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Zinc in PDB 2zkx: Crystal Structure of Human Cu-Zn Superoxide Dismutase Mutant G85R in Space Group I212121

Enzymatic activity of Crystal Structure of Human Cu-Zn Superoxide Dismutase Mutant G85R in Space Group I212121

All present enzymatic activity of Crystal Structure of Human Cu-Zn Superoxide Dismutase Mutant G85R in Space Group I212121:
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure of Human Cu-Zn Superoxide Dismutase Mutant G85R in Space Group I212121, PDB code: 2zkx was solved by S.Yoshikawa, M.Kukimoto-Niino, K.Ito, L.Chen, Z.Q.Fu, J.Chrzas, B.C.Wang, M.Shirouzu, M.Urushitani, R.Takahashi, S.Yokoyama, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.55 / 2.72
Space group I 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.105, 113.080, 146.375, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 24.6

Other elements in 2zkx:

The structure of Crystal Structure of Human Cu-Zn Superoxide Dismutase Mutant G85R in Space Group I212121 also contains other interesting chemical elements:

Copper (Cu) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Cu-Zn Superoxide Dismutase Mutant G85R in Space Group I212121 (pdb code 2zkx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Human Cu-Zn Superoxide Dismutase Mutant G85R in Space Group I212121, PDB code: 2zkx:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2zkx

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Cu-Zn Superoxide Dismutase Mutant G85R in Space Group I212121


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 Human Cu-Zn Superoxide Dismutase Mutant G85R in Space Group I212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:29.8
occ:1.00
 OD1 A:ASP83 1.8 25.3 1.0
ND1 A:HIS63 2.0 34.0 1.0
ND1 A:HIS80 2.0 15.3 1.0
ND1 A:HIS71 2.1 19.7 1.0
CG A:ASP83 2.7 22.9 1.0
CE1 A:HIS80 2.8 27.0 1.0
CE1 A:HIS63 2.9 30.8 1.0
OD2 A:ASP83 3.0 40.4 1.0
CG A:HIS63 3.0 29.2 1.0
CE1 A:HIS71 3.0 25.5 1.0
CG A:HIS80 3.1 19.6 1.0
CG A:HIS71 3.1 20.4 1.0
CB A:HIS63 3.4 23.3 1.0
CB A:HIS71 3.5 13.2 1.0
CB A:HIS80 3.6 31.3 1.0
O A:LYS136 3.6 33.8 1.0
CA A:HIS71 3.8 20.3 1.0
NE2 A:HIS80 4.0 24.5 1.0
NE2 A:HIS63 4.0 33.7 1.0
CD2 A:HIS63 4.1 33.3 1.0
CB A:ASP83 4.1 25.7 1.0
CD2 A:HIS80 4.1 19.8 1.0
NE2 A:HIS71 4.2 16.6 1.0
CD2 A:HIS71 4.2 15.9 1.0
N A:GLY72 4.5 32.6 1.0
C A:LYS136 4.7 37.0 1.0
CA A:ASP83 4.7 22.1 1.0
C A:HIS71 4.7 31.6 1.0
N A:HIS71 4.8 21.8 1.0
CA A:HIS80 4.8 32.1 1.0
CA A:HIS63 4.9 27.1 1.0
N A:ASP83 4.9 28.9 1.0
N A:HIS80 4.9 35.2 1.0
CD2 A:HIS46 4.9 39.0 1.0

Zinc binding site 2 out of 4 in 2zkx

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Zinc binding site 2 out of 4 in the Crystal Structure of Human Cu-Zn Superoxide Dismutase Mutant G85R in Space Group I212121


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 Human Cu-Zn Superoxide Dismutase Mutant G85R in Space Group I212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:32.7
occ:1.00
 ND1 B:HIS63 1.8 22.4 1.0
OD1 B:ASP83 1.9 24.1 1.0
ND1 B:HIS80 2.0 30.0 1.0
ND1 B:HIS71 2.2 29.1 1.0
CE1 B:HIS80 2.6 27.8 1.0
CE1 B:HIS63 2.6 32.8 1.0
CG B:ASP83 2.9 29.9 1.0
CG B:HIS63 2.9 24.9 1.0
CG B:HIS80 3.0 29.7 1.0
CE1 B:HIS71 3.1 36.1 1.0
OD2 B:ASP83 3.2 31.6 1.0
CG B:HIS71 3.2 26.5 1.0
CB B:HIS63 3.5 15.4 1.0
CB B:HIS71 3.6 22.7 1.0
CB B:HIS80 3.7 37.4 1.0
NE2 B:HIS80 3.7 31.3 1.0
NE2 B:HIS63 3.8 27.1 1.0
CA B:HIS71 3.9 29.3 1.0
O B:LYS136 3.9 41.2 1.0
CD2 B:HIS80 3.9 28.8 1.0
CD2 B:HIS63 4.0 25.5 1.0
CB B:ASP83 4.2 29.4 1.0
NE2 B:HIS71 4.2 20.6 1.0
CD2 B:HIS71 4.3 32.0 1.0
N B:GLY72 4.6 34.3 1.0
CA B:ASP83 4.7 24.5 1.0
C B:LYS136 4.8 34.6 1.0
C B:HIS71 4.8 31.6 1.0
N B:HIS80 4.8 37.2 1.0
N B:ASP83 4.8 24.7 1.0
CA B:HIS80 4.9 35.2 1.0
N B:HIS71 4.9 27.4 1.0
CA B:THR137 5.0 32.9 1.0
CA B:HIS63 5.0 18.2 1.0

