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Cadmium in PDB 2x05: 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: 2x05 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) 43.79 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.120, 121.800, 91.560, 90.00, 90.51, 90.00
R / Rfree (%) 18.401 / 24.816

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

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 2x05). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 19 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: 2x05:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 19 in 2x05

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Cadmium binding site 1 out of 19 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:29.6
occ:1.00
 O B:HOH2113 2.0 16.6 1.0
ND1 A:HIS310 2.6 12.8 1.0
O B:HOH2020 2.6 10.0 1.0
OD1 B:ASP68 2.6 25.1 1.0
NZ B:LYS187 2.7 12.8 1.0
O B:HOH2019 2.7 10.1 1.0
CE B:LYS187 2.9 11.8 1.0
OD2 B:ASP68 2.9 22.4 1.0
CG B:ASP68 3.2 23.0 1.0
CE1 A:HIS310 3.4 13.0 1.0
CG A:HIS310 3.6 13.1 1.0
ND2 A:ASN299 3.6 17.5 1.0
CB A:HIS310 3.9 12.4 1.0
CD B:LYS187 4.3 12.1 1.0
CG A:ASN299 4.4 15.3 1.0
NE2 A:HIS310 4.6 12.1 1.0
CA A:HIS310 4.7 12.2 1.0
CB B:ASP68 4.7 21.6 1.0
CD2 A:HIS310 4.7 11.9 1.0
O A:HOH2227 4.8 27.3 1.0
OD1 A:ASN299 4.8 17.0 1.0
O B:HOH2021 5.0 15.7 1.0

Cadmium binding site 2 out of 19 in 2x05

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Cadmium binding site 2 out of 19 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:11.9
occ:1.00
 OD2 A:ASP296 2.2 14.6 1.0
OD1 A:ASP296 2.3 20.4 1.0
O A:HOH2211 2.5 2.0 1.0
CG A:ASP296 2.6 17.4 1.0
CB A:ASP296 4.1 17.5 1.0
CE1 A:HIS244 4.2 9.1 1.0
ND1 A:HIS244 4.2 12.9 1.0
CA A:ASP296 5.0 17.4 1.0

Cadmium binding site 3 out of 19 in 2x05

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Cadmium binding site 3 out of 19 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
A:Cd1903

b:60.3
occ:1.00
 ND1 A:HIS178 2.4 31.7 1.0
O A:HOH2115 2.8 36.4 1.0
CE1 A:HIS178 3.3 32.2 1.0
CG A:HIS178 3.4 30.6 1.0
O A:HOH2055 3.5 51.2 1.0
CB A:HIS178 3.7 28.6 1.0
O A:GLN176 4.3 24.2 1.0
NE2 A:HIS178 4.3 32.1 1.0
CD2 A:HIS178 4.4 32.1 1.0
ND2 A:ASN152 4.9 18.3 1.0
O A:HOH2116 4.9 39.8 1.0
CA A:HIS178 4.9 28.5 1.0

Cadmium binding site 4 out of 19 in 2x05

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Cadmium binding site 4 out of 19 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 4 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:Cd1904

b:76.7
occ:1.00
 O A:HOH2104 2.3 27.1 1.0
OD1 A:ASP404 2.4 15.5 1.0
OD2 A:ASP404 2.5 18.9 1.0
CG A:ASP404 2.8 14.6 1.0
O A:HOH2299 2.9 42.6 1.0
O A:HOH2242 3.0 12.7 1.0
CE1 A:HIS458 4.0 11.8 1.0
CB A:ASP404 4.3 11.7 1.0
NH1 A:ARG311 4.3 15.9 1.0
NE2 A:HIS458 4.6 12.1 1.0
O A:HOH2341 5.0 7.2 1.0
CB A:ASP400 5.0 14.3 1.0

Cadmium binding site 5 out of 19 in 2x05

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Cadmium binding site 5 out of 19 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 5 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:Cd1905

b:12.8
occ:1.00
 OD1 A:ASP246 2.1 21.6 1.0
NE2 A:HIS244 2.1 11.0 1.0
CG A:ASP246 2.8 19.8 1.0
OD2 A:ASP246 2.9 19.8 1.0
CE1 A:HIS244 3.0 9.1 1.0
CD2 A:HIS244 3.2 11.4 1.0
ND1 A:HIS244 4.2 12.9 1.0
CB A:ASP246 4.2 19.4 1.0
CG A:HIS244 4.3 13.6 1.0
CA A:GLY294 4.5 16.6 1.0
CD2 A:LEU292 4.6 24.9 1.0
O A:ALA245 4.6 18.6 1.0
CA A:ASP246 4.8 19.2 1.0
C A:ALA245 5.0 18.4 1.0

Cadmium binding site 6 out of 19 in 2x05

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Cadmium binding site 6 out of 19 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 6 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:Cd1906

b:0.9
occ:1.00
 N A:ALA875 2.7 19.0 1.0
O A:GLY815 2.7 20.4 1.0
N A:THR874 3.1 18.6 1.0
O A:HOH2588 3.2 31.6 1.0
O A:HOH2585 3.3 20.1 1.0
CB A:ALA875 3.3 19.0 1.0
C A:THR874 3.5 19.0 1.0
CA A:ALA875 3.5 19.4 1.0
CA A:THR874 3.6 18.8 1.0
CB A:THR874 3.6 18.8 1.0
C A:ARG873 3.6 17.8 1.0
CB A:ARG873 3.7 16.8 1.0
C A:GLY815 3.7 20.4 1.0
CA A:ARG873 3.9 16.9 1.0
CA A:GLY815 4.1 20.6 1.0
O A:HOH2550 4.2 19.4 1.0
OG1 A:THR874 4.3 18.7 1.0
O A:ARG873 4.4 18.8 1.0
CG A:ARG873 4.5 16.5 1.0
O A:THR874 4.7 19.1 1.0
C A:ALA875 4.8 19.4 1.0
CG2 A:THR874 4.9 18.8 1.0
CD A:ARG873 4.9 16.1 1.0
N A:ASP876 4.9 20.2 1.0
N A:THR816 4.9 19.5 1.0

