Iron in PDB 4m06: Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145F in Complex with Cyanide
Enzymatic activity of Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145F in Complex with Cyanide
All present enzymatic activity of Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145F in Complex with Cyanide:
1.13.11.49;
Protein crystallography data
The structure of Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145F in Complex with Cyanide, PDB code: 4m06
was solved by
A.Hagmueller,
K.Gysel,
K.Djinovic-Carugo,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.45 /
2.60
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
136.210,
113.420,
118.840,
90.00,
117.94,
90.00
|
R / Rfree (%)
|
21.1 /
25.8
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145F in Complex with Cyanide
(pdb code 4m06). 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 W145F in Complex with Cyanide, PDB code: 4m06:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
Iron binding site 1 out
of 5 in 4m06
Go back to
Iron Binding Sites List in 4m06
Iron binding site 1 out
of 5 in the Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145F 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 Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145F in Complex with Cyanide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:81.3
occ:1.00
|
FE
|
A:HEM301
|
0.0
|
81.3
|
1.0
|
NC
|
A:HEM301
|
2.0
|
59.4
|
1.0
|
NB
|
A:HEM301
|
2.1
|
63.1
|
1.0
|
NA
|
A:HEM301
|
2.1
|
60.0
|
1.0
|
ND
|
A:HEM301
|
2.1
|
56.5
|
1.0
|
NE2
|
A:HIS160
|
2.1
|
88.2
|
1.0
|
C
|
A:CYN303
|
2.2
|
83.9
|
1.0
|
C1C
|
A:HEM301
|
3.0
|
67.6
|
1.0
|
C4D
|
A:HEM301
|
3.1
|
69.5
|
1.0
|
C4B
|
A:HEM301
|
3.1
|
67.5
|
1.0
|
C4C
|
A:HEM301
|
3.1
|
65.0
|
1.0
|
CE1
|
A:HIS160
|
3.1
|
85.9
|
1.0
|
C1A
|
A:HEM301
|
3.1
|
69.4
|
1.0
|
C1D
|
A:HEM301
|
3.1
|
62.0
|
1.0
|
C1B
|
A:HEM301
|
3.1
|
75.7
|
1.0
|
C4A
|
A:HEM301
|
3.1
|
82.3
|
1.0
|
CD2
|
A:HIS160
|
3.1
|
88.7
|
1.0
|
CHC
|
A:HEM301
|
3.4
|
58.2
|
1.0
|
CHA
|
A:HEM301
|
3.4
|
70.0
|
1.0
|
CHD
|
A:HEM301
|
3.4
|
59.5
|
1.0
|
N
|
A:CYN303
|
3.5
|
74.6
|
1.0
|
CHB
|
A:HEM301
|
3.5
|
82.1
|
1.0
|
ND1
|
A:HIS160
|
4.2
|
88.8
|
1.0
|
C2C
|
A:HEM301
|
4.3
|
66.7
|
1.0
|
CG
|
A:HIS160
|
4.3
|
88.2
|
1.0
|
C3C
|
A:HEM301
|
4.3
|
63.3
|
1.0
|
C3B
|
A:HEM301
|
4.3
|
74.0
|
1.0
|
C3D
|
A:HEM301
|
4.3
|
72.2
|
1.0
|
C2B
|
A:HEM301
|
4.3
|
77.8
|
1.0
|
C2A
|
A:HEM301
|
4.3
|
72.2
|
1.0
|
C3A
|
A:HEM301
|
4.3
|
77.3
|
1.0
|
C2D
|
A:HEM301
|
4.3
|
63.0
|
1.0
|
|
Iron binding site 2 out
of 5 in 4m06
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Iron Binding Sites List in 4m06
Iron binding site 2 out
of 5 in the Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145F 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 Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145F in Complex with Cyanide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe301
b:64.4
occ:1.00
|
FE
|
B:HEM301
|
0.0
|
64.4
|
1.0
|
NC
|
B:HEM301
|
2.0
|
57.9
|
1.0
|
NB
|
B:HEM301
|
2.1
|
51.8
|
1.0
|
NA
|
B:HEM301
|
2.1
|
66.5
|
1.0
|
ND
|
B:HEM301
|
2.1
|
53.5
|
1.0
|
C
|
B:CYN302
|
2.2
|
83.6
|
1.0
|
NE2
|
B:HIS160
|
2.2
|
89.8
|
1.0
|
C1C
|
B:HEM301
|
3.0
|
60.9
|
1.0
|
C4B
|
B:HEM301
|
3.0
|
58.8
|
1.0
|
C4C
|
B:HEM301
|
3.0
|
61.9
|
1.0
|
C1A
|
B:HEM301
|
3.1
|
67.3
|
1.0
|
C1B
|
B:HEM301
|
3.1
|
66.7
|
1.0
|
C1D
|
B:HEM301
|
3.1
|
53.2
|
1.0
|
C4D
|
B:HEM301
|
3.1
|
58.9
|
1.0
|
CE1
|
B:HIS160
|
3.1
|
87.4
|
1.0
|
C4A
|
B:HEM301
|
3.1
|
72.6
|
1.0
|
CD2
|
B:HIS160
|
3.2
|
84.4
|
1.0
|
CHC
|
B:HEM301
|
3.4
|
59.5
|
1.0
|
CHD
|
B:HEM301
|
3.4
|
52.8
|
1.0
|
CHA
|
B:HEM301
|
3.5
|
65.8
|
1.0
|
N
|
B:CYN302
|
3.5
|
72.8
|
1.0
|
CHB
|
B:HEM301
|
3.5
|
70.5
|
1.0
|
C2C
|
B:HEM301
|
4.2
|
59.9
|
1.0
|
C3C
|
B:HEM301
|
4.2
|
65.4
|
1.0
|
C3B
|
B:HEM301
|
4.3
|
68.3
|
1.0
|
ND1
|
B:HIS160
|
4.3
|
81.1
|
1.0
|
C2B
|
B:HEM301
|
4.3
|
71.4
|
1.0
|
C2A
|
B:HEM301
|
4.3
|
64.5
|
1.0
|
C3A
|
B:HEM301
|
4.3
|
69.1
|
1.0
|
C2D
|
B:HEM301
|
4.3
|
61.1
|
1.0
|
C3D
|
B:HEM301
|
4.4
|
65.8
|
1.0
|
CG
|
B:HIS160
|
4.4
|
79.0
|
1.0
|
|
Iron binding site 3 out
of 5 in 4m06
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Iron Binding Sites List in 4m06
Iron binding site 3 out
of 5 in the Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145F 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 Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145F in Complex with Cyanide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe301
b:64.8
occ:1.00
|
FE
|
C:HEM301
|
0.0
|
64.8
|
1.0
|
NA
|
C:HEM301
|
2.0
|
77.7
|
1.0
|
NB
|
C:HEM301
|
2.1
|
61.6
|
1.0
|
ND
|
C:HEM301
|
2.1
|
59.8
|
1.0
|
NC
|
C:HEM301
|
2.1
|
62.2
|
1.0
|
NE2
|
C:HIS160
|
2.1
|
98.0
|
1.0
|
C
|
C:CYN302
|
2.2
|
78.8
|
1.0
|
CE1
|
C:HIS160
|
3.0
|
94.6
|
1.0
|
C1A
|
C:HEM301
|
3.1
|
79.4
|
1.0
|
C1D
|
C:HEM301
|
3.1
|
56.7
|
1.0
|
C4B
|
C:HEM301
|
3.1
|
70.6
|
1.0
|
C4D
|
C:HEM301
|
3.1
|
65.8
|
1.0
|
C1C
|
C:HEM301
|
3.1
|
65.7
|
1.0
|
C1B
|
C:HEM301
|
3.1
|
72.1
|
1.0
|
C4A
|
C:HEM301
|
3.1
|
72.9
|
1.0
|
C4C
|
C:HEM301
|
3.1
|
57.1
|
1.0
|
CD2
|
C:HIS160
|
3.1
|
93.1
|
1.0
|
CHD
|
C:HEM301
|
3.4
|
54.0
|
1.0
|
CHA
|
C:HEM301
|
3.4
|
75.5
|
1.0
|
CHC
|
C:HEM301
|
3.4
|
64.6
|
1.0
|
CHB
|
C:HEM301
|
3.4
|
76.0
|
1.0
|
N
|
C:CYN302
|
3.5
|
62.0
|
1.0
|
ND1
|
C:HIS160
|
4.1
|
91.7
|
1.0
|
CG
|
C:HIS160
|
4.2
|
88.6
|
1.0
|
C2A
|
C:HEM301
|
4.3
|
71.3
|
1.0
|
C2B
|
C:HEM301
|
4.3
|
80.3
|
1.0
|
C3B
|
C:HEM301
|
4.3
|
78.1
|
1.0
|
C2C
|
C:HEM301
|
4.3
|
65.4
|
1.0
|
C3A
|
C:HEM301
|
4.3
|
67.1
|
1.0
|
C2D
|
C:HEM301
|
4.3
|
56.9
|
1.0
|
C3D
|
C:HEM301
|
4.3
|
59.2
|
1.0
|
C3C
|
C:HEM301
|
4.3
|
61.2
|
1.0
|
|
Iron binding site 4 out
of 5 in 4m06
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Iron Binding Sites List in 4m06
Iron binding site 4 out
of 5 in the Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145F 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 Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145F in Complex with Cyanide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe301
