Iron in PDB 3nn2: Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii in Complex with Cyanide
Enzymatic activity of Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii in Complex with Cyanide
All present enzymatic activity of Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii in Complex with Cyanide:
1.13.11.49;
Protein crystallography data
The structure of Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii in Complex with Cyanide, PDB code: 3nn2
was solved by
J.Kostan,
B.Sjoeblom,
F.Maixner,
G.Mlynek,
P.G.Furtmueller,
C.Obinger,
M.Wagner,
H.Daims,
K.Djinovic-Carugo,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
32.84 /
1.94
|
Space group
|
P 32 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
145.490,
145.490,
136.011,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
17.7 /
21.2
|
Iron Binding Sites:
The binding sites of Iron atom in the Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii in Complex with Cyanide
(pdb code 3nn2). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the
Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii in Complex with Cyanide, PDB code: 3nn2:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
Iron binding site 1 out
of 5 in 3nn2
Go back to
Iron Binding Sites List in 3nn2
Iron binding site 1 out
of 5 in the Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii in Complex with Cyanide
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii in Complex with Cyanide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe239
b:25.0
occ:1.00
|
FE
|
A:HEM239
|
0.0
|
25.0
|
1.0
|
C
|
A:CYN245
|
1.9
|
30.0
|
1.0
|
NB
|
A:HEM239
|
2.0
|
26.0
|
1.0
|
NA
|
A:HEM239
|
2.0
|
24.7
|
1.0
|
NC
|
A:HEM239
|
2.0
|
22.1
|
1.0
|
ND
|
A:HEM239
|
2.1
|
23.7
|
1.0
|
NE2
|
A:HIS160
|
2.2
|
25.3
|
1.0
|
C4B
|
A:HEM239
|
3.0
|
27.1
|
1.0
|
N
|
A:CYN245
|
3.0
|
25.4
|
1.0
|
C1C
|
A:HEM239
|
3.0
|
24.4
|
1.0
|
C1A
|
A:HEM239
|
3.0
|
23.1
|
1.0
|
C1B
|
A:HEM239
|
3.0
|
26.8
|
1.0
|
C4A
|
A:HEM239
|
3.0
|
25.7
|
1.0
|
C4D
|
A:HEM239
|
3.1
|
21.0
|
1.0
|
C4C
|
A:HEM239
|
3.1
|
23.3
|
1.0
|
CE1
|
A:HIS160
|
3.1
|
26.6
|
1.0
|
C1D
|
A:HEM239
|
3.1
|
22.0
|
1.0
|
CD2
|
A:HIS160
|
3.2
|
25.3
|
1.0
|
CHC
|
A:HEM239
|
3.4
|
23.9
|
1.0
|
CHA
|
A:HEM239
|
3.4
|
23.4
|
1.0
|
CHB
|
A:HEM239
|
3.4
|
26.3
|
1.0
|
CHD
|
A:HEM239
|
3.5
|
23.8
|
1.0
|
