Iron in PDB 8avl: Superoxide Dismutase SODFM2 From Bacteroides Fragilis
Enzymatic activity of Superoxide Dismutase SODFM2 From Bacteroides Fragilis
All present enzymatic activity of Superoxide Dismutase SODFM2 From Bacteroides Fragilis:
1.15.1.1;
Protein crystallography data
The structure of Superoxide Dismutase SODFM2 From Bacteroides Fragilis, PDB code: 8avl
was solved by
A.Basle,
A.Barwinska-Sendra,
K.M.Sendra,
K.Waldron,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
103.55 /
1.60
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
71.13,
100.11,
103.6,
90,
91.8,
90
|
|
R / Rfree (%)
|
13.3 /
20.4
|
Iron Binding Sites:
The binding sites of Iron atom in the Superoxide Dismutase SODFM2 From Bacteroides Fragilis
(pdb code 8avl). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the
Superoxide Dismutase SODFM2 From Bacteroides Fragilis, PDB code: 8avl:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 8avl
Go back to
Iron Binding Sites List in 8avl
Iron binding site 1 out
of 8 in the Superoxide Dismutase SODFM2 From Bacteroides Fragilis
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Superoxide Dismutase SODFM2 From Bacteroides Fragilis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:23.0
occ:1.00
|
OD2
|
A:ASP158
|
2.0
|
12.8
|
1.0
|
|
NE2
|
A:HIS74
|
2.1
|
14.8
|
1.0
|
|
O
|
A:HOH389
|
2.1
|
13.9
|
1.0
|
|
NE2
|
A:HIS162
|
2.2
|
15.9
|
1.0
|
|
NE2
|
A:HIS26
|
2.2
|
13.1
|
1.0
|
|
CD2
|
A:HIS162
|
3.0
|
17.2
|
1.0
|
|
HD2
|
A:HIS162
|
3.0
|
16.3
|
1.0
|
|
CE1
|
A:HIS74
|
3.0
|
16.0
|
1.0
|
|
CG
|
A:ASP158
|
3.0
|
13.7
|
1.0
|
|
HE1
|
A:HIS74
|
3.2
|
16.2
|
1.0
|
|
CD2
|
A:HIS74
|
3.2
|
14.0
|
1.0
|
|
CE1
|
A:HIS26
|
3.2
|
16.4
|
1.0
|
|
CD2
|
A:HIS26
|
3.2
|
17.4
|
1.0
|
|
CE1
|
A:HIS162
|
3.3
|
17.2
|
1.0
|
|
HD2
|
A:HIS26
|
3.3
|
16.8
|
1.0
|
|
HE1
|
A:HIS26
|
3.4
|
15.8
|
1.0
|
|
HD2
|
A:HIS74
|
3.4
|
13.4
|
1.0
|
|
OD1
|
A:ASP158
|
3.5
|
15.7
|
1.0
|
|
HZ2
|
A:TRP124
|
3.5
|
15.5
|
1.0
|
|
HE1
|
A:HIS162
|
3.6
|
16.4
|
1.0
|
|
HB2
|
A:TRP160
|
3.7
|
14.2
|
1.0
|
|
HB2
|
A:ALA163
|
4.0
|
16.7
|
1.0
|
|
ND1
|
A:HIS74
|
4.1
|
15.9
|
1.0
|
|
CZ2
|
A:TRP124
|
4.2
|
15.3
|
1.0
|
|
CG
|
