Zinc in PDB 7jvw: Crystal Structure of Human Histone Deacetylase 8 (HDAC8) G320R Mutation Complexed with M344

All present enzymatic activity of Crystal Structure of Human Histone Deacetylase 8 (HDAC8) G320R Mutation Complexed with M344:
3.5.1.98;

The structure of Crystal Structure of Human Histone Deacetylase 8 (HDAC8) G320R Mutation Complexed with M344, PDB code: 7jvw 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)	48.99 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.980, 82.750, 94.520, 90.00, 98.84, 90.00
R / Rfree (%)	19.5 / 25.4

The structure of Crystal Structure of Human Histone Deacetylase 8 (HDAC8) G320R Mutation Complexed with M344 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) G320R Mutation Complexed with M344 (pdb code 7jvw). 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) G320R Mutation Complexed with M344, PDB code: 7jvw:
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) G320R Mutation Complexed with M344


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) G320R Mutation Complexed with M344 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:32.4 occ:1.00 OD2 A:ASP178 2.0 32.1 1.0 ND1 A:HIS180 2.1 31.0 1.0 O2 A:B3N501 2.1 37.1 1.0 OD2 A:ASP267 2.1 31.6 1.0 O4 A:B3N501 2.2 30.2 1.0 OD1 A:ASP178 2.5 30.2 1.0 CG A:ASP178 2.6 29.9 1.0 C1 A:B3N501 2.7 41.2 1.0 CE1 A:HIS180 2.8 29.3 1.0 N3 A:B3N501 2.8 32.3 1.0 CG A:ASP267 3.1 22.6 1.0 CG A:HIS180 3.2 30.9 1.0 OD1 A:ASP267 3.4 26.4 1.0 CB A:HIS180 3.7 29.1 1.0 N A:HIS180 3.9 28.5 1.0 NE2 A:HIS180 4.0 30.6 1.0 CB A:ASP178 4.1 19.6 1.0 CA A:GLY304 4.1 27.0 1.0 C5 A:B3N501 4.2 35.2 1.0 N A:LEU179 4.2 32.4 1.0 CD2 A:HIS180 4.2 27.9 1.0 N A:GLY304 4.4 33.7 1.0 NE2 A:HIS142 4.4 20.6 1.0 CB A:ASP267 4.4 31.3 1.0 OH A:TYR306 4.4 29.6 1.0 CA A:HIS180 4.5 27.7 1.0 CB A:LEU179 4.5 27.1 1.0 C6 A:B3N501 4.7 33.1 1.0 CA A:LEU179 4.7 27.1 1.0 C A:LEU179 4.8 28.8 1.0 CE1 A:HIS142 4.8 24.6 1.0 CE1 A:TYR306 4.8 33.4 1.0 C A:ASP178 4.9 32.1 1.0 NE2 A:HIS143 4.9 34.1 1.0 CA A:ASP178 4.9 26.2 1.0 O A:HOH675 4.9 24.6 0.5

Zinc binding site 2 out of 2 in the Crystal Structure of Human Histone Deacetylase 8 (HDAC8) G320R Mutation Complexed with M344


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) G320R Mutation Complexed with M344 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:32.4 occ:1.00 ND1 B:HIS180 2.0 27.6 1.0 OD2 B:ASP178 2.0 29.6 1.0 O2 B:B3N401 2.0 37.2 1.0 O4 B:B3N401 2.2 34.1 1.0 OD2 B:ASP267 2.3 32.8 1.0 C1 B:B3N401 2.6 38.7 1.0 N3 B:B3N401 2.7 28.7 1.0 CG B:ASP178 2.7 30.0 1.0 CE1 B:HIS180 2.8 30.7 1.0 OD1 B:ASP178 2.8 27.1 1.0 CG B:HIS180 3.1 26.6 1.0 CG B:ASP267 3.1 32.2 1.0 OD1 B:ASP267 3.3 29.6 1.0 CB B:HIS180 3.6 25.8 1.0 N B:HIS180 3.7 33.9 1.0 NE2 B:HIS180 4.0 26.9 1.0 C5 B:B3N401 4.0 37.1 1.0 CD2 B:HIS180 4.1 26.7 1.0 CA B:GLY304 4.2 28.4 1.0 N B:LEU179 4.2 33.0 1.0 CB B:ASP178 4.2 28.9 1.0 CA B:HIS180 4.3 28.8 1.0 CB B:LEU179 4.3 27.5 1.0 NE2 B:HIS142 4.4 30.2 1.0 C6 B:B3N401 4.5 38.0 1.0 CB B:ASP267 4.5 28.9 1.0 N B:GLY304 4.6 31.8 1.0 C B:LEU179 4.6 33.6 1.0 CA B:LEU179 4.6 27.9 1.0 OH B:TYR306 4.7 31.8 1.0 O B:HOH545 4.7 22.9 0.5 CE1 B:TYR306 4.8 36.1 1.0 C B:ASP178 4.9 31.3 1.0 CE1 B:HIS142 4.9 26.9 1.0 CA B:ASP178 5.0 25.4 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