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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:

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; 11; 12; 13;

Cadmium binding site 1 out of 13 in 2vzo

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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

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Cadmium binding site 2 out of 13 in the Crystal Structure of Amycolatopsis Orientalis Exo- Chitosanase Csxa


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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

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Cadmium binding site 3 out of 13 in the Crystal Structure of Amycolatopsis Orientalis Exo- Chitosanase Csxa


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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

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Cadmium binding site 4 out of 13 in the Crystal Structure of Amycolatopsis Orientalis Exo- Chitosanase Csxa


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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

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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

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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

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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

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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

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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

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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

Cadmium binding site 11 out of 13 in 2vzo

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Cadmium binding site 11 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 11 of Crystal Structure of Amycolatopsis Orientalis Exo- Chitosanase Csxa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1903

b:34.8
occ:1.00
OE2 B:GLU541 2.5 24.6 1.0
OE1 B:GLU394 2.5 25.2 1.0
O B:HOH2172 2.6 18.3 1.0
OE2 B:GLU394 2.7 25.8 1.0
OE1 B:GLU541 2.8 29.8 1.0
CD B:GLU394 2.9 23.6 1.0
CD B:GLU541 3.0 26.7 1.0
C1 B:GOL1907 3.3 40.6 1.0
C3 B:GOL1907 3.7 39.8 1.0
SG B:CYS419 3.9 28.8 1.0
O3 B:GOL1907 4.0 38.9 1.0
CZ2 B:TRP642 4.0 18.4 1.0
OG B:SER468 4.0 24.1 1.0
C2 B:GOL1907 4.1 41.7 1.0
CH2 B:TRP642 4.3 18.6 1.0
CG B:GLU394 4.3 21.0 1.0
O1 B:GOL1907 4.3 39.7 1.0
CG B:GLU541 4.5 19.8 1.0
NH1 B:ARG392 4.5 16.8 1.0
CB B:CYS419 4.5 24.3 1.0
CE B:MET512 4.6 21.1 1.0
SD B:MET512 4.7 25.9 1.0
CE2 B:TRP642 4.8 19.8 1.0
NH2 B:ARG392 4.8 16.1 1.0

Cadmium binding site 12 out of 13 in 2vzo

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Cadmium binding site 12 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 12 of Crystal Structure of Amycolatopsis Orientalis Exo- Chitosanase Csxa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1904

b:0.7
occ:1.00
ND1 B:HIS178 2.8 36.6 1.0
O B:HOH2032 2.8 40.4 1.0
CG B:HIS178 3.6 35.4 1.0
CE1 B:HIS178 3.7 39.2 1.0
CB B:HIS178 3.8 33.7 1.0
O B:GLN176 4.2 30.2 1.0
CD2 B:HIS178 4.8 37.9 1.0
NE2 B:HIS178 4.8 39.8 1.0
ND2 B:ASN152 4.9 24.7 1.0
N B:HIS178 4.9 31.9 1.0
CA B:HIS178 5.0 33.4 1.0

Cadmium binding site 13 out of 13 in 2vzo

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Cadmium binding site 13 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 13 of Crystal Structure of Amycolatopsis Orientalis Exo- Chitosanase Csxa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1905

b:0.4
occ:1.00
OD1 B:ASP404 2.5 19.3 1.0
O B:HOH2105 2.9 22.6 1.0
OD2 B:ASP404 3.0 21.4 1.0
CG B:ASP404 3.1 21.1 1.0
O B:HOH2106 3.1 44.3 1.0
NH2 B:ARG311 3.7 23.9 1.0
CE1 B:HIS458 4.2 19.7 1.0
CB B:ASP404 4.6 18.7 1.0
NE2 B:HIS458 4.8 22.0 1.0
CZ B:ARG311 4.9 23.0 1.0
O B:HOH2136 5.0 24.9 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: Fri Aug 28 13:09:18 2020
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