Iron in PDB 2vxh: The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen
Enzymatic activity of The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen
All present enzymatic activity of The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen:
1.13.11.49;
Protein crystallography data
The structure of The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen, PDB code: 2vxh
was solved by
D.C.De Geus,
E.A.J.Thomassen,
P.L.Hagedoorn,
N.S.Pannu,
J.P.Abrahams,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.68 /
2.10
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
164.458,
169.335,
60.792,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.87 /
25.486
|
Iron Binding Sites:
The binding sites of Iron atom in the The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen
(pdb code 2vxh). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen, PDB code: 2vxh:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 2vxh
Go back to
Iron Binding Sites List in 2vxh
Iron binding site 1 out
of 6 in the The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1001
b:18.4
occ:1.00
|
FE
|
A:HEM1001
|
0.0
|
18.4
|
1.0
|
NE2
|
A:HIS170
|
2.1
|
21.5
|
1.0
|
NA
|
A:HEM1001
|
2.1
|
17.4
|
1.0
|
N
|
A:SCN1002
|
2.1
|
20.9
|
1.0
|
NC
|
A:HEM1001
|
2.1
|
17.1
|
1.0
|
ND
|
A:HEM1001
|
2.1
|
17.2
|
1.0
|
NB
|
A:HEM1001
|
2.1
|
18.0
|
1.0
|
CE1
|
A:HIS170
|
2.9
|
23.8
|
1.0
|
C1A
|
A:HEM1001
|
3.1
|
16.6
|
1.0
|
C4A
|
A:HEM1001
|
3.1
|
17.4
|
1.0
|
C4C
|
A:HEM1001
|
3.1
|
16.8
|
1.0
|
C1D
|
A:HEM1001
|
3.1
|
18.6
|
1.0
|
C1B
|
A:HEM1001
|
3.1
|
17.8
|
1.0
|
C1C
|
A:HEM1001
|
3.1
|
14.4
|
1.0
|
C4D
|
A:HEM1001
|
3.1
|
16.9
|
1.0
|
C4B
|
A:HEM1001
|
3.1
|
16.7
|
1.0
|
CD2
|
A:HIS170
|
3.2
|
22.2
|
1.0
|
C
|
A:SCN1002
|
3.3
|
19.8
|
1.0
|
CHD
|
A:HEM1001
|
3.4
|
16.5
|
1.0
|
CHA
|
A:HEM1001
|
3.4
|
15.6
|
1.0
|
CHB
|
A:HEM1001
|
3.5
|
18.4
|
1.0
|
CHC
|
A:HEM1001
|
3.5
|
15.8
|
1.0
|
ND1
|
A:HIS170
|
4.0
|
23.4
|
1.0
|
CG
|
A:HIS170
|
4.2
|
24.7
|
1.0
|
C2A
|
A:HEM1001
|
4.3
|
17.9
|
1.0
|
C3A
|
A:HEM1001
|
4.3
|
16.8
|
1.0
|
C3C
|
A:HEM1001
|
4.3
|
