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Manganese in PDB 4c7u: Crystal Structure of Manganese Superoxide Dismutase From Arabidopsis Thaliana

Enzymatic activity of Crystal Structure of Manganese Superoxide Dismutase From Arabidopsis Thaliana

All present enzymatic activity of Crystal Structure of Manganese Superoxide Dismutase From Arabidopsis Thaliana:
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure of Manganese Superoxide Dismutase From Arabidopsis Thaliana, PDB code: 4c7u was solved by A.Marques, S.P.Santos, M.Rosa, M.A.Carrondo, I.A.Abreu, C.V.Romao, C.Frazao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.985 / 1.95
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 58.952, 59.181, 107.980, 90.55, 90.51, 89.85
R / Rfree (%) 17.29 / n/a

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Manganese Superoxide Dismutase From Arabidopsis Thaliana (pdb code 4c7u). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of Manganese Superoxide Dismutase From Arabidopsis Thaliana, PDB code: 4c7u:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4c7u

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Manganese binding site 1 out of 8 in the Crystal Structure of Manganese Superoxide Dismutase From Arabidopsis Thaliana


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Manganese Superoxide Dismutase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn302

b:14.4
occ:1.00
 OD2 A:ASP163 1.9 10.9 1.0
NE2 A:HIS74 2.2 13.6 1.0
NE2 A:HIS167 2.2 19.3 1.0
NE2 A:HIS26 2.2 19.3 1.0
O A:HOH303 2.3 18.0 1.0
CG A:ASP163 3.0 13.5 1.0
CE1 A:HIS74 3.1 18.6 1.0
CD2 A:HIS26 3.1 12.5 1.0
CD2 A:HIS167 3.1 23.2 1.0
CD2 A:HIS74 3.2 13.4 1.0
CE1 A:HIS167 3.2 16.5 1.0
CE1 A:HIS26 3.3 22.5 1.0
OD1 A:ASP163 3.5 15.1 1.0
ND1 A:HIS74 4.2 12.6 1.0
CZ2 A:TRP126 4.3 15.1 1.0
CG A:HIS26 4.3 18.1 1.0
CG A:HIS167 4.3 19.2 1.0
CG A:HIS74 4.3 11.2 1.0
ND1 A:HIS167 4.3 16.5 1.0
CB A:ASP163 4.3 14.9 1.0
ND1 A:HIS26 4.3 20.7 1.0
NE2 A:GLN146 4.4 16.4 1.0
CB A:TRP165 4.6 12.7 1.0
CG A:TRP165 4.7 9.8 1.0
CH2 A:TRP126 4.8 13.1 1.0
CD1 A:TRP165 5.0 6.0 1.0
CB A:ALA168 5.0 14.5 1.0

Manganese binding site 2 out of 8 in 4c7u

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Manganese binding site 2 out of 8 in the Crystal Structure of Manganese Superoxide Dismutase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Manganese Superoxide Dismutase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn302

b:13.9
occ:1.00
 OD2 B:ASP163 2.0 14.4 1.0
NE2 B:HIS26 2.2 15.0 1.0
O B:HOH303 2.2 12.6 1.0
NE2 B:HIS74 2.2 10.9 1.0
NE2 B:HIS167 2.3 17.1 1.0
CE1 B:HIS26 3.0 20.0 1.0
CG B:ASP163 3.1 19.4 1.0
CD2 B:HIS74 3.2 19.8 1.0
CE1 B:HIS74 3.2 8.8 1.0
CD2 B:HIS167 3.3 15.3 1.0
CD2 B:HIS26 3.3 11.4 1.0
CE1 B:HIS167 3.3 13.7 1.0
OD1 B:ASP163 3.5 16.5 1.0
ND1 B:HIS26 4.2 12.9 1.0
CZ2 B:TRP126 4.3 17.9 1.0
ND1 B:HIS74 4.3 13.3 1.0
CG B:HIS74 4.3 10.5 1.0
CB B:ASP163 4.3 17.0 1.0
NE2 B:GLN146 4.3 15.1 1.0
CG B:HIS26 4.3 9.1 1.0
CG B:HIS167 4.4 16.2 1.0
ND1 B:HIS167 4.4 15.9 1.0
CB B:TRP165 4.6 22.6 1.0
CH2 B:TRP126 4.7 16.2 1.0
CG B:TRP165 4.8 14.4 1.0

