Zinc in PDB 6pzu: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Ap-1-62-A

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Ap-1-62-A, PDB code: 6pzu 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)	42.39 / 1.74
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.626, 84.273, 87.355, 90.00, 98.04, 90.00
R / Rfree (%)	n/a / n/a

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Ap-1-62-A 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 Ap-1-62-A (pdb code 6pzu). 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 Ap-1-62-A, PDB code: 6pzu:
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 Ap-1-62-A


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 Ap-1-62-A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:12.2 occ:1.00 OD2 A:ASP705 2.0 5.6 1.0 OD1 A:ASP612 2.1 7.5 1.0 ND1 A:HIS614 2.1 7.7 1.0 O35 A:A6I804 2.1 12.0 0.6 N34 A:A6I804 2.6 23.6 0.6 O01 A:A6I804 2.6 18.0 0.6 CG A:ASP612 2.8 6.4 1.0 OD2 A:ASP612 2.8 9.1 1.0 C02 A:A6I804 2.9 18.1 0.6 CE1 A:HIS614 2.9 10.6 1.0 CG A:ASP705 3.1 7.5 1.0 CG A:HIS614 3.2 7.7 1.0 OD1 A:ASP705 3.5 6.9 1.0 CB A:HIS614 3.7 7.0 1.0 N A:HIS614 3.9 4.5 1.0 NE2 A:HIS614 4.1 7.0 1.0 NE2 A:HIS573 4.2 9.1 1.0 CB A:ASP612 4.2 6.9 1.0 CA A:GLY743 4.2 5.0 1.0 CG1 A:VAL613 4.2 6.9 1.0 C03 A:A6I804 4.2 15.3 0.6 CD2 A:HIS614 4.3 6.7 1.0 N A:VAL613 4.3 4.7 1.0 CB A:ASP705 4.4 5.0 1.0 CA A:HIS614 4.4 3.9 1.0 OH A:TYR745 4.4 8.8 1.0 CE1 A:HIS573 4.5 8.8 1.0 CE2 A:TYR745 4.5 10.6 1.0 N A:GLY743 4.6 7.8 1.0 NE2 A:HIS574 4.7 9.0 1.0 C A:VAL613 4.8 5.8 1.0 C A:ASP612 4.8 7.2 1.0 C33 A:A6I804 4.9 17.5 0.6 CA A:ASP612 4.9 5.0 1.0 CA A:VAL613 5.0 5.9 1.0 CZ A:TYR745 5.0 12.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Ap-1-62-A


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 Ap-1-62-A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:12.7 occ:1.00 OD1 B:ASP612 2.0 11.6 1.0 OD2 B:ASP705 2.0 8.2 1.0 ND1 B:HIS614 2.1 10.0 1.0 O35 B:A6I804 2.1 25.8 1.0 O01 B:A6I804 2.7 21.5 1.0 N34 B:A6I804 2.7 37.8 1.0 CG B:ASP612 2.7 13.6 1.0 OD2 B:ASP612 2.7 9.3 1.0 C02 B:A6I804 2.9 26.2 1.0 CE1 B:HIS614 3.0 11.0 1.0 CG B:ASP705 3.1 9.2 1.0 CG B:HIS614 3.2 12.0 1.0 OD1 B:ASP705 3.5 10.8 1.0 CB B:HIS614 3.6 7.4 1.0 N B:HIS614 3.9 9.8 1.0 NE2 B:HIS573 4.1 8.6 1.0 NE2 B:HIS614 4.1 9.3 1.0 CB B:ASP612 4.2 7.4 1.0 CA B:GLY743 4.2 7.2 1.0 CD2 B:HIS614 4.2 9.8 1.0 CG1 B:VAL613 4.3 10.8 1.0 C03 B:A6I804 4.3 16.5 1.0 N B:VAL613 4.3 7.7 1.0 CB B:ASP705 4.4 6.0 1.0 CA B:HIS614 4.4 5.3 1.0 CE1 B:HIS573 4.4 9.0 1.0 OH B:TYR745 4.4 10.7 1.0 N B:GLY743 4.6 8.6 1.0 CE2 B:TYR745 4.6 11.4 1.0 NE2 B:HIS574 4.6 11.4 1.0 C B:ASP612 4.8 7.8 1.0 C B:VAL613 4.9 8.4 1.0 CA B:ASP612 4.9 6.0 1.0 C04 B:A6I804 5.0 20.0 1.0 CA B:VAL613 5.0 6.9 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