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Cadmium in PDB 2vzs: Chitosan Product Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa

Protein crystallography data

The structure of Chitosan Product Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa, PDB code: 2vzs was solved by A.Lammerts Van Bueren, M.G.Ghinet, K.Gregg, A.Fleury, R.Brzezinski, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.544, 121.810, 91.843, 90.00, 90.42, 90.00
R / Rfree (%) 17.3 / 22

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Chitosan Product Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa (pdb code 2vzs). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Chitosan Product Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa, PDB code: 2vzs:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 2vzs

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Cadmium binding site 1 out of 6 in the Chitosan Product Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Chitosan Product Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1899

b:0.4
occ:1.00
 NZ B:LYS187 2.5 20.6 1.0
ND2 A:ASN299 2.6 17.0 1.0
O B:HOH2031 2.7 18.2 1.0
CE B:LYS187 3.1 20.6 1.0
CE1 A:HIS310 3.5 16.2 1.0
OD1 B:ASP68 3.5 19.7 1.0
O B:HOH2016 3.5 16.8 1.0
ND1 A:HIS310 3.6 16.4 1.0
CG A:ASN299 3.8 15.7 1.0
CB B:SER62 3.8 18.8 1.0
CB A:ASN299 4.0 13.8 1.0
NE2 A:HIS310 4.1 15.6 1.0
OG B:SER62 4.1 19.8 1.0
CG A:HIS310 4.2 13.7 1.0
O B:SER62 4.2 20.0 1.0
O B:HOH2189 4.3 23.5 1.0
CG B:ASP68 4.3 19.7 1.0
OD2 B:ASP68 4.4 19.1 1.0
O B:VAL65 4.4 18.5 1.0
CD2 A:HIS310 4.5 14.1 1.0
O B:HOH2188 4.6 36.5 1.0
CD B:LYS187 4.6 17.5 1.0
O B:HOH2026 4.8 24.4 1.0
OD1 A:ASN299 4.9 13.7 1.0
CA B:SER62 4.9 18.4 1.0
C B:SER62 4.9 19.8 1.0

Cadmium binding site 2 out of 6 in 2vzs

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Cadmium binding site 2 out of 6 in the Chitosan Product Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Chitosan Product Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1900

b:37.5
occ:1.00
 O A:HOH2081 2.7 12.0 1.0
O A:HOH2174 2.7 21.7 1.0
CD A:PRO120 3.9 15.2 1.0
CG A:PRO120 3.9 14.9 1.0
CE1 A:TYR189 4.2 20.9 1.0
CD1 A:TYR189 4.6 19.4 1.0
O A:HOH2175 4.7 36.8 1.0

Cadmium binding site 3 out of 6 in 2vzs

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Cadmium binding site 3 out of 6 in the Chitosan Product Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Chitosan Product Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1901

b:0.2
occ:1.00
 O A:GLY433 2.4 23.0 1.0
O A:HOH2476 2.6 29.9 1.0
ND2 A:ASN428 2.7 17.2 1.0
O A:GLU431 2.9 23.9 1.0
O A:GLY429 2.9 25.4 1.0
O A:GLY425 3.5 18.4 1.0
C A:GLY433 3.6 23.1 1.0
CG A:ASN428 3.9 20.8 1.0
C A:GLY429 4.0 24.8 1.0
C A:GLU431 4.0 25.4 1.0
CA A:GLY425 4.1 18.5 1.0
N A:GLY433 4.2 24.4 1.0
C A:GLY425 4.2 19.2 1.0
CA A:GLY433 4.3 23.3 1.0
C A:LYS432 4.3 25.3 1.0
N A:GLY429 4.4 23.3 1.0
O A:LYS432 4.4 24.5 1.0
OD1 A:ASN428 4.4 23.9 1.0
C A:ASN428 4.5 21.6 1.0
N A:GLU434 4.6 23.0 1.0
N A:GLU431 4.7 26.4 1.0
CD A:PRO435 4.7 22.2 1.0
CA A:GLY429 4.7 24.2 1.0
O A:ASN428 4.7 20.6 1.0
CA A:GLU434 4.8 22.6 1.0
N A:PRO435 4.8 22.4 1.0
C A:GLU434 4.8 22.1 1.0
C A:GLU430 4.9 27.3 1.0
CA A:GLU431 4.9 26.4 1.0
N A:LYS432 4.9 25.2 1.0
CA A:LYS432 5.0 25.4 1.0
N A:GLU430 5.0 26.7 1.0

