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Copper 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:

Zinc (Zn) 4 atoms

Copper Binding Sites:

The binding sites of Copper 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 Copper atom.
In total 4 binding sites of Copper where determined in the Structure Solution and Molecular Dynamics Refinement of the Yeast Cu, Zn Enzyme Superoxide Dismutase, PDB code: 1sdy:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 1sdy

Go back to Copper Binding Sites List in 1sdy
Copper 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 Copper with other atoms in the Cu 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:Cu152

b:25.5
occ:1.00
 ND1 A:HIS44 1.8 28.9 1.0
O A:HOH154 1.9 48.4 1.0
NE2 A:HIS46 2.2 15.4 1.0
NE2 A:HIS118 2.2 12.7 1.0
NE2 A:HIS61 2.4 15.8 1.0
CG A:HIS44 2.8 22.2 1.0
CE1 A:HIS44 2.9 21.6 1.0
CD2 A:HIS61 3.1 15.1 1.0
CE1 A:HIS46 3.1 11.3 1.0
CB A:HIS44 3.2 26.7 1.0
CD2 A:HIS46 3.2 12.3 1.0
CE1 A:HIS118 3.2 7.1 1.0
CD2 A:HIS118 3.2 11.0 1.0
CE1 A:HIS61 3.6 30.0 1.0
NE2 A:HIS44 4.0 16.3 1.0
CD2 A:HIS44 4.0 14.6 1.0
ND1 A:HIS46 4.3 20.9 1.0
CG A:HIS46 4.3 18.9 1.0
CG A:HIS61 4.3 19.6 1.0
ND1 A:HIS118 4.3 24.8 1.0
CG A:HIS118 4.3 11.5 1.0
O A:HOH273 4.5 64.0 1.0
CA A:HIS44 4.6 31.1 1.0
ND1 A:HIS61 4.6 19.6 1.0
CG2 A:VAL116 4.7 6.6 1.0
N A:HIS44 4.8 21.7 1.0
CG1 A:VAL116 5.0 8.6 1.0

Copper binding site 2 out of 4 in 1sdy

Go back to Copper Binding Sites List in 1sdy
Copper 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 Copper with other atoms in the Cu 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:Cu152

b:22.0
occ:1.00
 ND1 B:HIS44 1.9 28.4 1.0
NE2 B:HIS118 2.0 10.5 1.0
O B:HOH154 2.1 39.8 1.0
NE2 B:HIS61 2.1 20.1 1.0
NE2 B:HIS46 2.3 14.6 1.0
CE1 B:HIS118 2.8 17.3 1.0
CD2 B:HIS61 2.8 21.7 1.0
CG B:HIS44 2.9 32.8 1.0
CE1 B:HIS44 2.9 12.6 1.0
CD2 B:HIS118 3.1 23.0 1.0
CE1 B:HIS46 3.1 9.6 1.0
CB B:HIS44 3.2 12.0 1.0
CE1 B:HIS61 3.2 19.3 1.0
CD2 B:HIS46 3.3 13.4 1.0
NE2 B:HIS44 4.0 24.1 1.0
ND1 B:HIS118 4.0 16.8 1.0
CD2 B:HIS44 4.0 17.4 1.0
CG B:HIS61 4.1 14.8 1.0
CG B:HIS118 4.2 27.7 1.0
ND1 B:HIS61 4.2 24.9 1.0
ND1 B:HIS46 4.3 20.1 1.0
CG B:HIS46 4.4 14.0 1.0
CA B:HIS44 4.6 13.9 1.0
CG2 B:VAL116 4.7 18.9 1.0
N B:HIS44 4.9 20.3 1.0
O B:HOH226 5.0 29.0 1.0

Copper binding site 3 out of 4 in 1sdy

Go back to Copper Binding Sites List in 1sdy
Copper 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 Copper with other atoms in the Cu 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:Cu152

b:22.1
occ:1.00
 O C:HOH154 1.8 31.5 1.0
ND1 C:HIS44 1.9 20.2 1.0
NE2 C:HIS61 2.0 24.6 1.0
NE2 C:HIS118 2.1 6.8 1.0
NE2 C:HIS46 2.3 9.0 1.0
CE1 C:HIS44 2.8 25.2 1.0
CD2 C:HIS61 2.9 11.7 1.0
CG C:HIS44 3.0 22.9 1.0
CE1 C:HIS118 3.0 14.3 1.0
CE1 C:HIS61 3.0 32.0 1.0
CD2 C:HIS118 3.2 24.0 1.0
CE1 C:HIS46 3.3 17.0 1.0
CD2 C:HIS46 3.3 21.5 1.0
CB C:HIS44 3.4 14.7 1.0
NE2 C:HIS44 4.0 11.1 1.0
CG C:HIS61 4.1 36.6 1.0
CD2 C:HIS44 4.1 12.5 1.0
ND1 C:HIS61 4.1 23.8 1.0
ND1 C:HIS118 4.2 17.3 1.0
O C:HOH240 4.2 30.5 1.0
CG C:HIS118 4.2 13.2 1.0
ND1 C:HIS46 4.4 16.5 1.0
CG C:HIS46 4.4 14.2 1.0
CA C:HIS44 4.6 10.7 1.0
N C:HIS44 4.8 15.8 1.0
CB C:VAL116 4.8 22.9 1.0
CG1 C:VAL116 4.9 10.1 1.0

Copper binding site 4 out of 4 in 1sdy

Go back to Copper Binding Sites List in 1sdy
Copper 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 Copper with other atoms in the Cu 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:Cu152

b:25.3
occ:1.00
 ND1 D:HIS44 1.8 15.2 1.0
NE2 D:HIS46 2.1 24.8 1.0
NE2 D:HIS61 2.2 22.7 1.0
NE2 D:HIS118 2.3 14.3 1.0
O D:HOH154 2.4 32.6 1.0
CE1 D:HIS44 2.8 22.0 1.0
CG D:HIS44 2.9 22.9 1.0
CD2 D:HIS61 2.9 19.9 1.0
CD2 D:HIS46 3.1 14.8 1.0
CE1 D:HIS46 3.1 15.5 1.0
CE1 D:HIS118 3.2 11.1 1.0
CD2 D:HIS118 3.3 25.6 1.0
CE1 D:HIS61 3.3 28.6 1.0
CB D:HIS44 3.3 31.5 1.0
NE2 D:HIS44 3.9 16.7 1.0
CD2 D:HIS44 4.0 12.7 1.0
CG D:HIS61 4.1 29.0 1.0
CG D:HIS46 4.2 21.6 1.0
ND1 D:HIS46 4.2 26.6 1.0
ND1 D:HIS61 4.3 13.7 1.0
ND1 D:HIS118 4.4 26.6 1.0
CG D:HIS118 4.4 19.3 1.0
CA D:HIS44 4.6 22.3 1.0
CG1 D:VAL116 4.7 9.9 1.0
CB D:VAL116 4.7 30.8 1.0
N D:HIS44 4.9 10.4 1.0
O D:HOH255 4.9 44.8 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: Mon Jul 14 00:24:47 2025

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