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Cadmium in PDB 2gj2: Crystal Structure of VP9 From White Spot Syndrome Virus

Protein crystallography data

The structure of Crystal Structure of VP9 From White Spot Syndrome Virus, PDB code: 2gj2 was solved by Y.Liu, J.L.Wu, J.X.Song, J.Sivaraman, C.L.Hew, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.00 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.133, 78.205, 78.979, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 27.5

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of VP9 From White Spot Syndrome Virus (pdb code 2gj2). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 8 binding sites of Cadmium where determined in the Crystal Structure of VP9 From White Spot Syndrome Virus, PDB code: 2gj2:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cadmium binding site 1 out of 8 in 2gj2

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Cadmium binding site 1 out of 8 in the Crystal Structure of VP9 From White Spot Syndrome Virus


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 VP9 From White Spot Syndrome Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:54.1
occ:1.00
OE2 D:GLU31 2.1 34.3 1.0
O A:HOH228 2.2 63.2 1.0
SG A:CYS46 2.3 39.6 1.0
OD2 A:ASP9 2.3 38.6 1.0
OD1 A:ASP9 2.4 32.1 1.0
CG A:ASP9 2.6 36.4 1.0
CD D:GLU31 3.1 39.7 1.0
CB A:CYS46 3.2 34.8 1.0
OE1 D:GLU31 3.4 33.1 1.0
CA A:CYS46 3.5 30.3 1.0
CD A:CD203 3.6 49.8 1.0
N A:LEU47 3.8 39.0 1.0
O A:LEU47 3.9 46.4 1.0
C A:CYS46 4.0 30.4 1.0
CB A:ASP9 4.1 36.2 1.0
O A:HOH218 4.2 40.6 1.0
O A:HOH230 4.3 44.0 1.0
CG D:GLU31 4.5 38.9 1.0
O D:HOH211 4.7 28.4 1.0
C A:LEU47 4.7 45.5 1.0
OE1 A:GLU31 4.7 26.6 1.0
SG D:CYS46 4.7 20.0 1.0
CA A:LEU47 4.8 43.5 1.0
N A:CYS46 4.9 30.3 1.0
CA A:ASP9 5.0 36.2 1.0
O A:CYS46 5.0 30.8 1.0

Cadmium binding site 2 out of 8 in 2gj2

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Cadmium binding site 2 out of 8 in the Crystal Structure of VP9 From White Spot Syndrome Virus


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 VP9 From White Spot Syndrome Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:49.8
occ:1.00
OE1 D:GLU31 1.9 33.1 1.0
OE1 A:GLU31 1.9 26.6 1.0
O D:HOH239 2.2 69.5 1.0
SG A:CYS46 2.3 39.6 1.0
SG D:CYS46 2.5 20.0 1.0
CD D:GLU31 3.0 39.7 1.0
CD A:GLU31 3.1 31.0 1.0
CB A:CYS46 3.3 34.8 1.0
CD D:CD204 3.4 47.3 1.0
OE2 D:GLU31 3.5 34.3 1.0
CB D:CYS46 3.5 36.3 1.0
CD A:CD201 3.6 54.1 1.0
OE2 A:GLU31 3.8 24.7 1.0
O A:HOH228 4.2 63.2 1.0
CG D:GLU31 4.2 38.9 1.0
O A:HOH230 4.2 44.0 1.0
CG A:GLU31 4.3 31.7 1.0
CB D:GLU31 4.5 42.1 1.0
CB A:GLU31 4.6 38.0 1.0
CA A:CYS46 4.8 30.3 1.0
CA D:CYS46 4.9 28.8 1.0

Cadmium binding site 3 out of 8 in 2gj2

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Cadmium binding site 3 out of 8 in the Crystal Structure of VP9 From White Spot Syndrome Virus


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 VP9 From White Spot Syndrome Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd202

b:35.7
occ:1.00
OE1 B:GLU31 2.3 34.9 1.0
OE1 C:GLU31 2.3 38.2 1.0
SG C:CYS46 2.5 30.2 1.0
SG B:CYS46 2.6 33.3 1.0
CB B:CYS46 3.3 24.8 1.0
CB C:CYS46 3.4 29.3 1.0
CD B:GLU31 3.4 39.1 1.0
CD C:GLU31 3.4 34.7 1.0
CD C:CD206 3.6 37.4 1.0
CD B:CD205 3.7 40.6 1.0
OE2 C:GLU31 4.0 32.2 1.0
OE2 B:GLU31 4.1 35.7 1.0
CG B:GLU31 4.4 37.9 1.0
CG C:GLU31 4.6 32.5 1.0
CA B:CYS46 4.8 29.4 1.0
CA C:CYS46 4.8 28.4 1.0
CB B:GLU31 4.9 41.4 1.0
CB C:GLU31 5.0 34.9 1.0

Cadmium binding site 4 out of 8 in 2gj2

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Cadmium binding site 4 out of 8 in the Crystal Structure of VP9 From White Spot Syndrome Virus


