Iron in PDB 1qnn: Cambialistic Superoxide Dismutase From Porphyromonas Gingivalis
Enzymatic activity of Cambialistic Superoxide Dismutase From Porphyromonas Gingivalis
All present enzymatic activity of Cambialistic Superoxide Dismutase From Porphyromonas Gingivalis:
1.15.1.1;
Protein crystallography data
The structure of Cambialistic Superoxide Dismutase From Porphyromonas Gingivalis, PDB code: 1qnn
was solved by
S.Sugio,
B.Y.Hiraoka,
F.Yamakura,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
1.80
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
75.470,
102.660,
99.590,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.9 /
22.3
|
Iron Binding Sites:
The binding sites of Iron atom in the Cambialistic Superoxide Dismutase From Porphyromonas Gingivalis
(pdb code 1qnn). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Cambialistic Superoxide Dismutase From Porphyromonas Gingivalis, PDB code: 1qnn:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 1qnn
Go back to
Iron Binding Sites List in 1qnn
Iron binding site 1 out
of 4 in the Cambialistic Superoxide Dismutase From Porphyromonas Gingivalis
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Cambialistic Superoxide Dismutase From Porphyromonas Gingivalis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:20.1
occ:1.00
|
OD2
|
A:ASP157
|
1.9
|
16.3
|
1.0
|
O
|
A:HOH2085
|
2.1
|
13.6
|
1.0
|
NE2
|
A:HIS161
|
2.1
|
14.7
|
1.0
|
NE2
|
A:HIS74
|
2.1
|
15.5
|
1.0
|
NE2
|
A:HIS27
|
2.1
|
6.2
|
1.0
|
CE1
|
A:HIS74
|
3.0
|
16.5
|
1.0
|
CE1
|
A:HIS27
|
3.0
|
9.2
|
1.0
|
CG
|
A:ASP157
|
3.0
|
15.9
|
1.0
|
CD2
|
A:HIS161
|
3.1
|
16.8
|
1.0
|
CE1
|
A:HIS161
|
3.1
|
15.7
|
1.0
|
CD2
|
A:HIS27
|
3.2
|
11.1
|
1.0
|
CD2
|
A:HIS74
|
3.2
|
16.6
|
1.0
|
OD1
|
A:ASP157
|
3.6
|
17.4
|
1.0
|
ND1
|
A:HIS27
|
4.1
|
7.9
|
1.0
|
CZ2
|
A:TRP123
|
4.2
|
15.4
|
1.0
|
ND1
|
A:HIS74
|
4.2
|
17.6
|
1.0
|
ND1
|
A:HIS161
|
4.2
|
14.7
|
1.0
|
CG
|
A:HIS161
|
4.2
|
15.0
|
1.0
|
CG
|
A:HIS27
|
4.3
|
9.5
|
1.0
|
CB
|
A:ASP157
|
4.3
|
15.6
|
1.0
|
CG
|
A:HIS74
|
4.3
|
17.2
|
1.0
|
CB
|
A:TRP159
|
4.5
|
12.0
|
1.0
|
CH2
|
A:TRP123
|
4.6
|
15.8
|
1.0
|
NE2
|
A:GLN70
|
4.7
|
18.5
|
1.0
|
CG
|
A:TRP159
|
4.7
|
11.4
|
1.0
|
CB
|
A:ALA162
|
4.9
|
12.6
|
1.0
|
|
Iron binding site 2 out
of 4 in 1qnn
Go back to
Iron Binding Sites List in 1qnn
Iron binding site 2 out
of 4 in the Cambialistic Superoxide Dismutase From Porphyromonas Gingivalis
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Cambialistic Superoxide Dismutase From Porphyromonas Gingivalis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe201
b:20.6
occ:1.00
|
OD2
|
B:ASP157
|
1.8
|
15.5
|
1.0
|
O
|
B:HOH2088
|
2.1
|
15.5
|
1.0
|
NE2
|
B:HIS161
|
2.1
|
16.1
|
1.0
|
NE2
|
B:HIS74
|
2.2
|
17.7
|
1.0
|
NE2
|
B:HIS27
|
2.2
|
10.3
|
1.0
|
CG
|
B:ASP157
|
3.0
|
18.6
|
1.0
|
CE1
|
B:HIS74
|
3.0
|
18.8
|
1.0
|
CE1
|
B:HIS161
|
3.1
|
17.2
|
1.0
|
CD2
|
B:HIS161
|
3.1
|
16.3
|
1.0
|
CE1
|
B:HIS27
|
3.1
|
11.9
|
1.0
|
CD2
|
B:HIS27
|
3.2
|
12.1
|
1.0
|
CD2
|
B:HIS74
|
3.2
|
18.4
|
1.0
|
OD1
|
B:ASP157
|
3.5
|
16.5
|
1.0
|
CZ2
|
B:TRP123
|
4.1
|
18.6
|
1.0
|
ND1
|
B:HIS74
|
4.2
|
19.5
|
1.0
|
ND1
|
B:HIS161
|
4.2
|
16.0
|
1.0
|
CB
|
B:ASP157
|
4.2
|
17.4
|
1.0
|
CG
|
B:HIS161
|
4.2
|