A:HIS162
|
4.2
|
15.8
|
1.0
|
|
CG
|
A:HIS74
|
4.2
|
13.3
|
1.0
|
|
ND1
|
A:HIS26
|
4.3
|
16.4
|
1.0
|
|
CG
|
A:HIS26
|
4.3
|
15.3
|
1.0
|
|
ND1
|
A:HIS162
|
4.3
|
15.4
|
1.0
|
|
CB
|
A:ASP158
|
4.3
|
12.9
|
1.0
|
|
HE2
|
A:TYR34
|
4.4
|
15.9
|
1.0
|
|
HB2
|
A:ASP158
|
4.4
|
12.3
|
1.0
|
|
HH2
|
A:TRP124
|
4.5
|
17.3
|
1.0
|
|
CB
|
A:TRP160
|
4.5
|
14.2
|
1.0
|
|
HB3
|
A:ASP158
|
4.5
|
12.8
|
1.0
|
|
NE2
|
A:GLN70
|
4.6
|
16.4
|
1.0
|
|
CH2
|
A:TRP124
|
4.7
|
18.4
|
1.0
|
|
HB3
|
A:TRP160
|
4.7
|
14.3
|
1.0
|
|
CG
|
A:TRP160
|
4.7
|
14.0
|
1.0
|
|
HA
|
A:ALA163
|
4.9
|
17.6
|
1.0
|
|
CB
|
A:ALA163
|
4.9
|
16.2
|
1.0
|
|
HB3
|
A:HIS30
|
4.9
|
17.2
|
1.0
|
|
H
|
A:ALA163
|
5.0
|
14.9
|
1.0
|
|
Iron binding site 2 out
of 8 in 8avl
Go back to
Iron Binding Sites List in 8avl
Iron binding site 2 out
of 8 in the Superoxide Dismutase SODFM2 From Bacteroides Fragilis
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Superoxide Dismutase SODFM2 From Bacteroides Fragilis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe202
b:24.1
occ:1.00
|
OD2
|
B:ASP158
|
2.0
|
15.9
|
1.0
|
|
O
|
B:HOH394
|
2.1
|
13.9
|
1.0
|
|
NE2
|
B:HIS74
|
2.2
|
16.5
|
1.0
|
|
NE2
|
B:HIS162
|
2.2
|
17.9
|
1.0
|
|
NE2
|
B:HIS26
|
2.2
|
12.0
|
1.0
|
|
CD2
|
B:HIS162
|
3.0
|
20.1
|
1.0
|
|
CG
|
B:ASP158
|
3.0
|
14.8
|
1.0
|
|
HD2
|
B:HIS162
|
3.1
|
18.9
|
1.0
|
|
CE1
|
B:HIS74
|
3.1
|
14.7
|
1.0
|
|
CD2
|
B:HIS26
|
3.2
|
14.1
|
1.0
|
|
CE1
|
B:HIS26
|
3.2
|
16.8
|
1.0
|
|
CD2
|
B:HIS74
|
3.2
|
17.0
|
1.0
|
|
HE1
|
B:HIS74
|
3.2
|
15.5
|
1.0
|
|
CE1
|
B:HIS162
|
3.3
|
16.3
|
1.0
|
|
HD2
|
B:HIS26
|
3.3
|
13.3
|
1.0
|
|
HE1
|
B:HIS26
|
3.4
|
15.0
|
1.0
|
|
HD2
|
B:HIS74
|
3.4
|
15.9
|
1.0
|
|
OD1
|
B:ASP158
|
3.5
|
16.2
|
1.0
|
|
HZ2
|
B:TRP124
|
3.5
|
14.1
|
1.0
|
|
HE1
|
B:HIS162
|
3.6
|
16.9
|
1.0
|
|
HB2
|
B:TRP160
|
3.7
|
13.8
|
1.0
|
|
HB2
|
B:ALA163
|
4.0
|
15.7
|
1.0
|
|
CZ2
|
B:TRP124
|
4.2
|
13.8
|
1.0
|
|
ND1
|
B:HIS74
|
4.2
|
14.9
|
1.0
|
|
CG
|
B:HIS162
|
4.2
|
17.4
|
1.0
|
|
HE2
|
B:TYR34
|
4.3
|
15.8
|
1.0
|
|
CG
|
B:HIS74
|
4.3
|
15.2
|
1.0
|
|
CB
|
B:ASP158
|
4.3
|
14.8
|
1.0
|
|
CG
|
B:HIS26
|
4.3
|
12.8
|
1.0
|
|
ND1
|
B:HIS26
