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Cadmium in PDB 2qp9: Crystal Structure of S.Cerevisiae VPS4

Protein crystallography data

The structure of Crystal Structure of S.Cerevisiae VPS4, PDB code: 2qp9 was solved by J.Xiao, Z.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.90
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 86.553, 86.553, 236.061, 90.00, 90.00, 120.00
R / Rfree (%) 25.8 / 28.8

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of S.Cerevisiae VPS4 (pdb code 2qp9). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Crystal Structure of S.Cerevisiae VPS4, PDB code: 2qp9:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 2qp9

Go back to Cadmium Binding Sites List in 2qp9
Cadmium binding site 1 out of 2 in the Crystal Structure of S.Cerevisiae VPS4


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 S.Cerevisiae VPS4 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Cd601

b:95.7
occ:1.00
OE1 X:GLU392 2.0 49.1 1.0
OD1 X:ASP394 2.2 55.2 1.0
CG X:ASP394 2.9 55.8 1.0
OD2 X:ASP394 3.0 57.2 1.0
CD X:GLU392 3.1 50.1 1.0
CG X:GLU392 3.9 50.0 1.0
OE2 X:GLU392 4.0 50.6 1.0
CB X:GLU392 4.0 50.7 1.0
CB X:ASP394 4.4 55.1 1.0
CG X:GLU395 4.7 56.8 1.0

Cadmium binding site 2 out of 2 in 2qp9

Go back to Cadmium Binding Sites List in 2qp9
Cadmium binding site 2 out of 2 in the Crystal Structure of S.Cerevisiae VPS4


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 S.Cerevisiae VPS4 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Cd603

b:0.1
occ:1.00
OE2 X:GLU189 2.0 55.0 1.0
CD X:GLU189 3.2 53.4 1.0
OE1 X:GLU189 4.0 54.1 1.0
CG X:GLU189 4.2 52.0 1.0
CD1 X:TRP132 4.9 69.7 1.0

Reference:

J.Xiao, H.Xia, K.Yoshino-Koh, J.Zhou, Z.Xu. Structural Characterization of the Atpase Reaction Cycle of Endosomal Aaa Protein VPS4. J.Mol.Biol. V. 374 655 2007.
ISSN: ISSN 0022-2836
PubMed: 17949747
DOI: 10.1016/J.JMB.2007.09.067
Page generated: Wed Oct 28 10:00:06 2020
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