Manganese binding site 3 out of 8 in 4c7u

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Manganese binding site 3 out of 8 in the Crystal Structure of Manganese Superoxide Dismutase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Manganese Superoxide Dismutase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn302

b:16.0
occ:1.00
 OD2 C:ASP163 2.0 19.8 1.0
NE2 C:HIS74 2.1 9.6 1.0
NE2 C:HIS26 2.2 13.0 1.0
O C:HOH303 2.2 11.7 1.0
NE2 C:HIS167 2.3 16.0 1.0
CD2 C:HIS74 3.0 9.9 1.0
CE1 C:HIS26 3.1 13.5 1.0
CG C:ASP163 3.1 17.4 1.0
CE1 C:HIS74 3.1 12.3 1.0
CD2 C:HIS26 3.2 9.7 1.0
CD2 C:HIS167 3.3 13.6 1.0
CE1 C:HIS167 3.4 13.5 1.0
OD1 C:ASP163 3.5 17.0 1.0
ND1 C:HIS74 4.2 16.7 1.0
CG C:HIS74 4.2 17.1 1.0
ND1 C:HIS26 4.2 14.8 1.0
CZ2 C:TRP126 4.2 17.7 1.0
CG C:HIS26 4.3 10.9 1.0
CB C:ASP163 4.3 12.1 1.0
CG C:HIS167 4.4 21.9 1.0
ND1 C:HIS167 4.4 18.6 1.0
NE2 C:GLN146 4.5 19.4 1.0
CB C:TRP165 4.6 19.9 1.0
CH2 C:TRP126 4.7 10.0 1.0
CG C:TRP165 4.8 11.5 1.0

Manganese binding site 4 out of 8 in 4c7u

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Manganese binding site 4 out of 8 in the Crystal Structure of Manganese Superoxide Dismutase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Manganese Superoxide Dismutase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn302

b:15.2
occ:1.00
 OD2 D:ASP163 2.0 16.8 1.0
NE2 D:HIS167 2.2 15.3 1.0
O D:HOH303 2.2 17.4 1.0
NE2 D:HIS74 2.2 10.9 1.0
NE2 D:HIS26 2.3 15.8 1.0
CG D:ASP163 3.0 14.0 1.0
CD2 D:HIS167 3.1 9.8 1.0
CE1 D:HIS74 3.1 12.3 1.0
CD2 D:HIS74 3.2 12.1 1.0
CE1 D:HIS167 3.2 15.5 1.0
CD2 D:HIS26 3.2 16.4 1.0
CE1 D:HIS26 3.3 14.4 1.0
OD1 D:ASP163 3.4 19.4 1.0
ND1 D:HIS74 4.2 10.2 1.0
CG D:HIS167 4.3 20.6 1.0
CZ2 D:TRP126 4.3 16.2 1.0
ND1 D:HIS167 4.3 14.2 1.0
CG D:HIS74 4.3 15.1 1.0
CB D:ASP163 4.3 13.4 1.0
NE2 D:GLN146 4.3 14.2 1.0
ND1 D:HIS26 4.4 12.3 1.0
CG D:HIS26 4.4 14.4 1.0
CB D:TRP165 4.6 8.0 1.0
CG D:TRP165 4.7 16.8 1.0
CH2 D:TRP126 4.8 21.4 1.0
CD1 D:TRP165 5.0 16.8 1.0

Manganese binding site 5 out of 8 in 4c7u

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Manganese binding site 5 out of 8 in the Crystal Structure of Manganese Superoxide Dismutase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Manganese Superoxide Dismutase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn302

b:17.6
occ:1.00
 OD2 E:ASP163 1.9 19.9 1.0
NE2 E:HIS74 2.1 18.9 1.0
NE2 E:HIS26 2.2 13.9 1.0
NE2 E:HIS167 2.3 23.0 1.0
O E:HOH303 2.3 10.0 1.0
CD2 E:HIS74 3.0 19.3 1.0
CE1 E:HIS74 3.1 23.8 1.0
CG E:ASP163 3.1 26.3 1.0
CE1 E:HIS26 3.2 18.9 1.0
CD2 E:HIS167 3.2 21.1 1.0
CD2 E:HIS26 3.2 15.9 1.0
CE1 E:HIS167 3.3 9.7 1.0
OD1 E:ASP163 3.6 21.4 1.0
ND1 E:HIS74 4.2 19.7 1.0
CG E:HIS74 4.2 22.0 1.0
CB E:ASP163 4.3 19.4 1.0
ND1 E:HIS26 4.3 21.1 1.0
CZ2 E:TRP126 4.3 19.2 1.0
CG E:HIS26 4.4 14.1 1.0
CG E:HIS167 4.4 26.9 1.0
ND1 E:HIS167 4.4 15.6 1.0
NE2 E:GLN146 4.5 17.5 1.0
CB E:TRP165 4.7 12.4 1.0
CG E:TRP165 4.7 23.3 1.0
CH2 E:TRP126 4.8 14.7 1.0
CD1 E:TRP165 4.9 13.5 1.0

