Zinc in PDB 8bjk: X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with An Inhibitor CPD11352

The structure of X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with An Inhibitor CPD11352, PDB code: 8bjk was solved by C.Barinka, L.Motlova, J.Pavlicek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.64 / 1.35
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.49, 83.78, 94.33, 90, 90, 90
R / Rfree (%)	16.8 / 20.7

The structure of X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with An Inhibitor CPD11352 also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Potassium	(K)	2 atoms

The binding sites of Zinc atom in the X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with An Inhibitor CPD11352 (pdb code 8bjk). 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 An Inhibitor CPD11352, PDB code: 8bjk:

Zinc binding site 1 out of 1 in the X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with An Inhibitor CPD11352


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 An Inhibitor CPD11352 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:13.7 occ:1.00 OD1 A:ASP612 2.0 7.7 1.0 OD2 A:ASP705 2.0 9.2 1.0 ND1 A:HIS614 2.0 8.1 1.0 N4 A:QXF804 2.1 9.0 1.0 O1 A:QXF804 2.6 10.6 1.0 CG A:ASP612 2.7 9.0 1.0 OD2 A:ASP612 2.7 8.3 1.0 N3 A:QXF804 2.9 8.4 1.0 CE1 A:HIS614 2.9 10.6 1.0 CG A:ASP705 3.0 10.0 1.0 C13 A:QXF804 3.1 6.8 1.0 CG A:HIS614 3.1 9.8 1.0 OD1 A:ASP705 3.3 8.6 1.0 CB A:HIS614 3.6 9.2 1.0 N A:HIS614 3.8 8.4 1.0 NE2 A:HIS614 4.1 10.6 1.0 NE2 A:HIS573 4.1 9.6 1.0 CB A:ASP612 4.1 7.6 1.0 CD2 A:HIS614 4.2 10.7 1.0 CG1 A:VAL613 4.2 9.0 1.0 CA A:GLY743 4.3 8.4 1.0 N A:VAL613 4.3 8.3 1.0 CB A:ASP705 4.3 9.4 1.0 CA A:HIS614 4.3 9.1 1.0 C11 A:QXF804 4.4 6.8 1.0 CE1 A:HIS573 4.5 8.4 1.0 OH A:TYR745 4.6 10.4 1.0 N A:GLY743 4.6 7.2 1.0 CE2 A:TYR745 4.8 11.1 1.0 C A:ASP612 4.8 7.8 1.0 NE2 A:HIS574 4.8 9.2 1.0 C A:VAL613 4.8 8.8 1.0 CA A:ASP612 4.8 8.4 1.0 C10 A:QXF804 4.9 8.2 1.0 CA A:VAL613 4.9 8.8 1.0

L.Motlova, I.Snajdr, Z.Kutil, E.Andris, J.Ptacek, A.Novotna, Z.Novakova, B.Havlinova, W.Tueckmantel, H.Draberova, P.Majer, M.Schutkowski, A.Kozikowski, L.Rulisek, C.Barinka. Comprehensive Mechanistic View of the Hydrolysis of Oxadiazole-Based Inhibitors By Histone Deacetylase 6 (HDAC6). Acs Chem.Biol. V. 18 1594 2023.
ISSN: ESSN 1554-8937
PubMed: 37392419
DOI: 10.1021/ACSCHEMBIO.3C00212