16.7
|
1.0
|
C2C
|
A:HEM1001
|
4.3
|
16.5
|
1.0
|
C2B
|
A:HEM1001
|
4.3
|
18.6
|
1.0
|
C3B
|
A:HEM1001
|
4.3
|
19.1
|
1.0
|
C2D
|
A:HEM1001
|
4.4
|
18.7
|
1.0
|
C3D
|
A:HEM1001
|
4.4
|
17.3
|
1.0
|
NE
|
A:ARG183
|
4.4
|
24.9
|
1.0
|
NH2
|
A:ARG183
|
4.5
|
25.0
|
1.0
|
CZ
|
A:ARG183
|
4.9
|
26.5
|
1.0
|
S
|
A:SCN1002
|
4.9
|
22.3
|
1.0
|
|
Iron binding site 2 out
of 6 in 2vxh
Go back to
Iron Binding Sites List in 2vxh
Iron binding site 2 out
of 6 in the The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1001
b:18.2
occ:1.00
|
FE
|
B:HEM1001
|
0.0
|
18.2
|
1.0
|
N
|
B:SCN1002
|
2.0
|
19.2
|
1.0
|
NE2
|
B:HIS170
|
2.1
|
22.4
|
1.0
|
NA
|
B:HEM1001
|
2.1
|
19.1
|
1.0
|
NC
|
B:HEM1001
|
2.1
|
19.4
|
1.0
|
ND
|
B:HEM1001
|
2.1
|
19.6
|
1.0
|
NB
|
B:HEM1001
|
2.1
|
18.8
|
1.0
|
CE1
|
B:HIS170
|
2.9
|
23.4
|
1.0
|
C1A
|
B:HEM1001
|
3.1
|
19.4
|
1.0
|
C4C
|
B:HEM1001
|
3.1
|
19.1
|
1.0
|
C1D
|
B:HEM1001
|
3.1
|
19.9
|
1.0
|
C4D
|
B:HEM1001
|
3.1
|
19.7
|
1.0
|
C4A
|
B:HEM1001
|
3.1
|
18.9
|
1.0
|
C1C
|
B:HEM1001
|
3.1
|
18.8
|
1.0
|
C1B
|
B:HEM1001
|
3.1
|
17.3
|
1.0
|
C4B
|
B:HEM1001
|
3.1
|
17.6
|
1.0
|
CD2
|
B:HIS170
|
3.2
|
22.9
|
1.0
|
C
|
B:SCN1002
|
3.2
|
18.8
|
1.0
|
CHD
|
B:HEM1001
|
3.4
|
18.9
|
1.0
|
CHA
|
B:HEM1001
|
3.4
|
19.5
|
1.0
|
CHB
|
B:HEM1001
|
3.5
|
17.9
|
1.0
|
CHC
|
B:HEM1001
|
3.5
|
18.9
|
1.0
|
ND1
|
B:HIS170
|
4.1
|
23.4
|
1.0
|
CG
|
B:HIS170
|
4.2
|
24.4
|
1.0
|
C3C
|
B:HEM1001
|
4.3
|
18.5
|
1.0
|
C2A
|
B:HEM1001
|
4.3
|
18.8
|
1.0
|
C2C
|
B:HEM1001
|
4.3
|
18.6
|
1.0
|
C3A
|
B:HEM1001
|
4.3
|
18.8
|
1.0
|
C2D
|
B:HEM1001
|
4.3
|
19.6
|
1.0
|
C2B
|
B:HEM1001
|
4.3
|
17.1
|
1.0
|
C3B
|
B:HEM1001
|
4.3
|
17.5
|
1.0
|
C3D
|
B:HEM1001
|
4.3
|
20.3
|
1.0
|
NH1
|
B:ARG183
|
4.6
|
27.4
|
1.0
|
S
|
B:SCN1002
|
4.9
|
20.6
|
1.0
|
CD
|
B:ARG183
|
4.9
|
23.0
|
1.0
|
|
Iron binding site 3 out
of 6 in 2vxh
Go back to
Iron Binding Sites List in 2vxh
Iron binding site 3 out
of 6 in the The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe1001
b:18.3
occ:1.00
|
FE
|
C:HEM1001
|
0.0
|
18.3
|
1.0
|
NA
|
C:HEM1001
|
2.1
|
19.7
|
