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Zinc in PDB 7bjk: Crystal Structure of the Chloroplastic Fe Superoxide Dismutase PAP9 From Arabidopsis Thaliana.

Enzymatic activity of Crystal Structure of the Chloroplastic Fe Superoxide Dismutase PAP9 From Arabidopsis Thaliana.

All present enzymatic activity of Crystal Structure of the Chloroplastic Fe Superoxide Dismutase PAP9 From Arabidopsis Thaliana.:
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure of the Chloroplastic Fe Superoxide Dismutase PAP9 From Arabidopsis Thaliana., PDB code: 7bjk was solved by D.Cobessi, R.Blanvillain, T.Pfannschmidt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.20 / 2.25
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 214.09, 83.01, 118.24, 90, 115.76, 90
R / Rfree (%) 17.9 / 22.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Chloroplastic Fe Superoxide Dismutase PAP9 From Arabidopsis Thaliana. (pdb code 7bjk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of the Chloroplastic Fe Superoxide Dismutase PAP9 From Arabidopsis Thaliana., PDB code: 7bjk:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 7bjk

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Zinc binding site 1 out of 5 in the Crystal Structure of the Chloroplastic Fe Superoxide Dismutase PAP9 From Arabidopsis Thaliana.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Chloroplastic Fe Superoxide Dismutase PAP9 From Arabidopsis Thaliana. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:34.4
occ:1.00
 OD2 A:ASP182 1.9 39.4 1.0
NE2 A:HIS186 2.0 26.5 1.0
NE2 A:HIS83 2.0 34.8 1.0
NE2 A:HIS31 2.1 30.3 1.0
O A:HOH422 2.2 22.8 1.0
CD2 A:HIS83 2.9 25.4 1.0
CE1 A:HIS186 3.0 30.1 1.0
CG A:ASP182 3.0 31.2 1.0
CD2 A:HIS186 3.0 27.8 1.0
CE1 A:HIS31 3.1 33.6 1.0
CE1 A:HIS83 3.1 35.7 1.0
CD2 A:HIS31 3.1 25.0 1.0
OD1 A:ASP182 3.5 34.0 1.0
CG A:HIS83 4.1 37.4 1.0
ND1 A:HIS83 4.1 39.4 1.0
ND1 A:HIS186 4.1 25.1 1.0
CG A:HIS186 4.2 31.1 1.0
ND1 A:HIS31 4.2 37.9 1.0
CG A:HIS31 4.2 30.8 1.0
CB A:ASP182 4.2 27.3 1.0
CH2 A:TRP132 4.3 35.0 1.0
CZ2 A:TRP132 4.4 28.8 1.0
CB A:TRP184 4.5 33.0 1.0
CB A:ALA187 4.7 32.7 1.0
CG A:TRP184 4.8 30.3 1.0
NE2 A:GLN79 5.0 36.0 1.0

Zinc binding site 2 out of 5 in 7bjk

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Zinc binding site 2 out of 5 in the Crystal Structure of the Chloroplastic Fe Superoxide Dismutase PAP9 From Arabidopsis Thaliana.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Chloroplastic Fe Superoxide Dismutase PAP9 From Arabidopsis Thaliana. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:32.8
occ:1.00
 OD2 B:ASP182 2.0 44.0 1.0
NE2 B:HIS186 2.0 27.1 1.0
NE2 B:HIS31 2.1 32.2 1.0
O B:HOH425 2.1 27.0 1.0
NE2 B:HIS83 2.1 34.1 1.0
CE1 B:HIS186 3.0 28.2 1.0
CE1 B:HIS31 3.0 30.5 1.0
CG B:ASP182 3.0 36.5 1.0
CD2 B:HIS186 3.0 27.9 1.0
CD2 B:HIS83 3.1 31.9 1.0
CE1 B:HIS83 3.1 33.3 1.0
CD2 B:HIS31 3.1 34.8 1.0
OD1 B:ASP182 3.4 34.2 1.0
ND1 B:HIS186 4.1 32.9 1.0
ND1 B:HIS83 4.1 40.6 1.0
ND1 B:HIS31 4.1 32.1 1.0
CG B:HIS83 4.1 41.4 1.0
CG B:HIS186 4.2 30.4 1.0
CG B:HIS31 4.2 36.6 1.0
CB B:ASP182 4.3 33.8 1.0
CH2 B:TRP132 4.3 37.6 1.0
CZ2 B:TRP132 4.4 33.1 1.0
CB B:TRP184 4.6 31.8 1.0
CG B:TRP184 4.8 20.4 1.0
CB B:ALA187 4.9 34.6 1.0

