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Zinc in PDB 1sdy: Structure Solution and Molecular Dynamics Refinement of the Yeast Cu, Zn Enzyme Superoxide Dismutase

Enzymatic activity of Structure Solution and Molecular Dynamics Refinement of the Yeast Cu, Zn Enzyme Superoxide Dismutase

All present enzymatic activity of Structure Solution and Molecular Dynamics Refinement of the Yeast Cu, Zn Enzyme Superoxide Dismutase:
1.15.1.1;

Protein crystallography data

The structure of Structure Solution and Molecular Dynamics Refinement of the Yeast Cu, Zn Enzyme Superoxide Dismutase, PDB code: 1sdy was solved by K.Djinovic, G.Gatti, A.Coda, L.Antolini, G.Pelosi, A.Desideri, M.Falconi, F.Marmocchi, G.Rotilio, M.Bolognesi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.50
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 105.300, 143.000, 62.100, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1sdy:

The structure of Structure Solution and Molecular Dynamics Refinement of the Yeast Cu, Zn Enzyme Superoxide Dismutase also contains other interesting chemical elements:

Copper (Cu) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure Solution and Molecular Dynamics Refinement of the Yeast Cu, Zn Enzyme Superoxide Dismutase (pdb code 1sdy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure Solution and Molecular Dynamics Refinement of the Yeast Cu, Zn Enzyme Superoxide Dismutase, PDB code: 1sdy:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1sdy

Go back to Zinc Binding Sites List in 1sdy
Zinc binding site 1 out of 4 in the Structure Solution and Molecular Dynamics Refinement of the Yeast Cu, Zn Enzyme Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure Solution and Molecular Dynamics Refinement of the Yeast Cu, Zn Enzyme Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn153

b:23.6
occ:1.00
OD1 A:ASP81 1.8 8.4 1.0
ND1 A:HIS69 1.9 15.3 1.0
ND1 A:HIS61 1.9 19.6 1.0
ND1 A:HIS78 2.0 27.4 1.0
CG A:ASP81 2.7 5.9 1.0
CE1 A:HIS61 2.8 30.0 1.0
OD2 A:ASP81 2.8 41.6 1.0
CE1 A:HIS78 2.8 25.4 1.0
CE1 A:HIS69 2.9 13.8 1.0
CG A:HIS69 3.0 13.9 1.0
CG A:HIS61 3.1 19.6 1.0
CG A:HIS78 3.2 16.5 1.0
CB A:HIS69 3.4 13.3 1.0
CB A:HIS61 3.6 17.4 1.0
CB A:HIS78 3.6 16.2 1.0
CA A:HIS69 3.9 15.4 1.0
O A:LYS134 3.9 23.0 1.0
NE2 A:HIS61 4.0 15.8 1.0
NE2 A:HIS78 4.0 21.5 1.0
NE2 A:HIS69 4.0 17.4 1.0
CB A:ASP81 4.1 15.8 1.0
CD2 A:HIS69 4.1 18.8 1.0
CD2 A:HIS61 4.2 15.1 1.0
CD2 A:HIS78 4.2 13.3 1.0
CA A:ASP81 4.6 14.9 1.0
N A:ASP81 4.7 30.7 1.0
N A:HIS69 4.8 22.8 1.0
N A:HIS78 4.8 24.6 1.0
C A:LYS134 4.8 29.5 1.0
N A:GLY70 4.8 25.4 1.0
CA A:HIS78 4.9 9.7 1.0
C A:HIS69 4.9 12.3 1.0

Zinc binding site 2 out of 4 in 1sdy

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Zinc binding site 2 out of 4 in the Structure Solution and Molecular Dynamics Refinement of the Yeast Cu, Zn Enzyme Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure Solution and Molecular Dynamics Refinement of the Yeast Cu, Zn Enzyme Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn153

b:23.6
occ:1.00
ND1 B:HIS69 1.9 26.5 1.0
OD1 B:ASP81 2.0 18.8 1.0
ND1 B:HIS78 2.0 20.5 1.0
ND1 B:HIS61 2.0 24.9 1.0
CE1 B:HIS69 2.8 14.1 1.0
CE1 B:HIS61 2.9 19.3 1.0
CG B:ASP81 2.9 50.3 1.0
CE1 B:HIS78 2.9 12.4 1.0
CG B:HIS69 3.0 23.0 1.0
CG B:HIS61 3.1 14.8 1.0
OD2 B:ASP81 3.1 37.0 1.0
CG B:HIS78 3.1 28.5 1.0
CB B:HIS61 3.5 14.7 1.0
CB B:HIS78 3.5 28.0 1.0
CB B:HIS69 3.5 11.2 1.0
O B:LYS134 3.8 32.0 1.0
NE2 B:HIS69 3.9 23.0 1.0
CA B:HIS69 3.9 11.0 1.0
NE2 B:HIS61 4.0 20.1 1.0
CD2 B:HIS69 4.1 22.6 1.0
NE2 B:HIS78 4.1 20.7 1.0
CD2 B:HIS61 4.1 21.7 1.0
CD2 B:HIS78 4.2 26.2 1.0
CB B:ASP81 4.3 10.9 1.0
N B:GLY70 4.8 33.6 1.0
CA B:ASP81 4.8 15.8 1.0
O B:HOH215 4.8 27.7 1.0
C B:LYS134 4.8 24.2 1.0
CA B:HIS78 4.9 19.7 1.0
N B:HIS78 4.9 27.3 1.0
C B:HIS69 4.9 19.2 1.0
N B:ASP81 4.9 22.6 1.0
N B:HIS69 4.9 17.9 1.0