|
4.3
|
15.3
|
1.0
|
|
ND1
|
B:HIS162
|
4.4
|
15.9
|
1.0
|
|
HB2
|
B:ASP158
|
4.4
|
14.5
|
1.0
|
|
HB3
|
B:ASP158
|
4.5
|
14.8
|
1.0
|
|
CB
|
B:TRP160
|
4.5
|
13.5
|
1.0
|
|
HH2
|
B:TRP124
|
4.5
|
15.4
|
1.0
|
|
NE2
|
B:GLN70
|
4.6
|
14.4
|
1.0
|
|
CH2
|
B:TRP124
|
4.7
|
15.0
|
1.0
|
|
CG
|
B:TRP160
|
4.7
|
13.1
|
1.0
|
|
HB3
|
B:TRP160
|
4.8
|
12.8
|
1.0
|
|
CB
|
B:ALA163
|
4.9
|
15.7
|
1.0
|
|
HA
|
B:ALA163
|
4.9
|
15.1
|
1.0
|
|
HB3
|
B:HIS30
|
4.9
|
14.2
|
1.0
|
|
CD1
|
B:TRP160
|
5.0
|
15.1
|
1.0
|
|
Iron binding site 3 out
of 8 in 8avl
Go back to
Iron Binding Sites List in 8avl
Iron binding site 3 out
of 8 in the Superoxide Dismutase SODFM2 From Bacteroides Fragilis
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Superoxide Dismutase SODFM2 From Bacteroides Fragilis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:28.5
occ:1.00
|
OD2
|
C:ASP158
|
2.0
|
18.5
|
1.0
|
|
NE2
|
C:HIS74
|
2.1
|
21.5
|
1.0
|
|
O
|
C:HOH364
|
2.2
|
19.5
|
1.0
|
|
NE2
|
C:HIS162
|
2.2
|
17.7
|
1.0
|
|
NE2
|
C:HIS26
|
2.3
|
17.2
|
1.0
|
|
CE1
|
C:HIS74
|
3.0
|
25.4
|
1.0
|
|
CD2
|
C:HIS162
|
3.0
|
19.8
|
1.0
|
|
CG
|
C:ASP158
|
3.1
|
20.6
|
1.0
|
|
HD2
|
C:HIS162
|
3.1
|
18.4
|
1.0
|
|
CD2
|
C:HIS74
|
3.1
|
23.9
|
1.0
|
|
HE1
|
C:HIS74
|
3.2
|
24.4
|
1.0
|
|
CD2
|
C:HIS26
|
3.2
|
23.2
|
1.0
|
|
CE1
|
C:HIS26
|
3.2
|
17.1
|
1.0
|
|
CE1
|
C:HIS162
|
3.3
|
21.0
|
1.0
|
|
HD2
|
C:HIS26
|
3.4
|
21.6
|
1.0
|
|
HD2
|
C:HIS74
|
3.4
|
22.4
|
1.0
|
|
HE1
|
C:HIS26
|
3.4
|
16.7
|
1.0
|
|
HZ2
|
C:TRP124
|
3.5
|
22.1
|
1.0
|
|
OD1
|
C:ASP158
|
3.5
|
19.1
|
1.0
|
|
HE1
|
C:HIS162
|
3.6
|
20.2
|
1.0
|
|
HB2
|
C:TRP160
|
3.7
|
15.5
|
1.0
|
|
HB2
|
C:ALA163
|
4.0
|
16.6
|
1.0
|
|
CZ2
|
C:TRP124
|
4.1
|
22.7
|
1.0
|
|
ND1
|
C:HIS74
|
4.1
|
22.0
|
1.0
|
|
CG
|
C:HIS74
|
4.2
|
19.2
|
1.0
|
|
CG
|
C:HIS162
|
4.2
|
17.5
|
1.0
|
|
ND1
|
C:HIS26
|
4.3
|
18.4
|
1.0
|
|
CB
|
C:ASP158
|
4.3
|
18.1
|
1.0
|
|
CG
|
C:HIS26
|
4.3
|
19.5
|
1.0
|
|
ND1
|
C:HIS162
|
4.3
|
19.8
|
1.0
|
|
HE2
|
C:TYR34
|
4.4
|
25.5
|
1.0
|
|
HB2
|
C:ASP158
|
4.4
|
17.9
|
1.0
|
|
HH2
|
C:TRP124
|
4.5
|
23.5
|
1.0
|
|
CB
|
C:TRP160
|
4.6
|
15.4
|
1.0
|
|
HB3
|
C:ASP158
|
