Zinc in PDB 6pzo: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Yx-153

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Yx-153:
3.5.1.98;

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Yx-153, PDB code: 6pzo was solved by J.D.Osko, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	66.88 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.810, 92.580, 96.730, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Yx-153 also contains other interesting chemical elements:

Fluorine	(F)	6 atoms
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 Yx-153 (pdb code 6pzo). 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 Yx-153, PDB code: 6pzo:
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 Yx-153


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 Yx-153 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:9.6 occ:1.00 O04 A:P6Y804 1.9 25.9 1.0 OD1 A:ASP612 2.0 8.0 1.0 OD2 A:ASP705 2.0 6.6 1.0 O A:HOH907 2.1 12.6 1.0 ND1 A:HIS614 2.1 7.6 1.0 N03 A:P6Y804 2.5 13.8 1.0 CG A:ASP612 2.7 8.2 1.0 OD2 A:ASP612 2.7 7.9 1.0 CE1 A:HIS614 3.0 8.2 1.0 CG A:ASP705 3.1 5.7 1.0 CG A:HIS614 3.2 7.7 1.0 C02 A:P6Y804 3.4 21.5 1.0 OD1 A:ASP705 3.4 8.1 1.0 O01 A:P6Y804 3.6 32.7 1.0 CB A:HIS614 3.6 5.7 1.0 N A:HIS614 4.0 5.3 1.0 NE2 A:HIS573 4.1 7.8 1.0 NE2 A:HIS614 4.1 9.7 1.0 CB A:ASP612 4.2 6.3 1.0 CD2 A:HIS614 4.3 8.6 1.0 CA A:GLY743 4.3 6.5 1.0 CG1 A:VAL613 4.3 4.9 1.0 OH A:TYR745 4.4 11.2 1.0 N A:VAL613 4.4 5.8 1.0 CB A:ASP705 4.4 4.5 1.0 CA A:HIS614 4.4 7.9 1.0 CE1 A:HIS573 4.5 8.2 1.0 C05 A:P6Y804 4.5 12.1 1.0 NE2 A:HIS574 4.6 8.2 1.0 CE2 A:TYR745 4.6 11.1 1.0 N A:GLY743 4.7 8.1 1.0 C A:VAL613 4.9 6.1 1.0 C A:ASP612 4.9 5.9 1.0 CA A:ASP612 4.9 4.4 1.0 C06 A:P6Y804 4.9 14.4 1.0 CZ A:TYR745 5.0 8.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Yx-153


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 Yx-153 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:9.6 occ:1.00 O04 B:P6Y804 2.0 12.0 1.0 OD1 B:ASP612 2.0 4.3 1.0 OD2 B:ASP705 2.0 4.3 1.0 ND1 B:HIS614 2.2 6.2 1.0 O01 B:P6Y804 2.6 14.7 1.0 CG B:ASP612 2.7 7.1 1.0 N03 B:P6Y804 2.7 18.3 1.0 OD2 B:ASP612 2.8 8.6 1.0 C02 B:P6Y804 2.9 16.6 1.0 CE1 B:HIS614 3.0 9.4 1.0 CG B:ASP705 3.1 5.4 1.0 CG B:HIS614 3.2 8.2 1.0 OD1 B:ASP705 3.4 7.3 1.0 CB B:HIS614 3.6 7.3 1.0 N B:HIS614 4.0 4.5 1.0 NE2 B:HIS573 4.1 6.9 1.0 CB B:ASP612 4.2 5.8 1.0 NE2 B:HIS614 4.2 10.7 1.0 C05 B:P6Y804 4.3 16.5 1.0 CD2 B:HIS614 4.3 8.6 1.0 CA B:GLY743 4.3 6.8 1.0 OH B:TYR745 4.3 12.1 1.0 CB B:ASP705 4.4 5.1 1.0 CG1 B:VAL613 4.4 6.0 1.0 N B:VAL613 4.4 6.5 1.0 CA B:HIS614 4.4 7.9 1.0 CE1 B:HIS573 4.5 7.2 1.0 NE2 B:HIS574 4.6 6.4 1.0 CE2 B:TYR745 4.6 9.3 1.0 N B:GLY743 4.7 5.4 1.0 C B:ASP612 4.9 7.4 1.0 C B:VAL613 4.9 6.1 1.0 CA B:ASP612 4.9 5.0 1.0 C24 B:P6Y804 5.0 12.9 1.0 CZ B:TYR745 5.0 10.3 1.0

J.D.Osko, N.J.Porter, P.A.Narayana Reddy, Y.C.Xiao, J.Rokka, M.Jung, J.M.Hooker, J.M.Salvino, D.W.Christianson. Exploring Structural Determinants of Inhibitor Affinity and Selectivity in Complexes with Histone Deacetylase 6. J.Med.Chem. V. 63 295 2020.
ISSN: ISSN 0022-2623
PubMed: 31793776
DOI: 10.1021/ACS.JMEDCHEM.9B01540