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

Cadmium in PDB 2vzo: Crystal Structure of Amycolatopsis Orientalis Exo- Chitosanase Csxa

Protein crystallography data

The structure of Crystal Structure of Amycolatopsis Orientalis Exo- Chitosanase Csxa, PDB code: 2vzo 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) 20.00 / 2.24
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.400, 122.035, 91.602, 90.00, 90.52, 90.00
R / Rfree (%) 17.5 / 22.3

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Cadmium atom in the Crystal Structure of Amycolatopsis Orientalis Exo- Chitosanase Csxa (pdb code 2vzo). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 13 binding sites of Cadmium where determined in the Crystal Structure of Amycolatopsis Orientalis Exo- Chitosanase Csxa, PDB code: 2vzo:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 13 in 2vzo

Go back to Cadmium Binding Sites List in 2vzo
Cadmium binding site 1 out of 13 in the Crystal Structure 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 Crystal Structure of Amycolatopsis Orientalis Exo- Chitosanase Csxa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1900

b:47.5
occ:1.00
ND1 A:HIS310 2.6 20.6 1.0
NZ B:LYS187 2.8 23.8 1.0
O A:HOH2031 2.9 27.8 1.0
OD2 B:ASP68 3.0 31.8 1.0
CE B:LYS187 3.0 21.5 1.0
O B:HOH2010 3.1 21.3 1.0
OD1 B:ASP68 3.1 37.6 1.0
CG B:ASP68 3.4 31.3 1.0
CE1 A:HIS310 3.5 19.3 1.0
CG A:HIS310 3.6 21.0 1.0
ND2 A:ASN299 3.6 22.5 1.0
CB A:HIS310 3.8 18.5 1.0
O B:HOH2048 4.2 28.4 1.0
CD B:LYS187 4.2 24.5 1.0
CG A:ASN299 4.4 21.2 1.0
NE2 A:HIS310 4.6 20.0 1.0
CA A:HIS310 4.7 19.1 1.0
CD2 A:HIS310 4.7 18.7 1.0
O A:HOH2095 4.7 33.1 1.0
CB B:ASP68 4.8 28.6 1.0
OD1 A:ASN299 4.9 23.9 1.0
O B:HOH2008 4.9 18.5 1.0

Cadmium binding site 2 out of 13 in 2vzo

Go back to Cadmium Binding Sites List in 2vzo
Cadmium binding site 2 out of 13 in the Crystal Structure 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 Crystal Structure of Amycolatopsis Orientalis Exo- Chitosanase Csxa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1901

b:37.2
occ:1.00
O A:HOH2301 2.4 17.9 1.0
OE2 A:GLU541 2.5 24.3 1.0
OE1 A:GLU394 2.5 22.9 1.0
OE1 A:GLU541 2.7 28.1 1.0
OE2 A:GLU394 2.8 27.5 1.0
CD A:GLU541 2.9 24.5 1.0
CD A:GLU394 3.0 21.3 1.0
C3 A:GOL1907 3.2 38.7 1.0
O1 A:GOL1907 3.7 39.8 1.0
C2 A:GOL1907 3.8 40.6 1.0
C1 A:GOL1907 3.8 39.4 1.0
OG A:SER468 3.9 26.4 1.0
SG A:CYS419 3.9 29.9 1.0
CZ2 A:TRP642 4.0 21.7 1.0
O3 A:GOL1907 4.3 36.2 1.0
CH2 A:TRP642 4.4 21.4 1.0
CG A:GLU541 4.4 21.6 1.0
CG A:GLU394 4.4 20.1 1.0
CB A:CYS419 4.5 23.6 1.0
NH2 A:ARG392 4.5 20.4 1.0
CE A:MET512 4.6 22.8 1.0
NH1 A:ARG392 4.6 21.8 1.0
SD A:MET512 4.6 27.5 1.0
CE2 A:TRP642 4.8 22.3 1.0
CZ A:ARG392 5.0 22.2 1.0

Cadmium binding site 3 out of 13 in 2vzo

Go back to Cadmium Binding Sites List in 2vzo
Cadmium binding site 3 out of 13 in the Crystal Structure 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 Crystal Structure of Amycolatopsis Orientalis Exo- Chitosanase Csxa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1902

b:53.2
occ:1.00
OE2 A:GLU469 2.5 28.1 1.0
OE1 A:GLU469 2.6 28.2 1.0
CD A:GLU469 2.9 26.7 1.0
O3 A:GOL1908 3.0 39.6 1.0
C3 A:GOL1908 3.2 42.5 1.0
C1 A:GOL1908 3.3 46.5 1.0
C2 A:GOL1908 3.7 43.8 1.0
SG A:CYS420 3.9 31.3 1.0
O2 A:GOL1908 4.1 43.5 1.0
O1 A:GOL1908 4.4 47.7 1.0
CG A:GLU469 4.4 25.1 1.0
O A:HOH2138 4.5 19.9 1.0
CE2 A:PHE470 4.7 25.1 1.0
O A:HOH2157 4.8 27.8 1.0
OD1 A:ASN428 5.0 49.8 1.0