1.0
|
NB
|
C:HEM1001
|
2.1
|
19.6
|
1.0
|
N
|
C:SCN1002
|
2.1
|
20.9
|
1.0
|
NC
|
C:HEM1001
|
2.1
|
18.5
|
1.0
|
NE2
|
C:HIS170
|
2.1
|
20.5
|
1.0
|
ND
|
C:HEM1001
|
2.1
|
19.1
|
1.0
|
CE1
|
C:HIS170
|
2.9
|
22.7
|
1.0
|
C1A
|
C:HEM1001
|
3.1
|
20.6
|
1.0
|
C4B
|
C:HEM1001
|
3.1
|
18.9
|
1.0
|
C4D
|
C:HEM1001
|
3.1
|
18.7
|
1.0
|
C1C
|
C:HEM1001
|
3.1
|
18.5
|
1.0
|
C4C
|
C:HEM1001
|
3.1
|
19.2
|
1.0
|
C1D
|
C:HEM1001
|
3.1
|
19.7
|
1.0
|
C1B
|
C:HEM1001
|
3.1
|
19.4
|
1.0
|
C4A
|
C:HEM1001
|
3.1
|
20.4
|
1.0
|
CD2
|
C:HIS170
|
3.2
|
23.6
|
1.0
|
C
|
C:SCN1002
|
3.2
|
20.7
|
1.0
|
CHA
|
C:HEM1001
|
3.4
|
20.0
|
1.0
|
CHC
|
C:HEM1001
|
3.4
|
18.2
|
1.0
|
CHD
|
C:HEM1001
|
3.5
|
17.9
|
1.0
|
CHB
|
C:HEM1001
|
3.5
|
19.1
|
1.0
|
ND1
|
C:HIS170
|
4.1
|
22.1
|
1.0
|
CG
|
C:HIS170
|
4.2
|
24.3
|
1.0
|
C3B
|
C:HEM1001
|
4.3
|
20.8
|
1.0
|
C2A
|
C:HEM1001
|
4.3
|
20.9
|
1.0
|
C2C
|
C:HEM1001
|
4.3
|
18.9
|
1.0
|
NE
|
C:ARG183
|
4.3
|
26.6
|
1.0
|
C3D
|
C:HEM1001
|
4.3
|
18.7
|
1.0
|
C3C
|
C:HEM1001
|
4.3
|
19.2
|
1.0
|
C2B
|
C:HEM1001
|
4.3
|
21.1
|
1.0
|
C3A
|
C:HEM1001
|
4.3
|
20.0
|
1.0
|
C2D
|
C:HEM1001
|
4.3
|
19.9
|
1.0
|
NH2
|
C:ARG183
|
4.5
|
26.8
|
1.0
|
CZ
|
C:ARG183
|
4.9
|
26.9
|
1.0
|
S
|
C:SCN1002
|
4.9
|
22.9
|
1.0
|
|
Iron binding site 4 out
of 6 in 2vxh
Go back to
Iron Binding Sites List in 2vxh
Iron binding site 4 out
of 6 in the The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe1001
b:25.1
occ:1.00
|
FE
|
D:HEM1001
|
0.0
|
25.1
|
1.0
|
N
|
D:SCN1002
|
2.0
|
18.7
|
1.0
|
NB
|
D:HEM1001
|
2.0
|
24.8
|
1.0
|
NC
|
D:HEM1001
|
2.1
|
24.0
|
1.0
|
NA
|
D:HEM1001
|
2.1
|
25.8
|
1.0
|
ND
|
D:HEM1001
|
2.1
|
23.6
|
1.0
|
NE2
|
D:HIS170
|
2.2
|
23.8
|
1.0
|
C4B
|
D:HEM1001
|
3.0
|
24.8
|
1.0
|
C1C
|
D:HEM1001
|
3.0
|
23.3
|
1.0
|
C1A
|
D:HEM1001
|
3.1
|
24.6
|
1.0
|
C1B
|
D:HEM1001
|
3.1
|
26.0
|
1.0
|
C4D
|
D:HEM1001
|
3.1
|
24.3
|
1.0
|
CE1
|
D:HIS170
|
3.1
|
23.9
|
1.0
|
C4A
|
D:HEM1001
|
3.1
|
26.3
|
1.0
|
C4C
|
D:HEM1001
|
3.1
|
22.9
|
1.0
|
C1D
|
D:HEM1001
|
3.1
|
24.5
|
1.0
|
C
|
D:SCN1002
|
3.1
|
18.6
|
1.0
|
CD2
|
D:HIS170
