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Cadmium in PDB 2vzt: Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa E541A with Pnp-Beta-D-Glucosamine

Protein crystallography data

The structure of Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa E541A with Pnp-Beta-D-Glucosamine, PDB code: 2vzt 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 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.690, 122.230, 91.860, 90.00, 90.52, 90.00
R / Rfree (%) 17.5 / 21.8

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa E541A with Pnp-Beta-D-Glucosamine (pdb code 2vzt). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa E541A with Pnp-Beta-D-Glucosamine, PDB code: 2vzt:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 2vzt

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Cadmium binding site 1 out of 6 in the Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa E541A with Pnp-Beta-D-Glucosamine


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa E541A with Pnp-Beta-D-Glucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1899

b:80.3
occ:1.00
CD A:PRO120 3.7 7.3 1.0
CG A:PRO120 3.8 6.5 1.0
CE1 A:TYR189 4.0 14.0 1.0
CD1 A:TYR189 4.4 12.8 1.0

Cadmium binding site 2 out of 6 in 2vzt

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Cadmium binding site 2 out of 6 in the Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa E541A with Pnp-Beta-D-Glucosamine


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa E541A with Pnp-Beta-D-Glucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1900

b:1.0
occ:1.00
O A:GLY433 2.5 19.1 1.0
ND2 A:ASN428 2.6 13.8 1.0
O A:GLU431 2.6 24.9 1.0
O A:GLY429 2.8 20.7 1.0
O A:GLY425 3.5 12.5 1.0
C A:GLY433 3.7 19.7 1.0
CG A:ASN428 3.7 16.1 1.0
C A:GLU431 3.8 25.2 1.0
C A:GLY429 3.9 20.6 1.0
OD1 A:ASN428 4.1 17.9 1.0
N A:GLY433 4.1 23.4 1.0
CA A:GLY425 4.1 12.1 1.0
N A:GLY429 4.2 18.4 1.0
C A:GLY425 4.2 12.4 1.0
C A:ASN428 4.4 17.2 1.0
CA A:GLY433 4.4 21.2 1.0
C A:LYS432 4.4 25.4 1.0
N A:GLU431 4.5 24.8 1.0
CA A:GLY429 4.5 20.1 1.0
O A:ASN428 4.6 17.4 1.0
N A:GLU434 4.7 18.6 1.0
CA A:GLU431 4.7 26.0 1.0
CD A:PRO435 4.7 15.8 1.0
N A:LYS432 4.7 25.4 1.0
C A:GLU430 4.7 23.8 1.0
O A:LYS432 4.8 27.5 1.0
N A:GLU430 4.8 21.8 1.0
CA A:GLU434 4.8 17.3 1.0
N A:PRO435 4.9 16.1 1.0
C A:GLU434 4.9 16.1 1.0
CB A:ASN428 4.9 15.6 1.0
CA A:GLU430 4.9 22.8 1.0
CA A:ASN428 5.0 15.8 1.0
CA A:LYS432 5.0 25.5 1.0

Cadmium binding site 3 out of 6 in 2vzt

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Cadmium binding site 3 out of 6 in the Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa E541A with Pnp-Beta-D-Glucosamine


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa E541A with Pnp-Beta-D-Glucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1899

b:9.6
occ:1.00
NE2 B:HIS244 2.2 5.8 1.0
OD1 B:ASP246 2.3 9.9 1.0
OD2 B:ASP246 2.6 4.7 1.0
CG B:ASP246 2.8 8.1 1.0
CE1 B:HIS244 3.2 5.5 1.0
CD2 B:HIS244 3.3 5.5 1.0
CB B:ASP246 4.3 7.9 1.0
ND1 B:HIS244 4.3 6.3 1.0
CG B:HIS244 4.4 6.8 1.0
CA B:GLY294 4.4 8.3 1.0
O B:ALA245 4.7 7.0 1.0
CD2 B:LEU292 4.7 16.6 1.0
CA B:ASP246 4.8 7.9 1.0