b:76.4
occ:1.00
|
FE
|
D:HEM301
|
0.0
|
76.4
|
1.0
|
NC
|
D:HEM301
|
2.0
|
63.5
|
1.0
|
NB
|
D:HEM301
|
2.0
|
71.0
|
1.0
|
NA
|
D:HEM301
|
2.1
|
79.7
|
1.0
|
ND
|
D:HEM301
|
2.1
|
73.9
|
1.0
|
NE2
|
D:HIS160
|
2.1
|
91.7
|
1.0
|
C
|
D:CYN302
|
2.1
|
69.2
|
1.0
|
CE1
|
D:HIS160
|
2.8
|
89.5
|
1.0
|
C4C
|
D:HEM301
|
3.0
|
67.9
|
1.0
|
C1C
|
D:HEM301
|
3.0
|
69.5
|
1.0
|
C4B
|
D:HEM301
|
3.1
|
72.1
|
1.0
|
C1B
|
D:HEM301
|
3.1
|
79.4
|
1.0
|
C1D
|
D:HEM301
|
3.1
|
70.0
|
1.0
|
C4A
|
D:HEM301
|
3.1
|
79.1
|
1.0
|
C1A
|
D:HEM301
|
3.1
|
79.7
|
1.0
|
C4D
|
D:HEM301
|
3.1
|
77.0
|
1.0
|
CD2
|
D:HIS160
|
3.3
|
90.7
|
1.0
|
N
|
D:CYN302
|
3.4
|
63.2
|
1.0
|
CHD
|
D:HEM301
|
3.4
|
66.0
|
1.0
|
CHC
|
D:HEM301
|
3.4
|
62.5
|
1.0
|
CHB
|
D:HEM301
|
3.4
|
79.5
|
1.0
|
CHA
|
D:HEM301
|
3.4
|
80.6
|
1.0
|
ND1
|
D:HIS160
|
4.0
|
88.1
|
1.0
|
C3C
|
D:HEM301
|
4.3
|
66.4
|
1.0
|
CG
|
D:HIS160
|
4.3
|
88.4
|
1.0
|
C2C
|
D:HEM301
|
4.3
|
70.3
|
1.0
|
C2B
|
D:HEM301
|
4.3
|
85.5
|
1.0
|
C3B
|
D:HEM301
|
4.3
|
84.4
|
1.0
|
C3A
|
D:HEM301
|
4.3
|
74.6
|
1.0
|
C2A
|
D:HEM301
|
4.3
|
77.0
|
1.0
|
C2D
|
D:HEM301
|
4.3
|
72.4
|
1.0
|
C3D
|
D:HEM301
|
4.3
|
74.5
|
1.0
|
|
Iron binding site 5 out
of 5 in 4m06
Go back to
Iron Binding Sites List in 4m06
Iron binding site 5 out
of 5 in the Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145F 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 Crystal Structure of Mutant Chlorite Dismutase From Candidatus Nitrospira Defluvii W145F in Complex with Cyanide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe301
b:70.4
occ:1.00
|
FE
|
E:HEM301
|
0.0
|
70.4
|
1.0
|
NB
|
E:HEM301
|
2.0
|
62.5
|
1.0
|
NC
|
E:HEM301
|
2.0
|
61.0
|
1.0
|
NA
|
E:HEM301
|
2.1
|
72.4
|
1.0
|
ND
|
E:HEM301
|
2.1
|
65.9
|
1.0
|
NE2
|
E:HIS160
|
2.1
|
0.3
|
1.0
|
C
|
E:CYN302
|
2.2
|
92.5
|
1.0
|
C1B
|
E:HEM301
|
3.0
|
71.7
|
1.0
|
C4B
|
E:HEM301
|
3.0
|
66.4
|
1.0
|
CE1
|
E:HIS160
|
3.1
|
0.7
|
1.0
|
C1C
|
E:HEM301
|
3.1
|
65.3
|
1.0
|
C4A
|
E:HEM301
|
3.1
|
75.3
|
1.0
|
C4C
|
E:HEM301
|
3.1
|
64.6
|
1.0
|
C1A
|
E:HEM301
|
3.1
|
73.7
|
1.0
|
C1D
|
E:HEM301
|
3.1
|
63.0
|
1.0
|
C4D
|
E:HEM301
|
3.1
|
71.4
|
1.0
|
CD2
|
E:HIS160
|
3.2
|
0.2
|
1.0
|
N
|
E:CYN302
|
3.3
|
87.9
|
1.0
|
CHB
|
E:HEM301
|
3.4
|
76.3
|
1.0
|
CHC
|
E:HEM301
|
3.4
|
70.0
|
1.0
|
CHD
|
E:HEM301
|
3.4
|
64.5
|
1.0
|
CHA
|
E:HEM301
|
3.5
|
76.9
|
1.0
|
ND1
|
E:HIS160
|
4.2
|
0.3
|
1.0
|
C2B
|
E:HEM301
|
4.3
|
78.2
|
1.0
|
C3B
|
E:HEM301
|
4.3
|
69.8
|
1.0
|
C3A
|
E:HEM301
|
4.3
|
67.5
|
1.0
|
CG
|
E:HIS160
|
4.3
|
95.0
|
1.0
|
C2C
|
E:HEM301
|
4.3
|
66.8
|
1.0
|
C2A
|
E:HEM301
|
4.3
|
65.7
|
1.0
|
C3C
|
E:HEM301
|
4.3
|
63.6
|
1.0
|
C2D
|
E:HEM301
|
4.3
|
62.2
|
1.0
|
C3D
|
E:HEM301
|
4.3
|
71.9
|
1.0
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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
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