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Zinc in PDB 1to5: Structure of the Cytosolic Cu,Zn Sod From S. Mansoni

Enzymatic activity of Structure of the Cytosolic Cu,Zn Sod From S. Mansoni

All present enzymatic activity of Structure of the Cytosolic Cu,Zn Sod From S. Mansoni:
1.15.1.1;

Protein crystallography data

The structure of Structure of the Cytosolic Cu,Zn Sod From S. Mansoni, PDB code: 1to5 was solved by R.M.F.Cardoso, C.H.T.P.Silva, A.P.Ulian De Araujo, T.Tanaka, M.Tanaka, R.C.Garratt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 58.80 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.640, 78.240, 95.180, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 24.1

Other elements in 1to5:

The structure of Structure of the Cytosolic Cu,Zn Sod From S. Mansoni also contains other interesting chemical elements:

Copper (Cu) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Cytosolic Cu,Zn Sod From S. Mansoni (pdb code 1to5). 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 of the Cytosolic Cu,Zn Sod From S. Mansoni, PDB code: 1to5:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1to5

Go back to Zinc Binding Sites List in 1to5
Zinc binding site 1 out of 4 in the Structure of the Cytosolic Cu,Zn Sod From S. Mansoni


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Cytosolic Cu,Zn Sod From S. Mansoni within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn711

b:10.1
occ:1.00
OD1 A:ASP82 2.0 6.2 1.0
ND1 A:HIS62 2.0 12.0 1.0
ND1 A:HIS70 2.0 8.0 1.0
ND1 A:HIS79 2.1 4.8 1.0
CG A:ASP82 2.8 6.1 1.0
CE1 A:HIS70 2.9 7.5 1.0
CE1 A:HIS62 2.9 13.3 1.0
OD2 A:ASP82 3.0 7.4 1.0
CE1 A:HIS79 3.1 4.9 1.0
CG A:HIS79 3.1 5.8 1.0
CG A:HIS62 3.1 13.4 1.0
CG A:HIS70 3.2 8.2 1.0
CB A:HIS79 3.4 6.2 1.0
CB A:HIS62 3.6 12.1 1.0
CB A:HIS70 3.7 10.3 1.0
CA A:HIS70 4.0 11.5 1.0
O A:VAL135 4.0 12.8 1.0
NE2 A:HIS62 4.0 14.5 1.0
NE2 A:HIS70 4.0 7.7 1.0
NE2 A:HIS79 4.1 3.1 1.0
CD2 A:HIS62 4.2 14.3 1.0
CD2 A:HIS79 4.2 5.6 1.0
CD2 A:HIS70 4.2 7.7 1.0
CB A:ASP82 4.2 7.6 1.0
CA A:HIS79 4.7 7.7 1.0
CA A:ASP82 4.7 8.2 1.0
N A:GLY71 4.8 10.6 1.0
CD2 A:HIS45 4.8 9.1 1.0
N A:HIS79 4.8 9.0 1.0
O A:HOH718 4.8 18.0 1.0
C A:VAL135 4.9 12.5 1.0
N A:ASP82 4.9 7.8 1.0
C A:HIS70 4.9 11.5 1.0
N A:HIS70 5.0 12.2 1.0

Zinc binding site 2 out of 4 in 1to5

Go back to Zinc Binding Sites List in 1to5
Zinc binding site 2 out of 4 in the Structure of the Cytosolic Cu,Zn Sod From S. Mansoni


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Cytosolic Cu,Zn Sod From S. Mansoni within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn721

b:9.1
occ:1.00
ND1 B:HIS70 2.0 4.6 1.0
OD1 B:ASP82 2.0 6.1 1.0
ND1 B:HIS62 2.1 10.0 1.0
ND1 B:HIS79 2.1 7.7 1.0
CG B:ASP82 2.7 8.7 1.0
OD2 B:ASP82 2.8 8.5 1.0
CE1 B:HIS70 2.9 5.7 1.0
CE1 B:HIS62 3.0 11.9 1.0
CE1 B:HIS79 3.0 8.6 1.0
CG B:HIS70 3.1 7.5 1.0
CG B:HIS62 3.1 9.3 1.0
CG B:HIS79 3.1 10.1 1.0
CB B:HIS62 3.5 7.3 1.0
CB B:HIS79 3.5 10.4 1.0
CB B:HIS70 3.5 6.1 1.0
O B:VAL135 3.9 10.6 1.0
CA B:HIS70 3.9 8.5 1.0
NE2 B:HIS70 4.0 6.6 1.0
NE2 B:HIS62 4.1 15.7 1.0
NE2 B:HIS79 4.1 6.4 1.0
CD2 B:HIS70 4.2 5.9 1.0
CB B:ASP82 4.2 9.0 1.0
CD2 B:HIS62 4.2 10.2 1.0
CD2 B:HIS79 4.2 7.8 1.0
O B:HOH756 4.6 7.0 1.0
CA B:ASP82 4.7 9.8 1.0
CA B:HIS79 4.8 9.6 1.0
N B:HIS79 4.8 11.3 1.0
C B:VAL135 4.8 10.8 1.0
N B:HIS70 4.8 11.1 1.0
N B:GLY71 4.8 10.6 1.0
N B:ASP82 4.9 9.6 1.0
C B:HIS70 4.9 9.7 1.0
CD2 B:HIS45 4.9 8.9 1.0
CA B:HIS62 5.0 8.8 1.0

