Zinc in PDB 5een: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Belinostat

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Belinostat:
3.5.1.98;

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Belinostat, PDB code: 5een was solved by Y.Hai, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.06 / 1.86
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.972, 95.483, 96.336, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 22.4

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Belinostat also contains other interesting chemical elements:

Potassium	(K)	4 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Belinostat (pdb code 5een). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Belinostat, PDB code: 5een:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Belinostat


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Belinostat within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn803 b:14.4 occ:1.00 OD1 B:ASP612 2.0 9.2 1.0 OD2 B:ASP705 2.2 12.4 1.0 O4 B:5OG804 2.2 27.1 1.0 ND1 B:HIS614 2.2 12.0 1.0 O3 B:5OG804 2.4 25.8 1.0 CG B:ASP612 2.7 10.3 1.0 N2 B:5OG804 2.7 26.8 1.0 OD2 B:ASP612 2.7 11.4 1.0 C12 B:5OG804 2.8 26.1 1.0 CE1 B:HIS614 3.1 12.0 1.0 CG B:ASP705 3.1 12.9 1.0 CG B:HIS614 3.2 12.1 1.0 OD1 B:ASP705 3.4 12.8 1.0 CB B:HIS614 3.6 12.2 1.0 N B:HIS614 3.9 11.9 1.0 C11 B:5OG804 4.1 25.5 1.0 CB B:ASP612 4.2 10.4 1.0 NE2 B:HIS573 4.2 11.3 1.0 NE2 B:HIS614 4.2 12.1 1.0 CG1 B:VAL613 4.2 12.9 1.0 N B:VAL613 4.3 11.7 1.0 CA B:GLY743 4.3 13.1 1.0 CD2 B:HIS614 4.3 11.8 1.0 CA B:HIS614 4.4 12.1 1.0 CB B:ASP705 4.4 12.5 1.0 CE1 B:HIS573 4.5 11.0 1.0 OH B:TYR745 4.6 13.2 1.0 N B:GLY743 4.7 13.2 1.0 C10 B:5OG804 4.7 25.1 1.0 CE2 B:TYR745 4.7 11.9 1.0 NE2 B:HIS574 4.7 11.2 1.0 C B:ASP612 4.8 11.4 1.0 C B:VAL613 4.8 12.7 1.0 CA B:ASP612 4.9 10.7 1.0 CA B:VAL613 5.0 12.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Belinostat


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Belinostat within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn803 b:12.8 occ:1.00 OD2 A:ASP705 2.1 9.2 1.0 O4 A:5OG804 2.1 27.1 1.0 OD1 A:ASP612 2.1 9.6 1.0 ND1 A:HIS614 2.2 10.4 1.0 O3 A:5OG804 2.6 25.5 1.0 N2 A:5OG804 2.6 26.9 1.0 OD2 A:ASP612 2.7 10.2 1.0 CG A:ASP612 2.7 9.9 1.0 C12 A:5OG804 2.8 25.9 1.0 CE1 A:HIS614 3.0 10.2 1.0 CG A:ASP705 3.1 10.0 1.0 CG A:HIS614 3.2 10.4 1.0 OD1 A:ASP705 3.4 10.0 1.0 CB A:HIS614 3.6 10.4 1.0 N A:HIS614 3.9 9.9 1.0 C11 A:5OG804 4.1 25.6 1.0 NE2 A:HIS614 4.2 10.4 1.0 NE2 A:HIS573 4.2 12.3 1.0 CB A:ASP612 4.2 9.9 1.0 CG1 A:VAL613 4.3 10.0 1.0 CD2 A:HIS614 4.3 10.6 1.0 CA A:GLY743 4.3 12.7 1.0 N A:VAL613 4.4 9.8 1.0 CA A:HIS614 4.4 10.0 1.0 CB A:ASP705 4.4 10.4 1.0 CE1 A:HIS573 4.5 12.2 1.0 OH A:TYR745 4.6 12.4 1.0 C10 A:5OG804 4.7 25.2 1.0 N A:GLY743 4.7 12.6 1.0 NE2 A:HIS574 4.7 11.4 1.0 CE2 A:TYR745 4.7 12.5 1.0 C A:ASP612 4.8 9.9 1.0 C A:VAL613 4.9 10.6 1.0 CA A:ASP612 4.9 10.0 1.0

Y.Hai, D.W.Christianson. Histone Deacetylase 6 Structure and Molecular Basis of Catalysis and Inhibition. Nat.Chem.Biol. V. 12 741 2016.
ISSN: ESSN 1552-4469
PubMed: 27454933
DOI: 10.1038/NCHEMBIO.2134