Zinc in PDB 5fcw: HDAC8 Complexed with A Hydroxamic Acid

All present enzymatic activity of HDAC8 Complexed with A Hydroxamic Acid:
3.5.1.98;

The structure of HDAC8 Complexed with A Hydroxamic Acid, PDB code: 5fcw was solved by K.E.Cole, K.Perry, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.66 / 1.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.443, 84.548, 94.307, 90.00, 100.08, 90.00
R / Rfree (%)	17.2 / 21.6

The structure of HDAC8 Complexed with A Hydroxamic Acid also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Zinc atom in the HDAC8 Complexed with A Hydroxamic Acid (pdb code 5fcw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the HDAC8 Complexed with A Hydroxamic Acid, PDB code: 5fcw:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the HDAC8 Complexed with A Hydroxamic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of HDAC8 Complexed with A Hydroxamic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:19.8 occ:1.00 OD2 A:ASP267 2.2 18.4 1.0 OD2 A:ASP178 2.2 16.1 1.0 ND1 A:HIS180 2.3 16.3 1.0 O2 A:5YA401 2.4 24.2 0.8 N1 A:5YA401 2.6 26.5 0.8 O1 A:5YA401 2.7 28.7 0.8 C17 A:5YA401 2.8 27.0 0.8 CG A:ASP178 2.9 16.6 1.0 OD1 A:ASP178 2.9 15.8 1.0 CG A:ASP267 3.1 20.5 1.0 CE1 A:HIS180 3.1 17.4 1.0 CG A:HIS180 3.3 14.5 1.0 OD1 A:ASP267 3.3 16.4 1.0 CB A:HIS180 3.7 13.5 1.0 N A:HIS180 3.8 14.5 1.0 C14 A:5YA401 4.0 22.0 0.8 CA A:GLY304 4.2 17.9 1.0 N A:LEU179 4.2 13.8 1.0 NE2 A:HIS180 4.3 17.1 1.0 CB A:ASP178 4.3 14.3 1.0 NE2 A:HIS142 4.4 17.5 1.0 CD2 A:HIS180 4.4 13.9 1.0 CA A:HIS180 4.4 11.4 1.0 CB A:ASP267 4.5 14.9 1.0 N A:GLY304 4.5 17.1 1.0 CB A:LEU179 4.5 13.7 1.0 O A:HOH655 4.6 30.6 1.0 C15 A:5YA401 4.7 22.5 0.8 C A:LEU179 4.7 15.7 1.0 OH A:TYR306 4.7 31.5 1.0 CA A:LEU179 4.7 12.1 1.0 CE1 A:HIS142 4.8 14.9 1.0 NE2 A:HIS143 4.8 18.3 1.0 CE2 A:TYR306 4.9 22.7 1.0 C A:ASP178 4.9 14.7 1.0 C13 A:5YA401 4.9 22.9 0.8

Zinc binding site 2 out of 2 in the HDAC8 Complexed with A Hydroxamic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of HDAC8 Complexed with A Hydroxamic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:20.0 occ:1.00 OD2 B:ASP267 2.1 19.4 1.0 OD2 B:ASP178 2.1 18.7 1.0 ND1 B:HIS180 2.3 18.2 1.0 O2 B:5YA401 2.3 31.2 0.9 O B:HOH501 2.4 23.5 1.0 CG B:ASP178 2.9 19.9 1.0 N1 B:5YA401 3.0 26.2 0.9 OD1 B:ASP178 3.0 18.5 1.0 CG B:ASP267 3.1 19.4 1.0 O1 B:5YA401 3.1 33.3 0.9 CE1 B:HIS180 3.2 21.3 1.0 CG B:HIS180 3.3 20.9 1.0 C17 B:5YA401 3.3 26.1 0.9 OD1 B:ASP267 3.4 16.4 1.0 CB B:HIS180 3.5 16.4 1.0 N B:HIS180 3.8 18.0 1.0 N B:LEU179 4.2 17.8 1.0 NE2 B:HIS142 4.3 20.2 1.0 CA B:HIS180 4.3 16.5 1.0 CA B:GLY304 4.3 20.2 1.0 NE2 B:HIS180 4.4 22.9 1.0 CB B:ASP178 4.4 20.2 1.0 CD2 B:HIS180 4.4 21.6 1.0 CB B:ASP267 4.4 14.1 1.0 CB B:LEU179 4.5 15.3 1.0 OH B:TYR306 4.5 26.7 1.0 N B:GLY304 4.6 17.4 1.0 C B:LEU179 4.7 18.9 1.0 C14 B:5YA401 4.7 26.9 0.9 CE1 B:HIS142 4.7 20.7 1.0 CA B:LEU179 4.7 16.0 1.0 CE2 B:TYR306 4.8 20.7 1.0 NE2 B:HIS143 4.8 22.9 1.0 C B:ASP178 4.9 19.9 1.0

A.A.Tabackman, R.Frankson, E.S.Marsan, K.Perry, K.E.Cole. Structure of 'Linkerless' Hydroxamic Acid Inhibitor-HDAC8 Complex Confirms the Formation of An Isoform-Specific Subpocket. J.Struct.Biol. V. 195 373 2016.
ISSN: ESSN 1095-8657
PubMed: 27374062
DOI: 10.1016/J.JSB.2016.06.023