4.6
|
18.1
|
1.0
|
|
NE2
|
C:GLN70
|
4.6
|
27.0
|
1.0
|
|
CH2
|
C:TRP124
|
4.7
|
24.9
|
1.0
|
|
CG
|
C:TRP160
|
4.7
|
16.0
|
1.0
|
|
HB3
|
C:TRP160
|
4.8
|
15.9
|
1.0
|
|
CE2
|
C:TRP124
|
5.0
|
20.4
|
1.0
|
|
CB
|
C:ALA163
|
5.0
|
16.8
|
1.0
|
|
HE1
|
C:TRP124
|
5.0
|
21.0
|
1.0
|
|
HB3
|
C:HIS30
|
5.0
|
20.0
|
1.0
|
|
HA
|
C:ALA163
|
5.0
|
15.8
|
1.0
|
|
Iron binding site 4 out
of 8 in 8avl
Go back to
Iron Binding Sites List in 8avl
Iron binding site 4 out
of 8 in the Superoxide Dismutase SODFM2 From Bacteroides Fragilis
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Superoxide Dismutase SODFM2 From Bacteroides Fragilis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe201
b:23.8
occ:1.00
|
OD2
|
D:ASP158
|
2.1
|
15.9
|
1.0
|
|
NE2
|
D:HIS74
|
2.1
|
16.2
|
1.0
|
|
NE2
|
D:HIS162
|
2.2
|
18.5
|
1.0
|
|
O
|
D:HOH369
|
2.2
|
15.3
|
1.0
|
|
NE2
|
D:HIS26
|
2.2
|
16.8
|
1.0
|
|
CD2
|
D:HIS162
|
3.0
|
18.9
|
1.0
|
|
CE1
|
D:HIS74
|
3.1
|
18.9
|
1.0
|
|
HD2
|
D:HIS162
|
3.1
|
17.6
|
1.0
|
|
CG
|
D:ASP158
|
3.1
|
15.6
|
1.0
|
|
CD2
|
D:HIS26
|
3.2
|
16.3
|
1.0
|
|
HE1
|
D:HIS74
|
3.2
|
17.5
|
1.0
|
|
CD2
|
D:HIS74
|
3.2
|
16.2
|
1.0
|
|
CE1
|
D:HIS26
|
3.2
|
17.6
|
1.0
|
|
CE1
|
D:HIS162
|
3.3
|
21.2
|
1.0
|
|
HD2
|
D:HIS26
|
3.3
|
16.3
|
1.0
|
|
HD2
|
D:HIS74
|
3.4
|
15.9
|
1.0
|
|
HE1
|
D:HIS26
|
3.4
|
17.1
|
1.0
|
|
HZ2
|
D:TRP124
|
3.5
|
16.0
|
1.0
|
|
OD1
|
D:ASP158
|
3.5
|
18.4
|
1.0
|
|
HE1
|
D:HIS162
|
3.6
|
20.2
|
1.0
|
|
HB2
|
D:TRP160
|
3.8
|
16.2
|
1.0
|
|
HB2
|
D:ALA163
|
4.0
|
18.4
|
1.0
|
|
CZ2
|
D:TRP124
|
4.1
|
15.9
|
1.0
|
|
ND1
|
D:HIS74
|
4.2
|
16.1
|
1.0
|
|
CG
|
D:HIS162
|
4.2
|
16.2
|
1.0
|
|
CG
|
D:HIS74
|
4.3
|
15.7
|
1.0
|
|
CG
|
D:HIS26
|
4.3
|
15.7
|
1.0
|
|
ND1
|
D:HIS26
|
4.3
|
16.4
|
1.0
|
|
ND1
|
D:HIS162
|
4.3
|
17.4
|
1.0
|
|
CB
|
D:ASP158
|
4.4
|
15.7
|
1.0
|
|
HE2
|
D:TYR34
|
4.4
|
20.6
|
1.0
|
|
HB2
|
D:ASP158
|
4.4
|
14.6
|
1.0
|
|
HH2
|
D:TRP124
|
4.5
|
18.8
|
1.0
|
|
HB3
|
D:ASP158
|
4.6
|
15.5
|
1.0
|
|
NE2
|
D:GLN70
|
4.6
|
16.3
|
1.0
|
|
CB
|
D:TRP160
|
4.6
|
16.6
|
1.0
|
|
CH2
|
D:TRP124
|
4.7
|
18.4
|
1.0
|
|
CG
|
D:TRP160
|
4.8
|
15.6
|
1.0
|
|
HB3
|
D:TRP160
|
4.8
|
16.4
|
1.0
|
|
CB
|
D:ALA163
|
5.0
|
18.4
|
1.0
|
|
HE1
|
D:TRP124
|
5.0
|
18.1
|
1.0
|
|
HA
|
D:ALA163
|
5.0
|
16.9
|
1.0
|
|
HB3
|
D:HIS30
|
5.0
|
17.4
|
1.0
|
|
CE2
|
D:TRP124
|
5.0
|
18.2
|
1.0
|
|
Iron binding site 5 out
of 8 in 8avl
Go back to
Iron Binding Sites List in 8avl
Iron binding site 5 out
of 8 in the Superoxide Dismutase SODFM2 From Bacteroides Fragilis
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Superoxide Dismutase SODFM2 From Bacteroides Fragilis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe201
b:25.4
occ:1.00
|
OD2
|
E:ASP158
|
2.0
|
16.7
|
1.0
|
|
NE2
|
E:HIS74
|
2.1
|
17.5
|
1.0
|
|
O
|
E:HOH383
|
2.2
|
17.5
|
1.0
|
|
NE2
|
E:HIS162
|
2.2
|
19.4
|
1.0
|
|
NE2
|
E:HIS26
|
2.3
|
17.1
|
1.0
|
|
CD2
|
E:HIS162
|
3.0
|
19.3
|
1.0
|
|
CE1
|
E:HIS74
|
3.0
|
16.4
|
1.0
|
|
HD2
|
E:HIS162
|
3.1
|
18.1
|
1.0
|
|
CG
|
E:ASP158
|
3.1
|
17.0
|
1.0
|
|
CD2
|
E:HIS74
|
3.2
|
20.0
|
1.0
|
|
HE1
|
E:HIS74
|
3.2
|
16.9
|
1.0
|
|
CD2
|
E:HIS26
|
3.2
|
18.7
|
1.0
|
|
CE1
|
E:HIS26
|
3.2
|
18.5
|
1.0
|
|
CE1
|
E:HIS162
|
3.3
|
18.4
|
1.0
|
|
HD2
|
E:HIS26
|
3.4
|
17.8
|
1.0
|
|
HD2
|
E:HIS74
|
3.4
|
18.1
|
1.0
|
|
HE1
|
E:HIS26
|
3.4
|
17.8
|
1.0
|
|
HZ2
|
E:TRP124
|
3.5
|
16.3
|
1.0
|
|
OD1
|
E:ASP158
|
3.5
|
17.9
|
1.0
|
|
HE1
|
E:HIS162
|
3.5
|
18.1
|
1.0
|
|
HB2
|
E:TRP160
|
3.7
|
15.7
|
1.0
|
|
HB2
|
E:ALA163
|
4.0
|
16.7
|
1.0
|
|
CZ2
|
E:TRP124
|
4.1
|
16.8
|
1.0
|
|
ND1
|
E:HIS74
|
4.2
|
17.3
|
1.0
|
|
CG
|
E:HIS162
|
4.2
|
18.0
|
1.0
|
|
CG
|
E:HIS74
|
4.2
|
18.4
|
1.0
|
|
ND1
|
E:HIS162
|
4.3
|
16.6
|
1.0
|
|
ND1
|
E:HIS26
|
4.3
|
17.6
|
1.0
|
|
CG
|
E:HIS26
|
4.3
|
16.0
|
1.0
|
|
HE2
|
E:TYR34
|
4.3
|
22.2
|
1.0
|
|
CB
|
E:ASP158
|
4.3
|
14.5
|
1.0
|
|
HB2
|
E:ASP158
|
4.4
|
14.9
|
1.0
|
|
HH2
|
E:TRP124
|
4.5
|
17.1
|
1.0
|
|
CB
|
E:TRP160
|
4.5
|
15.9
|
1.0
|
|
NE2
|
E:GLN70
|
4.6
|
20.1
|
1.0
|
|
HB3
|
E:ASP158
|
4.6
|
14.9
|
1.0
|
|
CH2
|
E:TRP124
|
4.7
|
16.9
|
1.0
|
|
CG
|
E:TRP160
|
4.7
|
16.5
|
1.0
|
|
HB3
|
E:TRP160
|
4.8
|
16.2
|
1.0
|
|
HA
|
E:ALA163
|
4.9
|
16.1
|
1.0
|
|
CB
|
E:ALA163
|
5.0
|
17.0
|
1.0
|
|
HB3
|
E:HIS30
|
5.0
|
19.5
|
1.0
|
|
CE2
|
E:TRP124
|
5.0
|
17.5
|
1.0
|
|
CD1
|
E:TRP160
|
5.0
|
15.3
|
1.0
|
|
HE1
|
E:TRP124
|
5.0
|
19.2
|
1.0
|
|
Iron binding site 6 out
of 8 in 8avl
Go back to
Iron Binding Sites List in 8avl
Iron binding site 6 out
of 8 in the Superoxide Dismutase SODFM2 From Bacteroides Fragilis
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Superoxide Dismutase SODFM2 From Bacteroides Fragilis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe201
b:23.3
occ:1.00
|
OD2
|
F:ASP158
|
2.0
|
16.0
|
1.0
|
|
NE2
|
F:HIS74
|
2.1
|
17.2
|
1.0
|
|
NE2
|
F:HIS162
|
2.2
|
15.3
|
1.0
|
|
O
|
F:HOH415
|
2.2
|
14.6
|
1.0
|
|
NE2
|
F:HIS26
|
2.2
|
14.0
|
1.0
|
|
CD2
|
F:HIS162
|
3.0
|
16.7
|
1.0
|
|
CE1
|
F:HIS74
|
3.0
|
14.8
|
1.0
|
|
CG
|
F:ASP158
|
3.1
|
13.4
|
1.0
|
|
HD2
|
F:HIS162
|
3.1
|
16.0
|
1.0
|
|
CD2
|
F:HIS74
|
3.1
|
17.0
|
1.0
|
|
CD2
|
F:HIS26
|
3.2
|
14.0
|
1.0
|
|
HE1
|
F:HIS74
|
3.2
|
15.6
|
1.0
|
|
CE1
|
F:HIS26
|
3.2
|
17.2
|
1.0
|
|
CE1
|
F:HIS162
|
3.3
|
18.2
|
1.0
|
|
HD2
|
F:HIS26
|
3.3
|
12.6
|
1.0
|
|
HD2
|
F:HIS74
|
3.3
|
16.9
|
1.0
|
|
HE1
|
F:HIS26
|
3.4
|
16.4
|
1.0
|
|
OD1
|
F:ASP158
|
3.5
|
14.8
|
1.0
|
|
HZ2
|
F:TRP124
|
3.5
|
16.7
|
1.0
|
|
HE1
|
F:HIS162
|
3.6
|
17.1
|
1.0
|
|
HB2
|
F:TRP160
|
3.7
|
14.2
|
1.0
|
|
HB2
|
F:ALA163
|
4.0
|
14.9
|
1.0
|
|
CZ2
|
F:TRP124
|
4.1
|
16.6
|
1.0
|
|
ND1
|
F:HIS74
|
4.1
|
15.7
|
1.0
|
|
CG
|
F:HIS74
|
4.2
|
15.3
|
1.0
|
|
CG
|
F:HIS162
|
4.2
|
14.9
|
1.0
|
|
ND1
|
F:HIS26
|
4.3
|
16.5
|
1.0
|
|
CG
|
F:HIS26
|
4.3
|
12.9
|
1.0
|
|
ND1
|
F:HIS162
|
4.3
|
17.3
|
1.0
|
|
CB
|
F:ASP158
|
4.3
|
18.1
|
1.0
|
|
HE2
|
F:TYR34
|
4.4
|
19.1
|
1.0
|
|
HB2
|
F:ASP158
|
4.4
|
16.7
|
1.0
|
|
HH2
|
F:TRP124
|
4.5
|
17.2
|
1.0
|
|
CB
|
F:TRP160
|
4.6
|
14.4
|
1.0
|
|
HB3
|
F:ASP158
|
4.6
|
17.6
|
1.0
|
|
NE2
|
F:GLN70
|
4.6
|
13.8
|
1.0
|
|
CH2
|
F:TRP124
|
4.7
|
18.3
|
1.0
|
|
CG
|
F:TRP160
|
4.8
|
13.3
|
1.0
|
|
HB3
|
F:TRP160
|
4.8
|
14.2
|
1.0
|
|
HA
|
F:ALA163
|
4.9
|
13.6
|
1.0
|
|
CB
|
F:ALA163
|
4.9
|
15.8
|
1.0
|
|
HB3
|
F:HIS30
|
5.0
|
15.4
|
1.0
|
|
CE2
|
F:TRP124
|
5.0
|
17.2
|
1.0
|
|
HE1
|
F:TRP124
|
5.0
|
16.8
|
1.0
|
|
Iron binding site 7 out
of 8 in 8avl
Go back to
