Zinc in PDB 6thv: X-Ray Structure of the Danio Rerio Histone Deacetylase 6 (HDAC6; Catalytic Domain 2) in Complex with Tubastatin A

The structure of X-Ray Structure of the Danio Rerio Histone Deacetylase 6 (HDAC6; Catalytic Domain 2) in Complex with Tubastatin A, PDB code: 6thv was solved by C.Barinka, L.Motlova, M.Svoboda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.90 / 1.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	84.278, 93.713, 51.574, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 16.9

The structure of X-Ray Structure of the Danio Rerio Histone Deacetylase 6 (HDAC6; Catalytic Domain 2) in Complex with Tubastatin A also contains other interesting chemical elements:

Potassium	(K)	3 atoms
Sodium	(Na)	1 atom

The binding sites of Zinc atom in the X-Ray Structure of the Danio Rerio Histone Deacetylase 6 (HDAC6; Catalytic Domain 2) in Complex with Tubastatin A (pdb code 6thv). 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 X-Ray Structure of the Danio Rerio Histone Deacetylase 6 (HDAC6; Catalytic Domain 2) in Complex with Tubastatin A, PDB code: 6thv:

Zinc binding site 1 out of 1 in the X-Ray Structure of the Danio Rerio Histone Deacetylase 6 (HDAC6; Catalytic Domain 2) in Complex with Tubastatin A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of the Danio Rerio Histone Deacetylase 6 (HDAC6; Catalytic Domain 2) in Complex with Tubastatin A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:8.7 occ:0.90 O1 A:N9W813 1.8 37.3 1.0 O A:HOH903 2.0 15.0 1.0 OD2 A:ASP705 2.0 8.9 1.0 OD1 A:ASP612 2.1 7.7 1.0 ND1 A:HIS614 2.1 7.7 1.0 N1 A:N9W813 2.4 26.9 1.0 CG A:ASP612 2.7 7.3 1.0 OD2 A:ASP612 2.7 9.3 1.0 CE1 A:HIS614 3.0 8.8 1.0 CG A:ASP705 3.0 8.2 1.0 CG A:HIS614 3.2 7.7 1.0 C1 A:N9W813 3.3 45.9 1.0 OD1 A:ASP705 3.4 8.8 1.0 CB A:HIS614 3.6 7.6 1.0 O2 A:N9W813 3.8 30.9 1.0 N A:HIS614 4.0 7.0 1.0 NE2 A:HIS573 4.1 9.8 1.0 NE2 A:HIS614 4.2 9.2 1.0 CB A:ASP612 4.2 7.4 1.0 CD2 A:HIS614 4.3 8.5 1.0 CA A:GLY743 4.3 9.7 1.0 CB A:ASP705 4.4 8.4 1.0 CG1 A:VAL613 4.4 8.1 1.0 CA A:HIS614 4.4 6.8 1.0 OH A:TYR745 4.4 13.4 1.0 N A:VAL613 4.4 6.8 1.0 C2 A:N9W813 4.5 41.0 1.0 NE2 A:HIS574 4.5 10.3 1.0 CE1 A:HIS573 4.6 8.8 1.0 N A:GLY743 4.7 8.8 1.0 CE2 A:TYR745 4.7 11.8 1.0 C A:ASP612 4.9 6.8 1.0 CA A:ASP612 4.9 6.8 1.0 C A:VAL613 4.9 6.7 1.0

C.Barinka, L.Motlova, M.Svoboda. X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with A Inhibitor Tubastatin A To Be Published.