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Cadmium in PDB 2vzu: Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa D469A with Pnp-Beta-D-Glucosamine

Protein crystallography data

The structure of Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa D469A with Pnp-Beta-D-Glucosamine, PDB code: 2vzu 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 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.600, 121.960, 91.810, 90.00, 90.42, 90.00
R / Rfree (%) 17.2 / 20.7

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa D469A with Pnp-Beta-D-Glucosamine (pdb code 2vzu). 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 D469A with Pnp-Beta-D-Glucosamine, PDB code: 2vzu:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 2vzu

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Cadmium binding site 1 out of 6 in the Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa D469A 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 D469A with Pnp-Beta-D-Glucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1899

b:99.8
occ:1.00
 CG A:PRO120 3.8 7.0 1.0
CD A:PRO120 3.8 8.1 1.0
CE1 A:TYR189 4.1 13.0 1.0
CD1 A:TYR189 4.5 12.1 1.0

Cadmium binding site 2 out of 6 in 2vzu

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Cadmium binding site 2 out of 6 in the Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa D469A 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 D469A with Pnp-Beta-D-Glucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1900

b:0.7
occ:1.00
 O A:GLY433 2.5 17.4 1.0
ND2 A:ASN428 2.6 14.8 1.0
O A:GLU431 2.7 20.7 1.0
O A:GLY429 2.9 22.8 1.0
O A:GLY425 3.5 12.6 1.0
C A:GLY433 3.7 17.8 1.0
CG A:ASN428 3.8 18.8 1.0
C A:GLU431 3.8 21.9 1.0
C A:GLY429 3.9 22.4 1.0
CA A:GLY425 4.1 12.8 1.0
N A:GLY429 4.2 20.2 1.0
C A:GLY425 4.2 12.6 1.0
OD1 A:ASN428 4.2 20.8 1.0
O A:LYS432 4.2 21.4 1.0
C A:LYS432 4.3 21.1 1.0
CA A:GLY433 4.3 18.5 1.0
C A:ASN428 4.4 19.0 1.0
N A:GLY433 4.4 19.7 1.0
N A:GLU431 4.5 23.3 1.0
O A:ASN428 4.6 19.0 1.0
CA A:GLY429 4.6 21.9 1.0
CA A:GLU431 4.7 22.7 1.0
C A:GLU430 4.7 24.2 1.0
N A:GLU434 4.7 17.2 1.0
CD A:PRO435 4.8 15.9 1.0
N A:LYS432 4.8 21.6 1.0
CA A:GLU434 4.9 16.6 1.0
N A:GLU430 4.9 23.8 1.0
CB A:ASN428 4.9 17.5 1.0
CA A:ASN428 4.9 18.1 1.0
C A:GLU434 5.0 15.9 1.0
N A:PRO435 5.0 15.8 1.0
CA A:LYS432 5.0 21.4 1.0

Cadmium binding site 3 out of 6 in 2vzu

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Cadmium binding site 3 out of 6 in the Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa D469A 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 D469A with Pnp-Beta-D-Glucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1899

b:10.9
occ:1.00
 NE2 B:HIS244 2.3 5.0 1.0
OD1 B:ASP246 2.4 11.4 1.0
OD2 B:ASP246 2.6 9.1 1.0
CG B:ASP246 2.8 9.4 1.0
CD2 B:HIS244 3.2 5.3 1.0
CE1 B:HIS244 3.2 2.6 1.0
CB B:ASP246 4.3 8.1 1.0
CA B:GLY294 4.3 9.9 1.0
ND1 B:HIS244 4.3 3.7 1.0
CG B:HIS244 4.3 5.4 1.0
CD2 B:LEU292 4.4 17.3 1.0
O B:ALA245 4.7 7.3 1.0
CA B:ASP246 4.9 7.4 1.0

Cadmium binding site 4 out of 6 in 2vzu

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Cadmium binding site 4 out of 6 in the Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa D469A 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 D469A with Pnp-Beta-D-Glucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1900

b:10.5
occ:1.00
 OD2 B:ASP296 2.4 11.8 1.0
OD1 B:ASP296 2.5 10.3 1.0
CG B:ASP296 2.8 12.4 1.0
CE1 B:HIS244 4.1 2.6 1.0
ND1 B:HIS244 4.2 3.7 1.0
CB B:ASP296 4.3 11.6 1.0

Cadmium binding site 5 out of 6 in 2vzu

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Cadmium binding site 5 out of 6 in the Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa D469A 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 D469A with Pnp-Beta-D-Glucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1901

b:0.0
occ:1.00
 NZ B:LYS187 2.1 28.9 1.0
CE B:LYS187 2.4 17.0 1.0
O A:HOH2122 2.7 11.4 1.0
ND1 A:HIS310 3.0 6.9 1.0
OD2 B:ASP68 3.0 8.8 1.0
ND2 A:ASN299 3.1 8.3 1.0
OD1 B:ASP68 3.3 7.0 1.0
CE1 A:HIS310 3.4 6.0 1.0
CG B:ASP68 3.5 9.3 1.0
CD B:LYS187 3.6 10.5 1.0
O B:HOH2013 3.8 11.1 1.0
CG A:HIS310 4.0 4.5 1.0
O B:HOH2012 4.1 27.8 1.0
CG A:ASN299 4.3 7.9 1.0
NE2 A:HIS310 4.5 5.5 1.0
CB A:HIS310 4.6 6.3 1.0
CD2 A:HIS310 4.8 3.2 1.0
CG B:LYS187 4.8 7.6 1.0
O B:HOH2004 4.9 8.8 1.0

Cadmium binding site 6 out of 6 in 2vzu

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Cadmium binding site 6 out of 6 in the Complex of Amycolatopsis Orientalis Exo-Chitosanase Csxa D469A 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 D469A with Pnp-Beta-D-Glucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1902

b:97.6
occ:1.00
 O B:GLY433 2.5 14.0 1.0
O B:HOH2197 2.5 30.2 1.0
O B:GLU431 2.7 17.6 1.0
OD1 B:ASN428 2.7 14.9 1.0
O B:GLY429 2.9 22.4 1.0
C B:GLY433 3.6 14.8 1.0
O B:GLY425 3.7 11.7 1.0
C B:GLU431 3.7 19.2 1.0
CG B:ASN428 3.8 15.9 1.0
C B:GLY429 4.0 22.7 1.0
O B:LYS432 4.1 18.8 1.0
C B:LYS432 4.1 18.4 1.0
N B:GLY433 4.1 16.6 1.0
CA B:GLY425 4.2 11.2 1.0
N B:GLU431 4.2 21.8 1.0
CA B:GLY433 4.2 15.0 1.0
ND2 B:ASN428 4.2 11.9 1.0
N B:GLY429 4.4 20.1 1.0
C B:GLY425 4.4 11.6 1.0
C B:GLU430 4.5 23.9 1.0
CA B:GLU431 4.5 19.9 1.0
C B:ASN428 4.5 18.7 1.0
N B:GLU434 4.7 13.1 1.0
N B:LYS432 4.7 18.8 1.0
CA B:GLY429 4.7 21.8 1.0
CA B:LYS432 4.8 19.3 1.0
O B:ASN428 4.8 18.4 1.0
CA B:GLU430 4.8 25.1 1.0
N B:GLU430 4.8 23.4 1.0
CA B:GLU434 4.9 13.2 1.0
CD B:PRO435 4.9 11.1 1.0
CB B:ASN428 4.9 16.6 1.0
O B:GLU430 4.9 24.5 1.0
CB B:GLU431 5.0 20.4 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: Sat Dec 12 08:18:22 2020

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