Iron in PDB 3nn1: Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii in Complex with Imidazole
Enzymatic activity of Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii in Complex with Imidazole
All present enzymatic activity of Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii in Complex with Imidazole:
1.13.11.49;
Protein crystallography data
The structure of Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii in Complex with Imidazole, PDB code: 3nn1
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)
|
47.68 /
1.85
|
Space group
|
P 32 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
145.670,
145.670,
136.440,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
18 /
21
|
Iron Binding Sites:
The binding sites of Iron atom in the Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii in Complex with Imidazole
(pdb code 3nn1). 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 Imidazole, PDB code: 3nn1:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
Iron binding site 1 out
of 5 in 3nn1
Go back to
Iron Binding Sites List in 3nn1
Iron binding site 1 out
of 5 in the Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii in Complex with Imidazole
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 Imidazole within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe239
b:24.8
occ:1.00
|
FE
|
A:HEM239
|
0.0
|
24.8
|
1.0
|
NB
|
A:HEM239
|
2.0
|
25.5
|
1.0
|
NA
|
A:HEM239
|
2.0
|
24.1
|
1.0
|
NC
|
A:HEM239
|
2.0
|
23.5
|
1.0
|
ND
|
A:HEM239
|
2.1
|
22.2
|
1.0
|
NE2
|
A:HIS160
|
2.1
|
27.1
|
1.0
|
N3
|
A:IMD243
|
2.2
|
26.8
|
1.0
|
C4B
|
A:HEM239
|
3.0
|
24.6
|
1.0
|
C1C
|
A:HEM239
|
3.0
|
23.6
|
1.0
|
CE1
|
A:HIS160
|
3.0
|
27.9
|
1.0
|
C4
|
A:IMD243
|
3.0
|
26.2
|
1.0
|
C1A
|
A:HEM239
|
3.0
|
23.7
|
1.0
|
C1B
|
A:HEM239
|
3.0
|
25.0
|
1.0
|
C4A
|
A:HEM239
|
3.0
|
26.4
|
1.0
|
C4D
|
A:HEM239
|
3.1
|
23.2
|
1.0
|
C4C
|
A:HEM239
|
3.1
|
22.3
|
1.0
|
C1D
|
A:HEM239
|
3.1
|
21.9
|
1.0
|
CD2
|
A:HIS160
|
3.1
|
28.0
|
1.0
|
C2
|
A:IMD243
|
3.2
|
26.9
|
1.0
|
CHC
|
A:HEM239
|
3.3
|
24.9
|
1.0
|
CHA
|
A:HEM239
|
3.4
|
23.4
|
1.0
|
CHB
|
A:HEM239
|
3.4
|
25.7
|
1.0
|
CHD
|
A:HEM239
|
3.5
|
22.2
|
1.0
|
ND1
|
A:HIS160
|
4.2
|
25.8
|
1.0
|
C5
|
A:IMD243
|
4.2
|
26.1
|
1.0
|
C3B
|
A:HEM239
|
4.2
|
25.9
|
1.0
|
C2C
|
A:HEM239
|
4.2
|
25.1
|
1.0
|
C2B
|
A:HEM239
|
4.2
|
25.4
|
1.0
|
C2A
|
A:HEM239
|
4.2
|
23.8
|
1.0
|
CG
|
A:HIS160
|
4.2
|
25.1
|
1.0
|
C3C
|
A:HEM239
|
4.3
|
25.4
|
1.0
|
C3A
|
A:HEM239
|
4.3
|
26.0
|
1.0
|
N1
|
A:IMD243
|
4.3
|
28.5
|
1.0
|
C3D
|
A:HEM239
|
4.3
|
21.9
|
1.0
|
C2D
|
A:HEM239
|
4.3
|
23.6
|
1.0
|
CE
|
A:MET157
|
4.9
|
25.9
|
1.0
|
|
Iron binding site 2 out
of 5 in 3nn1
Go back to
Iron Binding Sites List in 3nn1
Iron binding site 2 out
of 5 in the Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii in Complex with Imidazole
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 Imidazole within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe239
b:20.8
occ:1.00
|
FE
|
B:HEM239
|
0.0
|
20.8
|
1.0
|
NA
|
B:HEM239
|
2.0
|
20.9
|
1.0
|
NC
|
B:HEM239
|
2.0
|
19.5
|
1.0
|
NB
|
B:HEM239
|
2.1
|
20.5
|
1.0
|
ND
|
B:HEM239
|
2.1
|
19.1
|
1.0
|
N3
|
B:IMD243
|
2.1
|
26.6
|
1.0
|
NE2
|
B:HIS160
|
2.1
|
22.5
|
1.0
|
C4C
|
B:HEM239
|
3.0
|
21.5
|
1.0
|
C4A
|
B:HEM239
|
3.0
|
22.4
|
1.0
|
C1D
|
B:HEM239
|
3.0
|
21.6
|
1.0
|
C1B
|
B:HEM239
|
3.0
|
21.6
|
1.0
|
C4
|
B:IMD243
|
3.0
|
27.2
|
1.0
|
CE1
|
B:HIS160
|
3.1
|
23.0
|
1.0
|
C1A
|
B:HEM239
|
3.1
|
19.9
|
1.0
|
C4B
|
B:HEM239
|
3.1
|
19.3
|
1.0
|
C1C
|
B:HEM239
|
3.1
|
17.8
|
1.0
|
C4D
|
B:HEM239
|
3.1
|
21.9
|
1.0
|
CD2
|
B:HIS160
|
3.2
|
22.1
|
1.0
|
C2
|
B:IMD243
|
3.2
|
24.6
|
1.0
|
CHD
|
B:HEM239
|
3.3
|
21.4
|
1.0
|
CHB
|
B:HEM239
|
3.4
|
22.2
|
1.0
|
CHC
|
B:HEM239
|
3.5
|
19.1
|
1.0
|
CHA
|
B:HEM239
|
3.5
|
21.8
|
1.0
|
ND1
|
B:HIS160
|
4.2
|
21.1
|
1.0
|
C3C
|
B:HEM239
|
4.2
|
21.5
|
1.0
|
C5
|
B:IMD243
|
4.2
|
24.7
|
1.0
|
C3A
|
B:HEM239
|
4.2
|
20.5
|
1.0
|
C2B
|
B:HEM239
|
4.3
|
21.9
|
1.0
|
N1
|
B:IMD243
|
4.3
|
27.5
|
1.0
|
C2A
|
B:HEM239
|
4.3
|
23.1
|
1.0
|
CG
|
B:HIS160
|
4.3
|
22.2
|
1.0
|
C2D
|
B:HEM239
|
4.3
|
23.1
|
1.0
|
C2C
|
B:HEM239
|
4.3
|
20.1
|
1.0
|
C3B
|
B:HEM239
|
4.3
|
21.4
|
1.0
|
C3D
|
B:HEM239
|
4.3
|
20.4
|
1.0
|
CE
|
B:MET157
|
5.0
|
23.9
|
1.0
|
|
Iron binding site 3 out
of 5 in 3nn1
Go back to
Iron Binding Sites List in 3nn1
Iron binding site 3 out
of 5 in the Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii in Complex with Imidazole
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 Imidazole within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe239
b:21.9
occ:1.00
|
FE
|
C:HEM239
|
0.0
|
21.9
|
1.0
|
NB
|
C:HEM239
|
1.9
|
22.2
|
1.0
|
ND
|
C:HEM239
|
2.0
|
20.6
|
1.0
|
NA
|
C:HEM239
|
2.1
|
20.5
|
1.0
|
NC
|
C:HEM239
|
2.1
|
20.8
|
1.0
|
N3
|
C:IMD242
|
2.1
|
23.6
|
1.0
|
NE2
|
C:HIS160
|
2.1
|
22.7
|
1.0
|
C1B
|
C:HEM239
|
3.0
|
23.9
|
1.0
|
C4B
|
C:HEM239
|
3.0
|
22.6
|
1.0
|
C1D
|
C:HEM239
|
3.0
|
21.9
|
1.0
|
C4
|
C:IMD242
|
3.0
|
25.2
|
1.0
|
C4C
|
C:HEM239
|
3.0
|
20.8
|
1.0
|
C4A
|
C:HEM239
|
3.0
|
21.2
|
1.0
|
C4D
|
C:HEM239
|
3.1
|
21.0
|
1.0
|
C1A
|
C:HEM239
|
3.1
|
20.0
|
1.0
|
C1C
|
C:HEM239
|
3.1
|
20.5
|
1.0
|
CE1
|
C:HIS160
|
3.1
|
21.4
|
1.0
|
CD2
|
C:HIS160
|
3.1
|
23.1
|
1.0
|
C2
|
C:IMD242
|
3.2
|
24.8
|
1.0
|
CHD
|
C:HEM239
|
3.4
|
20.9
|
1.0
|
CHB
|
C:HEM239
|
3.4
|
23.8
|
1.0
|
CHC
|
C:HEM239
|
3.4
|
21.9
|
1.0
|
CHA
|
C:HEM239
|
3.4
|
22.4
|
1.0
|
C2B
|
C:HEM239
|
4.2
|
25.8
|
1.0
|
ND1
|
C:HIS160
|
4.2
|
21.0
|
1.0
|
C3B
|
C:HEM239
|
4.2
|
26.2
|
1.0
|
C5
|
C:IMD242
|
4.2
|
23.3
|
1.0
|
C3C
|
C:HEM239
|
4.3
|
20.0
|
1.0
|
CG
|
C:HIS160
|
4.3
|
23.4
|
1.0
|
C2D
|
C:HEM239
|
4.3
|
23.5
|
1.0
|
C3A
|
C:HEM239
|
4.3
|
20.8
|
1.0
|
C3D
|
C:HEM239
|
4.3
|
22.8
|
1.0
|
N1
|
C:IMD242
|
4.3
|
25.2
|
1.0
|
C2A
|
C:HEM239
|
4.3
|
21.5
|
1.0
|
C2C
|
C:HEM239
|
4.3
|
19.6
|
1.0
|
CE
|
C:MET157
|
4.9
|
27.7
|
1.0
|
|
Iron binding site 4 out
of 5 in 3nn1
Go back to
Iron Binding Sites List in 3nn1
Iron binding site 4 out
of 5 in the Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii in Complex with Imidazole
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 Imidazole within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe239
b:28.1
occ:1.00
|
FE
|
D:HEM239
|
0.0
|
28.1
|
1.0
|
NB
|
D:HEM239
|
1.9
|
27.2
|
1.0
|
ND
|
D:HEM239
|
1.9
|
27.0
|
1.0
|
NA
|
D:HEM239
|
2.1
|
27.2
|
1.0
|
NC
|
D:HEM239
|
2.1
|
25.7
|
1.0
|
NE2
|
D:HIS160
|
2.1
|
29.6
|
1.0
|
N3
|
D:IMD243
|
2.3
|
32.3
|
1.0
|
C1B
|
D:HEM239
|
2.9
|
29.5
|
1.0
|
C4
|
D:IMD243
|
2.9
|
32.0
|
1.0
|
C4B
|
D:HEM239
|
3.0
|
27.3
|
1.0
|
C1D
|
D:HEM239
|
3.0
|
27.8
|
1.0
|
CE1
|
D:HIS160
|
3.0
|
31.0
|
1.0
|
C4A
|
D:HEM239
|
3.0
|
27.3
|
1.0
|
C4D
|
D:HEM239
|
3.1
|
26.9
|
1.0
|
C4C
|
D:HEM239
|
3.1
|
25.2
|
1.0
|
C1A
|
D:HEM239
|
3.1
|
26.9
|
1.0
|
C1C
|
D:HEM239
|
3.1
|
25.1
|
1.0
|
CD2
|
D:HIS160
|
3.1
|
32.6
|
1.0
|
CHB
|
D:HEM239
|
3.3
|
29.0
|
1.0
|
CHD
|
D:HEM239
|
3.4
|
26.1
|
1.0
|
C2
|
D:IMD243
|
3.4
|
35.1
|
1.0
|
CHC
|
D:HEM239
|
3.4
|
27.1
|
1.0
|
CHA
|
D:HEM239
|
3.5
|
27.9
|
1.0
|
C2B
|
D:HEM239
|
4.1
|
30.4
|
1.0
|
ND1
|
D:HIS160
|
4.2
|
28.7
|
1.0
|
C3B
|
D:HEM239
|
4.2
|
30.4
|
1.0
|
C2D
|
D:HEM239
|
4.2
|
28.3
|
1.0
|
C5
|
D:IMD243
|
4.2
|
33.3
|
1.0
|
CG
|
D:HIS160
|
4.2
|
29.9
|
1.0
|
C3D
|
D:HEM239
|
4.2
|
28.8
|
1.0
|
C3A
|
D:HEM239
|
4.3
|
29.5
|
1.0
|
C2A
|
D:HEM239
|
4.3
|
29.6
|
1.0
|
C3C
|
D:HEM239
|
4.3
|
24.8
|
1.0
|
C2C
|
D:HEM239
|
4.3
|
26.3
|
1.0
|
N1
|
D:IMD243
|
4.4
|
33.3
|
1.0
|
CE
|
D:MET157
|
5.0
|
35.2
|
1.0
|
|
Iron binding site 5 out
of 5 in 3nn1
Go back to
Iron Binding Sites List in 3nn1
Iron binding site 5 out
of 5 in the Structure of Chlorite Dismutase From Candidatus Nitrospira Defluvii in Complex with Imidazole
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 Imidazole within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe239
b:28.4
occ:1.00
|
FE
|
E:HEM239
|
0.0
|
28.4
|
1.0
|
NA
|
E:HEM239
|
1.9
|
27.1
|
1.0
|
NC
|
E:HEM239
|
1.9
|
27.2
|
1.0
|
NB
|
E:HEM239
|
2.0
|
27.5
|
1.0
|
ND
|
E:HEM239
|
2.1
|
25.9
|
1.0
|
NE2
|
E:HIS160
|
2.1
|
29.2
|
1.0
|
N1
|
E:IMD244
|
2.2
|
31.9
|
1.0
|
C4A
|
E:HEM239
|
2.9
|
28.2
|
1.0
|
C4C
|
E:HEM239
|
3.0
|
28.9
|
1.0
|
CE1
|
E:HIS160
|
3.0
|
30.1
|
1.0
|
C1B
|
E:HEM239
|
3.0
|
26.6
|
1.0
|
C1D
|
E:HEM239
|
3.0
|
27.7
|
1.0
|
C1A
|
E:HEM239
|
3.0
|
26.4
|
1.0
|
C1C
|
E:HEM239
|
3.1
|
26.5
|
1.0
|
C4B
|
E:HEM239
|
3.1
|
26.4
|
1.0
|
C5
|
E:IMD244
|
3.1
|
33.8
|
1.0
|
C4D
|
E:HEM239
|
3.1
|
26.9
|
1.0
|
CD2
|
E:HIS160
|
3.2
|
32.2
|
1.0
|
C2
|
E:IMD244
|
3.2
|
33.8
|
1.0
|
CHB
|
E:HEM239
|
3.3
|
28.1
|
1.0
|
CHD
|
E:HEM239
|
3.3
|
26.8
|
1.0
|
CHA
|
E:HEM239
|
3.5
|
26.7
|
1.0
|
CHC
|
E:HEM239
|
3.5
|
26.7
|
1.0
|
ND1
|
E:HIS160
|
4.1
|
30.3
|
1.0
|
C3A
|
E:HEM239
|
4.2
|
30.5
|
1.0
|
C3C
|
E:HEM239
|
4.2
|
28.9
|
1.0
|
C2A
|
E:HEM239
|
4.2
|
28.8
|
1.0
|
C2B
|
E:HEM239
|
4.2
|
27.3
|
1.0
|
C2C
|
E:HEM239
|
4.2
|
27.2
|
1.0
|
CG
|
E:HIS160
|
4.3
|
30.1
|
1.0
|
C3B
|
E:HEM239
|
4.3
|
27.0
|
1.0
|
C2D
|
E:HEM239
|
4.3
|
28.9
|
1.0
|
C4
|
E:IMD244
|
4.3
|
32.4
|
1.0
|
C3D
|
E:HEM239
|
4.3
|
27.9
|
1.0
|
N3
|
E:IMD244
|
4.3
|
33.8
|
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
Page generated: Sun Aug 4 16:36:05 2024
|