Zinc in PDB 6r0k: X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with A Inhibitor SS208

The structure of X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with A Inhibitor SS208, PDB code: 6r0k was solved by C.Barinka, K.Ustinova, L.Motlova, J.Pavlicek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.94 / 1.15
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	84.028, 93.886, 51.679, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 17.8

The structure of X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with A Inhibitor SS208 also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Zinc atom in the X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with A Inhibitor SS208 (pdb code 6r0k). 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 Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with A Inhibitor SS208, PDB code: 6r0k:

Zinc binding site 1 out of 1 in the X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with A Inhibitor SS208


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 Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with A Inhibitor SS208 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:14.5 occ:0.85 OD2 A:ASP705 2.0 12.6 1.0 O2 A:JNN2004 2.0 15.9 0.5 O2 A:JNN2004 2.0 23.9 0.5 OD1 A:ASP612 2.0 11.9 1.0 ND1 A:HIS614 2.1 12.9 1.0 O1 A:JNN2004 2.2 15.6 0.5 O1 A:JNN2004 2.3 23.9 0.5 CG A:ASP612 2.7 12.2 1.0 OD2 A:ASP612 2.7 13.1 1.0 N1 A:JNN2004 2.7 18.2 0.5 C1 A:JNN2004 2.7 17.7 0.5 N1 A:JNN2004 2.8 27.5 0.5 C1 A:JNN2004 2.8 26.2 0.5 CE1 A:HIS614 3.0 12.9 1.0 CG A:ASP705 3.0 12.3 1.0 CG A:HIS614 3.2 12.4 1.0 OD1 A:ASP705 3.4 13.1 1.0 CB A:HIS614 3.6 11.8 1.0 N A:HIS614 4.0 11.2 1.0 C2 A:JNN2004 4.0 17.2 0.5 C2 A:JNN2004 4.0 25.6 0.5 NE2 A:HIS573 4.1 14.8 1.0 NE2 A:HIS614 4.1 13.2 1.0 CB A:ASP612 4.2 11.8 1.0 CA A:GLY743 4.3 12.0 1.0 CD2 A:HIS614 4.3 12.6 1.0 CG1 A:VAL613 4.3 11.7 1.0 CB A:ASP705 4.3 11.9 1.0 N A:VAL613 4.4 10.9 1.0 CA A:HIS614 4.4 11.2 1.0 OH A:TYR745 4.4 14.7 1.0 N3 A:JNN2004 4.5 26.5 0.5 CE1 A:HIS573 4.6 13.4 1.0 N3 A:JNN2004 4.6 17.9 0.5 N A:GLY743 4.6 12.4 1.0 CE2 A:TYR745 4.7 14.2 1.0 NE2 A:HIS574 4.7 13.2 1.0 C A:ASP612 4.9 11.1 1.0 CA A:ASP612 4.9 11.3 1.0 C A:VAL613 4.9 10.8 1.0

S.Shen, M.Hadley, K.Ustinova, J.Pavlicek, T.Knox, S.Noonepalle, M.T.Tavares, C.A.Zimprich, G.Zhang, M.B.Robers, C.Barinka, A.P.Kozikowski, A.Villagra. Discovery of A New Isoxazole-3-Hydroxamate-Based Histone Deacetylase 6 Inhibitor Ss-208 with Antitumor Activity in Syngeneic Melanoma Mouse Models. J.Med.Chem. V. 62 8557 2019.
ISSN: ISSN 0022-2623
PubMed: 31414801
DOI: 10.1021/ACS.JMEDCHEM.9B00946