14.2
|
1.0
|
ND1
|
B:HIS27
|
4.3
|
11.8
|
1.0
|
CG
|
B:HIS74
|
4.3
|
18.9
|
1.0
|
CG
|
B:HIS27
|
4.3
|
12.1
|
1.0
|
CB
|
B:TRP159
|
4.5
|
14.0
|
1.0
|
CH2
|
B:TRP123
|
4.6
|
16.9
|
1.0
|
NE2
|
B:GLN70
|
4.6
|
21.4
|
1.0
|
CG
|
B:TRP159
|
4.7
|
14.0
|
1.0
|
CB
|
B:ALA162
|
4.9
|
18.1
|
1.0
|
|
Iron binding site 3 out
of 4 in 1qnn
Go back to
Iron Binding Sites List in 1qnn
Iron binding site 3 out
of 4 in the Cambialistic Superoxide Dismutase From Porphyromonas Gingivalis
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Cambialistic Superoxide Dismutase From Porphyromonas Gingivalis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:18.9
occ:1.00
|
OD2
|
C:ASP157
|
1.8
|
13.7
|
1.0
|
O
|
C:HOH2117
|
2.1
|
18.6
|
1.0
|
NE2
|
C:HIS74
|
2.1
|
16.2
|
1.0
|
NE2
|
C:HIS161
|
2.2
|
12.6
|
1.0
|
NE2
|
C:HIS27
|
2.2
|
11.9
|
1.0
|
CG
|
C:ASP157
|
2.9
|
16.9
|
1.0
|
CE1
|
C:HIS74
|
2.9
|
14.7
|
1.0
|
CD2
|
C:HIS161
|
3.1
|
15.8
|
1.0
|
CE1
|
C:HIS27
|
3.2
|
12.8
|
1.0
|
CD2
|
C:HIS74
|
3.2
|
16.3
|
1.0
|
CD2
|
C:HIS27
|
3.2
|
13.1
|
1.0
|
CE1
|
C:HIS161
|
3.2
|
15.2
|
1.0
|
OD1
|
C:ASP157
|
3.4
|
17.8
|
1.0
|
ND1
|
C:HIS74
|
4.1
|
13.5
|
1.0
|
CZ2
|
C:TRP123
|
4.1
|
15.4
|
1.0
|
CB
|
C:ASP157
|
4.2
|
14.8
|
1.0
|
CG
|
C:HIS74
|
4.3
|
15.5
|
1.0
|
ND1
|
C:HIS27
|
4.3
|
11.3
|
1.0
|
CG
|
C:HIS161
|
4.3
|
14.6
|
1.0
|
ND1
|
C:HIS161
|
4.3
|
11.4
|
1.0
|
CG
|
C:HIS27
|
4.3
|
11.0
|
1.0
|
CB
|
C:TRP159
|
4.5
|
12.0
|
1.0
|
NE2
|
C:GLN70
|
4.6
|
13.6
|
1.0
|
CH2
|
C:TRP123
|
4.6
|
13.2
|
1.0
|
CG
|
C:TRP159
|
4.7
|
11.2
|
1.0
|
CB
|
C:ALA162
|
4.8
|
15.0
|
1.0
|
CE2
|
C:TRP123
|
5.0
|
14.5
|
1.0
|
|
Iron binding site 4 out
of 4 in 1qnn
Go back to
Iron Binding Sites List in 1qnn
Iron binding site 4 out
of 4 in the Cambialistic Superoxide Dismutase From Porphyromonas Gingivalis
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Cambialistic Superoxide Dismutase From Porphyromonas Gingivalis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe201
b:27.4
occ:1.00
|
OD2
|
D:ASP157
|
1.9
|
20.1
|
1.0
|
NE2
|
D:HIS161
|
2.2
|
21.1
|
1.0
|
O
|
D:HOH2056
|
2.2
|
19.2
|
1.0
|
NE2
|
D:HIS74
|
2.2
|
29.9
|
1.0
|
NE2
|
D:HIS27
|
2.2
|
24.3
|
1.0
|
CG
|
D:ASP157
|
3.0
|
22.9
|
1.0
|
CD2
|
D:HIS161
|
3.1
|
21.9
|
1.0
|
CE1
|
D:HIS74
|
3.1
|
29.7
|
1.0
|
CD2
|
D:HIS27
|
3.1
|
24.3
|
1.0
|
CE1
|
D:HIS161
|
3.2
|
20.5
|
1.0
|
CE1
|
D:HIS27
|
3.2
|
25.4
|
1.0
|
CD2
|
D:HIS74
|
3.2
|
30.4
|
1.0
|
OD1
|
D:ASP157
|
3.5
|
23.3
|
1.0
|
ND1
|
D:HIS161
|
4.3
|
22.3
|
1.0
|
CB
|
D:ASP157
|
4.3
|
22.0
|
1.0
|
ND1
|
D:HIS74
|
4.3
|
29.8
|
1.0
|
CG
|
D:HIS161
|
4.3
|
21.6
|
1.0
|
CZ2
|
D:TRP123
|
4.3
|
25.7
|
1.0
|
ND1
|
D:HIS27
|
4.3
|
24.1
|
1.0
|
CG
|
D:HIS27
|
4.3
|
25.2
|
1.0
|
CG
|
D:HIS74
|
4.4
|
30.6
|
1.0
|
CB
|
D:TRP159
|
4.5
|
16.3
|
1.0
|
NE2
|
D:GLN70
|
4.6
|
26.1
|
1.0
|
CG
|
D:TRP159
|
4.7
|
16.1
|
1.0
|
CH2
|
D:TRP123
|
4.8
|
24.8
|
1.0
|
CB
|
D:ALA162
|
4.9
|
22.2
|
1.0
|
CD1
|
D:TRP159
|
5.0
|
15.8
|
1.0
|
|
Reference:
S.Sugio,
B.Y.Hiraoka,
F.Yamakura.
Crystal Structure of Cambialistic Superoxide Dismutase From Porphyromonas Gingivalis Eur.J.Biochem. V. 267 3487 2000.
ISSN: ISSN 0014-2956
PubMed: 10848964
DOI: 10.1046/J.1432-1327.2000.01373.X
Page generated: Sat Aug 3 13:36:08 2024
|