Zinc in PDB 8tq0: Crystal Structure of Danio Reroof Histone Deacetylase 6 Catalytic Domain 2 Complexed with (R)-Lipoic Acid

The structure of Crystal Structure of Danio Reroof Histone Deacetylase 6 Catalytic Domain 2 Complexed with (R)-Lipoic Acid, PDB code: 8tq0 was solved by P.R.Watson, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.60 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.894, 92.156, 96.666, 90, 90, 90
R / Rfree (%)	20.7 / 24.8

The structure of Crystal Structure of Danio Reroof Histone Deacetylase 6 Catalytic Domain 2 Complexed with (R)-Lipoic Acid also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of Danio Reroof Histone Deacetylase 6 Catalytic Domain 2 Complexed with (R)-Lipoic Acid (pdb code 8tq0). 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 Reroof Histone Deacetylase 6 Catalytic Domain 2 Complexed with (R)-Lipoic Acid, PDB code: 8tq0:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Danio Reroof Histone Deacetylase 6 Catalytic Domain 2 Complexed with (R)-Lipoic Acid


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 Reroof Histone Deacetylase 6 Catalytic Domain 2 Complexed with (R)-Lipoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:15.0 occ:1.00 OD2 A:ASP705 1.9 12.9 1.0 OD1 A:ASP612 2.1 12.3 1.0 S8 A:RED801 2.3 16.9 1.0 ND1 A:HIS614 2.3 15.2 1.0 CG A:ASP612 2.8 16.7 1.0 OD2 A:ASP612 2.8 12.9 1.0 CG A:ASP705 3.0 12.8 1.0 CE1 A:HIS614 3.2 20.8 1.0 CG A:HIS614 3.3 16.7 1.0 OD1 A:ASP705 3.4 12.9 1.0 C8 A:RED801 3.5 19.7 1.0 CB A:HIS614 3.6 15.8 1.0 C7 A:RED801 3.8 19.2 1.0 N A:HIS614 3.9 12.8 1.0 NE2 A:HIS573 4.1 12.9 1.0 CB A:ASP705 4.2 13.0 1.0 CG1 A:VAL613 4.2 9.7 1.0 CE1 A:HIS573 4.2 14.2 1.0 CB A:ASP612 4.3 12.5 1.0 CA A:GLY743 4.3 12.6 1.0 CA A:HIS614 4.4 14.4 1.0 N A:VAL613 4.4 13.6 1.0 NE2 A:HIS614 4.4 16.0 1.0 CD2 A:HIS614 4.4 14.9 1.0 NE2 A:HIS574 4.4 14.4 1.0 OH A:TYR745 4.5 17.6 1.0 CE2 A:TYR745 4.6 12.4 1.0 C6 A:RED801 4.7 21.1 1.0 N A:GLY743 4.8 17.5 1.0 C A:VAL613 4.8 14.0 1.0 C A:ASP612 4.9 14.1 1.0 CA A:ASP612 5.0 12.7 1.0 CA A:VAL613 5.0 12.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Danio Reroof Histone Deacetylase 6 Catalytic Domain 2 Complexed with (R)-Lipoic Acid


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 Reroof Histone Deacetylase 6 Catalytic Domain 2 Complexed with (R)-Lipoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn802 b:15.3 occ:1.00 OD2 B:ASP705 1.9 12.9 1.0 OD1 B:ASP612 2.0 12.1 1.0 ND1 B:HIS614 2.3 15.9 1.0 S8 B:RED801 2.4 15.1 1.0 CG B:ASP612 2.8 15.7 1.0 OD2 B:ASP612 2.9 11.5 1.0 CG B:ASP705 3.0 13.1 1.0 CG B:HIS614 3.2 17.9 1.0 CE1 B:HIS614 3.3 16.4 1.0 OD1 B:ASP705 3.4 13.3 1.0 CB B:HIS614 3.5 11.6 1.0 C8 B:RED801 3.7 21.1 1.0 N B:HIS614 3.8 15.3 1.0 C7 B:RED801 3.8 20.6 1.0 NE2 B:HIS573 4.1 14.9 1.0 CE1 B:HIS573 4.2 15.0 1.0 CG1 B:VAL613 4.2 11.9 1.0 CB B:ASP612 4.2 13.4 1.0 CA B:HIS614 4.2 13.4 1.0 CB B:ASP705 4.3 14.7 1.0 CA B:GLY743 4.3 11.7 1.0 N B:VAL613 4.3 15.8 1.0 CD2 B:HIS614 4.4 16.8 1.0 NE2 B:HIS614 4.4 19.4 1.0 OH B:TYR745 4.5 18.1 1.0 NE2 B:HIS574 4.5 10.8 1.0 CE2 B:TYR745 4.6 13.8 1.0 C B:VAL613 4.7 14.6 1.0 N B:GLY743 4.8 16.0 1.0 C B:ASP612 4.8 13.9 1.0 C6 B:RED801 4.9 21.0 1.0 CA B:ASP612 4.9 13.3 1.0 CA B:VAL613 4.9 14.0 1.0 O B:HIS614 5.0 14.4 1.0

P.R.Watson, J.Goulart Stollmaier, D.W.Christianson. Crystal Structure of Danio Reroof Histone Deacetylase 6 Catalytic Domain 2 Complexed with (R)-Lipoic Acid To Be Published.