Atomistry » Cadmium » PDB 4qe1-5ai3 » 4yo1
Atomistry »
  Cadmium »
    PDB 4qe1-5ai3 »
      4yo1 »

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

Protein crystallography data

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

Cadmium Binding Sites:

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 4yo1

Go back to Cadmium Binding Sites List in 4yo1
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 4yo1

Go back to Cadmium Binding Sites List in 4yo1
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 4yo1

Go back to Cadmium Binding Sites List in 4yo1
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 4yo1

Go back to Cadmium Binding Sites List in 4yo1
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 4yo1

Go back to Cadmium Binding Sites List in 4yo1
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

Reference:

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
Page generated: Fri Jul 19 18:06:35 2024

Last articles

Zn in 7YZZ
Zn in 7Z10
Zn in 7Z0U
Zn in 7YUI
Zn in 7Z0R
Zn in 7Z00
Zn in 7Z0I
Zn in 7YX8
Zn in 7YXM
Zn in 7YSF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy