Zinc in PDB 5d1c: Crystal Structure of D233G-Y306F HDAC8 in Complex with A Tetrapeptide Substrate

All present enzymatic activity of Crystal Structure of D233G-Y306F HDAC8 in Complex with A Tetrapeptide Substrate:
3.5.1.98;

The structure of Crystal Structure of D233G-Y306F HDAC8 in Complex with A Tetrapeptide Substrate, PDB code: 5d1c was solved by C.Decroos, N.H.Christianson, L.E.Gullett, C.M.Bowman, K.E.Christianson, M.A.Deardorff, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.35 / 1.42
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	83.031, 97.936, 104.656, 90.00, 90.00, 90.00
R / Rfree (%)	14.6 / 16.7

The structure of Crystal Structure of D233G-Y306F HDAC8 in Complex with A Tetrapeptide Substrate also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of D233G-Y306F HDAC8 in Complex with A Tetrapeptide Substrate (pdb code 5d1c). 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 D233G-Y306F HDAC8 in Complex with A Tetrapeptide Substrate, PDB code: 5d1c:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of D233G-Y306F HDAC8 in Complex with A Tetrapeptide Substrate


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 D233G-Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:11.1 occ:1.00 OD2 A:ASP178 2.0 9.7 1.0 OD2 A:ASP267 2.0 9.9 1.0 OH C:ALY5 2.1 10.5 1.0 ND1 A:HIS180 2.1 9.2 1.0 O A:HOH547 2.1 11.6 1.0 CG A:ASP178 2.8 10.4 1.0 CE1 A:HIS180 3.0 8.5 1.0 CH C:ALY5 3.0 12.4 1.0 OD1 A:ASP178 3.1 10.8 1.0 CG A:ASP267 3.1 10.2 1.0 CG A:HIS180 3.2 8.4 1.0 OD1 A:ASP267 3.4 9.6 1.0 CB A:HIS180 3.6 8.7 1.0 NZ C:ALY5 3.8 10.6 1.0 N A:HIS180 3.8 9.2 1.0 CE C:ALY5 3.9 10.8 1.0 CH3 C:ALY5 3.9 13.5 1.0 CA A:GLY304 4.1 10.4 1.0 NE2 A:HIS180 4.1 9.6 1.0 CD2 A:HIS180 4.2 9.6 1.0 CB A:ASP178 4.3 10.7 1.0 N A:GLY304 4.3 10.3 1.0 N A:LEU179 4.3 9.0 1.0 NE2 A:HIS142 4.3 12.4 1.0 CA A:HIS180 4.4 9.0 1.0 CB A:ASP267 4.4 8.8 1.0 CB A:LEU179 4.6 9.8 1.0 NE2 A:HIS143 4.6 10.7 1.0 C A:LEU179 4.8 9.7 1.0 CE2 A:PHE306 4.8 10.5 1.0 CA A:LEU179 4.8 9.2 1.0 CE1 A:HIS142 4.9 11.7 1.0 C A:ASP178 5.0 9.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of D233G-Y306F HDAC8 in Complex with A Tetrapeptide Substrate


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 D233G-Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:10.7 occ:1.00 OD2 B:ASP178 2.0 9.0 1.0 OD2 B:ASP267 2.0 10.2 1.0 OH D:ALY5 2.1 9.9 1.0 O B:HOH554 2.1 10.8 1.0 ND1 B:HIS180 2.1 8.9 1.0 CG B:ASP178 2.9 9.4 1.0 CE1 B:HIS180 3.0 8.6 1.0 CH D:ALY5 3.0 10.5 1.0 OD1 B:ASP178 3.0 10.1 1.0 CG B:ASP267 3.1 10.3 1.0 CG B:HIS180 3.2 8.2 1.0 OD1 B:ASP267 3.4 9.9 1.0 CB B:HIS180 3.6 7.7 1.0 NZ D:ALY5 3.8 8.8 1.0 N B:HIS180 3.8 8.8 1.0 CE D:ALY5 3.9 9.8 1.0 CH3 D:ALY5 3.9 11.7 1.0 NE2 B:HIS180 4.1 8.7 1.0 CA B:GLY304 4.2 9.1 1.0 CD2 B:HIS180 4.2 8.3 1.0 CB B:ASP178 4.3 9.8 1.0 NE2 B:HIS142 4.3 11.4 1.0 N B:LEU179 4.3 9.3 1.0 CA B:HIS180 4.4 9.0 1.0 N B:GLY304 4.4 9.3 1.0 CB B:ASP267 4.4 9.3 1.0 CB B:LEU179 4.5 9.1 1.0 NE2 B:HIS143 4.6 9.8 1.0 C B:LEU179 4.8 9.4 1.0 CA B:LEU179 4.8 8.9 1.0 CE2 B:PHE306 4.8 10.9 1.0 CE1 B:HIS142 4.9 10.2 1.0 C B:ASP178 5.0 8.8 1.0

C.Decroos, N.H.Christianson, L.E.Gullett, C.M.Bowman, K.E.Christianson, M.A.Deardorff, D.W.Christianson. Biochemical and Structural Characterization of HDAC8 Mutants Associated with Cornelia De Lange Syndrome Spectrum Disorders. Biochemistry V. 54 6501 2015.
ISSN: ISSN 0006-2960
PubMed: 26463496
DOI: 10.1021/ACS.BIOCHEM.5B00881