Zinc in PDB 6vnr: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Bishydroxamic Acid Inhibitor

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Bishydroxamic Acid Inhibitor, PDB code: 6vnr was solved by J.D.Osko, N.J.Porter, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.38 / 1.94
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.380, 107.140, 74.350, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 21.1

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Bishydroxamic Acid Inhibitor 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 (CD2) Complexed with Bishydroxamic Acid Inhibitor (pdb code 6vnr). 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 (CD2) Complexed with Bishydroxamic Acid Inhibitor, PDB code: 6vnr:
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 (CD2) Complexed with Bishydroxamic Acid Inhibitor


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 (CD2) Complexed with Bishydroxamic Acid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:11.9 occ:1.00 OD2 A:ASP705 2.0 9.5 1.0 OD1 A:ASP612 2.0 4.0 1.0 O01 A:R5G804 2.1 30.8 1.0 ND1 A:HIS614 2.2 7.5 1.0 O A:HOH901 2.2 13.8 1.0 CG A:ASP612 2.7 5.8 1.0 OD2 A:ASP612 2.7 8.1 1.0 N02 A:R5G804 2.8 17.3 1.0 CG A:ASP705 3.0 7.8 1.0 CE1 A:HIS614 3.1 7.2 1.0 CG A:HIS614 3.2 6.0 1.0 O24 A:R5G804 3.3 32.8 1.0 C03 A:R5G804 3.3 17.5 1.0 OD1 A:ASP705 3.4 7.8 1.0 CB A:HIS614 3.6 8.5 1.0 N A:HIS614 3.9 4.7 1.0 CB A:ASP612 4.2 4.6 1.0 NE2 A:HIS573 4.2 7.7 1.0 NE2 A:HIS614 4.2 9.3 1.0 CG1 A:VAL613 4.3 5.0 1.0 CD2 A:HIS614 4.3 8.8 1.0 CA A:GLY743 4.3 5.0 1.0 CB A:ASP705 4.3 4.6 1.0 N A:VAL613 4.4 7.1 1.0 OH A:TYR745 4.4 17.4 1.0 CA A:HIS614 4.4 5.9 1.0 CE1 A:HIS573 4.6 7.9 1.0 C04 A:R5G804 4.6 13.6 1.0 NE2 A:HIS574 4.7 9.8 1.0 CE2 A:TYR745 4.7 9.6 1.0 N A:GLY743 4.7 7.5 1.0 C A:ASP612 4.9 5.2 1.0 C A:VAL613 4.9 7.1 1.0 CA A:ASP612 4.9 5.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Bishydroxamic Acid Inhibitor


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 (CD2) Complexed with Bishydroxamic Acid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:11.8 occ:1.00 O01 B:R5G804 2.0 24.1 1.0 OD2 B:ASP705 2.1 9.3 1.0 OD1 B:ASP612 2.1 6.3 1.0 O B:HOH915 2.2 13.6 1.0 ND1 B:HIS614 2.2 7.4 1.0 N02 B:R5G804 2.4 14.6 1.0 CG B:ASP612 2.8 8.9 1.0 OD2 B:ASP612 2.8 6.7 1.0 CE1 B:HIS614 3.0 8.6 1.0 CG B:ASP705 3.1 8.8 1.0 CG B:HIS614 3.3 5.5 1.0 C03 B:R5G804 3.4 18.8 1.0 OD1 B:ASP705 3.5 8.3 1.0 CB B:HIS614 3.7 7.4 1.0 O24 B:R5G804 3.8 29.8 1.0 N B:HIS614 3.8 5.3 1.0 NE2 B:HIS573 4.2 6.8 1.0 CG1 B:VAL613 4.2 4.1 1.0 NE2 B:HIS614 4.2 7.0 1.0 N B:VAL613 4.2 7.5 1.0 CB B:ASP612 4.2 5.6 1.0 CD2 B:HIS614 4.3 8.3 1.0 CA B:GLY743 4.3 9.7 1.0 CA B:HIS614 4.4 4.8 1.0 OH B:TYR745 4.4 12.9 1.0 CB B:ASP705 4.4 4.7 1.0 C04 B:R5G804 4.5 19.2 1.0 CE1 B:HIS573 4.6 5.9 1.0 NE2 B:HIS574 4.6 11.2 1.0 CE2 B:TYR745 4.6 8.2 1.0 N B:GLY743 4.7 8.3 1.0 C B:VAL613 4.7 9.8 1.0 C B:ASP612 4.8 6.5 1.0 CA B:VAL613 4.9 6.6 1.0 CA B:ASP612 4.9 7.2 1.0 C05 B:R5G804 4.9 14.6 1.0

A.K.Miller, M.Morgen, R.R.Steimbach, M.Geraldy, L.Hellweg, P.Sehr, J.Ridinger, O.Witt, I.Oehme, C.J.Herbst-Gervasoni, J.D.Osko, N.J.Porter, D.W.Christianson, N.Gunkel. Design and Synthesis of Dihydroxamic Acids As HDAC6/8/10 Inhibitors. Chemmedchem 2020.
ISSN: ESSN 1860-7187
PubMed: 32348628
DOI: 10.1002/CMDC.202000149