Zinc in PDB 8a8z: Crystal Structure of Danio Rerio HDAC6 CD2 in Complex with in Situ Enzymatically Hydrolyzed Dfmo-Based ITF5924

The structure of Crystal Structure of Danio Rerio HDAC6 CD2 in Complex with in Situ Enzymatically Hydrolyzed Dfmo-Based ITF5924, PDB code: 8a8z was solved by K.Zrubek, G.Sandrone, C.D.Cukier, A.Stevenazzi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.88 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.372, 118.924, 60.263, 90, 93.87, 90
R / Rfree (%)	15.5 / 19

The structure of Crystal Structure of Danio Rerio HDAC6 CD2 in Complex with in Situ Enzymatically Hydrolyzed Dfmo-Based ITF5924 also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio HDAC6 CD2 in Complex with in Situ Enzymatically Hydrolyzed Dfmo-Based ITF5924 (pdb code 8a8z). 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 Rerio HDAC6 CD2 in Complex with in Situ Enzymatically Hydrolyzed Dfmo-Based ITF5924, PDB code: 8a8z:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Danio Rerio HDAC6 CD2 in Complex with in Situ Enzymatically Hydrolyzed Dfmo-Based ITF5924


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 Rerio HDAC6 CD2 in Complex with in Situ Enzymatically Hydrolyzed Dfmo-Based ITF5924 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:16.0 occ:1.00 OD2 A:ASP705 1.9 18.3 1.0 OD1 A:ASP612 2.0 16.1 1.0 ND1 A:HIS614 2.1 16.4 1.0 N8 A:LDL801 2.1 26.1 1.0 O1 A:LDL801 2.5 26.4 1.0 CG A:ASP612 2.7 17.2 1.0 OD2 A:ASP612 2.7 17.9 1.0 N7 A:LDL801 2.8 29.2 1.0 C19 A:LDL801 2.9 29.6 1.0 CG A:ASP705 2.9 18.5 1.0 CE1 A:HIS614 3.0 19.3 1.0 CG A:HIS614 3.2 15.8 1.0 OD1 A:ASP705 3.3 17.2 1.0 CB A:HIS614 3.6 15.4 1.0 N A:HIS614 3.9 13.7 1.0 NE2 A:HIS614 4.2 18.7 1.0 CB A:ASP612 4.2 16.4 1.0 NE2 A:HIS573 4.2 18.9 1.0 CD2 A:HIS614 4.2 18.9 1.0 C1 A:LDL801 4.3 27.4 1.0 CB A:ASP705 4.3 16.8 1.0 CA A:GLY743 4.3 17.4 1.0 CG1 A:VAL613 4.3 17.1 1.0 N A:VAL613 4.4 14.9 1.0 O A:HOH999 4.4 38.0 1.0 OH A:TYR745 4.4 23.5 1.0 CA A:HIS614 4.4 15.1 1.0 CE1 A:HIS573 4.6 17.3 1.0 N A:GLY743 4.7 16.3 1.0 CE2 A:TYR745 4.7 22.0 1.0 C4 A:LDL801 4.8 28.5 1.0 NE2 A:HIS574 4.8 19.6 1.0 CA A:ASP612 4.8 15.9 1.0 C A:ASP612 4.8 16.4 1.0 C A:VAL613 4.9 13.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Danio Rerio HDAC6 CD2 in Complex with in Situ Enzymatically Hydrolyzed Dfmo-Based ITF5924


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 Rerio HDAC6 CD2 in Complex with in Situ Enzymatically Hydrolyzed Dfmo-Based ITF5924 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn802 b:17.4 occ:1.00 OD2 B:ASP705 2.0 17.5 1.0 OD1 B:ASP612 2.0 16.9 1.0 ND1 B:HIS614 2.1 19.3 1.0 N8 B:LDL801 2.1 26.2 1.0 O1 B:LDL801 2.4 27.5 1.0 CG B:ASP612 2.7 17.2 1.0 OD2 B:ASP612 2.7 17.9 1.0 N7 B:LDL801 2.8 31.1 1.0 C19 B:LDL801 2.9 32.4 1.0 CG B:ASP705 3.0 19.3 1.0 CE1 B:HIS614 3.0 20.3 1.0 CG B:HIS614 3.2 20.3 1.0 OD1 B:ASP705 3.4 18.0 1.0 CB B:HIS614 3.6 16.7 1.0 N B:HIS614 3.9 16.7 1.0 CB B:ASP612 4.1 15.9 1.0 O B:HOH934 4.2 56.1 1.0 NE2 B:HIS614 4.2 19.4 1.0 NE2 B:HIS573 4.2 20.2 1.0 C1 B:LDL801 4.2 29.7 1.0 CD2 B:HIS614 4.2 19.7 1.0 CB B:ASP705 4.3 19.3 1.0 CG1 B:VAL613 4.3 17.7 1.0 CA B:GLY743 4.3 18.5 1.0 N B:VAL613 4.3 16.2 1.0 CA B:HIS614 4.4 17.1 1.0 OH B:TYR745 4.4 26.5 1.0 CE1 B:HIS573 4.6 19.8 1.0 N B:GLY743 4.6 18.7 1.0 CE2 B:TYR745 4.7 21.2 1.0 C4 B:LDL801 4.8 35.4 1.0 C B:ASP612 4.8 16.4 1.0 CA B:ASP612 4.8 15.9 1.0 C B:VAL613 4.9 17.2 1.0 NE2 B:HIS574 4.9 19.3 1.0

E.Cellupica, G.Caprini, P.Cordella, C.Cukier, G.Fossati, M.Marchini, I.Rocchio, G.Sandrone, M.A.Vanoni, B.Vergani, K.Zrubek, A.Stevenazzi, C.Steinkuhler. Difluoromethyl-1,3,4-Oxadiazoles Are Slow-Binding Substrate Analog Inhibitors of Histone Deacetylase 6 with Unprecedented Isotype Selectivity. J.Biol.Chem. V. 299 02800 2022.
ISSN: ESSN 1083-351X
PubMed: 36528061
DOI: 10.1016/J.JBC.2022.102800