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Cadmium in PDB 6hj4: Crystal Structure of Whitewater Arroyo Virus GP1 Glycoprotein at pH 7.5

Protein crystallography data

The structure of Crystal Structure of Whitewater Arroyo Virus GP1 Glycoprotein at pH 7.5, PDB code: 6hj4 was solved by R.Pryce, W.M.Ng, A.Zeltina, Y.Watanabe, K.El Omari, A.Wagner, T.A.Bowden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.47 / 2.43
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 106.660, 106.660, 74.810, 90.00, 90.00, 120.00
R / Rfree (%) 22 / 25.2

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Whitewater Arroyo Virus GP1 Glycoprotein at pH 7.5 (pdb code 6hj4). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Crystal Structure of Whitewater Arroyo Virus GP1 Glycoprotein at pH 7.5, PDB code: 6hj4:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 6hj4

Go back to Cadmium Binding Sites List in 6hj4
Cadmium binding site 1 out of 5 in the Crystal Structure of Whitewater Arroyo Virus GP1 Glycoprotein at pH 7.5


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 Whitewater Arroyo Virus GP1 Glycoprotein at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd304

b:86.8
occ:1.00
OD1 A:ASP154 2.8 96.0 1.0
CD2 A:HIS156 3.0 0.7 1.0
CG A:ASP154 3.3 73.2 1.0
CG A:HIS156 3.4 0.1 1.0
NE2 A:HIS156 3.4 0.9 1.0
OD2 A:ASP154 3.5 78.9 1.0
CB A:HIS156 4.0 95.0 1.0
ND1 A:HIS156 4.0 0.8 1.0
CE1 A:HIS156 4.0 0.1 1.0
N A:HIS156 4.1 80.2 1.0
CB A:ASP154 4.4 83.2 1.0
N A:HIS155 4.4 77.9 1.0
CA A:ASP154 4.5 75.3 1.0
CA A:HIS156 4.7 76.5 1.0
C A:ASP154 4.8 86.8 1.0

Cadmium binding site 2 out of 5 in 6hj4

Go back to Cadmium Binding Sites List in 6hj4
Cadmium binding site 2 out of 5 in the Crystal Structure of Whitewater Arroyo Virus GP1 Glycoprotein at pH 7.5


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 Whitewater Arroyo Virus GP1 Glycoprotein at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd305

b:87.2
occ:1.00
NE2 A:HIS155 2.8 0.9 1.0
CE1 A:HIS155 3.1 0.4 1.0
CD2 A:HIS155 3.8 0.9 1.0
ND1 A:HIS155 4.2 0.1 1.0
CG A:HIS155 4.5 0.3 1.0
O A:HIS153 4.6 84.8 1.0

Cadmium binding site 3 out of 5 in 6hj4

Go back to Cadmium Binding Sites List in 6hj4
Cadmium binding site 3 out of 5 in the Crystal Structure of Whitewater Arroyo Virus GP1 Glycoprotein at pH 7.5


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 Whitewater Arroyo Virus GP1 Glycoprotein at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd306

b:96.8
occ:1.00
O A:HIS156 2.7 89.4 1.0
OD2 A:ASP181 2.8 92.9 1.0
NE2 A:HIS182 2.8 88.7 1.0
CD2 A:HIS182 3.5 84.4 1.0
C A:HIS156 3.6 86.5 1.0
CE1 A:HIS182 3.6 90.7 1.0
CG A:ASP181 3.8 0.1 1.0
OG1 A:THR158 3.9 90.8 1.0
OD1 A:ASP181 4.2 0.6 1.0
CA A:HIS156 4.3 76.5 1.0
N A:THR158 4.4 77.8 1.0
N A:PHE157 4.4 84.1 1.0
CG A:HIS182 4.6 93.7 1.0
CB A:HIS156 4.6 95.0 1.0
ND1 A:HIS182 4.6 93.8 1.0
CA A:PHE157 4.6 74.2 1.0

Cadmium binding site 4 out of 5 in 6hj4

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Cadmium binding site 4 out of 5 in the Crystal Structure of Whitewater Arroyo Virus GP1 Glycoprotein at pH 7.5


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 Whitewater Arroyo Virus GP1 Glycoprotein at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd307

b:0.6
occ:1.00
OE1 A:GLU107 2.7 0.3 1.0
NE2 A:HIS91 2.9 0.1 1.0
CD2 A:HIS91 3.0 0.8 1.0
CD A:GLU107 3.7 0.7 1.0
NZ A:LYS105 3.8 0.3 1.0
CE A:LYS105 3.8 0.2 1.0
CB A:GLU107 4.1 0.0 1.0
CE1 A:HIS91 4.2 0.7 1.0
CG A:HIS91 4.3 0.7 1.0
CG A:GLU107 4.4 0.3 1.0
OE2 A:GLU107 4.5 0.9 1.0
ND1 A:HIS91 4.8 0.4 1.0

Cadmium binding site 5 out of 5 in 6hj4

Go back to Cadmium Binding Sites List in 6hj4
Cadmium binding site 5 out of 5 in the Crystal Structure of Whitewater Arroyo Virus GP1 Glycoprotein at pH 7.5


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 Whitewater Arroyo Virus GP1 Glycoprotein at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd308

b:0.2
occ:0.33
OE1 A:GLU99 2.8 0.8 1.0
OE2 A:GLU99 2.9 0.2 1.0
CD A:GLU99 3.1 0.9 1.0
CG A:GLU99 4.5 92.1 1.0

Reference:

R.Pryce, W.M.Ng, A.Zeltina, Y.Watanabe, K.El Omari, A.Wagner, T.A.Bowden. Structure-Based Classification Defines the Discrete Conformational Classes Adopted By the Arenaviral GP1. J. Virol. V. 93 2019.
ISSN: ESSN 1098-5514
PubMed: 30305351
DOI: 10.1128/JVI.01048-18
Page generated: Sat Dec 12 08:28:39 2020

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