Atomistry » Cadmium » PDB 2mpa-2w5f » 2vzs
Atomistry »
  Cadmium »
    PDB 2mpa-2w5f »
      2vzs »

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

Go back to Cadmium Binding Sites List in 2vzs
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

Go back to Cadmium Binding Sites List in 2vzs
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

Go back to Cadmium Binding Sites List in 2vzs
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

Go back to Cadmium Binding Sites List in 2vzs
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

Go back to Cadmium Binding Sites List in 2vzs
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

Go back to Cadmium Binding Sites List in 2vzs
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: Sat Dec 12 08:18:20 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy