Zinc in PDB 6dvl: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-115

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-115, PDB code: 6dvl 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)	60.21 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.982, 82.601, 88.910, 90.00, 98.49, 90.00
R / Rfree (%)	17.6 / 20.3

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-115 also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-115 (pdb code 6dvl). 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 Ddk-115, PDB code: 6dvl:
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 Ddk-115


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 Ddk-115 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:10.3 occ:1.00 OD2 A:ASP705 2.0 9.5 1.0 OD1 A:ASP612 2.0 6.0 1.0 O A:HOH930 2.1 14.0 1.0 ND1 A:HIS614 2.1 7.6 1.0 O29 A:HBG804 2.1 41.1 1.0 N28 A:HBG804 2.6 19.2 1.0 CG A:ASP612 2.7 7.8 1.0 OD2 A:ASP612 2.7 8.9 1.0 CE1 A:HIS614 3.0 8.3 1.0 CG A:ASP705 3.1 10.5 1.0 CG A:HIS614 3.1 7.3 1.0 CB A:HIS614 3.5 6.1 1.0 OD1 A:ASP705 3.6 9.1 1.0 C26 A:HBG804 3.6 16.9 1.0 N A:HIS614 3.8 3.4 1.0 O27 A:HBG804 3.9 27.8 1.0 NE2 A:HIS614 4.2 10.7 1.0 NE2 A:HIS573 4.2 6.1 1.0 CB A:ASP612 4.2 4.5 1.0 CG1 A:VAL613 4.2 6.2 1.0 CD2 A:HIS614 4.2 7.7 1.0 CA A:GLY743 4.2 10.5 1.0 CA A:HIS614 4.3 5.5 1.0 N A:VAL613 4.3 5.4 1.0 CB A:ASP705 4.3 8.4 1.0 CE1 A:HIS573 4.5 6.9 1.0 NE2 A:HIS574 4.5 9.6 1.0 OH A:TYR745 4.6 18.4 1.0 C25 A:HBG804 4.7 13.8 1.0 N A:GLY743 4.7 11.1 1.0 CE2 A:TYR745 4.7 15.7 1.0 C A:VAL613 4.7 6.2 1.0 C A:ASP612 4.8 7.7 1.0 CA A:VAL613 4.9 7.5 1.0 CA A:ASP612 4.9 4.7 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 Ddk-115


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 Ddk-115 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:17.9 occ:1.00 OD2 B:ASP705 2.0 11.7 1.0 OD1 B:ASP612 2.1 13.5 1.0 O B:HOH914 2.1 19.6 1.0 O29 B:HBG804 2.2 35.5 1.0 ND1 B:HIS614 2.2 19.8 1.0 OD2 B:ASP612 2.7 11.4 1.0 N28 B:HBG804 2.7 23.2 1.0 CG B:ASP612 2.7 14.2 1.0 CG B:ASP705 3.1 14.7 1.0 CE1 B:HIS614 3.1 17.4 1.0 CG B:HIS614 3.2 16.7 1.0 CB B:HIS614 3.5 12.2 1.0 OD1 B:ASP705 3.5 13.4 1.0 C26 B:HBG804 3.6 24.6 1.0 N B:HIS614 3.7 9.0 1.0 O27 B:HBG804 3.9 30.4 1.0 NE2 B:HIS573 4.1 13.4 1.0 CB B:ASP612 4.2 9.9 1.0 CG1 B:VAL613 4.2 10.3 1.0 CA B:GLY743 4.2 13.1 1.0 NE2 B:HIS614 4.2 17.6 1.0 CA B:HIS614 4.2 12.7 1.0 N B:VAL613 4.3 10.2 1.0 CD2 B:HIS614 4.3 15.2 1.0 CB B:ASP705 4.3 13.5 1.0 CE1 B:HIS573 4.4 13.2 1.0 NE2 B:HIS574 4.5 16.5 1.0 N B:GLY743 4.6 14.0 1.0 C25 B:HBG804 4.7 18.9 1.0 C B:VAL613 4.7 10.9 1.0 OH B:TYR745 4.7 24.4 1.0 C B:ASP612 4.8 13.3 1.0 CE2 B:TYR745 4.9 14.8 1.0 CA B:VAL613 4.9 10.8 1.0 CA B:ASP612 4.9 10.1 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