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Iron in PDB 1ma1: Structure and Properties of the Atypical Iron Superoxide Dismutase From Methanobacterium Thermoautotrophicum

Enzymatic activity of Structure and Properties of the Atypical Iron Superoxide Dismutase From Methanobacterium Thermoautotrophicum

All present enzymatic activity of Structure and Properties of the Atypical Iron Superoxide Dismutase From Methanobacterium Thermoautotrophicum:
1.15.1.1;

Protein crystallography data

The structure of Structure and Properties of the Atypical Iron Superoxide Dismutase From Methanobacterium Thermoautotrophicum, PDB code: 1ma1 was solved by J.J.Adams, B.F.Anderson, J.P.Renault, C.Verchere-Beaur, I.Morgenstern-Badarau, G.B.Jameson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 187.619, 114.082, 58.087, 90.00, 94.95, 90.00
R / Rfree (%) 21.5 / 24.7

Iron Binding Sites:

The binding sites of Iron atom in the Structure and Properties of the Atypical Iron Superoxide Dismutase From Methanobacterium Thermoautotrophicum (pdb code 1ma1). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Structure and Properties of the Atypical Iron Superoxide Dismutase From Methanobacterium Thermoautotrophicum, PDB code: 1ma1:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 1ma1

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Iron binding site 1 out of 6 in the Structure and Properties of the Atypical Iron Superoxide Dismutase From Methanobacterium Thermoautotrophicum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure and Properties of the Atypical Iron Superoxide Dismutase From Methanobacterium Thermoautotrophicum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe206

b:43.3
occ:0.50
 O A:HOH272 1.9 2.4 0.5
OD2 A:ASP166 1.9 16.0 1.0
NE2 A:HIS32 2.1 20.9 1.0
NE2 A:HIS170 2.1 27.7 1.0
NE2 A:HIS80 2.1 18.6 1.0
CD2 A:HIS170 2.9 21.7 1.0
CE1 A:HIS80 2.9 16.1 1.0
CD2 A:HIS32 3.0 17.2 1.0
CE1 A:HIS32 3.1 21.5 1.0
CG A:ASP166 3.1 14.9 1.0
CD2 A:HIS80 3.2 16.5 1.0
CE1 A:HIS170 3.3 23.5 1.0
OD1 A:ASP166 3.7 16.7 1.0
ND1 A:HIS80 4.0 17.0 1.0
CG A:HIS170 4.1 19.4 1.0
ND1 A:HIS32 4.1 19.4 1.0
CG A:HIS32 4.1 16.4 1.0
CG A:HIS80 4.2 17.2 1.0
ND1 A:HIS170 4.3 20.6 1.0
CB A:TRP168 4.3 13.7 1.0
CB A:ASP166 4.3 12.6 1.0
CZ2 A:TRP131 4.4 18.0 1.0
CG A:TRP168 4.5 14.9 1.0
CH2 A:TRP131 4.5 17.1 1.0
CB A:ALA171 4.7 19.5 1.0
CD1 A:TRP168 4.8 12.1 1.0
CB A:HIS36 4.9 19.9 1.0

Iron binding site 2 out of 6 in 1ma1

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Iron binding site 2 out of 6 in the Structure and Properties of the Atypical Iron Superoxide Dismutase From Methanobacterium Thermoautotrophicum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure and Properties of the Atypical Iron Superoxide Dismutase From Methanobacterium Thermoautotrophicum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe206

b:23.6
occ:0.50
 O B:HOH246 1.9 5.5 0.5
OD2 B:ASP166 1.9 24.6 1.0
NE2 B:HIS32 2.1 30.4 1.0
NE2 B:HIS170 2.1 24.8 1.0
NE2 B:HIS80 2.1 34.7 1.0
CD2 B:HIS170 2.9 21.4 1.0
CE1 B:HIS80 2.9 35.2 1.0
CD2 B:HIS32 3.0 27.6 1.0
CE1 B:HIS32 3.1 28.0 1.0
CG B:ASP166 3.1 19.2 1.0
CD2 B:HIS80 3.2 33.8 1.0
CE1 B:HIS170 3.3 21.7 1.0
OD1 B:ASP166 3.7 17.6 1.0
ND1 B:HIS80 4.0 33.4 1.0
CG B:HIS170 4.1 21.6 1.0
CG B:HIS32 4.1 24.7 1.0
ND1 B:HIS32 4.1 24.8 1.0
CG B:HIS80 4.2 30.9 1.0
ND1 B:HIS170 4.3 21.3 1.0
CB B:TRP168 4.3 19.6 1.0
CB B:ASP166 4.3 19.0 1.0
CZ2 B:TRP131 4.4 19.2 1.0
CH2 B:TRP131 4.5 19.8 1.0
CG B:TRP168 4.5 18.8 1.0
CB B:ALA171 4.8 23.8 1.0
CD1 B:TRP168 4.8 19.9 1.0
CB B:HIS36 4.9 24.8 1.0
CE2 B:TYR40 5.0 28.9 1.0
CD2 B:TRP168 5.0 17.2 1.0

