Zinc in PDB 8gd4: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Dmfo Inhibitor 6

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Dmfo Inhibitor 6, PDB code: 8gd4 was solved by P.R.Watson, A.D.Craigin, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.56 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.803, 92.364, 96.474, 90, 90, 90
R / Rfree (%)	18.5 / 22.2

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Dmfo Inhibitor 6 also contains other interesting chemical elements:

Fluorine	(F)	4 atoms
Potassium	(K)	4 atoms

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Dmfo Inhibitor 6 (pdb code 8gd4). 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 Complexed with Dmfo Inhibitor 6, PDB code: 8gd4:
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 Complexed with Dmfo Inhibitor 6


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 Complexed with Dmfo Inhibitor 6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:12.6 occ:1.00 OD1 A:ASP612 2.0 9.2 1.0 N05 A:Z4I801 2.0 16.6 1.0 OD2 A:ASP705 2.0 9.5 1.0 ND1 A:HIS614 2.1 12.3 1.0 CG A:ASP612 2.8 11.2 1.0 OD2 A:ASP612 2.9 10.5 1.0 C04 A:Z4I801 2.9 16.5 1.0 CG A:ASP705 3.0 9.9 1.0 CE1 A:HIS614 3.0 14.3 1.0 O23 A:Z4I801 3.0 23.6 1.0 N06 A:Z4I801 3.1 23.2 1.0 CG A:HIS614 3.2 12.4 1.0 O22 A:Z4I801 3.3 23.4 1.0 OD1 A:ASP705 3.3 10.8 1.0 C07 A:Z4I801 3.6 20.9 1.0 CB A:HIS614 3.6 9.8 1.0 N A:HIS614 3.9 10.6 1.0 CG1 A:VAL613 4.2 11.0 1.0 NE2 A:HIS614 4.2 13.6 1.0 CB A:ASP612 4.2 7.6 1.0 N A:VAL613 4.3 10.2 1.0 NE2 A:HIS573 4.3 11.0 1.0 CD2 A:HIS614 4.3 14.4 1.0 C02 A:Z4I801 4.3 17.3 1.0 CB A:ASP705 4.3 8.4 1.0 OH A:TYR745 4.3 13.7 1.0 CA A:GLY743 4.4 9.0 1.0 CA A:HIS614 4.4 9.9 1.0 NE2 A:HIS574 4.5 12.8 1.0 CE1 A:HIS573 4.7 9.6 1.0 CE2 A:TYR745 4.7 13.3 1.0 C A:VAL613 4.8 10.8 1.0 N A:GLY743 4.8 10.7 1.0 C A:ASP612 4.8 10.5 1.0 F01 A:Z4I801 4.9 18.8 1.0 CA A:VAL613 4.9 9.3 1.0 CA A:ASP612 4.9 7.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Dmfo Inhibitor 6


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 Complexed with Dmfo Inhibitor 6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn802 b:12.7 occ:1.00 OD1 B:ASP612 2.0 5.3 1.0 N05 B:Z4I801 2.0 13.6 1.0 OD2 B:ASP705 2.0 10.1 1.0 ND1 B:HIS614 2.1 13.3 1.0 CG B:ASP612 2.8 9.0 1.0 OD2 B:ASP612 2.9 11.0 1.0 C04 B:Z4I801 2.9 14.9 1.0 CG B:ASP705 3.0 9.6 1.0 N06 B:Z4I801 3.0 17.4 1.0 O23 B:Z4I801 3.1 22.5 1.0 CE1 B:HIS614 3.1 12.3 1.0 CG B:HIS614 3.2 14.8 1.0 OD1 B:ASP705 3.2 12.3 1.0 O22 B:Z4I801 3.3 18.1 1.0 CB B:HIS614 3.5 11.0 1.0 C07 B:Z4I801 3.5 19.8 1.0 N B:HIS614 3.8 7.6 1.0 CB B:ASP612 4.2 6.9 1.0 NE2 B:HIS573 4.2 13.1 1.0 NE2 B:HIS614 4.2 13.5 1.0 OH B:TYR745 4.2 11.9 1.0 CA B:HIS614 4.3 10.4 1.0 CD2 B:HIS614 4.3 14.8 1.0 N B:VAL613 4.3 8.8 1.0 CG1 B:VAL613 4.3 8.2 1.0 CB B:ASP705 4.3 9.4 1.0 C02 B:Z4I801 4.3 14.3 1.0 CA B:GLY743 4.4 8.1 1.0 NE2 B:HIS574 4.6 9.2 1.0 CE1 B:HIS573 4.6 14.2 1.0 CE2 B:TYR745 4.7 12.2 1.0 C B:VAL613 4.8 9.0 1.0 N B:GLY743 4.8 9.4 1.0 C B:ASP612 4.8 11.4 1.0 F01 B:Z4I801 4.9 20.8 1.0 CA B:ASP612 4.9 8.7 1.0 CA B:VAL613 5.0 10.8 1.0 CZ B:TYR745 5.0 12.5 1.0 C08 B:Z4I801 5.0 18.0 1.0

B.Konig, P.R.Watson, N.Rebing, A.D.Craigin, L.Schaker-Hubner, D.W.Christianson, F.K.Hansen. Difluoromethyl-1,3,4-Oxadiazoles Are Selective, Mechanism-Based, and Essentially Irreversible Inhibitors of Histone Deacetylase 6 To Be Published.