|
3.3
|
23.9
|
1.0
|
CHC
|
D:HEM1001
|
3.4
|
24.8
|
1.0
|
CHA
|
D:HEM1001
|
3.4
|
25.4
|
1.0
|
CHB
|
D:HEM1001
|
3.5
|
25.1
|
1.0
|
CHD
|
D:HEM1001
|
3.5
|
22.6
|
1.0
|
ND1
|
D:HIS170
|
4.2
|
24.6
|
1.0
|
C3B
|
D:HEM1001
|
4.3
|
25.4
|
1.0
|
C2B
|
D:HEM1001
|
4.3
|
25.3
|
1.0
|
C2C
|
D:HEM1001
|
4.3
|
22.8
|
1.0
|
C2A
|
D:HEM1001
|
4.3
|
26.2
|
1.0
|
C3C
|
D:HEM1001
|
4.3
|
22.2
|
1.0
|
C3D
|
D:HEM1001
|
4.3
|
24.1
|
1.0
|
C3A
|
D:HEM1001
|
4.3
|
25.6
|
1.0
|
C2D
|
D:HEM1001
|
4.4
|
23.0
|
1.0
|
CG
|
D:HIS170
|
4.4
|
25.2
|
1.0
|
NH1
|
D:ARG183
|
4.5
|
27.3
|
1.0
|
S
|
D:SCN1002
|
4.8
|
20.3
|
1.0
|
CD
|
D:ARG183
|
4.9
|
23.1
|
1.0
|
|
Iron binding site 5 out
of 6 in 2vxh
Go back to
Iron Binding Sites List in 2vxh
Iron binding site 5 out
of 6 in the The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe1001
b:17.6
occ:1.00
|
FE
|
E:HEM1001
|
0.0
|
17.6
|
1.0
|
N
|
E:SCN1002
|
1.9
|
17.1
|
1.0
|
NB
|
E:HEM1001
|
2.1
|
19.4
|
1.0
|
ND
|
E:HEM1001
|
2.1
|
16.2
|
1.0
|
NC
|
E:HEM1001
|
2.1
|
17.2
|
1.0
|
NA
|
E:HEM1001
|
2.1
|
18.2
|
1.0
|
NE2
|
E:HIS170
|
2.2
|
20.2
|
1.0
|
CE1
|
E:HIS170
|
3.0
|
22.8
|
1.0
|
C1B
|
E:HEM1001
|
3.1
|
20.5
|
1.0
|
C1D
|
E:HEM1001
|
3.1
|
17.7
|
1.0
|
C4B
|
E:HEM1001
|
3.1
|
19.1
|
1.0
|
C
|
E:SCN1002
|
3.1
|
16.8
|
1.0
|
C4D
|
E:HEM1001
|
3.1
|
17.3
|
1.0
|
C1C
|
E:HEM1001
|
3.1
|
16.8
|
1.0
|
C4C
|
E:HEM1001
|
3.1
|
17.7
|
1.0
|
C4A
|
E:HEM1001
|
3.1
|
19.3
|
1.0
|
C1A
|
E:HEM1001
|
3.2
|
17.8
|
1.0
|
CD2
|
E:HIS170
|
3.3
|
21.3
|
1.0
|
CHD
|
E:HEM1001
|
3.4
|
17.0
|
1.0
|
CHC
|
E:HEM1001
|
3.4
|
16.7
|
1.0
|
CHB
|
E:HEM1001
|
3.5
|
19.6
|
1.0
|
CHA
|
E:HEM1001
|
3.5
|
16.0
|
1.0
|
ND1
|
E:HIS170
|
4.1
|
22.4
|
1.0
|
C2B
|
E:HEM1001
|
4.3
|
22.1
|
1.0
|
C3B
|
E:HEM1001
|
4.3
|
20.7
|
1.0
|
NE
|
E:ARG183
|
4.3
|
24.7
|
1.0
|
CG
|
E:HIS170
|
4.3
|
23.3
|
1.0
|
C2D
|
E:HEM1001
|
4.3
|
16.9
|
1.0
|
C3D
|
E:HEM1001
|
4.3
|
15.9
|
1.0
|
C2C
|
E:HEM1001
|
4.3
|
17.4
|
1.0
|
C3C
|
E:HEM1001
|
4.3
|
17.5
|
1.0
|
C3A
|
E:HEM1001
|
4.4
|
19.6
|
1.0
|
C2A
|
E:HEM1001
|
4.4
|
18.7
|
1.0
|
NH2
|
E:ARG183
|
4.5
|
23.8
|
1.0
|
S
|
E:SCN1002
|
4.8
|
17.6
|
1.0
|
CZ
|
E:ARG183
|
4.8
|
25.6
|
1.0
|
|
Iron binding site 6 out
of 6 in 2vxh
Go back to
Iron Binding Sites List in 2vxh
Iron binding site 6 out
of 6 in the The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of The Crystal Structure of Chlorite Dismutase: A Detox Enzyme Producing Molecular Oxygen within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe1001
b:23.8
occ:1.00
|
FE
|
F:HEM1001
|
0.0
|
23.8
|
1.0
|
NB
|
F:HEM1001
|
2.0
|
25.2
|
1.0
|
N
|
F:SCN1002
|
2.1
|
22.9
|
1.0
|
NA
|
F:HEM1001
|
2.1
|
26.6
|
1.0
|
ND
|
F:HEM1001
|
2.1
|
25.2
|
1.0
|
NE2
|
F:HIS170
|
2.1
|
22.7
|
1.0
|
NC
|
F:HEM1001
|
2.1
|
24.5
|
1.0
|
CE1
|
F:HIS170
|
3.0
|
23.5
|
1.0
|
C1B
|
F:HEM1001
|
3.0
|
25.5
|
1.0
|
C4B
|
F:HEM1001
|
3.0
|
25.7
|
1.0
|
C4D
|
F:HEM1001
|
3.1
|
24.0
|
1.0
|
C4A
|
F:HEM1001
|
3.1
|
26.6
|
1.0
|
CD2
|
F:HIS170
|
3.1
|
23.3
|
1.0
|
C1D
|
F:HEM1001
|
3.1
|
24.2
|
1.0
|
C1A
|
F:HEM1001
|
3.1
|
26.1
|
1.0
|
C1C
|
F:HEM1001
|
3.1
|
24.5
|
1.0
|
C4C
|
F:HEM1001
|
3.1
|
24.9
|
1.0
|
C
|
F:SCN1002
|
3.2
|
21.6
|
1.0
|
CHB
|
F:HEM1001
|
3.4
|
25.4
|
1.0
|
CHC
|
F:HEM1001
|
3.4
|
25.2
|
1.0
|
CHA
|
F:HEM1001
|
3.5
|
24.6
|
1.0
|
CHD
|
F:HEM1001
|
3.5
|
24.0
|
1.0
|
ND1
|
F:HIS170
|
4.1
|
24.1
|
1.0
|
CG
|
F:HIS170
|
4.2
|
24.1
|
1.0
|
NH1
|
F:ARG183
|
4.2
|
27.5
|
1.0
|
C2B
|
F:HEM1001
|
4.2
|
25.6
|
1.0
|
C3B
|
F:HEM1001
|
4.3
|
25.6
|
1.0
|
C3D
|
F:HEM1001
|
4.3
|
24.2
|
1.0
|
C3A
|
F:HEM1001
|
4.3
|
26.6
|
1.0
|
C2D
|
F:HEM1001
|
4.3
|
25.1
|
1.0
|
C2A
|
F:HEM1001
|
4.3
|
26.5
|
1.0
|
C2C
|
F:HEM1001
|
4.4
|
25.2
|
1.0
|
C3C
|
F:HEM1001
|
4.4
|
25.7
|
1.0
|
CD
|
F:ARG183
|
4.9
|
23.5
|
1.0
|
S
|
F:SCN1002
|
4.9
|
22.6
|
1.0
|
|
Reference:
D.C.De Geus,
E.A.J.Thomassen,
P.L.Hagedoorn,
N.S.Pannu,
E.Van Duijn,
J.P.Abrahams.
Crystal Structure of Chlorite Dismutase, A Detoxifying Enzyme Producing Molecular Oxygen J.Mol.Biol. V. 387 192 2009.
ISSN: ISSN 0022-2836
PubMed: 19361444
DOI: 10.1016/J.JMB.2009.01.036
Page generated: Sun Aug 4 03:10:51 2024
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