Zinc in PDB 6dvo: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Bavarostat

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

Resolution Low / High (Å)	42.10 / 1.98
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	97.230, 97.230, 78.900, 90.00, 90.00, 120.00
R / Rfree (%)	16.8 / 21.6

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

Fluorine	(F)	1 atom
Potassium	(K)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Bavarostat (pdb code 6dvo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Bavarostat, PDB code: 6dvo:

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


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 Bavarostat within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:16.3 occ:1.00 OD2 A:ASP705 2.0 11.8 1.0 O01 A:HBV805 2.0 27.5 1.0 OD1 A:ASP612 2.0 12.1 1.0 ND1 A:HIS614 2.2 14.0 1.0 O02 A:HBV805 2.2 26.5 1.0 N02 A:HBV805 2.4 27.3 1.0 C07 A:HBV805 2.6 26.5 1.0 CG A:ASP612 2.8 12.2 1.0 OD2 A:ASP612 2.8 11.7 1.0 CG A:ASP705 3.1 12.5 1.0 CE1 A:HIS614 3.1 14.0 1.0 CG A:HIS614 3.2 14.3 1.0 CB A:HIS614 3.5 14.0 1.0 OD1 A:ASP705 3.6 13.2 1.0 N A:HIS614 3.9 14.0 1.0 C06 A:HBV805 3.9 25.3 1.0 NE2 A:HIS573 4.2 12.8 1.0 NE2 A:HIS614 4.2 14.7 1.0 CB A:ASP612 4.2 12.6 1.0 CD2 A:HIS614 4.3 14.5 1.0 CG1 A:VAL613 4.3 13.2 1.0 CA A:GLY743 4.3 15.3 1.0 CB A:ASP705 4.3 12.7 1.0 CA A:HIS614 4.3 14.4 1.0 N A:VAL613 4.4 14.1 1.0 OH A:TYR745 4.4 18.8 1.0 CE1 A:HIS573 4.5 12.8 1.0 C08 A:HBV805 4.5 24.8 1.0 CE2 A:TYR745 4.6 18.2 1.0 N A:GLY743 4.7 15.0 1.0 NE2 A:HIS574 4.7 10.3 1.0 C A:VAL613 4.8 13.8 1.0 C A:ASP612 4.9 14.3 1.0 CA A:ASP612 4.9 13.4 1.0 CZ A:TYR745 5.0 18.2 1.0

N.J.Porter, J.D.Osko, D.Diedrich, T.Kurz, J.M.Hooker, F.K.Hansen, D.W.Christianson. Histone Deacetylase 6-Selective Inhibitors and the Influence of Capping Groups on Hydroxamate-Zinc Denticity. J. Med. Chem. V. 61 8054 2018.
ISSN: ISSN 1520-4804
PubMed: 30118224
DOI: 10.1021/ACS.JMEDCHEM.8B01013