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 VP9 From White Spot Syndrome Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd205

b:40.6
occ:1.00
OE2 C:GLU31 2.1 32.2 1.0
OD2 B:ASP9 2.4 36.5 1.0
SG B:CYS46 2.5 33.3 1.0
CD C:GLU31 2.9 34.7 1.0
OD1 B:ASP9 3.0 31.5 1.0
CG B:ASP9 3.0 33.3 1.0
OE1 C:GLU31 3.1 38.2 1.0
CB B:CYS46 3.4 24.8 1.0
CD B:CD202 3.7 35.7 1.0
CA B:CYS46 3.9 29.4 1.0
SG C:CYS46 4.0 30.2 1.0
N B:LEU47 4.3 33.3 1.0
CG C:GLU31 4.3 32.5 1.0
CB B:ASP9 4.4 32.7 1.0
O B:LEU47 4.5 34.2 1.0
C B:CYS46 4.5 30.1 1.0
CD C:CD206 4.5 37.4 1.0
OE1 B:GLU31 4.8 34.9 1.0

Cadmium binding site 5 out of 8 in 2gj2

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Cadmium binding site 5 out of 8 in the Crystal Structure of VP9 From White Spot Syndrome Virus


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 VP9 From White Spot Syndrome Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd206

b:37.4
occ:1.00
OE2 B:GLU31 2.0 35.7 1.0
SG C:CYS46 2.4 30.2 1.0
OD2 C:ASP9 2.4 35.7 1.0
OE1 B:GLU31 2.7 34.9 1.0
CD B:GLU31 2.7 39.1 1.0
OD1 C:ASP9 2.8 25.3 1.0
CG C:ASP9 2.9 31.0 1.0
CB C:CYS46 3.5 29.3 1.0
CD B:CD202 3.6 35.7 1.0
CA C:CYS46 4.0 28.4 1.0
SG B:CYS46 4.0 33.3 1.0
O B:HOH218 4.0 50.7 1.0
CG B:GLU31 4.2 37.9 1.0
O C:LEU47 4.3 36.1 1.0
N C:LEU47 4.3 30.5 1.0
CB C:ASP9 4.4 31.1 1.0
C C:CYS46 4.5 26.6 1.0
CD B:CD205 4.5 40.6 1.0
OE1 C:GLU31 4.9 38.2 1.0
CB B:GLU31 5.0 41.4 1.0

Cadmium binding site 6 out of 8 in 2gj2

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Cadmium binding site 6 out of 8 in the Crystal Structure of VP9 From White Spot Syndrome Virus


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 VP9 From White Spot Syndrome Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd208

b:44.4
occ:1.00
OE1 C:GLU60 1.6 24.7 1.0
CD C:GLU60 2.6 33.5 1.0
OE2 C:GLU60 3.1 36.7 1.0
O C:HOH236 3.3 49.1 1.0
CG C:GLU60 3.9 30.4 1.0
CB C:ALA2 3.9 49.5 1.0
O C:ALA2 4.4 46.2 1.0
N C:ILE59 4.6 27.7 1.0
CA C:GLY58 4.6 27.3 1.0
O C:GLY57 4.9 37.3 1.0

Cadmium binding site 7 out of 8 in 2gj2

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Cadmium binding site 7 out of 8 in the Crystal Structure of VP9 From White Spot Syndrome Virus


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 VP9 From White Spot Syndrome Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd204

b:47.3
occ:1.00
SG D:CYS46 1.8 20.0 1.0
OE2 A:GLU31 1.9 24.7 1.0
O A:HOH230 1.9 44.0 1.0
OD2 D:ASP9 2.3 36.4 1.0
CD A:GLU31 2.7 31.0 1.0
OE1 A:GLU31 2.8 26.6 1.0
OD1 D:ASP9 2.9 29.9 1.0
CG D:ASP9 2.9 32.5 1.0
CB D:CYS46 3.0 36.3 1.0
CD A:CD203 3.4 49.8 1.0
CA D:CYS46 3.7 28.8 1.0
O A:HOH228 3.9 63.2 1.0
O D:HOH225 4.0 48.6 1.0
N D:LEU47 4.1 33.5 1.0
CG A:GLU31 4.2 31.7 1.0
SG A:CYS46 4.3 39.6 1.0
C D:CYS46 4.3 28.6 1.0
CB D:ASP9 4.4 33.8 1.0
O D:LEU47 4.4 38.8 1.0
OE1 D:GLU31 4.8 33.1 1.0
O A:HOH222 5.0 50.1 1.0

Cadmium binding site 8 out of 8 in 2gj2

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Cadmium binding site 8 out of 8 in the Crystal Structure of VP9 From White Spot Syndrome Virus


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 VP9 From White Spot Syndrome Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd207

b:42.5
occ:1.00
OE1 D:GLU72 2.4 30.6 1.0
OE2 D:GLU72 2.7 27.8 1.0
CD D:GLU72 2.9 27.6 1.0
CD1 D:ILE59 4.2 37.7 1.0
O D:HOH215 4.4 36.7 1.0
CG D:GLU72 4.4 27.1 1.0
O D:HOH237 4.6 61.4 1.0
NH2 D:ARG63 4.9 30.4 1.0

Reference:

Y.Liu, J.L.Wu, J.X.Song, J.Sivaraman, C.L.Hew. Identification of A Novel Nonstructural Protein, VP9, From White Spot Syndrome Virus: Its Structure Reveals A Ferredoxin Fold with Specific Metal Binding Sites J.Virol. V. 80 10419 2006.
ISSN: ISSN 0022-538X
PubMed: 16956937
DOI: 10.1128/JVI.00698-06
Page generated: Sun Jan 24 09:43:33 2021

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