
|
FE1
|
X:WCC1003
|
3.5
|
7.0
|
0.7
|
|
S4
|
X:WCC1003
|
3.6
|
8.4
|
0.7
|
|
NE2
|
X:HIS261
|
3.6
|
12.5
|
1.0
|
|
O
|
X:HOH2495
|
3.6
|
13.5
|
1.0
|
|
CB
|
X:CYS295
|
3.6
|
8.6
|
0.3
|
|
H
|
X:CYS526
|
3.7
|
8.7
|
1.0
|
|
CB
|
X:CYS295
|
3.7
|
10.1
|
0.7
|
|
HB2
|
X:CYS295
|
3.9
|
12.1
|
0.7
|
|
HA2
|
X:GLY475
|
3.9
|
9.0
|
1.0
|
|
HA3
|
X:GLY475
|
3.9
|
9.0
|
1.0
|
|
HB3
|
X:CYS526
|
4.0
|
11.0
|
1.0
|
|
N
|
X:0NM1005
|
4.0
|
7.9
|
0.6
|
|
FE3
|
X:WCC1003
|
4.0
|
6.8
|
0.7
|
|
HZ3
|
X:LYS563
|
4.1
|
16.3
|
1.0
|
|
H
|
X:CYS295
|
4.2
|
8.9
|
0.7
|
|
H
|
X:CYS476
|
4.2
|
9.6
|
1.0
|
|
N
|
X:CYS526
|
4.3
|
7.2
|
1.0
|
|
HB3
|
X:CYS295
|
4.3
|
10.4
|
0.3
|
|
HD2
|
X:HIS261
|
4.3
|
15.3
|
1.0
|
|
CD2
|
X:HIS261
|
4.4
|
12.8
|
1.0
|
|
CA
|
X:GLY475
|
4.4
|
7.5
|
1.0
|
|
HB3
|
X:CYS295
|
4.4
|
12.1
|
0.7
|
|
SG
|
X:CYS294
|
4.4
|
14.0
|
0.2
|
|
CA
|
X:CYS526
|
4.4
|
7.3
|
1.0
|
|
N
|
X:CYS295
|
4.5
|
7.4
|
0.7
|
|
HA
|
X:CYS295
|
4.5
|
9.3
|
0.7
|
|
H
|
X:CYS295
|
4.5
|
11.2
|
0.3
|
|
CA
|
X:CYS295
|
4.5
|
7.8
|
0.7
|
|
CE1
|
X:HIS261
|
4.6
|
9.7
|
1.0
|
|
HZ2
|
X:LYS563
|
4.6
|
16.3
|
1.0
|
|
CA
|
X:CYS295
|
4.7
|
7.4
|
0.3
|
|
HE1
|
X:HIS261
|
4.7
|
11.6
|
1.0
|
|
N
|
X:CYS295
|
4.7
|
9.3
|
0.3
|
|
SG
|
X:CYS476
|
4.7
|
11.4
|
1.0
|
|
O
|
X:HOH2496
|
4.8
|
10.3
|
1.0
|
|
HA
|
X:CYS295
|
4.8
|
8.9
|
0.3
|
|
NZ
|
X:LYS563
|
4.8
|
10.8
|
1.0
|
|
HA
|
X:CYS526
|
4.8
|
8.8
|
1.0
|
|
N
|
X:CYS476
|
4.8
|
8.0
|
1.0
|
|
O
|
X:HOH2242
|
4.9
|
11.3
|
0.7
|
|
O
|
X:HOH2677
|
4.9
|
15.4
|
0.3
|
|
S2
|
X:WCC1003
|
5.0
|
7.2
|
0.7
|
|
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
|