Cadmium binding site 7 out of 19 in 2x05

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Cadmium binding site 7 out of 19 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 7 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:Cd1907

b:0.2
occ:1.00
 O A:ARG87 2.8 14.4 1.0
N A:THR89 2.8 10.9 1.0
O A:PHE368 2.9 12.6 1.0
O A:LEU369 3.0 13.4 1.0
C A:LEU369 3.2 13.4 1.0
CA A:SER88 3.2 12.0 1.0
C A:SER88 3.4 11.5 1.0
N A:ARG370 3.5 13.5 1.0
OG1 A:THR89 3.5 10.0 1.0
CB A:ALA92 3.6 15.2 1.0
CG2 A:THR89 3.7 11.4 1.0
C A:ARG87 3.7 13.8 1.0
CA A:ARG370 3.8 13.4 1.0
N A:SER88 3.9 12.8 1.0
CA A:THR89 3.9 10.8 1.0
C A:PHE368 3.9 12.2 1.0
CB A:THR89 3.9 10.3 1.0
CA A:LEU369 4.0 13.3 1.0
O A:HOH2029 4.0 19.4 1.0
CB A:LEU369 4.0 12.6 1.0
CB A:SER88 4.2 11.9 1.0
CG A:ARG370 4.3 13.1 1.0
N A:LEU369 4.4 13.0 1.0
CG1 A:VAL216 4.6 12.9 1.0
O A:SER88 4.6 11.1 1.0
CB A:ARG370 4.6 13.9 1.0
O A:THR89 4.7 10.4 1.0
C A:THR89 4.9 10.7 1.0
OG A:SER88 4.9 15.2 1.0
C A:ARG370 4.9 14.3 1.0

Cadmium binding site 8 out of 19 in 2x05

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Cadmium binding site 8 out of 19 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 8 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:Cd1908

b:0.1
occ:1.00
 OD1 A:ASP421 2.8 16.3 1.0
O A:GLU418 2.8 14.5 1.0
N A:GLU424 2.9 12.8 1.0
O A:ASP421 2.9 13.7 1.0
N A:ASP421 2.9 14.7 1.0
C A:CYS419 3.2 16.0 1.0
N A:TRP423 3.2 11.6 1.0
C A:ASP421 3.2 13.8 1.0
CB A:TRP423 3.3 11.6 1.0
O A:CYS419 3.4 16.3 1.0
N A:CYS420 3.4 15.9 1.0
CA A:TRP423 3.5 11.8 1.0
CA A:ASP421 3.5 14.7 1.0
C A:TRP423 3.6 12.1 1.0
CB A:GLU424 3.6 12.5 1.0
CG A:ASP421 3.6 16.9 1.0
CA A:CYS419 3.7 15.7 1.0
CG A:GLU424 3.7 12.3 1.0
C A:GLU418 3.7 14.3 1.0
CA A:GLU424 3.8 13.1 1.0
N A:LYS422 4.0 13.0 1.0
C A:CYS420 4.0 15.8 1.0
C A:LYS422 4.0 12.2 1.0
N A:CYS419 4.1 14.9 1.0
CB A:ASP421 4.2 15.0 1.0
CA A:CYS420 4.3 16.0 1.0
CG A:TRP423 4.3 10.5 1.0
CD A:GLU424 4.4 11.8 1.0
CD1 A:TRP423 4.4 10.2 1.0
CG A:GLU418 4.5 13.4 1.0
OD2 A:ASP421 4.6 19.1 1.0
CA A:LYS422 4.6 12.5 1.0
C A:GLU424 4.7 13.6 1.0
O A:TRP423 4.7 12.0 1.0
O A:LYS422 4.8 11.9 1.0
N A:GLY425 4.8 13.8 1.0
OE1 A:GLU424 4.9 14.6 1.0
O A:HOH2310 4.9 15.2 1.0
OE2 A:GLU424 5.0 12.3 1.0
CA A:GLU418 5.0 13.6 1.0

Cadmium binding site 9 out of 19 in 2x05

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Cadmium binding site 9 out of 19 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 9 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:Cd1909

b:14.1
occ:1.00
 CD A:PRO120 4.0 14.8 1.0
CG A:PRO120 4.3 14.8 1.0
CE1 A:TYR189 4.3 15.1 1.0
CD1 A:TYR189 4.5 13.7 1.0

Cadmium binding site 10 out of 19 in 2x05

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Cadmium binding site 10 out of 19 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 10 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:69.2
occ:1.00
 ND1 B:HIS178 2.7 33.1 1.0
O B:HOH2085 3.6 38.7 1.0
CG B:HIS178 3.6 31.7 1.0
CE1 B:HIS178 3.6 34.3 1.0
CB B:HIS178 3.8 29.9 1.0
O B:GLN176 4.3 24.9 1.0
NE2 B:HIS178 4.7 35.0 1.0
CD2 B:HIS178 4.7 33.5 1.0
ND2 B:ASN152 4.7 27.6 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 15:21:41 2024

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