Cadmium binding site 4 out of 6 in 2vzs

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Cadmium binding site 4 out of 6 in the Chitosan Product Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Chitosan Product Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1899

b:18.2
occ:1.00
 OD1 B:ASP246 2.3 22.4 1.0
NE2 B:HIS244 2.3 14.2 1.0
OD2 B:ASP246 2.7 19.4 1.0
CG B:ASP246 2.8 17.4 1.0
CD2 B:HIS244 3.1 15.3 1.0
CE1 B:HIS244 3.3 13.7 1.0
CB B:ASP246 4.3 16.6 1.0
CA B:GLY294 4.3 17.8 1.0
CG B:HIS244 4.3 15.1 1.0
ND1 B:HIS244 4.4 13.3 1.0
O B:ALA245 4.6 16.9 1.0
CA B:ASP246 4.8 16.2 1.0
CD2 B:LEU292 5.0 29.4 1.0

Cadmium binding site 5 out of 6 in 2vzs

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Cadmium binding site 5 out of 6 in the Chitosan Product Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Chitosan Product Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1900

b:18.1
occ:1.00
 OD2 B:ASP296 2.3 18.8 1.0
OD1 B:ASP296 2.5 13.9 1.0
O B:HOH2319 2.5 8.5 1.0
CG B:ASP296 2.7 17.4 1.0
CE1 B:HIS244 3.9 13.7 1.0
ND1 B:HIS244 4.1 13.3 1.0
CB B:ASP296 4.2 18.0 1.0
O B:HOH2279 4.4 44.4 1.0

Cadmium binding site 6 out of 6 in 2vzs

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Cadmium binding site 6 out of 6 in the Chitosan Product Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Chitosan Product Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1901

b:76.5
occ:1.00
 O B:GLU431 2.5 22.4 1.0
O B:GLY433 2.5 21.5 1.0
OD1 B:ASN428 2.7 19.4 1.0
O B:GLY429 2.7 25.9 1.0
C B:GLU431 3.7 23.4 1.0
C B:GLY433 3.7 21.5 1.0
CG B:ASN428 3.8 19.3 1.0
C B:GLY429 3.8 26.8 1.0
O B:GLY425 4.0 20.1 1.0
C B:LYS432 4.0 21.9 1.0
N B:GLY433 4.0 20.8 1.0
N B:GLU431 4.2 25.4 1.0
O B:LYS432 4.2 21.2 1.0
CA B:GLY433 4.2 20.7 1.0
ND2 B:ASN428 4.3 16.2 1.0
N B:GLY429 4.3 24.2 1.0
C B:ASN428 4.4 23.1 1.0
C B:GLU430 4.4 27.5 1.0
CA B:GLY425 4.4 18.4 1.0
CA B:GLU431 4.5 24.5 1.0
N B:LYS432 4.6 22.8 1.0
O B:ASN428 4.6 22.4 1.0
CA B:LYS432 4.6 22.8 1.0
N B:GLU430 4.6 27.5 1.0
C B:GLY425 4.7 18.6 1.0
CA B:GLU430 4.7 28.8 1.0
CA B:GLY429 4.7 25.4 1.0
N B:GLU434 4.7 20.5 1.0
CB B:ASN428 4.9 21.1 1.0
CA B:ASN428 5.0 21.5 1.0

Reference:

A.Lammerts Van Bueren, M.G.Ghinet, K.Gregg, A.Fleury, R.Brzezinski, A.B.Boraston. The Structural Basis of Substrate Recognition in An Exo-Beta-D-Glucosaminidase Involved in Chitosan Hydrolysis. J.Mol.Biol. V. 385 131 2009.
ISSN: ISSN 0022-2836
PubMed: 18976664
DOI: 10.1016/J.JMB.2008.10.031
Page generated: Wed Oct 28 10:00:24 2020
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