Zinc in PDB 7jvu: Crystal Structure of Human Histone Deacetylase 8 (HDAC8) I45T Mutation Complexed with Saha

All present enzymatic activity of Crystal Structure of Human Histone Deacetylase 8 (HDAC8) I45T Mutation Complexed with Saha:
3.5.1.98;

The structure of Crystal Structure of Human Histone Deacetylase 8 (HDAC8) I45T Mutation Complexed with Saha, PDB code: 7jvu was solved by J.D.Osko, D.W.Christianson, C.Decroos, N.J.Porter, M.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	16.00 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.314, 84.118, 94.281, 90.00, 99.06, 90.00
R / Rfree (%)	16.4 / 18.5

The structure of Crystal Structure of Human Histone Deacetylase 8 (HDAC8) I45T Mutation Complexed with Saha also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of Human Histone Deacetylase 8 (HDAC8) I45T Mutation Complexed with Saha (pdb code 7jvu). 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 Human Histone Deacetylase 8 (HDAC8) I45T Mutation Complexed with Saha, PDB code: 7jvu:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Human Histone Deacetylase 8 (HDAC8) I45T Mutation Complexed with Saha


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 Human Histone Deacetylase 8 (HDAC8) I45T Mutation Complexed with Saha within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:12.6 occ:1.00 OD2 A:ASP178 2.0 12.1 1.0 OD2 A:ASP267 2.0 12.7 1.0 O1 A:SHH404 2.0 14.3 1.0 ND1 A:HIS180 2.1 13.0 1.0 O2 A:SHH404 2.2 14.5 1.0 N1 A:SHH404 2.7 17.3 1.0 C1 A:SHH404 2.8 16.6 1.0 CG A:ASP178 2.9 11.1 1.0 CE1 A:HIS180 3.0 12.2 1.0 CG A:ASP267 3.0 12.4 1.0 OD1 A:ASP178 3.1 13.1 1.0 CG A:HIS180 3.2 12.0 1.0 OD1 A:ASP267 3.3 11.9 1.0 CB A:HIS180 3.6 11.4 1.0 N A:HIS180 3.8 11.4 1.0 CA A:GLY304 4.1 13.5 1.0 NE2 A:HIS180 4.1 12.8 1.0 C2 A:SHH404 4.2 22.7 1.0 CD2 A:HIS180 4.3 12.8 1.0 CB A:ASP178 4.3 12.9 1.0 N A:LEU179 4.3 11.7 1.0 CB A:ASP267 4.3 11.0 1.0 N A:GLY304 4.4 12.0 1.0 CA A:HIS180 4.4 12.6 1.0 NE2 A:HIS142 4.4 13.4 1.0 CB A:LEU179 4.5 12.2 1.0 OH A:TYR306 4.6 16.5 1.0 C A:LEU179 4.7 11.7 1.0 C3 A:SHH404 4.7 27.1 1.0 CA A:LEU179 4.7 11.9 1.0 CE1 A:TYR306 4.8 11.3 1.0 CE1 A:HIS142 4.8 13.5 1.0 C A:ASP178 4.9 11.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human Histone Deacetylase 8 (HDAC8) I45T Mutation Complexed with Saha


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 Human Histone Deacetylase 8 (HDAC8) I45T Mutation Complexed with Saha within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:12.8 occ:1.00 OD2 B:ASP267 2.0 12.2 1.0 OD2 B:ASP178 2.0 11.9 1.0 O1 B:SHH404 2.0 16.1 1.0 ND1 B:HIS180 2.1 12.1 1.0 O2 B:SHH404 2.2 13.4 1.0 N1 B:SHH404 2.8 15.6 1.0 C1 B:SHH404 2.8 16.6 1.0 CG B:ASP178 2.9 12.5 1.0 CE1 B:HIS180 3.0 11.0 1.0 CG B:ASP267 3.0 14.5 1.0 OD1 B:ASP178 3.1 11.8 1.0 CG B:HIS180 3.2 11.5 1.0 OD1 B:ASP267 3.4 13.3 1.0 CB B:HIS180 3.6 11.9 1.0 N B:HIS180 3.8 12.4 1.0 CA B:GLY304 4.1 12.4 1.0 NE2 B:HIS180 4.1 10.5 1.0 C2 B:SHH404 4.2 19.2 1.0 CD2 B:HIS180 4.3 11.6 1.0 CB B:ASP178 4.3 13.6 1.0 N B:LEU179 4.3 11.6 1.0 CB B:ASP267 4.3 12.7 1.0 N B:GLY304 4.4 11.9 1.0 CA B:HIS180 4.4 12.6 1.0 NE2 B:HIS142 4.4 15.0 1.0 CB B:LEU179 4.5 12.4 1.0 OH B:TYR306 4.6 15.9 1.0 C3 B:SHH404 4.7 20.5 1.0 C B:LEU179 4.7 13.0 1.0 CA B:LEU179 4.7 11.7 1.0 CE1 B:TYR306 4.7 14.7 1.0 CE1 B:HIS142 4.8 13.5 1.0 C B:ASP178 5.0 12.4 1.0

J.D.Osko, N.J.Porter, C.Decroos, M.Lee, P.Watson, M.Deardorff, D.W.Christianson. Structural Analysis of Histone Deacetylase 8 Mutants Associated with Cornelia De Lange Syndrome Spectrum Disorders J.Struct.Biol. 2020.
ISSN: ESSN 1095-8657