Zinc binding site 3 out of 5 in 7bjk

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Zinc binding site 3 out of 5 in the Crystal Structure of the Chloroplastic Fe Superoxide Dismutase PAP9 From Arabidopsis Thaliana.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Chloroplastic Fe Superoxide Dismutase PAP9 From Arabidopsis Thaliana. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:35.3
occ:1.00
 OD2 C:ASP182 2.0 49.2 1.0
NE2 C:HIS186 2.0 29.6 1.0
NE2 C:HIS83 2.1 38.5 1.0
NE2 C:HIS31 2.1 41.8 1.0
O C:HOH442 2.5 32.9 1.0
CD2 C:HIS186 3.0 33.9 1.0
CD2 C:HIS83 3.0 36.1 1.0
CG C:ASP182 3.0 37.3 1.0
CE1 C:HIS186 3.0 30.6 1.0
CE1 C:HIS31 3.1 32.7 1.0
CE1 C:HIS83 3.1 45.9 1.0
CD2 C:HIS31 3.1 37.9 1.0
OD1 C:ASP182 3.4 36.0 1.0
CG C:HIS83 4.1 41.0 1.0
ND1 C:HIS83 4.1 51.3 1.0
ND1 C:HIS186 4.1 27.0 1.0
CG C:HIS186 4.1 31.4 1.0
ND1 C:HIS31 4.2 34.0 1.0
CG C:HIS31 4.2 32.5 1.0
CB C:ASP182 4.3 31.8 1.0
CH2 C:TRP132 4.4 35.7 1.0
CZ2 C:TRP132 4.4 35.0 1.0
CB C:TRP184 4.5 31.5 1.0
CG C:TRP184 4.8 33.5 1.0
CB C:ALA187 4.8 37.4 1.0
NE2 C:GLN79 4.9 29.3 1.0

Zinc binding site 4 out of 5 in 7bjk

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Zinc binding site 4 out of 5 in the Crystal Structure of the Chloroplastic Fe Superoxide Dismutase PAP9 From Arabidopsis Thaliana.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Chloroplastic Fe Superoxide Dismutase PAP9 From Arabidopsis Thaliana. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:35.8
occ:1.00
 OD2 D:ASP182 1.9 49.2 1.0
NE2 D:HIS186 2.0 32.1 1.0
NE2 D:HIS31 2.2 42.8 1.0
NE2 D:HIS83 2.2 35.9 1.0
O D:HOH431 2.2 33.9 1.0
CD2 D:HIS186 3.0 31.9 1.0
CG D:ASP182 3.0 34.0 1.0
CD2 D:HIS83 3.0 30.8 1.0
CE1 D:HIS186 3.1 30.3 1.0
CE1 D:HIS31 3.1 42.8 1.0
CD2 D:HIS31 3.1 41.9 1.0
CE1 D:HIS83 3.2 37.4 1.0
OD1 D:ASP182 3.4 32.5 1.0
CG D:HIS186 4.1 33.8 1.0
ND1 D:HIS186 4.1 24.8 1.0
CG D:HIS83 4.2 40.9 1.0
ND1 D:HIS31 4.2 42.4 1.0
ND1 D:HIS83 4.3 42.6 1.0
CG D:HIS31 4.3 39.9 1.0
CB D:ASP182 4.3 27.5 1.0
CH2 D:TRP132 4.3 31.7 1.0
CZ2 D:TRP132 4.4 27.5 1.0
CB D:TRP184 4.5 33.4 1.0
CB D:ALA187 4.7 32.6 1.0
CG D:TRP184 4.8 35.6 1.0

Zinc binding site 5 out of 5 in 7bjk

Go back to Zinc Binding Sites List in 7bjk
Zinc binding site 5 out of 5 in the Crystal Structure of the Chloroplastic Fe Superoxide Dismutase PAP9 From Arabidopsis Thaliana.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Chloroplastic Fe Superoxide Dismutase PAP9 From Arabidopsis Thaliana. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:39.5
occ:1.00
 NE2 E:HIS31 1.9 52.4 1.0
OD2 E:ASP182 2.0 54.2 1.0
NE2 E:HIS186 2.2 30.1 1.0
NE2 E:HIS83 2.3 36.7 1.0
O E:HOH437 2.3 28.9 1.0
CE1 E:HIS31 2.7 45.3 1.0
CD2 E:HIS83 3.0 33.0 1.0
CD2 E:HIS31 3.0 51.0 1.0
CG E:ASP182 3.0 29.3 1.0
CD2 E:HIS186 3.1 32.2 1.0
CE1 E:HIS186 3.2 38.2 1.0
CE1 E:HIS83 3.4 45.0 1.0
OD1 E:ASP182 3.4 31.9 1.0
ND1 E:HIS31 3.8 41.8 1.0
CG E:HIS31 4.0 41.9 1.0
CG E:HIS83 4.2 42.7 1.0
CB E:ASP182 4.2 33.4 1.0
CG E:HIS186 4.2 41.4 1.0
ND1 E:HIS186 4.3 43.3 1.0
CH2 E:TRP132 4.4 27.6 1.0
ND1 E:HIS83 4.4 44.6 1.0
CZ2 E:TRP132 4.4 32.5 1.0
CB E:TRP184 4.5 30.4 1.0
CG E:TRP184 4.8 30.7 1.0
CB E:ALA187 4.9 34.6 1.0
NE2 E:GLN79 5.0 29.5 1.0

Reference:

A.Favier, P.Gans, E.Boeri Erba, L.Signor, S.S.Muthukumar, T.Pfannschmidt, R.Blanvillain, D.Cobessi. The Plastid-Encoded Rna Polymerase-Associated Protein PAP9 Is A Superoxide Dismutase with Unusual Structural Features Front Plant Sci 2021.
ISSN: ESSN 1664-462X
DOI: 10.3389/FPLS.2021.668897
Page generated: Thu Aug 21 22:48:49 2025

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