Iron in PDB 4m05: Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii R173E
Enzymatic activity of Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii R173E
All present enzymatic activity of Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii R173E:
1.13.11.49;
Protein crystallography data
The structure of Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii R173E, PDB code: 4m05
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)
|
44.22 /
2.28
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
136.470,
112.390,
119.250,
90.00,
117.84,
90.00
|
R / Rfree (%)
|
26.8 /
32
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii R173E
(pdb code 4m05). 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 R173E, PDB code: 4m05:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
Iron binding site 1 out
of 5 in 4m05
Go back to
Iron Binding Sites List in 4m05
Iron binding site 1 out
of 5 in the Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii R173E
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 R173E within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:44.1
occ:1.00
|
FE
|
A:HEM301
|
0.0
|
44.1
|
1.0
|
NC
|
A:HEM301
|
2.0
|
43.5
|
1.0
|
NB
|
A:HEM301
|
2.1
|
47.7
|
1.0
|
ND
|
A:HEM301
|
2.1
|
43.1
|
1.0
|
NA
|
A:HEM301
|
2.1
|
50.0
|
1.0
|
NE2
|
A:HIS160
|
2.1
|
75.0
|
1.0
|
C4C
|
A:HEM301
|
3.0
|
72.5
|
1.0
|
C1C
|
A:HEM301
|
3.0
|
45.1
|
1.0
|
CE1
|
A:HIS160
|
3.0
|
69.3
|
1.0
|
C1D
|
A:HEM301
|
3.0
|
52.3
|
1.0
|
C1B
|
A:HEM301
|
3.0
|
64.4
|
1.0
|
C4A
|
A:HEM301
|
3.1
|
45.9
|
1.0
|
C4B
|
A:HEM301
|
3.1
|
46.6
|
1.0
|
C4D
|
A:HEM301
|
3.1
|
71.6
|
1.0
|
CD2
|
A:HIS160
|
3.1
|
60.4
|
1.0
|
C1A
|
A:HEM301
|
3.2
|
44.7
|
1.0
|
CHD
|
A:HEM301
|
3.3
|
42.1
|
1.0
|
CHC
|
A:HEM301
|
3.4
|
44.8
|
1.0
|
CHB
|
A:HEM301
|
3.4
|
60.7
|
1.0
|
CHA
|
A:HEM301
|
3.5
|
81.4
|
1.0
|
ND1
|
A:HIS160
|
4.1
|
72.9
|
1.0
|
C3C
|
A:HEM301
|
4.2
|
42.5
|
1.0
|
C2C
|
A:HEM301
|
4.2
|
43.2
|
1.0
|
CG
|
A:HIS160
|
4.2
|
77.1
|
1.0
|
C2B
|
A:HEM301
|
4.3
|
47.1
|
1.0
|
C2D
|
A:HEM301
|
4.3
|
41.8
|
1.0
|
C3B
|
A:HEM301
|
4.3
|
64.6
|
1.0
|
C3A
|
A:HEM301
|
4.3
|
46.6
|
1.0
|
C3D
|
A:HEM301
|
4.3
|
42.3
|
1.0
|
C2A
|
A:HEM301
|
4.4
|
45.6
|
1.0
|
CE
|
A:MET157
|
5.0
|
89.8
|
1.0
|
|
Iron binding site 2 out
of 5 in 4m05
Go back to
Iron Binding Sites List in 4m05
Iron binding site 2 out
of 5 in the Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii R173E
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 R173E within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe301
b:38.5
occ:1.00
|
FE
|
B:HEM301
|
0.0
|
38.5
|
1.0
|
NC
|
B:HEM301
|
1.9
|
38.1
|
1.0
|
ND
|
B:HEM301
|
2.1
|
37.9
|
1.0
|
NE2
|
B:HIS160
|
2.1
|
75.5
|
1.0
|
NA
|
B:HEM301
|
2.1
|
39.0
|
1.0
|
NB
|
B:HEM301
|
2.1
|
39.2
|
1.0
|
CE1
|
B:HIS160
|
2.9
|
64.6
|
1.0
|
C4C
|
B:HEM301
|
2.9
|
89.8
|
1.0
|
C1D
|
B:HEM301
|
2.9
|
37.4
|
1.0
|
C1C
|
B:HEM301
|
3.0
|
42.2
|
1.0
|
C4A
|
B:HEM301
|
3.0
|
39.6
|
1.0
|
C1B
|
B:HEM301
|
3.1
|
60.3
|
1.0
|
C4B
|
B:HEM301
|
3.1
|
45.6
|
1.0
|
C4D
|
B:HEM301
|
3.1
|
42.9
|
1.0
|
C1A
|
B:HEM301
|
3.2
|
42.0
|
1.0
|
CD2
|
B:HIS160
|
3.2
|
46.8
|
1.0
|
CHD
|
B:HEM301
|
3.2
|
37.2
|
1.0
|
CHB
|
B:HEM301
|
3.4
|
39.9
|
1.0
|
CHC
|
B:HEM301
|
3.5
|
38.9
|
1.0
|
CHA
|
B:HEM301
|
3.6
|
38.5
|
1.0
|
ND1
|
B:HIS160
|
4.1
|
63.8
|
1.0
|
C3C
|
B:HEM301
|
4.2
|
37.4
|
1.0
|
C2C
|
B:HEM301
|
4.2
|
37.9
|
1.0
|
CG
|
B:HIS160
|
4.2
|
51.6
|
1.0
|
C2D
|
B:HEM301
|
4.2
|
42.5
|
1.0
|
C2B
|
B:HEM301
|
4.3
|
44.7
|
1.0
|
C3A
|
B:HEM301
|
4.3
|
50.5
|
1.0
|
C3D
|
B:HEM301
|
4.3
|
37.5
|
1.0
|
C3B
|
B:HEM301
|
4.3
|
47.6
|
1.0
|
C2A
|
B:HEM301
|
4.4
|
39.6
|
1.0
|
CE
|
B:MET157
|
5.0
|
0.7
|
1.0
|
|
Iron binding site 3 out
of 5 in 4m05
Go back to
Iron Binding Sites List in 4m05
Iron binding site 3 out
of 5 in the Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii R173E
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 R173E within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe301
b:53.6
occ:1.00
|
FE
|
C:HEM301
|
0.0
|
53.6
|
1.0
|
NC
|
C:HEM301
|
2.0
|
40.0
|
1.0
|
NB
|
C:HEM301
|
2.0
|
41.4
|
1.0
|
NA
|
C:HEM301
|
2.0
|
40.8
|
1.0
|
ND
|
C:HEM301
|
2.0
|
39.4
|
1.0
|
NE2
|
C:HIS160
|
2.2
|
87.2
|
1.0
|
CE1
|
C:HIS160
|
2.9
|
78.9
|
1.0
|
C1B
|
C:HEM301
|
3.0
|
42.1
|
1.0
|
C1C
|
C:HEM301
|
3.0
|
43.9
|
1.0
|
C4C
|
C:HEM301
|
3.0
|
41.0
|
1.0
|
C4B
|
C:HEM301
|
3.0
|
78.6
|
1.0
|
C4D
|
C:HEM301
|
3.0
|
39.3
|
1.0
|
C4A
|
C:HEM301
|
3.0
|
55.3
|
1.0
|
C1D
|
C:HEM301
|
3.0
|
84.8
|
1.0
|
C1A
|
C:HEM301
|
3.1
|
50.8
|
1.0
|
CD2
|
C:HIS160
|
3.3
|
73.7
|
1.0
|
CHB
|
C:HEM301
|
3.4
|
63.3
|
1.0
|
CHD
|
C:HEM301
|
3.4
|
38.8
|
1.0
|
CHC
|
C:HEM301
|
3.4
|
41.3
|
1.0
|
CHA
|
C:HEM301
|
3.4
|
39.9
|
1.0
|
ND1
|
C:HIS160
|
4.1
|
60.3
|
1.0
|
C2B
|
C:HEM301
|
4.2
|
62.8
|
1.0
|
C3B
|
C:HEM301
|
4.2
|
42.6
|
1.0
|
C2C
|
C:HEM301
|
4.2
|
47.1
|
1.0
|
C3C
|
C:HEM301
|
4.2
|
39.4
|
1.0
|
C3D
|
C:HEM301
|
4.3
|
38.7
|
1.0
|
C3A
|
C:HEM301
|
4.3
|
41.7
|
1.0
|
C2D
|
C:HEM301
|
4.3
|
38.3
|
1.0
|
C2A
|
C:HEM301
|
4.3
|
41.1
|
1.0
|
CG
|
C:HIS160
|
4.3
|
67.5
|
1.0
|
|
Iron binding site 4 out
of 5 in 4m05
Go back to
Iron Binding Sites List in 4m05
Iron binding site 4 out
of 5 in the Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii R173E
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 R173E within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe301
b:62.7
occ:1.00
|
FE
|
D:HEM301
|
0.0
|
62.7
|
1.0
|
NC
|
D:HEM301
|
2.0
|
57.7
|
1.0
|
NB
|
D:HEM301
|
2.0
|
54.7
|
1.0
|
NA
|
D:HEM301
|
2.0
|
62.5
|
1.0
|
ND
|
D:HEM301
|
2.1
|
56.0
|
1.0
|
NE2
|
D:HIS160
|
2.2
|
64.3
|
1.0
|
CE1
|
D:HIS160
|
2.8
|
69.7
|
1.0
|
C4C
|
D:HEM301
|
3.0
|
60.0
|
1.0
|
C1B
|
D:HEM301
|
3.0
|
66.3
|
1.0
|
C4A
|
D:HEM301
|
3.0
|
64.7
|
1.0
|
C1C
|
D:HEM301
|
3.0
|
50.2
|
1.0
|
C1A
|
D:HEM301
|
3.0
|
64.8
|
1.0
|
C4B
|
D:HEM301
|
3.1
|
58.1
|
1.0
|
C1D
|
D:HEM301
|
3.1
|
52.4
|
1.0
|
C4D
|
D:HEM301
|
3.1
|
56.4
|
1.0
|
CHD
|
D:HEM301
|
3.4
|
55.0
|
1.0
|
CHB
|
D:HEM301
|
3.4
|
73.2
|
1.0
|
CD2
|
D:HIS160
|
3.4
|
43.6
|
1.0
|
CHC
|
D:HEM301
|
3.4
|
55.1
|
1.0
|
CHA
|
D:HEM301
|
3.4
|
66.5
|
1.0
|
ND1
|
D:HIS160
|
4.0
|
53.7
|
1.0
|
C3C
|
D:HEM301
|
4.2
|
53.7
|
1.0
|
C2A
|
D:HEM301
|
4.2
|
66.8
|
1.0
|
C2B
|
D:HEM301
|
4.2
|
66.4
|
1.0
|
C3A
|
D:HEM301
|
4.2
|
44.0
|
1.0
|
C2C
|
D:HEM301
|
4.3
|
45.6
|
1.0
|
C3B
|
D:HEM301
|
4.3
|
63.3
|
1.0
|
CG
|
D:HIS160
|
4.3
|
57.0
|
1.0
|
C2D
|
D:HEM301
|
4.3
|
40.6
|
1.0
|
C3D
|
D:HEM301
|
4.4
|
45.6
|
1.0
|
|
Iron binding site 5 out
of 5 in 4m05
Go back to
Iron Binding Sites List in 4m05
Iron binding site 5 out
of 5 in the Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii R173E
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 R173E within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe301
b:44.2
occ:1.00
|
FE
|
E:HEM301
|
0.0
|
44.2
|
1.0
|
NB
|
E:HEM301
|
2.0
|
43.8
|
1.0
|
NC
|
E:HEM301
|
2.0
|
42.2
|
1.0
|
ND
|
E:HEM301
|
2.1
|
42.1
|
1.0
|
NA
|
E:HEM301
|
2.1
|
43.8
|
1.0
|
NE2
|
E:HIS160
|
2.2
|
86.5
|
1.0
|
CE1
|
E:HIS160
|
2.7
|
81.3
|
1.0
|
C4B
|
E:HEM301
|
3.0
|
43.9
|
1.0
|
C1B
|
E:HEM301
|
3.0
|
44.6
|
1.0
|
C4C
|
E:HEM301
|
3.0
|
44.1
|
1.0
|
C1C
|
E:HEM301
|
3.0
|
42.5
|
1.0
|
C1D
|
E:HEM301
|
3.1
|
41.4
|
1.0
|
C4D
|
E:HEM301
|
3.1
|
42.3
|
1.0
|
C4A
|
E:HEM301
|
3.1
|
67.5
|
1.0
|
C1A
|
E:HEM301
|
3.1
|
53.0
|
1.0
|
CD2
|
E:HIS160
|
3.4
|
42.5
|
1.0
|
CHC
|
E:HEM301
|
3.4
|
43.2
|
1.0
|
CHD
|
E:HEM301
|
3.4
|
41.1
|
1.0
|
CHB
|
E:HEM301
|
3.4
|
44.9
|
1.0
|
CHA
|
E:HEM301
|
3.5
|
45.0
|
1.0
|
ND1
|
E:HIS160
|
3.9
|
83.8
|
1.0
|
C3B
|
E:HEM301
|
4.2
|
49.4
|
1.0
|
C2B
|
E:HEM301
|
4.2
|
45.2
|
1.0
|
C3C
|
E:HEM301
|
4.2
|
41.2
|
1.0
|
C2C
|
E:HEM301
|
4.2
|
41.8
|
1.0
|
CG
|
E:HIS160
|
4.3
|
72.4
|
1.0
|
C2D
|
E:HEM301
|
4.3
|
41.1
|
1.0
|
C3D
|
E:HEM301
|
4.3
|
47.2
|
1.0
|
C3A
|
E:HEM301
|
4.4
|
45.0
|
1.0
|
C2A
|
E:HEM301
|
4.4
|
58.6
|
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 06:30:16 2024
|