Zinc binding site 3 out of 4 in 1sdy

Go back to Zinc Binding Sites List in 1sdy
Zinc binding site 3 out of 4 in the Structure Solution and Molecular Dynamics Refinement of the Yeast Cu, Zn Enzyme Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure Solution and Molecular Dynamics Refinement of the Yeast Cu, Zn Enzyme Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn153

b:21.1
occ:1.00
ND1 C:HIS78 1.9 18.3 1.0
ND1 C:HIS69 1.9 27.5 1.0
OD1 C:ASP81 2.1 7.6 1.0
ND1 C:HIS61 2.2 23.8 1.0
CE1 C:HIS78 2.7 5.5 1.0
CE1 C:HIS69 2.8 12.9 1.0
CG C:ASP81 2.9 46.6 1.0
CG C:HIS69 3.0 21.5 1.0
OD2 C:ASP81 3.1 18.6 1.0
CG C:HIS78 3.1 17.8 1.0
CE1 C:HIS61 3.1 32.0 1.0
CG C:HIS61 3.2 36.6 1.0
CB C:HIS69 3.4 14.8 1.0
CB C:HIS61 3.5 7.2 1.0
CB C:HIS78 3.6 20.7 1.0
O C:LYS134 3.8 18.6 1.0
NE2 C:HIS78 3.9 5.0 1.0
CA C:HIS69 3.9 20.9 1.0
NE2 C:HIS69 4.0 22.1 1.0
CD2 C:HIS78 4.1 5.0 1.0
CD2 C:HIS69 4.1 10.2 1.0
NE2 C:HIS61 4.3 24.6 1.0
CB C:ASP81 4.3 12.7 1.0
CD2 C:HIS61 4.4 11.7 1.0
CA C:ASP81 4.7 18.1 1.0
N C:GLY70 4.8 27.3 1.0
O C:HOH191 4.8 27.6 1.0
C C:LYS134 4.9 16.1 1.0
N C:ASP81 4.9 28.9 1.0
N C:HIS78 4.9 15.4 1.0
C C:HIS69 4.9 45.9 1.0
CA C:HIS78 4.9 23.9 1.0
N C:HIS69 5.0 16.6 1.0

Zinc binding site 4 out of 4 in 1sdy

Go back to Zinc Binding Sites List in 1sdy
Zinc binding site 4 out of 4 in the Structure Solution and Molecular Dynamics Refinement of the Yeast Cu, Zn Enzyme Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure Solution and Molecular Dynamics Refinement of the Yeast Cu, Zn Enzyme Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn153

b:20.6
occ:1.00
OD1 D:ASP81 1.8 15.7 1.0
ND1 D:HIS78 1.9 14.5 1.0
ND1 D:HIS61 2.0 13.7 1.0
ND1 D:HIS69 2.1 30.6 1.0
CE1 D:HIS78 2.7 18.7 1.0
CG D:ASP81 2.7 19.1 1.0
CE1 D:HIS61 2.9 28.6 1.0
OD2 D:ASP81 2.9 29.9 1.0
CE1 D:HIS69 3.0 26.3 1.0
CG D:HIS61 3.0 29.0 1.0
CG D:HIS78 3.1 15.5 1.0
CG D:HIS69 3.2 31.3 1.0
CB D:HIS61 3.5 14.3 1.0
CB D:HIS69 3.6 12.5 1.0
CB D:HIS78 3.7 21.8 1.0
O D:LYS134 3.8 24.7 1.0
NE2 D:HIS78 3.9 16.8 1.0
CA D:HIS69 3.9 8.9 1.0
NE2 D:HIS61 4.1 22.7 1.0
CD2 D:HIS61 4.1 19.9 1.0
CD2 D:HIS78 4.1 10.0 1.0
CB D:ASP81 4.1 22.5 1.0
NE2 D:HIS69 4.2 30.2 1.0
CD2 D:HIS69 4.3 23.8 1.0
CA D:ASP81 4.7 23.9 1.0
C D:LYS134 4.8 34.8 1.0
CA D:THR135 4.8 21.6 1.0
N D:GLY70 4.9 24.9 1.0
N D:HIS69 4.9 28.0 1.0
C D:HIS69 4.9 26.5 1.0
N D:HIS78 4.9 22.6 1.0
CA D:HIS61 5.0 24.8 1.0
CA D:HIS78 5.0 20.8 1.0
N D:ASP81 5.0 40.0 1.0

Reference:

K.Djinovic, G.Gatti, A.Coda, L.Antolini, G.Pelosi, A.Desideri, M.Falconi, F.Marmocchi, G.Rolilio, M.Bolognesi. Structure Solution and Molecular Dynamics Refinement of the Yeast Cu,Zn Enzyme Superoxide Dismutase. Acta Crystallogr.,Sect.B V. 47 918 1991.
ISSN: ISSN 0108-7681
PubMed: 1772629
DOI: 10.1107/S0108768191004949
Page generated: Wed Dec 16 03:03:37 2020

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