Zinc binding site 3 out of 4 in 2zkx

Go back to Zinc Binding Sites List in 2zkx
Zinc binding site 3 out of 4 in the Crystal Structure of Human Cu-Zn Superoxide Dismutase Mutant G85R in Space Group I212121


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 Human Cu-Zn Superoxide Dismutase Mutant G85R in Space Group I212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn403

b:32.3
occ:1.00
 OD1 C:ASP83 1.9 26.8 1.0
ND1 C:HIS80 1.9 33.6 1.0
ND1 C:HIS71 2.0 30.4 1.0
ND1 C:HIS63 2.1 20.8 1.0
CG C:ASP83 2.6 30.9 1.0
CE1 C:HIS80 2.7 22.1 1.0
OD2 C:ASP83 2.8 31.4 1.0
CE1 C:HIS71 2.8 39.0 1.0
CG C:HIS63 3.0 21.1 1.0
CG C:HIS80 3.1 28.9 1.0
CE1 C:HIS63 3.1 23.1 1.0
CG C:HIS71 3.1 35.0 1.0
CB C:HIS63 3.2 19.8 1.0
CB C:HIS71 3.6 32.3 1.0
CB C:HIS80 3.6 32.9 1.0
NE2 C:HIS80 3.9 24.7 1.0
CA C:HIS71 3.9 31.9 1.0
NE2 C:HIS71 4.0 34.2 1.0
CB C:ASP83 4.0 25.1 1.0
O C:LYS136 4.1 56.5 1.0
CD2 C:HIS80 4.1 25.7 1.0
CD2 C:HIS63 4.1 26.9 1.0
CD2 C:HIS71 4.2 31.1 1.0
NE2 C:HIS63 4.2 25.5 1.0
CA C:ASP83 4.7 30.6 1.0
N C:GLY72 4.7 32.0 1.0
CA C:HIS63 4.7 26.4 1.0
N C:HIS80 4.7 31.1 1.0
CA C:HIS80 4.8 29.6 1.0
C C:LYS136 4.8 54.1 1.0
N C:ASP83 4.9 26.3 1.0
C C:HIS71 4.9 33.5 1.0
CD2 C:HIS46 4.9 27.7 1.0
N C:HIS71 5.0 32.5 1.0

Zinc binding site 4 out of 4 in 2zkx

Go back to Zinc Binding Sites List in 2zkx
Zinc binding site 4 out of 4 in the Crystal Structure of Human Cu-Zn Superoxide Dismutase Mutant G85R in Space Group I212121


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 Human Cu-Zn Superoxide Dismutase Mutant G85R in Space Group I212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn404

b:0.4
occ:1.00
 ND1 D:HIS63 1.8 63.8 1.0
OD1 D:ASP83 2.3 0.4 1.0
CG D:HIS63 2.7 63.8 1.0
CE1 D:HIS63 2.8 70.7 1.0
CB D:HIS63 3.0 55.8 1.0
CG D:ASP83 3.2 98.5 1.0
OD2 D:ASP83 3.4 0.5 1.0
CD2 D:HIS63 3.8 68.8 1.0
NE2 D:HIS63 3.8 74.0 1.0
O D:GLY82 4.2 96.0 1.0
CA D:HIS63 4.5 51.8 1.0
CB D:ASP83 4.6 96.9 1.0
C D:GLY82 4.8 96.6 1.0
CD2 D:HIS46 4.9 45.1 1.0

Reference:

S.Yoshikawa, M.Kukimoto-Niino, K.Ito, L.Chen, Z.Q.Fu, J.Chrzas, B.C.Wang, M.Shirouzu, M.Urushitani, R.Takahashi, S.Yokoyama. Crystal Structure of Human Cu-Zn Superoxide Dismutase Mutant G85R in Space Group I212121 To Be Published.
Page generated: Thu Oct 24 10:48:46 2024

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