Manganese binding site 6 out of 8 in 4c7u

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Manganese binding site 6 out of 8 in the Crystal Structure of Manganese Superoxide Dismutase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Manganese Superoxide Dismutase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn302

b:18.7
occ:1.00
 OD2 F:ASP163 1.9 11.1 1.0
NE2 F:HIS74 2.1 28.0 1.0
NE2 F:HIS26 2.2 21.1 1.0
O F:HOH303 2.2 18.1 1.0
NE2 F:HIS167 2.3 19.3 1.0
CG F:ASP163 3.0 24.6 1.0
CE1 F:HIS74 3.1 27.2 1.0
CD2 F:HIS74 3.1 22.6 1.0
CD2 F:HIS26 3.1 13.3 1.0
CE1 F:HIS26 3.2 21.4 1.0
CD2 F:HIS167 3.2 15.9 1.0
CE1 F:HIS167 3.3 22.2 1.0
OD1 F:ASP163 3.5 19.7 1.0
ND1 F:HIS74 4.2 20.5 1.0
CG F:HIS74 4.2 20.3 1.0
CZ2 F:TRP126 4.3 12.0 1.0
CB F:ASP163 4.3 18.1 1.0
ND1 F:HIS26 4.3 23.3 1.0
CG F:HIS26 4.3 30.9 1.0
ND1 F:HIS167 4.4 19.0 1.0
CG F:HIS167 4.4 19.0 1.0
NE2 F:GLN146 4.5 18.9 1.0
CB F:TRP165 4.6 8.3 1.0
CG F:TRP165 4.7 17.0 1.0
CH2 F:TRP126 4.7 18.9 1.0

Manganese binding site 7 out of 8 in 4c7u

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Manganese binding site 7 out of 8 in the Crystal Structure of Manganese Superoxide Dismutase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Manganese Superoxide Dismutase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn302

b:20.7
occ:1.00
 OD2 G:ASP163 2.0 22.6 1.0
NE2 G:HIS74 2.1 30.5 1.0
NE2 G:HIS26 2.2 15.6 1.0
NE2 G:HIS167 2.3 19.6 1.0
O G:HOH303 2.4 14.3 1.0
CE1 G:HIS74 3.0 17.6 1.0
CG G:ASP163 3.1 22.5 1.0
CD2 G:HIS74 3.1 22.8 1.0
CE1 G:HIS26 3.1 25.4 1.0
CD2 G:HIS167 3.2 14.3 1.0
CD2 G:HIS26 3.3 17.8 1.0
CE1 G:HIS167 3.3 15.4 1.0
OD1 G:ASP163 3.5 24.6 1.0
ND1 G:HIS74 4.2 22.9 1.0
CG G:HIS74 4.2 23.0 1.0
ND1 G:HIS26 4.3 27.2 1.0
CB G:ASP163 4.3 15.9 1.0
CZ2 G:TRP126 4.4 14.3 1.0
CG G:HIS26 4.4 19.3 1.0
CG G:HIS167 4.4 15.3 1.0
ND1 G:HIS167 4.4 12.4 1.0
NE2 G:GLN146 4.5 14.2 1.0
CB G:TRP165 4.7 15.2 1.0
CG G:TRP165 4.7 15.9 1.0
CH2 G:TRP126 4.8 15.3 1.0
CD1 G:TRP165 5.0 15.1 1.0

Manganese binding site 8 out of 8 in 4c7u

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Manganese binding site 8 out of 8 in the Crystal Structure of Manganese Superoxide Dismutase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Manganese Superoxide Dismutase From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn302

b:18.4
occ:1.00
 OD2 H:ASP163 1.9 12.4 1.0
NE2 H:HIS74 2.1 24.2 1.0
NE2 H:HIS167 2.2 22.7 1.0
NE2 H:HIS26 2.3 22.7 1.0
O H:HOH303 2.3 16.9 1.0
CE1 H:HIS74 2.9 25.5 1.0
CG H:ASP163 3.0 23.6 1.0
CD2 H:HIS74 3.1 29.1 1.0
CE1 H:HIS167 3.1 23.0 1.0
CD2 H:HIS167 3.2 19.1 1.0
CD2 H:HIS26 3.3 20.5 1.0
CE1 H:HIS26 3.3 27.9 1.0
OD1 H:ASP163 3.4 24.4 1.0
ND1 H:HIS74 4.1 20.5 1.0
CG H:HIS74 4.2 17.0 1.0
CB H:ASP163 4.2 17.4 1.0
ND1 H:HIS167 4.3 20.4 1.0
CZ2 H:TRP126 4.3 18.4 1.0
CG H:HIS167 4.3 20.8 1.0
ND1 H:HIS26 4.4 27.3 1.0
CG H:HIS26 4.4 20.2 1.0
NE2 H:GLN146 4.5 15.2 1.0
CB H:TRP165 4.6 21.4 1.0
CG H:TRP165 4.7 22.0 1.0
CH2 H:TRP126 4.8 21.5 1.0

Reference:

A.Marques, S.P.Santos, M.Rosa, M.A.Carrondo, I.A.Abreu, C.V.Romao, C.Frazao. Crystal Structure of the Arabidopsis Thaliana Manganese Superoxide Dismutase at 1.95 A Resolution To Be Published.
Page generated: Sat Oct 5 18:53:44 2024

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