C3B
|
A:HEM239
|
4.2
|
28.9
|
1.0
|
C2B
|
A:HEM239
|
4.2
|
27.5
|
1.0
|
ND1
|
A:HIS160
|
4.2
|
24.8
|
1.0
|
C2A
|
A:HEM239
|
4.2
|
22.8
|
1.0
|
C2C
|
A:HEM239
|
4.2
|
25.5
|
1.0
|
C3A
|
A:HEM239
|
4.2
|
24.2
|
1.0
|
C3C
|
A:HEM239
|
4.3
|
24.7
|
1.0
|
C3D
|
A:HEM239
|
4.3
|
23.6
|
1.0
|
CG
|
A:HIS160
|
4.3
|
24.4
|
1.0
|
C2D
|
A:HEM239
|
4.3
|
21.2
|
1.0
|
O3
|
A:GOL246
|
4.7
|
59.1
|
1.0
|
|
Iron binding site 2 out
of 5 in 3nn2
Go back to
Iron Binding Sites List in 3nn2
Iron binding site 2 out
of 5 in the Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii in Complex with Cyanide
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii in Complex with Cyanide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe239
b:20.7
occ:1.00
|
FE
|
B:HEM239
|
0.0
|
20.7
|
1.0
|
C
|
B:CYN244
|
1.9
|
20.9
|
1.0
|
NC
|
B:HEM239
|
2.0
|
20.4
|
1.0
|
NA
|
B:HEM239
|
2.0
|
20.2
|
1.0
|
NB
|
B:HEM239
|
2.0
|
21.6
|
1.0
|
ND
|
B:HEM239
|
2.1
|
21.1
|
1.0
|
NE2
|
B:HIS160
|
2.2
|
20.0
|
1.0
|
C4C
|
B:HEM239
|
3.0
|
21.8
|
1.0
|
C4A
|
B:HEM239
|
3.0
|
19.8
|
1.0
|
C1B
|
B:HEM239
|
3.0
|
22.0
|
1.0
|
C1D
|
B:HEM239
|
3.0
|
20.0
|
1.0
|
N
|
B:CYN244
|
3.1
|
27.6
|
1.0
|
C1A
|
B:HEM239
|
3.1
|
21.4
|
1.0
|
C1C
|
B:HEM239
|
3.1
|
21.6
|
1.0
|
CE1
|
B:HIS160
|
3.1
|
22.3
|
1.0
|
C4B
|
B:HEM239
|
3.1
|
20.4
|
1.0
|
C4D
|
B:HEM239
|
3.1
|
21.5
|
1.0
|
CD2
|
B:HIS160
|
3.1
|
22.2
|
1.0
|
CHD
|
B:HEM239
|
3.3
|
19.6
|
1.0
|
CHB
|
B:HEM239
|
3.3
|
20.1
|
1.0
|
CHC
|
B:HEM239
|
3.5
|
19.7
|
1.0
|
CHA
|
B:HEM239
|
3.5
|
21.4
|
1.0
|
C3C
|
B:HEM239
|
4.2
|
22.6
|
1.0
|
C3A
|
B:HEM239
|
4.2
|
20.9
|
1.0
|
ND1
|
B:HIS160
|
4.2
|
20.5
|
1.0
|
C2A
|
B:HEM239
|
4.3
|
21.1
|
1.0
|
CG
|
B:HIS160
|
4.3
|
19.6
|
1.0
|
C2C
|
B:HEM239
|
4.3
|
21.5
|
1.0
|
C2B
|
B:HEM239
|
4.3
|
22.4
|
1.0
|
C2D
|
B:HEM239
|
4.3
|
19.5
|
1.0
|
C3B
|
B:HEM239
|
4.3
|
21.6
|
1.0
|
C3D
|
B:HEM239
|
4.3
|
17.5
|
1.0
|
|
Iron binding site 3 out
of 5 in 3nn2
Go back to
Iron Binding Sites List in 3nn2
Iron binding site 3 out
of 5 in the Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii in Complex with Cyanide
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii in Complex with Cyanide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe239
b:22.3
occ:1.00
|
FE
|
C:HEM239
|
0.0
|
22.3
|
1.0
|
C
|
C:CYN243
|
1.9
|
25.8
|
1.0
|
NB
|
C:HEM239