Iron binding site 3 out of 6 in 1ma1

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Iron binding site 3 out of 6 in the Structure and Properties of the Atypical Iron Superoxide Dismutase From Methanobacterium Thermoautotrophicum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure and Properties of the Atypical Iron Superoxide Dismutase From Methanobacterium Thermoautotrophicum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe206

b:33.6
occ:0.50
 O C:HOH290 1.9 2.4 0.5
OD2 C:ASP166 1.9 24.1 1.0
NE2 C:HIS32 2.1 29.1 1.0
NE2 C:HIS170 2.1 19.4 1.0
NE2 C:HIS80 2.1 16.6 1.0
CD2 C:HIS170 2.9 17.8 1.0
CE1 C:HIS80 2.9 16.1 1.0
CD2 C:HIS32 3.0 24.0 1.0
CE1 C:HIS32 3.1 28.6 1.0
CG C:ASP166 3.1 20.7 1.0
CD2 C:HIS80 3.2 14.2 1.0
CE1 C:HIS170 3.3 19.6 1.0
OD1 C:ASP166 3.7 23.8 1.0
ND1 C:HIS80 4.0 16.1 1.0
CG C:HIS32 4.1 24.6 1.0
ND1 C:HIS32 4.1 28.1 1.0
CG C:HIS170 4.1 14.8 1.0
CG C:HIS80 4.2 14.2 1.0
ND1 C:HIS170 4.3 15.1 1.0
CB C:ASP166 4.3 17.2 1.0
CB C:TRP168 4.4 15.9 1.0
CZ2 C:TRP131 4.4 15.7 1.0
CG C:TRP168 4.5 18.0 1.0
CH2 C:TRP131 4.6 16.7 1.0
CD1 C:TRP168 4.8 15.7 1.0
CB C:ALA171 4.8 16.1 1.0
CB C:HIS36 4.9 21.1 1.0
CE2 C:TYR40 5.0 17.4 1.0

Iron binding site 4 out of 6 in 1ma1

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Iron binding site 4 out of 6 in the Structure and Properties of the Atypical Iron Superoxide Dismutase From Methanobacterium Thermoautotrophicum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure and Properties of the Atypical Iron Superoxide Dismutase From Methanobacterium Thermoautotrophicum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe206

b:39.3
occ:0.50
 O D:HOH286 1.9 2.4 0.5
OD2 D:ASP166 1.9 11.3 1.0
NE2 D:HIS32 2.1 21.4 1.0
NE2 D:HIS170 2.1 24.9 1.0
NE2 D:HIS80 2.1 25.9 1.0
CD2 D:HIS170 2.9 22.7 1.0
CE1 D:HIS80 2.9 28.0 1.0
CD2 D:HIS32 3.0 18.1 1.0
CE1 D:HIS32 3.1 23.1 1.0
CG D:ASP166 3.1 11.7 1.0
CD2 D:HIS80 3.2 22.7 1.0
CE1 D:HIS170 3.3 26.0 1.0
OD1 D:ASP166 3.7 8.2 1.0
ND1 D:HIS80 4.0 25.5 1.0
CG D:HIS32 4.1 20.5 1.0
CG D:HIS170 4.1 21.8 1.0
ND1 D:HIS32 4.1 22.4 1.0
CG D:HIS80 4.2 22.4 1.0
ND1 D:HIS170 4.3 24.5 1.0
CB D:TRP168 4.3 15.4 1.0
CB D:ASP166 4.3 11.5 1.0
CZ2 D:TRP131 4.4 14.1 1.0
CH2 D:TRP131 4.5 16.9 1.0
CG D:TRP168 4.5 17.5 1.0
CB D:ALA171 4.7 18.4 1.0
CD1 D:TRP168 4.8 17.9 1.0
CB D:HIS36 4.9 20.6 1.0
CE2 D:TYR40 5.0 19.5 1.0

Iron binding site 5 out of 6 in 1ma1

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Iron binding site 5 out of 6 in the Structure and Properties of the Atypical Iron Superoxide Dismutase From Methanobacterium Thermoautotrophicum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure and Properties of the Atypical Iron Superoxide Dismutase From Methanobacterium Thermoautotrophicum within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe206

b:31.8
occ:0.50
 O E:HOH299 1.9 2.4 0.5
OD2 E:ASP166 1.9 22.1 1.0
NE2 E:HIS32 2.1 25.6 1.0
NE2 E:HIS170 2.1 26.7 1.0
NE2 E:HIS80 2.1 21.0 1.0
CD2 E:HIS170 2.9 23.5 1.0
CE1 E:HIS80 2.9 20.9 1.0
CD2 E:HIS32 3.0 24.1 1.0
CE1 E:HIS32 3.1 23.5 1.0
CG E:ASP166 3.1 19.1 1.0
CD2 E:HIS80 3.2 16.7 1.0
CE1 E:HIS170 3.3 24.8 1.0
OD1 E:ASP166 3.6 20.9 1.0
ND1 E:HIS80 4.0 18.2 1.0
CG E:HIS32 4.1 23.6 1.0
ND1 E:HIS32 4.1 24.0 1.0
CG E:HIS170 4.1 20.6 1.0
CG E:HIS80 4.2 17.1 1.0
ND1 E:HIS170 4.3 19.9 1.0
CB E:TRP168 4.3 11.5 1.0
CB E:ASP166 4.3 15.3 1.0
CZ2 E:TRP131 4.4 13.4 1.0
CG E:TRP168 4.5 11.9 1.0
CH2 E:TRP131 4.5 8.6 1.0
CB E:ALA171 4.8 19.2 1.0
CD1 E:TRP168 4.8 11.2 1.0
CE2 E:TYR40 5.0 14.6 1.0
CB E:HIS36 5.0 21.4 1.0
CD2 E:TRP168 5.0 11.8 1.0

Iron binding site 6 out of 6 in 1ma1

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Iron binding site 6 out of 6 in the Structure and Properties of the Atypical Iron Superoxide Dismutase From Methanobacterium Thermoautotrophicum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure and Properties of the Atypical Iron Superoxide Dismutase From Methanobacterium Thermoautotrophicum within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe206

b:28.5
occ:0.50
 O F:HOH265 1.9 2.4 0.5
OD2 F:ASP166 1.9 21.9 1.0
NE2 F:HIS170 2.1 28.7 1.0
NE2 F:HIS80 2.1 26.7 1.0
NE2 F:HIS32 2.1 27.5 1.0
CD2 F:HIS170 2.9 24.3 1.0
CD2 F:HIS32 2.9 25.6 1.0
CE1 F:HIS80 2.9 25.1 1.0
CG F:ASP166 3.1 18.8 1.0
CD2 F:HIS80 3.2 23.6 1.0
CE1 F:HIS170 3.3 27.2 1.0
CE1 F:HIS32 3.3 27.5 1.0
OD1 F:ASP166 3.7 20.3 1.0
ND1 F:HIS80 4.0 23.2 1.0
CG F:HIS170 4.1 21.5 1.0
CG F:HIS32 4.1 24.4 1.0
CG F:HIS80 4.2 21.9 1.0
ND1 F:HIS170 4.3 24.3 1.0
CB F:TRP168 4.3 15.0 1.0
ND1 F:HIS32 4.3 24.6 1.0
CB F:ASP166 4.3 18.2 1.0
CZ2 F:TRP131 4.4 22.2 1.0
CG F:TRP168 4.4 14.5 1.0
CH2 F:TRP131 4.5 23.1 1.0
CD1 F:TRP168 4.7 13.4 1.0
CB F:ALA171 4.8 19.1 1.0
CB F:HIS36 4.9 19.2 1.0
CE2 F:TYR40 5.0 18.0 1.0

Reference:

J.J.Adams, B.F.Anderson, J.P.Renault, C.Verchere-Beaur, I.Morgenstern-Badarau, G.B.Jameson. Structure and Properties of the Atypical Iron Superoxide Dismutase From Methanobacterium Thermoautotrophicum To Be Published.
Page generated: Sat Aug 3 10:37:40 2024

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