Cadmium in PDB 4yo1: Structure of Legionella Pneumophila Degq (Delta PDZ2 Variant)

The structure of Structure of Legionella Pneumophila Degq (Delta PDZ2 Variant), PDB code: 4yo1 was solved by R.Wrase, R.Hilgenfeld, G.Hansen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.04 / 2.80
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	110.870, 110.870, 68.210, 90.00, 90.00, 120.00
R / Rfree (%)	21.9 / 27.5

The binding sites of Cadmium atom in the Structure of Legionella Pneumophila Degq (Delta PDZ2 Variant) (pdb code 4yo1). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Structure of Legionella Pneumophila Degq (Delta PDZ2 Variant), PDB code: 4yo1:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Structure of Legionella Pneumophila Degq (Delta PDZ2 Variant)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Legionella Pneumophila Degq (Delta PDZ2 Variant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd401 b:71.7 occ:1.00 OE2 A:GLU200 2.3 59.5 1.0 OE1 A:GLU200 2.4 57.8 1.0 CD A:GLU200 2.7 56.8 1.0 NZ A:LYS132 3.4 78.3 1.0 CE A:LYS132 3.5 74.7 1.0 CG A:GLU200 4.2 53.7 1.0 ND2 A:ASN196 4.5 42.8 1.0 CD A:LYS198 4.7 56.3 1.0 CB A:GLU200 5.0 49.8 1.0 CD A:LYS132 5.0 72.2 1.0

Cadmium binding site 2 out of 5 in the Structure of Legionella Pneumophila Degq (Delta PDZ2 Variant)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Legionella Pneumophila Degq (Delta PDZ2 Variant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd402 b:0.4 occ:1.00 OD2 A:ASP131 2.5 65.4 1.0 OE1 A:GLN276 2.6 90.0 1.0 CG A:ASP131 3.4 63.9 1.0 OD1 A:ASP131 3.6 62.9 1.0 CD A:GLN276 3.8 89.2 1.0 ND2 A:ASN225 4.4 44.8 1.0 NE2 A:GLN276 4.6 89.3 1.0 CG A:GLN276 4.6 88.5 1.0 CB A:ASP131 4.8 62.9 1.0

Cadmium binding site 3 out of 5 in the Structure of Legionella Pneumophila Degq (Delta PDZ2 Variant)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of Legionella Pneumophila Degq (Delta PDZ2 Variant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd403 b:91.1 occ:1.00 OE2 A:GLU109 2.3 69.9 1.0 CD A:GLU109 2.9 68.9 1.0 OE1 A:GLU109 3.3 71.9 1.0 NZ A:LYS306 3.3 74.8 1.0 OD1 A:ASP107 4.0 59.6 1.0 CG A:GLU109 4.0 64.2 1.0 O A:ILE240 4.1 66.2 1.0 CE A:LYS306 4.7 75.2 1.0 OG A:SER108 4.9 70.5 1.0 N A:SER108 5.0 63.1 1.0 CB A:SER108 5.0 67.3 1.0

Cadmium binding site 4 out of 5 in the Structure of Legionella Pneumophila Degq (Delta PDZ2 Variant)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of Legionella Pneumophila Degq (Delta PDZ2 Variant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd404 b:0.6 occ:1.00 OE1 A:GLU134 2.4 75.9 1.0 CD A:GLU134 3.5 72.7 1.0 OE2 A:GLU134 3.8 74.4 1.0 CG A:GLU134 4.7 66.0 1.0

Cadmium binding site 5 out of 5 in the Structure of Legionella Pneumophila Degq (Delta PDZ2 Variant)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of Legionella Pneumophila Degq (Delta PDZ2 Variant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd405 b:0.6 occ:1.00 OD1 A:ASP325 3.7 92.0 1.0 CB A:ASP325 3.8 89.4 1.0 CG A:ASP325 4.1 91.9 1.0 CA A:ASP325 4.7 88.0 1.0 N A:ASP325 4.9 86.8 1.0

A.Schubert, R.Wrase, R.Hilgenfeld, G.Hansen. Structures of Degq From Legionella Pneumophila Define Distinct on and Off States. J.Mol.Biol. V. 427 2840 2015.
ISSN: ESSN 1089-8638
PubMed: 26205420
DOI: 10.1016/J.JMB.2015.06.023