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

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

Go back to Cadmium Binding Sites List in 2vzu
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

Go back to Cadmium Binding Sites List in 2vzu
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

Go back to Cadmium Binding Sites List in 2vzu
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

Go back to Cadmium Binding Sites List in 2vzu
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

Go back to Cadmium Binding Sites List in 2vzu
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

Go back to Cadmium Binding Sites List in 2vzu
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: Fri Jul 19 15:17:10 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy