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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

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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

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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

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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

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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

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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

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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

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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

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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: Thu Aug 7 13:32:16 2025

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