Zinc in PDB 6cw8: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Rts-V5

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Rts-V5, PDB code: 6cw8 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)	45.72 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	48.310, 128.430, 260.490, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 18.8

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Rts-V5 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 Rts-V5 (pdb code 6cw8). 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 Rts-V5, PDB code: 6cw8:
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 Rts-V5


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 Rts-V5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:6.1 occ:1.00 OD2 A:ASP705 2.0 7.6 1.0 O04 A:FGY804 2.0 45.0 1.0 OD1 A:ASP612 2.0 3.6 1.0 ND1 A:HIS614 2.1 3.6 1.0 O A:HOH903 2.1 12.5 1.0 N03 A:FGY804 2.4 7.0 1.0 OD2 A:ASP612 2.7 6.5 1.0 CG A:ASP612 2.7 3.8 1.0 CE1 A:HIS614 3.0 6.4 1.0 CG A:ASP705 3.0 7.1 1.0 CG A:HIS614 3.2 4.3 1.0 C02 A:FGY804 3.4 23.1 1.0 OD1 A:ASP705 3.4 6.4 1.0 CB A:HIS614 3.6 4.1 1.0 O01 A:FGY804 3.8 18.9 1.0 N A:HIS614 4.0 4.6 1.0 NE2 A:HIS614 4.1 7.1 1.0 NE2 A:HIS573 4.2 5.8 1.0 CB A:ASP612 4.2 3.4 1.0 CD2 A:HIS614 4.3 3.3 1.0 CG1 A:VAL613 4.3 2.7 1.0 C05 A:FGY804 4.4 5.8 1.0 CB A:ASP705 4.4 6.8 1.0 N A:VAL613 4.4 2.0 1.0 CA A:GLY743 4.4 9.4 1.0 CA A:HIS614 4.4 2.7 1.0 OH A:TYR745 4.5 15.1 1.0 NE2 A:HIS574 4.5 5.2 1.0 CE1 A:HIS573 4.6 6.2 1.0 C38 A:FGY804 4.7 6.0 1.0 N A:GLY743 4.7 8.5 1.0 CE2 A:TYR745 4.8 4.9 1.0 C A:ASP612 4.9 3.2 1.0 C A:VAL613 4.9 2.6 1.0 CA A:ASP612 4.9 2.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Rts-V5


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 Rts-V5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:10.0 occ:1.00 OD1 B:ASP612 2.0 5.7 1.0 OD2 B:ASP705 2.0 10.2 1.0 O04 B:FGY804 2.1 40.2 1.0 O B:HOH902 2.1 15.9 1.0 ND1 B:HIS614 2.1 6.5 1.0 N03 B:FGY804 2.4 13.2 1.0 CG B:ASP612 2.7 11.4 1.0 OD2 B:ASP612 2.8 11.6 1.0 CG B:ASP705 3.1 12.8 1.0 CE1 B:HIS614 3.1 14.3 1.0 CG B:HIS614 3.2 7.5 1.0 C02 B:FGY804 3.4 21.6 1.0 OD1 B:ASP705 3.4 10.1 1.0 CB B:HIS614 3.5 7.0 1.0 O01 B:FGY804 3.8 25.2 1.0 N B:HIS614 3.9 4.8 1.0 NE2 B:HIS573 4.1 10.4 1.0 CB B:ASP612 4.2 6.8 1.0 NE2 B:HIS614 4.2 10.7 1.0 CD2 B:HIS614 4.3 8.0 1.0 CA B:GLY743 4.3 12.2 1.0 CA B:HIS614 4.3 6.0 1.0 CG1 B:VAL613 4.4 10.2 1.0 CB B:ASP705 4.4 10.8 1.0 N B:VAL613 4.4 3.8 1.0 C05 B:FGY804 4.4 18.0 1.0 OH B:TYR745 4.5 18.1 1.0 CE1 B:HIS573 4.5 13.6 1.0 NE2 B:HIS574 4.6 5.6 1.0 CE2 B:TYR745 4.6 10.1 1.0 N B:GLY743 4.7 15.7 1.0 C38 B:FGY804 4.8 14.9 1.0 C B:ASP612 4.9 4.3 1.0 C B:VAL613 4.9 4.5 1.0 CA B:ASP612 4.9 6.9 1.0

S.Bhatia, V.Krieger, M.Groll, J.D.Osko, H.Ahlert, A.Borkhardt, T.Kurz, D.W.Christianson, J.Hauer, F.K.Hansen. Discovery of the First-in-Class Dual Histone Deacetylase-Proteasome Inhibitor. J. Med. Chem. V. 61 10299 2018.
ISSN: ISSN 1520-4804
PubMed: 30365892
DOI: 10.1021/ACS.JMEDCHEM.8B01487