|
1.9
|
23.8
|
1.0
|
ND
|
C:HEM239
|
2.0
|
21.5
|
1.0
|
NC
|
C:HEM239
|
2.1
|
21.9
|
1.0
|
NA
|
C:HEM239
|
2.1
|
22.5
|
1.0
|
NE2
|
C:HIS160
|
2.2
|
22.7
|
1.0
|
C4B
|
C:HEM239
|
3.0
|
24.9
|
1.0
|
C1D
|
C:HEM239
|
3.0
|
20.6
|
1.0
|
C1B
|
C:HEM239
|
3.0
|
24.5
|
1.0
|
C4D
|
C:HEM239
|
3.0
|
21.4
|
1.0
|
N
|
C:CYN243
|
3.1
|
27.9
|
1.0
|
C4C
|
C:HEM239
|
3.1
|
20.2
|
1.0
|
C1A
|
C:HEM239
|
3.1
|
21.1
|
1.0
|
CE1
|
C:HIS160
|
3.1
|
22.3
|
1.0
|
C1C
|
C:HEM239
|
3.1
|
21.1
|
1.0
|
C4A
|
C:HEM239
|
3.1
|
20.4
|
1.0
|
CD2
|
C:HIS160
|
3.2
|
22.7
|
1.0
|
CHD
|
C:HEM239
|
3.4
|
19.0
|
1.0
|
CHC
|
C:HEM239
|
3.4
|
23.8
|
1.0
|
CHA
|
C:HEM239
|
3.4
|
21.5
|
1.0
|
CHB
|
C:HEM239
|
3.4
|
23.5
|
1.0
|
C3B
|
C:HEM239
|
4.2
|
27.8
|
1.0
|
C2B
|
C:HEM239
|
4.2
|
25.4
|
1.0
|
ND1
|
C:HIS160
|
4.2
|
21.3
|
1.0
|
C3D
|
C:HEM239
|
4.2
|
21.2
|
1.0
|
C2D
|
C:HEM239
|
4.2
|
21.7
|
1.0
|
C3C
|
C:HEM239
|
4.3
|
20.0
|
1.0
|
C2A
|
C:HEM239
|
4.3
|
22.4
|
1.0
|
C3A
|
C:HEM239
|
4.3
|
23.1
|
1.0
|
C2C
|
C:HEM239
|
4.3
|
22.0
|
1.0
|
CG
|
C:HIS160
|
4.3
|
23.1
|
1.0
|
O1
|
C:GOL244
|
4.8
|
62.3
|
1.0
|
|
Iron binding site 4 out
of 5 in 3nn2
Go back to
Iron Binding Sites List in 3nn2
Iron binding site 4 out
of 5 in the Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii in Complex with Cyanide
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii in Complex with Cyanide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe239
b:28.2
occ:1.00
|
FE
|
D:HEM239
|
0.0
|
28.2
|
1.0
|
C
|
D:CYN244
|
1.9
|
34.6
|
1.0
|
NB
|
D:HEM239
|
1.9
|
26.2
|
1.0
|
ND
|
D:HEM239
|
2.0
|
25.7
|
1.0
|
NC
|
D:HEM239
|
2.0
|
24.9
|
1.0
|
NA
|
D:HEM239
|
2.0
|
29.0
|
1.0
|
NE2
|
D:HIS160
|
2.2
|
28.0
|
1.0
|
N
|
D:CYN244
|
3.0
|
31.9
|
1.0
|
C1B
|
D:HEM239
|
3.0
|
29.3
|
1.0
|
C4B
|
D:HEM239
|
3.0
|
27.3
|
1.0
|
C4A
|
D:HEM239
|
3.0
|
27.9
|
1.0
|
C1D
|
D:HEM239
|
3.0
|
25.2
|
1.0
|
C4D
|
D:HEM239
|
3.0
|
26.1
|
1.0
|
C4C
|
D:HEM239
|
3.0
|
24.0
|
1.0
|
C1A
|
D:HEM239
|
3.1
|
26.8
|
1.0
|
C1C
|
D:HEM239
|
3.1
|
25.0
|
1.0
|
CE1
|
D:HIS160
|
3.1
|
29.2
|
1.0
|
CD2
|
D:HIS160
|
3.2
|
29.3
|
1.0
|
CHB
|
D:HEM239
|
3.4
|
29.8
|
1.0
|
CHD
|
D:HEM239
|
3.4
|
25.4
|
1.0
|
CHC
|
D:HEM239
|
3.4
|
26.5
|
1.0
|
CHA
|
D:HEM239
|
3.4
|
27.3
|
1.0
|
C2B
|
D:HEM239
|
4.2
|
28.9
|
1.0
|
C3B
|
D:HEM239
|
4.2
|
28.9
|
1.0
|
ND1
|
D:HIS160
