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Cadmium in PDB 2x09: Inhibition of the Exo-Beta-D-Glucosaminidase Csxa By A Glucosamine-Configured Castanospermine and An Amino- Australine Analogue

Enzymatic activity of Inhibition of the Exo-Beta-D-Glucosaminidase Csxa By A Glucosamine-Configured Castanospermine and An Amino- Australine Analogue

All present enzymatic activity of Inhibition of the Exo-Beta-D-Glucosaminidase Csxa By A Glucosamine-Configured Castanospermine and An Amino- Australine Analogue:
3.2.1.165;

Protein crystallography data

The structure of Inhibition of the Exo-Beta-D-Glucosaminidase Csxa By A Glucosamine-Configured Castanospermine and An Amino- Australine Analogue, PDB code: 2x09 was solved by B.Pluvinage, M.G.Ghinet, R.Brzezinski, A.B.Boraston, K.A.Stubbs, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.750, 121.950, 92.050, 90.00, 90.65, 90.00
R / Rfree (%) 17.602 / 24.032

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Inhibition of the Exo-Beta-D-Glucosaminidase Csxa By A Glucosamine-Configured Castanospermine and An Amino- Australine Analogue (pdb code 2x09). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Inhibition of the Exo-Beta-D-Glucosaminidase Csxa By A Glucosamine-Configured Castanospermine and An Amino- Australine Analogue, PDB code: 2x09:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in 2x09

Go back to Cadmium Binding Sites List in 2x09
Cadmium binding site 1 out of 3 in the Inhibition of the Exo-Beta-D-Glucosaminidase Csxa By A Glucosamine-Configured Castanospermine and An Amino- Australine Analogue


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Inhibition of the Exo-Beta-D-Glucosaminidase Csxa By A Glucosamine-Configured Castanospermine and An Amino- Australine Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1901

b:11.5
occ:1.00
 OD1 A:ASP246 1.9 11.3 1.0
NE2 A:HIS244 2.2 6.0 1.0
O A:HOH2212 2.3 2.0 1.0
CG A:ASP246 2.8 11.3 1.0
OD2 A:ASP246 3.0 9.6 1.0
CE1 A:HIS244 3.1 7.1 1.0
CD2 A:HIS244 3.2 9.1 1.0
CB A:ASP246 4.2 11.4 1.0
ND1 A:HIS244 4.2 6.2 1.0
CG A:HIS244 4.3 9.9 1.0
CA A:GLY294 4.6 13.1 1.0
CD2 A:LEU292 4.6 19.0 1.0
O A:ALA245 4.8 11.7 1.0
CA A:ASP246 4.8 11.4 1.0

Cadmium binding site 2 out of 3 in 2x09

Go back to Cadmium Binding Sites List in 2x09
Cadmium binding site 2 out of 3 in the Inhibition of the Exo-Beta-D-Glucosaminidase Csxa By A Glucosamine-Configured Castanospermine and An Amino- Australine Analogue


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Inhibition of the Exo-Beta-D-Glucosaminidase Csxa By A Glucosamine-Configured Castanospermine and An Amino- Australine Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1902

b:9.9
occ:1.00
 OD2 A:ASP296 2.1 13.8 1.0
OD1 A:ASP296 2.4 15.9 1.0
O A:HOH2261 2.5 2.0 1.0
CG A:ASP296 2.6 14.3 1.0
ND1 A:HIS244 4.0 6.2 1.0
CE1 A:HIS244 4.1 7.1 1.0
CB A:ASP296 4.1 14.3 1.0
O A:HOH2262 4.9 34.5 1.0
CA A:ASP296 5.0 13.9 1.0

Cadmium binding site 3 out of 3 in 2x09

Go back to Cadmium Binding Sites List in 2x09
Cadmium binding site 3 out of 3 in the Inhibition of the Exo-Beta-D-Glucosaminidase Csxa By A Glucosamine-Configured Castanospermine and An Amino- Australine Analogue


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Inhibition of the Exo-Beta-D-Glucosaminidase Csxa By A Glucosamine-Configured Castanospermine and An Amino- Australine Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1901

b:66.0
occ:1.00
 O B:GLU431 2.5 18.1 1.0
OD1 B:ASN428 2.6 17.3 1.0
O B:GLY429 2.6 22.1 1.0
O B:GLY433 2.7 16.0 1.0
O B:HOH2371 2.8 26.8 1.0
C B:GLU431 3.6 18.7 1.0
CG B:ASN428 3.7 19.1 1.0
C B:GLY429 3.7 22.0 1.0
C B:GLY433 3.9 16.6 1.0
N B:GLU431 4.0 20.7 1.0
O B:GLY425 4.0 14.1 1.0
O B:HOH2375 4.1 29.2 1.0
C B:GLU430 4.2 22.0 1.0
N B:GLY429 4.2 21.1 1.0
C B:ASN428 4.2 20.5 1.0
C B:LYS432 4.2 18.2 1.0
N B:GLY433 4.3 17.5 1.0
ND2 B:ASN428 4.3 19.7 1.0
CA B:GLU431 4.3 19.9 1.0
O B:LYS432 4.4 17.9 1.0
O B:ASN428 4.4 20.3 1.0
CA B:GLY433 4.4 16.8 1.0
CA B:GLY425 4.5 14.2 1.0
CA B:GLU430 4.5 22.9 1.0
N B:GLU430 4.5 22.2 1.0
CA B:GLY429 4.5 21.6 1.0
N B:LYS432 4.6 18.4 1.0
O B:GLU430 4.6 22.6 1.0
C B:GLY425 4.7 14.8 1.0
CB B:ASN428 4.8 19.8 1.0
CA B:LYS432 4.8 18.6 1.0
CA B:ASN428 4.8 19.9 1.0
CB B:GLU431 4.8 20.0 1.0
O B:HOH2377 4.8 21.0 1.0
N B:ASN428 5.0 19.5 1.0
N B:GLU434 5.0 16.1 1.0

Reference:

B.Pluvinage, M.G.Ghinet, R.Brzezinski, A.B.Boraston, K.A.Stubbs. Inhibition of the Exo-Beta-D-Glucosaminidase Csxa By A Glucosamine-Configured Castanospermine and An Amino-Australine Analogue. Org.Biomol.Chem. V. 7 4169 2009.
ISSN: ISSN 1477-0520
PubMed: 19795054
DOI: 10.1039/B913235J
Page generated: Fri Jul 19 15:23:41 2024

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