Iron Binding Sites List in 8avl
Iron binding site 7 out
of 8 in the Superoxide Dismutase SODFM2 From Bacteroides Fragilis
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Superoxide Dismutase SODFM2 From Bacteroides Fragilis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Fe201
b:26.4
occ:1.00
|
OD2
|
G:ASP158
|
2.0
|
16.4
|
1.0
|
|
NE2
|
G:HIS74
|
2.2
|
18.4
|
1.0
|
|
O
|
G:HOH382
|
2.2
|
17.6
|
1.0
|
|
NE2
|
G:HIS162
|
2.2
|
15.8
|
1.0
|
|
NE2
|
G:HIS26
|
2.2
|
15.0
|
1.0
|
|
CG
|
G:ASP158
|
3.0
|
18.0
|
1.0
|
|
CD2
|
G:HIS162
|
3.0
|
18.9
|
1.0
|
|
HD2
|
G:HIS162
|
3.1
|
16.8
|
1.0
|
|
CE1
|
G:HIS74
|
3.1
|
18.8
|
1.0
|
|
CD2
|
G:HIS74
|
3.2
|
18.9
|
1.0
|
|
CD2
|
G:HIS26
|
3.2
|
19.4
|
1.0
|
|
HE1
|
G:HIS74
|
3.2
|
17.8
|
1.0
|
|
CE1
|
G:HIS26
|
3.2
|
16.2
|
1.0
|
|
CE1
|
G:HIS162
|
3.3
|
17.2
|
1.0
|
|
HD2
|
G:HIS26
|
3.4
|
18.4
|
1.0
|
|
HD2
|
G:HIS74
|
3.4
|
18.4
|
1.0
|
|
HE1
|
G:HIS26
|
3.4
|
16.1
|
1.0
|
|
OD1
|
G:ASP158
|
3.5
|
18.2
|
1.0
|
|
HZ2
|
G:TRP124
|
3.5
|
17.4
|
1.0
|
|
HE1
|
G:HIS162
|
3.6
|
17.0
|
1.0
|
|
HB2
|
G:TRP160
|
3.7
|
17.0
|
1.0
|
|
HB2
|
G:ALA163
|
4.0
|
17.2
|
1.0
|
|
CZ2
|
G:TRP124
|
4.1
|
18.5
|
1.0
|
|
ND1
|
G:HIS74
|
4.2
|
15.8
|
1.0
|
|
CG
|
G:HIS162
|
4.2
|
17.1
|
1.0
|
|
CG
|
G:HIS74
|
4.3
|
17.9
|
1.0
|
|
CB
|
G:ASP158
|
4.3
|
17.5
|
1.0
|
|
CG
|
G:HIS26
|
4.3
|
15.9
|
1.0
|
|
ND1
|
G:HIS26
|
4.3
|
18.4
|
1.0
|
|
ND1
|
G:HIS162
|
4.3
|
17.6
|
1.0
|
|
HE2
|
G:TYR34
|
4.3
|
18.3
|
1.0
|
|
HB2
|
G:ASP158
|
4.4
|
17.4
|
1.0
|
|
HB3
|
G:ASP158
|
4.5
|
17.3
|
1.0
|
|
HH2
|
G:TRP124
|
4.5
|
18.9
|
1.0
|
|
CB
|
G:TRP160
|
4.5
|
17.0
|
1.0
|
|
NE2
|
G:GLN70
|
4.6
|
15.3
|
1.0
|
|
CH2
|
G:TRP124
|
4.7
|
19.9
|
1.0
|
|
CG
|
G:TRP160
|
4.7
|
16.3
|
1.0
|
|
HB3
|
G:TRP160
|
4.8
|
17.5
|
1.0
|
|
CB
|
G:ALA163
|
4.9
|
16.7
|
1.0
|
|
HB3
|
G:HIS30
|
4.9
|
16.5
|
1.0
|
|
HA
|
G:ALA163
|
4.9
|
17.8
|
1.0
|
|
CE2
|
G:TRP124
|
4.9
|
16.6
|
1.0
|
|
HE1
|
G:TRP124
|
4.9
|
16.5
|
1.0
|
|
CD1
|
G:TRP160
|
5.0
|
16.3
|
1.0
|
|
Iron binding site 8 out
of 8 in 8avl
Go back to
Iron Binding Sites List in 8avl
Iron binding site 8 out
of 8 in the Superoxide Dismutase SODFM2 From Bacteroides Fragilis