|
4.2
|
26.0
|
1.0
|
C3A
|
D:HEM239
|
4.2
|
28.6
|
1.0
|
C2A
|
D:HEM239
|
4.3
|
29.8
|
1.0
|
C3D
|
D:HEM239
|
4.3
|
25.7
|
1.0
|
C3C
|
D:HEM239
|
4.3
|
24.2
|
1.0
|
C2D
|
D:HEM239
|
4.3
|
26.4
|
1.0
|
C2C
|
D:HEM239
|
4.3
|
25.6
|
1.0
|
CG
|
D:HIS160
|
4.3
|
27.7
|
1.0
|
C3
|
D:GOL245
|
4.6
|
64.0
|
1.0
|
|
Iron binding site 5 out
of 5 in 3nn2
Go back to
Iron Binding Sites List in 3nn2
Iron binding site 5 out
of 5 in the Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii in Complex with Cyanide
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii in Complex with Cyanide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe239
b:27.0
occ:1.00
|
FE
|
E:HEM239
|
0.0
|
27.0
|
1.0
|
NC
|
E:HEM239
|
1.9
|
22.4
|
1.0
|
C
|
E:CYN242
|
1.9
|
30.8
|
1.0
|
NA
|
E:HEM239
|
2.0
|
24.6
|
1.0
|
NB
|
E:HEM239
|
2.0
|
28.0
|
1.0
|
ND
|
E:HEM239
|
2.1
|
25.8
|
1.0
|
NE2
|
E:HIS160
|
2.2
|
26.8
|
1.0
|
C4C
|
E:HEM239
|
2.9
|
24.7
|
1.0
|
N
|
E:CYN242
|
2.9
|
28.7
|
1.0
|
C4A
|
E:HEM239
|
2.9
|
25.8
|
1.0
|
C1B
|
E:HEM239
|
3.0
|
25.8
|
1.0
|
C1C
|
E:HEM239
|
3.0
|
25.7
|
1.0
|
C1D
|
E:HEM239
|
3.0
|
24.4
|
1.0
|
C4B
|
E:HEM239
|
3.1
|
26.1
|
1.0
|
C1A
|
E:HEM239
|
3.1
|
28.7
|
1.0
|
CE1
|
E:HIS160
|
3.1
|
28.3
|
1.0
|
C4D
|
E:HEM239
|
3.1
|
24.7
|
1.0
|
CD2
|
E:HIS160
|
3.1
|
28.1
|
1.0
|
CHD
|
E:HEM239
|
3.3
|
25.4
|
1.0
|
CHB
|
E:HEM239
|
3.3
|
26.0
|
1.0
|
CHC
|
E:HEM239
|
3.5
|
25.7
|
1.0
|
CHA
|
E:HEM239
|
3.5
|
27.6
|
1.0
|
C3C
|
E:HEM239
|
4.1
|
23.4
|
1.0
|
C3A
|
E:HEM239
|
4.2
|
27.2
|
1.0
|
C2C
|
E:HEM239
|
4.2
|
20.6
|
1.0
|
ND1
|
E:HIS160
|
4.2
|
28.2
|
1.0
|
C2B
|
E:HEM239
|
4.2
|
28.8
|
1.0
|
C2A
|
E:HEM239
|
4.3
|
25.0
|
1.0
|
CG
|
E:HIS160
|
4.3
|
27.9
|
1.0
|
C3B
|
E:HEM239
|
4.3
|
28.0
|
1.0
|
C2D
|
E:HEM239
|
4.3
|
27.1
|
1.0
|
C3D
|
E:HEM239
|
4.3
|
24.1
|
1.0
|
O3
|
E:GOL243
|
4.6
|
64.2
|
1.0
|
|
Reference:
J.Kostan,
B.Sjoeblom,
F.Maixner,
G.Mlynek,
P.G.Furtmueller,
C.Obinger,
M.Wagner,
H.Daims,
K.Djinovic-Carugo.
Structural and Functional Characterisation of the Chlorite Dismutase From the Nitrite-Oxidizing Bacterium "Candidatus Nitrospira Defluvii": Identification of A Catalytically Important Amino Acid Residue J.Struct.Biol. V. 172 331 2010.
ISSN: ISSN 1047-8477
PubMed: 20600954
DOI: 10.1016/J.JSB.2010.06.014
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