Cadmium binding site 4 out of 6 in 2vzt

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Cadmium binding site 4 out of 6 in the Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa E541A with Pnp-Beta-D-Glucosamine


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa E541A with Pnp-Beta-D-Glucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1900

b:9.8
occ:1.00
OD2 B:ASP296 2.3 8.5 1.0
OD1 B:ASP296 2.5 7.9 1.0
O B:HOH2107 2.5 2.1 1.0
CG B:ASP296 2.7 10.9 1.0
CE1 B:HIS244 4.2 5.5 1.0
ND1 B:HIS244 4.2 6.3 1.0
CB B:ASP296 4.2 10.1 1.0

Cadmium binding site 5 out of 6 in 2vzt

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Cadmium binding site 5 out of 6 in the Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa E541A with Pnp-Beta-D-Glucosamine


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa E541A with Pnp-Beta-D-Glucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1901

b:0.2
occ:1.00
NZ B:LYS187 2.3 25.4 1.0
CE B:LYS187 2.6 16.4 1.0
ND1 A:HIS310 2.8 4.0 1.0
OD2 B:ASP68 3.0 9.3 1.0
O A:HOH2113 3.3 13.4 1.0
ND2 A:ASN299 3.4 4.4 1.0
OD1 B:ASP68 3.5 6.8 1.0
CE1 A:HIS310 3.5 4.2 1.0
CG B:ASP68 3.6 10.0 1.0
CD B:LYS187 3.7 11.5 1.0
O B:HOH2010 3.7 18.0 1.0
CG A:HIS310 3.8 5.1 1.0
O B:HOH2009 4.1 14.2 1.0
CB A:HIS310 4.2 5.4 1.0
CG A:ASN299 4.5 5.3 1.0
NE2 A:HIS310 4.6 5.3 1.0
CD2 A:HIS310 4.8 4.5 1.0
O B:HOH2011 4.9 14.4 1.0
OH B:TYR189 4.9 7.3 1.0

Cadmium binding site 6 out of 6 in 2vzt

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Cadmium binding site 6 out of 6 in the Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa E541A with Pnp-Beta-D-Glucosamine


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa E541A with Pnp-Beta-D-Glucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1902

b:87.7
occ:1.00
O B:GLY433 2.5 11.6 1.0
OD1 B:ASN428 2.5 15.2 1.0
O B:HOH2183 2.5 21.3 1.0
O B:GLU431 2.6 18.2 1.0
O B:GLY429 2.8 21.9 1.0
CG B:ASN428 3.6 15.1 1.0
C B:GLY433 3.6 12.7 1.0
C B:GLU431 3.7 19.1 1.0
O B:GLY425 3.8 11.0 1.0
C B:GLY429 3.9 22.1 1.0
C B:LYS432 4.0 16.0 1.0
O B:LYS432 4.0 16.1 1.0
N B:GLY433 4.1 14.1 1.0
N B:GLU431 4.2 22.0 1.0
ND2 B:ASN428 4.2 10.2 1.0
CA B:GLY433 4.2 12.9 1.0
CA B:GLY425 4.2 10.8 1.0
N B:GLY429 4.3 20.2 1.0
C B:GLU430 4.4 23.4 1.0
C B:ASN428 4.4 19.2 1.0
CA B:GLU431 4.5 20.2 1.0
C B:GLY425 4.5 11.1 1.0
O B:ASN428 4.6 19.8 1.0
N B:LYS432 4.6 17.9 1.0
CA B:GLY429 4.7 21.4 1.0
N B:GLU434 4.7 11.9 1.0
CA B:LYS432 4.7 17.3 1.0
N B:GLU430 4.7 23.0 1.0
CA B:GLU430 4.7 24.4 1.0
O B:GLU430 4.8 23.6 1.0
CB B:ASN428 4.8 17.5 1.0
CA B:ASN428 4.9 18.0 1.0
CB B:GLU431 4.9 20.6 1.0
CA B:GLU434 4.9 12.3 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: Fri Aug 28 13:10:03 2020
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