Zinc in PDB 8qh9: X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with A S-29B

The structure of X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with A S-29B, PDB code: 8qh9 was solved by C.Barinka, L.Motlova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.13 / 1.59
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	84.39, 94.26, 51.65, 90, 90, 90
R / Rfree (%)	19.7 / 22.6

The structure of X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with A S-29B also contains other interesting chemical elements:

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 A S-29B (pdb code 8qh9). 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 S-29B, PDB code: 8qh9:

Zinc binding site 1 out of 1 in the X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with A S-29B


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 S-29B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:11.8 occ:0.85 OD1 A:ASP612 2.0 15.0 1.0 OD2 A:ASP705 2.0 11.9 1.0 O1 A:V9F2004 2.0 22.4 1.0 ND1 A:HIS614 2.1 14.0 1.0 O2 A:V9F2004 2.3 21.4 1.0 N1 A:V9F2004 2.5 25.4 1.0 C1 A:V9F2004 2.7 24.2 1.0 CG A:ASP612 2.7 15.7 1.0 OD2 A:ASP612 2.8 15.4 1.0 CE1 A:HIS614 3.0 14.2 1.0 CG A:ASP705 3.1 15.1 1.0 CG A:HIS614 3.2 15.4 1.0 OD1 A:ASP705 3.5 12.8 1.0 CB A:HIS614 3.5 12.8 1.0 N A:HIS614 3.9 13.6 1.0 C2 A:V9F2004 4.1 22.7 1.0 NE2 A:HIS573 4.2 16.0 1.0 CB A:ASP612 4.2 14.4 1.0 NE2 A:HIS614 4.2 15.1 1.0 CD2 A:HIS614 4.3 14.8 1.0 CG1 A:VAL613 4.3 13.8 1.0 CA A:HIS614 4.3 14.0 1.0 CB A:ASP705 4.3 13.0 1.0 N A:VAL613 4.3 15.8 1.0 OH A:TYR745 4.4 21.1 1.0 CA A:GLY743 4.4 17.1 1.0 CE1 A:HIS573 4.5 14.6 1.0 CE2 A:TYR745 4.6 18.7 1.0 C7 A:V9F2004 4.7 22.7 1.0 N A:GLY743 4.7 15.8 1.0 NE2 A:HIS574 4.8 16.5 1.0 C A:VAL613 4.8 15.6 1.0 C A:ASP612 4.9 15.2 1.0 CA A:ASP612 4.9 14.3 1.0

S.Scheuerer, L.Motlova, L.Schaker-Hubner, A.Sellmer, F.Feller, F.J.Ertl, P.Koch, F.K.Hansen, C.Barinka, S.Mahboobi. Biological and Structural Investigation of Tetrahydro-Beta-Carboline-Based Selective HDAC6 Inhibitors with Improved Stability. Eur.J.Med.Chem. V. 276 16676 2024.
ISSN: ISSN 0223-5234
PubMed: 39067437
DOI: 10.1016/J.EJMECH.2024.116676