Cadmium in PDB 2jf5: Crystal Structure of LYS63-Linked Di-Ubiquitin

The structure of Crystal Structure of LYS63-Linked Di-Ubiquitin, PDB code: 2jf5 was solved by D.Komander, P.Odenwaelder, D.Barford, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.95
Space group	P 43 3 2
Cell size a, b, c (Å), α, β, γ (°)	105.021, 105.021, 105.021, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 25

The structure of Crystal Structure of LYS63-Linked Di-Ubiquitin also contains other interesting chemical elements:

Cobalt	(Co)	2 atoms
Magnesium	(Mg)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Cadmium atom in the Crystal Structure of LYS63-Linked Di-Ubiquitin (pdb code 2jf5). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Crystal Structure of LYS63-Linked Di-Ubiquitin, PDB code: 2jf5:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Crystal Structure of LYS63-Linked Di-Ubiquitin


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 LYS63-Linked Di-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1076 b:54.7 occ:0.50 CD A:CD1076 0.0 54.7 0.5 CD A:CD1076 1.9 37.4 0.5 OE2 A:GLU18 2.1 45.7 1.0 OD1 A:ASP21 2.2 39.8 1.0 CG A:ASP21 3.0 39.5 1.0 CD A:GLU18 3.1 42.8 1.0 OD2 A:ASP21 3.3 37.2 1.0 CG A:GLU18 3.4 41.9 1.0 O A:HOH2006 3.6 41.8 0.3 ND2 A:ASN25 4.1 36.4 1.0 OE1 A:GLU18 4.1 41.1 1.0 O A:HOH2008 4.3 35.7 1.0 CB A:ASP21 4.3 40.1 1.0 CA A:ASP21 4.6 41.0 1.0 CB A:GLU18 4.6 40.8 1.0

Cadmium binding site 2 out of 4 in the Crystal Structure of LYS63-Linked Di-Ubiquitin


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 LYS63-Linked Di-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1076 b:37.4 occ:0.50 CD A:CD1076 0.0 37.4 0.5 CD A:CD1076 1.9 54.7 0.5 OD1 A:ASP21 2.2 39.8 1.0 OD2 A:ASP21 2.6 37.2 1.0 CG A:ASP21 2.8 39.5 1.0 NZ A:LYS29 3.3 45.1 1.0 CE A:LYS29 3.5 44.1 1.0 OE2 A:GLU18 3.7 45.7 1.0 O A:HOH2006 4.0 41.8 0.3 CB A:ASP21 4.3 40.1 1.0 CD A:GLU18 4.3 42.8 1.0 CG A:GLU18 4.3 41.9 1.0 ND2 A:ASN25 4.4 36.4 1.0 N A:GLU18 4.7 40.0 1.0 CB A:ASN25 4.7 37.1 1.0 CG A:ASN25 4.9 37.8 1.0 CD A:LYS29 5.0 43.8 1.0

Cadmium binding site 3 out of 4 in the Crystal Structure of LYS63-Linked Di-Ubiquitin


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 LYS63-Linked Di-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd1077 b:24.9 occ:0.50 CD B:CD1077 0.0 24.9 0.5 CD B:CD1077 1.6 26.2 0.5 OD1 B:ASP21 2.3 37.6 1.0 OD2 B:ASP21 2.6 34.9 1.0 CL B:CL1080 2.7 66.5 1.0 CG B:ASP21 2.8 37.5 1.0 NZ B:LYS29 2.9 43.2 1.0 CE B:LYS29 3.3 42.0 1.0 OE1 B:GLU18 3.7 44.2 1.0 CG B:GLU18 4.2 40.1 1.0 CB B:ASP21 4.3 35.5 1.0 ND2 B:ASN25 4.3 31.6 1.0 CD B:GLU18 4.4 43.0 1.0 N B:GLU18 4.6 36.6 1.0 CB B:ASN25 4.6 32.2 1.0 CB B:GLU18 4.8 36.3 1.0 CD B:LYS29 4.8 43.8 1.0 O B:HOH2018 4.8 25.2 1.0 CG B:ASN25 4.9 33.6 1.0 CA B:VAL17 4.9 36.7 1.0

Cadmium binding site 4 out of 4 in the Crystal Structure of LYS63-Linked Di-Ubiquitin


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 LYS63-Linked Di-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd1077 b:26.2 occ:0.50 CD B:CD1077 0.0 26.2 0.5 CD B:CD1077 1.6 24.9 0.5 OE1 B:GLU18 2.3 44.2 1.0 OD1 B:ASP21 2.4 37.6 1.0 CL B:CL1080 3.2 66.5 1.0 CG B:ASP21 3.2 37.5 1.0 OD2 B:ASP21 3.3 34.9 1.0 CD B:GLU18 3.3 43.0 1.0 CG B:GLU18 3.6 40.1 1.0 CB B:GLU18 4.2 36.3 1.0 ND2 B:ASN25 4.3 31.6 1.0 NZ B:LYS29 4.4 43.2 1.0 OE2 B:GLU18 4.5 43.3 1.0 CB B:ASP21 4.6 35.5 1.0 O B:HOH2017 4.6 29.7 1.0 N B:GLU18 4.8 36.6 1.0 CA B:ASP21 4.9 35.8 1.0 CE B:LYS29 4.9 42.0 1.0

D.Komander, F.Reyes-Turcu, J.D.F.Licchesi, P.Odenwaelder, K.D.Wilkinson, D.Barford. Molecular Discrimination of Structurally Equivalent Lys 63-Linked and Linear Polyubiquitin Chains. Embo Rep. V. 10 466 2009.
ISSN: ISSN 1469-221X
PubMed: 19373254
DOI: 10.1038/EMBOR.2009.55