Zinc binding site 3 out of 4 in 1to5

Go back to Zinc Binding Sites List in 1to5
Zinc binding site 3 out of 4 in the Structure of the Cytosolic Cu,Zn Sod From S. Mansoni


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Cytosolic Cu,Zn Sod From S. Mansoni within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn731

b:9.3
occ:1.00
ND1 C:HIS70 2.0 9.3 1.0
OD1 C:ASP82 2.0 6.7 1.0
ND1 C:HIS62 2.1 12.5 1.0
ND1 C:HIS79 2.1 3.4 1.0
CE1 C:HIS70 2.9 9.9 1.0
CG C:ASP82 2.9 7.7 1.0
CE1 C:HIS62 2.9 13.0 1.0
CE1 C:HIS79 2.9 4.3 1.0
OD2 C:ASP82 3.0 10.0 1.0
CG C:HIS79 3.1 7.2 1.0
CG C:HIS70 3.1 10.0 1.0
CG C:HIS62 3.2 11.6 1.0
CB C:HIS79 3.5 4.9 1.0
CB C:HIS70 3.6 8.8 1.0
CB C:HIS62 3.6 10.0 1.0
CA C:HIS70 3.9 11.2 1.0
NE2 C:HIS70 4.0 10.8 1.0
O C:VAL135 4.0 9.7 1.0
NE2 C:HIS79 4.1 4.5 1.0
NE2 C:HIS62 4.1 14.3 1.0
CD2 C:HIS70 4.2 10.5 1.0
CD2 C:HIS79 4.2 3.9 1.0
CD2 C:HIS62 4.2 12.8 1.0
CB C:ASP82 4.3 8.5 1.0
N C:GLY71 4.7 10.5 1.0
CA C:ASP82 4.8 8.0 1.0
CA C:HIS79 4.8 6.0 1.0
N C:HIS79 4.8 6.6 1.0
CD2 C:HIS45 4.8 8.4 1.0
C C:HIS70 4.9 10.2 1.0
C C:VAL135 4.9 7.8 1.0
O C:HOH744 4.9 12.7 1.0
N C:HIS70 4.9 9.8 1.0
N C:ASP82 5.0 6.9 1.0
CA C:THR136 5.0 9.4 1.0

Zinc binding site 4 out of 4 in 1to5

Go back to Zinc Binding Sites List in 1to5
Zinc binding site 4 out of 4 in the Structure of the Cytosolic Cu,Zn Sod From S. Mansoni


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Cytosolic Cu,Zn Sod From S. Mansoni within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn741

b:10.7
occ:1.00
OD1 D:ASP82 1.9 9.5 1.0
ND1 D:HIS70 2.0 6.1 1.0
ND1 D:HIS79 2.0 7.3 1.0
ND1 D:HIS62 2.1 10.0 1.0
CG D:ASP82 2.7 9.9 1.0
CE1 D:HIS70 2.8 6.6 1.0
OD2 D:ASP82 2.9 8.9 1.0
CE1 D:HIS79 2.9 9.7 1.0
CE1 D:HIS62 3.0 12.3 1.0
CG D:HIS79 3.1 10.1 1.0
CG D:HIS70 3.1 7.8 1.0
CG D:HIS62 3.2 10.8 1.0
CB D:HIS79 3.5 11.6 1.0
CB D:HIS62 3.5 7.7 1.0
CB D:HIS70 3.6 8.7 1.0
CA D:HIS70 3.9 10.6 1.0
NE2 D:HIS79 4.0 7.2 1.0
O D:VAL135 4.0 8.7 1.0
NE2 D:HIS70 4.0 9.1 1.0
CD2 D:HIS79 4.1 7.8 1.0
CB D:ASP82 4.1 7.9 1.0
NE2 D:HIS62 4.1 13.6 1.0
CD2 D:HIS70 4.2 6.5 1.0
CD2 D:HIS62 4.2 11.5 1.0
CA D:ASP82 4.6 10.1 1.0
O D:HOH769 4.7 7.2 1.0
N D:GLY71 4.7 10.7 1.0
CA D:HIS79 4.8 12.5 1.0
N D:HIS79 4.8 14.2 1.0
N D:ASP82 4.8 10.0 1.0
CD2 D:HIS45 4.8 12.2 1.0
C D:VAL135 4.9 10.8 1.0
C D:HIS70 4.9 11.6 1.0
N D:HIS70 4.9 12.9 1.0

Reference:

R.M.Cardoso, C.H.Silva, A.P.Ulian De Araujo, T.Tanaka, M.Tanaka, R.C.Garratt. Structure of the Cytosolic Cu,Zn Superoxide Dismutase From Schistosoma Mansoni. Acta Crystallogr.,Sect.D V. 60 1569 2004.
ISSN: ISSN 0907-4449
PubMed: 15333927
DOI: 10.1107/S0907444904016798
Page generated: Wed Dec 16 03:05:15 2020

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