Cadmium binding site 4 out of 13 in 2vzo

Go back to Cadmium Binding Sites List in 2vzo
Cadmium binding site 4 out of 13 in the Crystal Structure 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 Crystal Structure of Amycolatopsis Orientalis Exo- Chitosanase Csxa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1903

b:0.5
occ:1.00
OD2 A:ASP404 3.1 25.8 1.0
OD1 A:ASP404 3.2 21.0 1.0
CB A:ASP400 3.3 24.1 1.0
NE2 A:HIS458 3.4 23.2 1.0
CE1 A:HIS458 3.4 20.3 1.0
CG A:ASP404 3.5 20.5 1.0
OD2 A:ASP400 3.9 34.7 1.0
O A:ASP400 4.0 22.2 1.0
CG A:ASP400 4.0 29.2 1.0
C A:ASP400 4.1 22.0 1.0
CA A:ASP400 4.1 22.8 1.0
N A:GLU401 4.7 21.3 1.0
ND1 A:HIS458 4.7 18.3 1.0
CD2 A:HIS458 4.8 19.5 1.0
CB A:ASP404 4.8 18.6 1.0

Cadmium binding site 5 out of 13 in 2vzo

Go back to Cadmium Binding Sites List in 2vzo
Cadmium binding site 5 out of 13 in the Crystal Structure 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 Crystal Structure of Amycolatopsis Orientalis Exo- Chitosanase Csxa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1904

b:1.0
occ:1.00
CB A:ASP130 3.4 49.3 1.0
OD2 A:ASP130 3.5 52.9 1.0
O A:HOH2022 3.7 32.8 1.0
O B:HOH2150 3.8 47.9 1.0
CG A:ASP130 4.0 52.3 1.0
CA A:ASP130 4.7 48.9 1.0

Cadmium binding site 6 out of 13 in 2vzo

Go back to Cadmium Binding Sites List in 2vzo
Cadmium binding site 6 out of 13 in the Crystal Structure 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 Crystal Structure of Amycolatopsis Orientalis Exo- Chitosanase Csxa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1905

b:76.7
occ:1.00
ND1 A:HIS178 2.5 33.9 1.0
CG A:HIS178 3.3 32.0 1.0
CB A:HIS178 3.4 30.9 1.0
CE1 A:HIS178 3.5 33.6 1.0
O A:GLN176 4.3 28.9 1.0
CD2 A:HIS178 4.5 34.3 1.0
NE2 A:HIS178 4.6 32.6 1.0
CA A:HIS178 4.8 31.0 1.0
ND2 A:ASN152 4.9 22.7 1.0
N A:HIS178 5.0 29.2 1.0

Cadmium binding site 7 out of 13 in 2vzo

Go back to Cadmium Binding Sites List in 2vzo
Cadmium binding site 7 out of 13 in the Crystal Structure 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 7 of Crystal Structure of Amycolatopsis Orientalis Exo- Chitosanase Csxa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1909

b:29.0
occ:1.00
O A:HOH2019 2.6 5.4 1.0
CD A:PRO120 4.1 20.0 1.0
CE1 A:TYR189 4.2 21.0 1.0
CG A:PRO120 4.2 20.3 1.0
CD1 A:TYR189 4.5 21.3 1.0

Cadmium binding site 8 out of 13 in 2vzo

Go back to Cadmium Binding Sites List in 2vzo
Cadmium binding site 8 out of 13 in the Crystal Structure 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 8 of Crystal Structure of Amycolatopsis Orientalis Exo- Chitosanase Csxa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1900

b:25.5
occ:1.00
OD1 B:ASP246 2.2 26.9 1.0
NE2 B:HIS244 2.2 19.1 1.0
OD2 B:ASP246 2.8 23.8 1.0
CG B:ASP246 2.8 24.8 1.0
CE1 B:HIS244 3.1 17.6 1.0
CD2 B:HIS244 3.2 15.3 1.0
CB B:ASP246 4.3 22.9 1.0
ND1 B:HIS244 4.3 15.5 1.0
CA B:GLY294 4.3 22.3 1.0
CG B:HIS244 4.3 19.0 1.0
O B:ALA245 4.6 20.6 1.0
CD2 B:LEU292 4.7 29.8 1.0
CA B:ASP246 4.8 23.2 1.0

Cadmium binding site 9 out of 13 in 2vzo

Go back to Cadmium Binding Sites List in 2vzo
Cadmium binding site 9 out of 13 in the Crystal Structure 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 9 of Crystal Structure of Amycolatopsis Orientalis Exo- Chitosanase Csxa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1901

b:25.4
occ:1.00
OD2 B:ASP296 2.4 27.4 1.0
OD1 B:ASP296 2.6 26.1 1.0
CG B:ASP296 2.8 25.3 1.0
CE1 B:HIS244 4.1 17.6 1.0
ND1 B:HIS244 4.1 15.5 1.0
CB B:ASP296 4.3 24.6 1.0
N B:ASP296 5.0 23.9 1.0

Cadmium binding site 10 out of 13 in 2vzo

Go back to Cadmium Binding Sites List in 2vzo
Cadmium binding site 10 out of 13 in the Crystal Structure 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 10 of Crystal Structure of Amycolatopsis Orientalis Exo- Chitosanase Csxa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1902

b:48.4
occ:1.00
OE1 B:GLU469 2.5 28.1 1.0
OE2 B:GLU469 2.8 27.4 1.0
CD B:GLU469 2.9 26.8 1.0
O B:HOH2149 3.2 35.2 1.0
O B:HOH2174 3.7 37.3 1.0
SG B:CYS420 3.8 29.7 1.0
O B:HOH2148 4.3 18.3 1.0
CG B:GLU469 4.4 25.2 1.0
CE2 B:PHE470 4.8 25.3 1.0
O3 B:GOL1907 5.0 38.9 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: Thu Jul 10 12:05:55 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy