Cobalt 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:

Cadmium	(Cd)	4 atoms
Magnesium	(Mg)	1 atom
Chlorine	(Cl)	1 atom

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

Cobalt binding site 1 out of 2 in the Crystal Structure of LYS63-Linked Di-Ubiquitin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of LYS63-Linked Di-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Co1079 b:28.2 occ:1.00 N B:MET1 1.9 43.0 1.0 O B:HOH2047 2.3 41.8 1.0 OE2 B:GLU16 2.4 48.6 1.0 OE1 B:GLU16 2.6 49.6 1.0 CD B:GLU16 2.8 46.6 1.0 CA B:MET1 3.0 43.3 1.0 C B:MET1 3.3 43.1 1.0 O B:MET1 3.6 44.3 1.0 N B:GLN2 4.1 41.5 1.0 O B:HOH2001 4.3 37.6 1.0 CB B:MET1 4.3 43.4 1.0 CG B:GLU16 4.4 42.7 1.0 O B:VAL17 5.0 37.0 1.0 CA B:GLN2 5.0 41.4 1.0

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


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of LYS63-Linked Di-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Co1081 b:30.7 occ:1.00 O B:HOH2039 2.0 23.3 1.0 OE1 B:GLU64 2.4 40.9 1.0 CD B:GLU64 3.2 40.8 1.0 OE2 B:GLU64 3.3 45.2 1.0 CE B:LYS63 4.5 40.5 0.5 CG B:GLU64 4.7 38.8 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