Iron in PDB 4m08: Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145V
Enzymatic activity of Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145V
All present enzymatic activity of Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145V:
1.13.11.49;
Protein crystallography data
The structure of Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145V, PDB code: 4m08
was solved by
K.Gysel,
A.Hagmueller,
K.Djinovic-Carugo,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
63.15 /
2.80
|
Space group
|
P 32 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
145.830,
145.830,
137.225,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
22.1 /
28
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145V
(pdb code 4m08). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the
Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145V, PDB code: 4m08:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
Iron binding site 1 out
of 5 in 4m08
Go back to
Iron Binding Sites List in 4m08
Iron binding site 1 out
of 5 in the Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145V
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145V within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:45.0
occ:1.00
|
FE
|
A:HEM301
|
0.0
|
45.0
|
1.0
|
NC
|
A:HEM301
|
2.0
|
26.9
|
1.0
|
NA
|
A:HEM301
|
2.1
|
30.9
|
1.0
|
NB
|
A:HEM301
|
2.1
|
36.8
|
1.0
|
ND
|
A:HEM301
|
2.1
|
36.3
|
1.0
|
N3
|
A:IMD306
|
2.5
|
29.0
|
1.0
|
NE2
|
A:HIS160
|
2.5
|
56.6
|
1.0
|
C2
|
A:IMD306
|
2.8
|
36.2
|
1.0
|
C4C
|
A:HEM301
|
3.0
|
43.4
|
1.0
|
C1C
|
A:HEM301
|
3.1
|
45.9
|
1.0
|
C4A
|
A:HEM301
|
3.1
|
29.8
|
1.0
|
C1B
|
A:HEM301
|
3.1
|
55.8
|
1.0
|
C1A
|
A:HEM301
|
3.1
|
29.9
|
1.0
|
C4B
|
A:HEM301
|
3.1
|
43.8
|
1.0
|
C1D
|
A:HEM301
|
3.1
|
31.3
|
1.0
|
C4D
|
A:HEM301
|
3.1
|
44.1
|
1.0
|
CD2
|
A:HIS160
|
3.3
|
51.1
|
1.0
|
CHB
|
A:HEM301
|
3.4
|
44.4
|
1.0
|
CHD
|
A:HEM301
|
3.4
|
37.6
|
1.0
|
CHC
|
A:HEM301
|
3.4
|
42.6
|
1.0
|
CHA
|
A:HEM301
|
3.5
|
35.8
|
1.0
|
CE1
|
A:HIS160
|
3.6
|
73.7
|
1.0
|
C4
|
A:IMD306
|
3.8
|
36.4
|
1.0
|
N1
|
A:IMD306
|
4.1
|
53.3
|
1.0
|
C3C
|
A:HEM301
|
4.3
|
36.9
|
1.0
|
C2C
|
A:HEM301
|
4.3
|
41.6
|
1.0
|
C2B
|
A:HEM301
|
4.3
|
58.6
|
1.0
|
C3A
|
A:HEM301
|
4.3
|
39.4
|
1.0
|
C2A
|
A:HEM301
|
4.3
|
40.8
|
1.0
|
C3B
|
A:HEM301
|
4.3
|
56.0
|
1.0
|
C2D
|
A:HEM301
|
4.4
|
34.9
|
1.0
|
C3D
|
A:HEM301
|
4.4
|
39.8
|
1.0
|
CG
|
A:HIS160
|
4.5
|
59.8
|
1.0
|
C5
|
A:IMD306
|
4.5
|
48.7
|
1.0
|
ND1
|
A:HIS160
|
4.6
|
74.6
|
1.0
|
|
Iron binding site 2 out
of 5 in 4m08
Go back to
Iron Binding Sites List in 4m08
Iron binding site 2 out
of 5 in the Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145V
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145V within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe301
b:29.8
occ:1.00
|
FE
|
B:HEM301
|
0.0
|
29.8
|
1.0
|
NA
|
B:HEM301
|
2.0
|
17.1
|
1.0
|
NB
|
B:HEM301
|
2.1
|
43.9
|
1.0
|
NC
|
B:HEM301
|
2.1
|
30.9
|
1.0
|
ND
|
B:HEM301
|
2.1
|
33.4
|
1.0
|
NE2
|
B:HIS160
|
2.3
|
19.1
|
1.0
|
N3
|
B:IMD305
|
2.5
|
16.9
|
1.0
|
C4
|
B:IMD305
|
2.9
|
23.4
|
1.0
|
C1A
|
B:HEM301
|
3.0
|
23.4
|
1.0
|
C4A
|
B:HEM301
|
3.0
|
31.9
|
1.0
|
C4B
|
B:HEM301
|
3.1
|
45.2
|
1.0
|
C1B
|
B:HEM301
|
3.1
|
30.0
|
1.0
|
C4D
|
B:HEM301
|
3.1
|
30.3
|
1.0
|
C1C
|
B:HEM301
|
3.1
|
31.4
|
1.0
|
C4C
|
B:HEM301
|
3.1
|
32.7
|
1.0
|
C1D
|
B:HEM301
|
3.1
|
32.4
|
1.0
|
CE1
|
B:HIS160
|
3.3
|
30.7
|
1.0
|
CD2
|
B:HIS160
|
3.4
|
21.0
|
1.0
|
CHA
|
B:HEM301
|
3.4
|
35.2
|
1.0
|
CHB
|
B:HEM301
|
3.4
|
34.5
|
1.0
|
CHC
|
B:HEM301
|
3.4
|
40.2
|
1.0
|
CHD
|
B:HEM301
|
3.5
|
30.2
|
1.0
|
C2
|
B:IMD305
|
3.8
|
49.4
|
1.0
|
C3B
|
B:HEM301
|
4.3
|
33.2
|
1.0
|
C2A
|
B:HEM301
|
4.3
|
32.1
|
1.0
|
C3A
|
B:HEM301
|
4.3
|
17.4
|
1.0
|
C2B
|
B:HEM301
|
4.3
|
25.7
|
1.0
|
C5
|
B:IMD305
|
4.3
|
30.1
|
1.0
|
C2C
|
B:HEM301
|
4.3
|
30.8
|
1.0
|
C3C
|
B:HEM301
|
4.3
|
27.8
|
1.0
|
C3D
|
B:HEM301
|
4.3
|
24.3
|
1.0
|
C2D
|
B:HEM301
|
4.4
|
24.4
|
1.0
|
ND1
|
B:HIS160
|
4.4
|
38.6
|
1.0
|
CG
|
B:HIS160
|
4.5
|
18.4
|
1.0
|
N1
|
B:IMD305
|
4.7
|
25.8
|
1.0
|
|
Iron binding site 3 out
of 5 in 4m08
Go back to
Iron Binding Sites List in 4m08
Iron binding site 3 out
of 5 in the Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145V
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145V within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe302
b:23.1
occ:1.00
|
FE
|
C:HEM302
|
0.0
|
23.1
|
1.0
|
NA
|
C:HEM302
|
2.0
|
30.4
|
1.0
|
NC
|
C:HEM302
|
2.1
|
15.5
|
1.0
|
NB
|
C:HEM302
|
2.1
|
13.1
|
1.0
|
ND
|
C:HEM302
|
2.1
|
36.5
|
1.0
|
NE2
|
C:HIS160
|
2.4
|
22.4
|
1.0
|
N3
|
C:IMD305
|
2.5
|
13.9
|
1.0
|
C2
|
C:IMD305
|
2.9
|
26.7
|
1.0
|
C1A
|
C:HEM302
|
3.1
|
33.0
|
1.0
|
C4A
|
C:HEM302
|
3.1
|
30.7
|
1.0
|
C4C
|
C:HEM302
|
3.1
|
24.9
|
1.0
|
C1D
|
C:HEM302
|
3.1
|
24.5
|
1.0
|
C4D
|
C:HEM302
|
3.1
|
33.4
|
1.0
|
C4B
|
C:HEM302
|
3.1
|
26.4
|
1.0
|
C1C
|
C:HEM302
|
3.1
|
16.9
|
1.0
|
C1B
|
C:HEM302
|
3.1
|
19.5
|
1.0
|
CD2
|
C:HIS160
|
3.3
|
28.3
|
1.0
|
CE1
|
C:HIS160
|
3.3
|
28.4
|
1.0
|
CHD
|
C:HEM302
|
3.4
|
31.9
|
1.0
|
CHA
|
C:HEM302
|
3.4
|
30.8
|
1.0
|
CHB
|
C:HEM302
|
3.4
|
36.0
|
1.0
|
CHC
|
C:HEM302
|
3.5
|
12.9
|
1.0
|
C4
|
C:IMD305
|
3.6
|
31.8
|
1.0
|
N1
|
C:IMD305
|
4.1
|
32.9
|
1.0
|
C2A
|
C:HEM302
|
4.3
|
28.5
|
1.0
|
C3A
|
C:HEM302
|
4.3
|
15.3
|
1.0
|
C3C
|
C:HEM302
|
4.3
|
12.7
|
1.0
|
C2D
|
C:HEM302
|
4.3
|
38.9
|
1.0
|
C2C
|
C:HEM302
|
4.3
|
24.7
|
1.0
|
C3D
|
C:HEM302
|
4.3
|
32.8
|
1.0
|
C3B
|
C:HEM302
|
4.3
|
42.0
|
1.0
|
C2B
|
C:HEM302
|
4.3
|
35.6
|
1.0
|
C5
|
C:IMD305
|
4.4
|
45.0
|
1.0
|
ND1
|
C:HIS160
|
4.4
|
36.7
|
1.0
|
CG
|
C:HIS160
|
4.4
|
28.1
|
1.0
|
|
Iron binding site 4 out
of 5 in 4m08
Go back to
Iron Binding Sites List in 4m08
Iron binding site 4 out
of 5 in the Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145V
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145V within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe301
b:53.5
occ:1.00
|
FE
|
D:HEM301
|
0.0
|
53.5
|
1.0
|
NA
|
D:HEM301
|
2.0
|
61.2
|
1.0
|
NB
|
D:HEM301
|
2.1
|
57.3
|
1.0
|
NC
|
D:HEM301
|
2.1
|
60.3
|
1.0
|
ND
|
D:HEM301
|
2.1
|
59.0
|
1.0
|
NE2
|
D:HIS160
|
2.5
|
45.5
|
1.0
|
N1
|
D:IMD304
|
2.6
|
73.3
|
1.0
|
C2
|
D:IMD304
|
2.9
|
75.8
|
1.0
|
C4A
|
D:HEM301
|
3.1
|
70.2
|
1.0
|
C1B
|
D:HEM301
|
3.1
|
61.2
|
1.0
|
C1A
|
D:HEM301
|
3.1
|
65.5
|
1.0
|
C4C
|
D:HEM301
|
3.1
|
57.3
|
1.0
|
C4B
|
D:HEM301
|
3.1
|
66.1
|
1.0
|
C1D
|
D:HEM301
|
3.1
|
53.4
|
1.0
|
C4D
|
D:HEM301
|
3.1
|
69.4
|
1.0
|
C1C
|
D:HEM301
|
3.1
|
49.8
|
1.0
|
CD2
|
D:HIS160
|
3.4
|
51.4
|
1.0
|
CHB
|
D:HEM301
|
3.4
|
72.8
|
1.0
|
CHD
|
D:HEM301
|
3.4
|
57.3
|
1.0
|
CHA
|
D:HEM301
|
3.5
|
70.9
|
1.0
|
CHC
|
D:HEM301
|
3.5
|
55.6
|
1.0
|
CE1
|
D:HIS160
|
3.5
|
53.5
|
1.0
|
C5
|
D:IMD304
|
3.6
|
76.0
|
1.0
|
N3
|
D:IMD304
|
4.0
|
87.1
|
1.0
|
C3A
|
D:HEM301
|
4.3
|
67.9
|
1.0
|
C2B
|
D:HEM301
|
4.3
|
58.4
|
1.0
|
C2A
|
D:HEM301
|
4.3
|
71.8
|
1.0
|
C3B
|
D:HEM301
|
4.3
|
65.7
|
1.0
|
C3C
|
D:HEM301
|
4.3
|
46.2
|
1.0
|
C4
|
D:IMD304
|
4.3
|
83.5
|
1.0
|
C2D
|
D:HEM301
|
4.3
|
45.1
|
1.0
|
C2C
|
D:HEM301
|
4.3
|
41.0
|
1.0
|
C3D
|
D:HEM301
|
4.3
|
63.2
|
1.0
|
CG
|
D:HIS160
|
4.6
|
51.8
|
1.0
|
ND1
|
D:HIS160
|
4.6
|
56.9
|
1.0
|
|
Iron binding site 5 out
of 5 in 4m08
Go back to
Iron Binding Sites List in 4m08
Iron binding site 5 out
of 5 in the Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145V
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145V within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe301
b:62.5
occ:1.00
|
FE
|
E:HEM301
|
0.0
|
62.5
|
1.0
|
NC
|
E:HEM301
|
2.1
|
62.0
|
1.0
|
NB
|
E:HEM301
|
2.1
|
74.4
|
1.0
|
ND
|
E:HEM301
|
2.1
|
47.3
|
1.0
|
NA
|
E:HEM301
|
2.1
|
56.5
|
1.0
|
NE2
|
E:HIS160
|
2.5
|
53.3
|
1.0
|
N1
|
E:IMD304
|
2.5
|
88.3
|
1.0
|
C5
|
E:IMD304
|
2.9
|
87.5
|
1.0
|
C4D
|
E:HEM301
|
3.1
|
59.1
|
1.0
|
C4C
|
E:HEM301
|
3.1
|
55.6
|
1.0
|
C1D
|
E:HEM301
|
3.1
|
56.6
|
1.0
|
C4B
|
E:HEM301
|
3.1
|
68.8
|
1.0
|
C1C
|
E:HEM301
|
3.1
|
61.5
|
1.0
|
C1A
|
E:HEM301
|
3.1
|
58.6
|
1.0
|
C1B
|
E:HEM301
|
3.1
|
70.9
|
1.0
|
C4A
|
E:HEM301
|
3.1
|
63.0
|
1.0
|
CD2
|
E:HIS160
|
3.2
|
63.6
|
1.0
|
CHA
|
E:HEM301
|
3.4
|
59.0
|
1.0
|
CHD
|
E:HEM301
|
3.4
|
49.5
|
1.0
|
CHC
|
E:HEM301
|
3.4
|
60.4
|
1.0
|
CHB
|
E:HEM301
|
3.5
|
68.3
|
1.0
|
C2
|
E:IMD304
|
3.6
|
87.9
|
1.0
|
CE1
|
E:HIS160
|
3.6
|
70.1
|
1.0
|
C4
|
E:IMD304
|
4.1
|
87.4
|
1.0
|
C3C
|
E:HEM301
|
4.3
|
54.2
|
1.0
|
C2C
|
E:HEM301
|
4.3
|
61.8
|
1.0
|
C3D
|
E:HEM301
|
4.3
|
67.2
|
1.0
|
C3B
|
E:HEM301
|
4.3
|
64.5
|
1.0
|
C2B
|
E:HEM301
|
4.3
|
65.1
|
1.0
|
C2A
|
E:HEM301
|
4.3
|
62.6
|
1.0
|
C3A
|
E:HEM301
|
4.3
|
66.0
|
1.0
|
C2D
|
E:HEM301
|
4.3
|
63.0
|
1.0
|
N3
|
E:IMD304
|
4.4
|
90.9
|
1.0
|
CG
|
E:HIS160
|
4.4
|
75.2
|
1.0
|
ND1
|
E:HIS160
|
4.6
|
76.6
|
1.0
|
|
Reference:
S.Hofbauer,
K.Gysel,
M.Bellei,
A.Hagmuller,
I.Schaffner,
G.Mlynek,
J.Kostan,
K.F.Pirker,
H.Daims,
P.G.Furtmuller,
G.Battistuzzi,
K.Djinovic-Carugo,
C.Obinger.
Manipulating Conserved Heme Cavity Residues of Chlorite Dismutase: Effect on Structure, Redox Chemistry, and Reactivity. Biochemistry V. 53 77 2014.
ISSN: ISSN 0006-2960
PubMed: 24364531
DOI: 10.1021/BI401042Z
Page generated: Mon Aug 5 06:30:39 2024
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