Zinc in PDB 8g20: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Inhibitor MZ327

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Inhibitor MZ327, PDB code: 8g20 was solved by M.A.Tararina, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.05 / 1.77
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	48.244, 55.544, 74.399, 73, 89.9, 82.82
R / Rfree (%)	19.3 / 23.1

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Inhibitor MZ327 also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Inhibitor MZ327 (pdb code 8g20). 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 Histone Deacetylase 6 Catalytic Domain 2 Complexed with Inhibitor MZ327, PDB code: 8g20:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Inhibitor MZ327


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 Histone Deacetylase 6 Catalytic Domain 2 Complexed with Inhibitor MZ327 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn805 b:12.1 occ:1.00 OD2 A:ASP705 2.0 14.1 1.0 O01 A:YJ5801 2.0 15.0 1.0 OD1 A:ASP612 2.1 10.5 1.0 ND1 A:HIS614 2.2 11.3 1.0 O22 A:YJ5801 2.4 18.6 1.0 N02 A:YJ5801 2.6 16.1 1.0 OD2 A:ASP612 2.7 11.2 1.0 CG A:ASP612 2.8 10.3 1.0 C03 A:YJ5801 2.8 17.1 1.0 CG A:ASP705 3.1 11.8 1.0 CE1 A:HIS614 3.1 14.6 1.0 CG A:HIS614 3.3 13.3 1.0 OD1 A:ASP705 3.5 9.7 1.0 CB A:HIS614 3.7 11.3 1.0 N A:HIS614 4.0 10.5 1.0 NE2 A:HIS573 4.2 10.8 1.0 C04 A:YJ5801 4.2 14.7 1.0 OH A:TYR745 4.2 15.7 1.0 CB A:ASP612 4.3 9.2 1.0 NE2 A:HIS614 4.3 13.3 1.0 CA A:GLY743 4.3 12.2 1.0 CB A:ASP705 4.3 11.4 1.0 CG1 A:VAL613 4.3 11.4 1.0 CD2 A:HIS614 4.4 12.2 1.0 N A:VAL613 4.4 11.8 1.0 CE1 A:HIS573 4.5 11.7 1.0 CA A:HIS614 4.5 11.6 1.0 CE2 A:TYR745 4.6 15.4 1.0 N A:GLY743 4.6 10.9 1.0 NE2 A:HIS574 4.7 12.9 1.0 C05 A:YJ5801 4.7 16.4 1.0 C A:VAL613 4.9 11.2 1.0 C A:ASP612 4.9 10.7 1.0 CZ A:TYR745 4.9 13.8 1.0 CA A:ASP612 5.0 9.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Inhibitor MZ327


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 Histone Deacetylase 6 Catalytic Domain 2 Complexed with Inhibitor MZ327 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn807 b:14.0 occ:1.00 O01 B:YJ5801 1.9 12.6 1.0 OD2 B:ASP705 2.0 14.2 1.0 OD1 B:ASP612 2.1 10.2 1.0 ND1 B:HIS614 2.2 14.3 1.0 O22 B:YJ5801 2.3 16.8 1.0 N02 B:YJ5801 2.6 18.6 1.0 C03 B:YJ5801 2.7 17.5 1.0 CG B:ASP612 2.8 15.6 1.0 OD2 B:ASP612 2.8 11.5 1.0 CE1 B:HIS614 3.0 16.2 1.0 CG B:ASP705 3.1 14.7 1.0 CG B:HIS614 3.3 14.2 1.0 OD1 B:ASP705 3.5 14.1 1.0 CB B:HIS614 3.7 13.0 1.0 N B:HIS614 3.9 11.4 1.0 NE2 B:HIS573 4.1 10.1 1.0 C04 B:YJ5801 4.2 16.9 1.0 NE2 B:HIS614 4.2 13.7 1.0 CB B:ASP612 4.2 8.8 1.0 OH B:TYR745 4.3 15.8 1.0 CA B:GLY743 4.3 11.7 1.0 CD2 B:HIS614 4.3 15.5 1.0 N B:VAL613 4.4 12.2 1.0 CB B:ASP705 4.4 11.4 1.0 CG1 B:VAL613 4.4 15.2 1.0 CA B:HIS614 4.4 11.1 1.0 CE1 B:HIS573 4.4 12.7 1.0 CE2 B:TYR745 4.6 14.7 1.0 N B:GLY743 4.7 13.8 1.0 C05 B:YJ5801 4.7 16.2 1.0 NE2 B:HIS574 4.7 13.2 1.0 C B:VAL613 4.9 13.0 1.0 C B:ASP612 4.9 12.9 1.0 CZ B:TYR745 4.9 13.6 1.0 CA B:ASP612 5.0 9.5 1.0

L.Sinatra, A.Vogelmann, F.Friedrich, M.A.Tararina, E.Neuwirt, A.Colcerasa, P.Konig, L.Toy, T.Z.Yesiloglu, S.Hilscher, L.Gaitzsch, N.Papenkordt, S.Zhai, L.Zhang, C.Romier, O.Einsle, W.Sippl, M.Schutkowski, O.Gross, G.Bendas, D.W.Christianson, F.K.Hansen, M.Jung, M.Schiedel. Development of First-in-Class Dual SIRT2/HDAC6 Inhibitors As Molecular Tools For Dual Inhibition of Tubulin Deacetylation. J.Med.Chem. V. 66 14787 2023.
ISSN: ISSN 0022-2623
PubMed: 37902787
DOI: 10.1021/ACS.JMEDCHEM.3C01385