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Superoxide Dismutase SODFM2 From Bacteroides Fragilis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Fe201
b:25.0
occ:1.00
|
OD2
|
H:ASP158
|
2.0
|
15.7
|
1.0
|
|
NE2
|
H:HIS162
|
2.2
|
18.3
|
1.0
|
|
O
|
H:HOH387
|
2.2
|
15.4
|
1.0
|
|
NE2
|
H:HIS74
|
2.2
|
15.9
|
1.0
|
|
NE2
|
H:HIS26
|
2.2
|
15.0
|
1.0
|
|
CD2
|
H:HIS162
|
3.0
|
20.0
|
1.0
|
|
HD2
|
H:HIS162
|
3.0
|
18.1
|
1.0
|
|
CE1
|
H:HIS74
|
3.1
|
19.6
|
1.0
|
|
CG
|
H:ASP158
|
3.1
|
15.4
|
1.0
|
|
CD2
|
H:HIS26
|
3.2
|
17.8
|
1.0
|
|
CD2
|
H:HIS74
|
3.2
|
16.8
|
1.0
|
|
CE1
|
H:HIS26
|
3.2
|
17.8
|
1.0
|
|
HE1
|
H:HIS74
|
3.2
|
18.2
|
1.0
|
|
CE1
|
H:HIS162
|
3.2
|
20.1
|
1.0
|
|
HD2
|
H:HIS26
|
3.3
|
16.9
|
1.0
|
|
HD2
|
H:HIS74
|
3.4
|
16.7
|
1.0
|
|
HE1
|
H:HIS26
|
3.4
|
17.7
|
1.0
|
|
HZ2
|
H:TRP124
|
3.5
|
16.4
|
1.0
|
|
OD1
|
H:ASP158
|
3.5
|
16.3
|
1.0
|
|
HE1
|
H:HIS162
|
3.5
|
19.5
|
1.0
|
|
HB2
|
H:TRP160
|
3.7
|
14.4
|
1.0
|
|
HB2
|
H:ALA163
|
4.0
|
15.5
|
1.0
|
|
CZ2
|
H:TRP124
|
4.1
|
16.2
|
1.0
|
|
ND1
|
H:HIS74
|
4.2
|
16.0
|
1.0
|
|
CG
|
H:HIS162
|
4.2
|
17.6
|
1.0
|
|
CG
|
H:HIS74
|
4.2
|
15.0
|
1.0
|
|
CG
|
H:HIS26
|
4.3
|
17.8
|
1.0
|
|
ND1
|
H:HIS26
|
4.3
|
18.6
|
1.0
|
|
ND1
|
H:HIS162
|
4.3
|
18.9
|
1.0
|
|
CB
|
H:ASP158
|
4.3
|
15.3
|
1.0
|
|
HE2
|
H:TYR34
|
4.4
|
18.1
|
1.0
|
|
HB2
|
H:ASP158
|
4.4
|
15.0
|
1.0
|
|
HH2
|
H:TRP124
|
4.5
|
18.3
|
1.0
|
|
CB
|
H:TRP160
|
4.5
|
14.2
|
1.0
|
|
HB3
|
H:ASP158
|
4.6
|
14.9
|
1.0
|
|
NE2
|
H:GLN70
|
4.7
|
21.4
|
1.0
|
|
CH2
|
H:TRP124
|
4.7
|
19.6
|
1.0
|
|
HB3
|
H:TRP160
|
4.7
|
14.3
|
1.0
|
|
CG
|
H:TRP160
|
4.8
|
15.1
|
1.0
|
|
HA
|
H:ALA163
|
4.9
|
15.8
|
1.0
|
|
HB3
|
H:HIS30
|
4.9
|
20.6
|
1.0
|
|
CB
|
H:ALA163
|
4.9
|
15.6
|
1.0
|
|
CE2
|
H:TRP124
|
5.0
|
16.1
|
1.0
|
|
Reference:
K.M.Sendra,
A.Barwinska-Sendra,
E.S.Mackenzie,
A.Basle,
T.E.Kehl-Fie,
K.J.Waldron.
An Ancient Metalloenzyme Evolves Through Metal Preference Modulation. Nat Ecol Evol 2023.
ISSN: ISSN 2397-334X
PubMed: 37037909
DOI: 10.1038/S41559-023-02012-0
Page generated: Fri Aug 9 18:42:28 2024
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