Zinc in PDB 6pye: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with NR160

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with NR160, PDB code: 6pye 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)	60.32 / 1.48
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.000, 83.130, 88.590, 90.00, 98.33, 90.00
R / Rfree (%)	16.4 / 18.2

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with NR160 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 NR160 (pdb code 6pye). 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 NR160, PDB code: 6pye:
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 NR160


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 NR160 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn804 b:7.8 occ:0.89 OD2 A:ASP705 2.0 10.2 1.0 O37 A:P5Y801 2.0 19.9 0.9 OD2 A:ASP612 2.0 7.3 1.0 ND1 A:HIS614 2.1 8.2 1.0 O01 A:P5Y801 2.5 15.6 0.9 N36 A:P5Y801 2.7 24.5 0.9 CG A:ASP612 2.7 8.6 1.0 OD1 A:ASP612 2.8 9.1 1.0 C02 A:P5Y801 2.9 17.8 0.9 CE1 A:HIS614 3.0 7.5 1.0 CG A:ASP705 3.0 7.7 1.0 CG A:HIS614 3.2 5.1 1.0 OD1 A:ASP705 3.4 8.1 1.0 CB A:HIS614 3.6 6.6 1.0 N A:HIS614 3.9 4.9 1.0 NE2 A:HIS614 4.1 8.4 1.0 NE2 A:HIS573 4.2 9.8 1.0 CB A:ASP612 4.2 7.5 1.0 CD2 A:HIS614 4.3 8.7 1.0 CG1 A:VAL613 4.3 7.5 1.0 CA A:GLY743 4.3 6.5 1.0 CB A:ASP705 4.3 7.3 1.0 N A:VAL613 4.4 6.7 1.0 C03 A:P5Y801 4.4 11.4 0.9 CA A:HIS614 4.4 7.0 1.0 OH A:TYR745 4.4 15.1 1.0 CE1 A:HIS573 4.6 8.8 1.0 CE2 A:TYR745 4.6 9.7 1.0 N A:GLY743 4.7 7.1 1.0 NE2 A:HIS574 4.8 11.2 1.0 C A:VAL613 4.8 5.4 1.0 C A:ASP612 4.9 6.5 1.0 CA A:ASP612 4.9 4.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with NR160


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 NR160 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn807 b:10.0 occ:0.89 O37 B:P5Y801 1.9 23.2 0.9 OD2 B:ASP705 2.0 10.8 1.0 OD1 B:ASP612 2.0 10.2 1.0 ND1 B:HIS614 2.1 10.7 1.0 O01 B:P5Y801 2.5 22.5 0.9 N36 B:P5Y801 2.6 32.4 0.9 CG B:ASP612 2.7 10.6 1.0 OD2 B:ASP612 2.8 10.3 1.0 C02 B:P5Y801 2.8 24.5 0.9 CE1 B:HIS614 2.9 10.5 1.0 CG B:ASP705 3.0 9.1 1.0 CG B:HIS614 3.2 9.6 1.0 OD1 B:ASP705 3.4 9.9 1.0 CB B:HIS614 3.7 8.1 1.0 N B:HIS614 3.9 9.1 1.0 NE2 B:HIS614 4.1 13.0 1.0 NE2 B:HIS573 4.2 10.9 1.0 CB B:ASP612 4.2 9.2 1.0 CD2 B:HIS614 4.3 11.7 1.0 CG1 B:VAL613 4.3 9.6 1.0 C03 B:P5Y801 4.3 16.9 0.9 CB B:ASP705 4.3 8.0 1.0 CA B:GLY743 4.3 7.5 1.0 N B:VAL613 4.4 8.1 1.0 CA B:HIS614 4.4 10.7 1.0 OH B:TYR745 4.4 14.8 1.0 CE1 B:HIS573 4.6 11.0 1.0 CE2 B:TYR745 4.6 12.9 1.0 NE2 B:HIS574 4.7 12.9 1.0 N B:GLY743 4.7 9.5 1.0 C B:VAL613 4.9 9.7 1.0 C B:ASP612 4.9 8.2 1.0 CA B:ASP612 4.9 8.0 1.0 CA B:VAL613 5.0 10.0 1.0

N.Ressing, M.Sonnichsen, J.D.Osko, A.Scholer, J.Schliehe-Diecks, A.Skerhut, A.Borkhardt, J.Hauer, M.U.Kassack, D.W.Christianson, S.Bhatia, F.K.Hansen. Multicomponent Synthesis, Binding Mode, and Structure-Activity Relationship of Selective Histone Deacetylase 6 (HDAC6) Inhibitors with Bifurcated Capping Groups. J.Med.Chem. V. 63 10339 2020.
ISSN: ISSN 0022-2623
PubMed: 32803970
DOI: 10.1021/ACS.JMEDCHEM.9B01888