Zinc in PDB 3ezp: Crystal Structure Analysis of Human HDAC8 D101N Variant

All present enzymatic activity of Crystal Structure Analysis of Human HDAC8 D101N Variant:
3.5.1.98;

The structure of Crystal Structure Analysis of Human HDAC8 D101N Variant, PDB code: 3ezp was solved by D.P.Dowling, S.L.Gantt, S.G.Gattis, C.A.Fierke, D.W.Christianon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.23 / 2.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.310, 85.874, 94.642, 90.00, 93.60, 90.00
R / Rfree (%)	22.5 / 26.2

The structure of Crystal Structure Analysis of Human HDAC8 D101N Variant also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Zinc atom in the Crystal Structure Analysis of Human HDAC8 D101N Variant (pdb code 3ezp). 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 Analysis of Human HDAC8 D101N Variant, PDB code: 3ezp:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure Analysis of Human HDAC8 D101N Variant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure Analysis of Human HDAC8 D101N Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:54.8 occ:1.00 OD2 A:ASP178 1.8 51.7 1.0 OD2 A:ASP267 1.9 47.4 1.0 ND1 A:HIS180 2.2 33.3 1.0 O2 A:B3N501 2.2 84.7 0.5 O4 A:B3N501 2.3 62.2 0.5 O2 A:B3N501 2.3 52.9 0.5 O4 A:B3N501 2.3 91.1 0.5 C1 A:B3N501 2.9 85.5 0.5 N3 A:B3N501 2.9 56.4 0.5 C1 A:B3N501 2.9 54.4 0.5 CG A:ASP267 2.9 51.1 1.0 CE1 A:HIS180 2.9 31.2 1.0 CG A:ASP178 3.0 56.0 1.0 N3 A:B3N501 3.0 87.5 0.5 OD1 A:ASP267 3.3 55.2 1.0 CG A:HIS180 3.3 35.7 1.0 OD1 A:ASP178 3.5 60.8 1.0 CB A:HIS180 3.8 39.4 1.0 N A:HIS180 3.8 50.0 1.0 CA A:GLY304 4.0 51.1 1.0 NE2 A:HIS180 4.1 34.3 1.0 N A:LEU179 4.2 52.4 1.0 CB A:ASP178 4.2 55.4 1.0 CB A:ASP267 4.3 50.6 1.0 N A:GLY304 4.3 53.0 1.0 CD2 A:HIS180 4.3 35.2 1.0 C5 A:B3N501 4.4 84.6 0.5 C5 A:B3N501 4.4 54.7 0.5 CB A:LEU179 4.4 48.7 1.0 CA A:HIS180 4.4 46.5 1.0 OH A:TYR306 4.5 73.3 1.0 NE2 A:HIS142 4.5 58.7 1.0 C A:LEU179 4.6 51.8 1.0 CA A:LEU179 4.6 50.1 1.0 CE1 A:TYR306 4.7 69.7 1.0 C6 A:B3N501 4.8 82.1 0.5 C6 A:B3N501 4.8 52.8 0.5 C A:ASP178 4.8 55.4 1.0 CE1 A:HIS142 4.9 58.1 1.0 CA A:ASP178 5.0 54.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure Analysis of Human HDAC8 D101N Variant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure Analysis of Human HDAC8 D101N Variant within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:53.3 occ:1.00 OD2 B:ASP178 1.9 53.0 1.0 OD2 B:ASP267 1.9 48.8 1.0 O4 B:B3N500 2.0 58.6 0.5 O2 B:B3N500 2.0 62.4 0.5 O4 B:B3N500 2.0 60.8 0.5 ND1 B:HIS180 2.2 29.5 1.0 O2 B:B3N500 2.4 59.1 0.5 C1 B:B3N500 2.6 62.2 0.5 N3 B:B3N500 2.6 61.6 0.5 N3 B:B3N500 2.8 58.8 0.5 C1 B:B3N500 2.9 59.8 0.5 CG B:ASP267 3.0 51.1 1.0 CE1 B:HIS180 3.0 31.2 1.0 CG B:ASP178 3.0 56.7 1.0 CG B:HIS180 3.3 31.4 1.0 OD1 B:ASP267 3.3 55.1 1.0 OD1 B:ASP178 3.6 61.4 1.0 CB B:HIS180 3.8 38.1 1.0 N B:HIS180 3.8 45.5 1.0 CA B:GLY304 4.0 48.4 1.0 C5 B:B3N500 4.1 63.3 0.5 N B:LEU179 4.1 51.3 1.0 NE2 B:HIS180 4.2 31.0 1.0 CB B:ASP178 4.2 56.0 1.0 CB B:ASP267 4.3 50.6 1.0 CD2 B:HIS180 4.3 31.4 1.0 N B:GLY304 4.4 50.5 1.0 C5 B:B3N500 4.4 61.0 0.5 CB B:LEU179 4.4 50.1 1.0 CA B:HIS180 4.4 42.3 1.0 OH B:TYR306 4.5 66.1 1.0 NE2 B:HIS142 4.5 58.1 1.0 C6 B:B3N500 4.6 62.6 0.5 C B:LEU179 4.6 49.5 1.0 CA B:LEU179 4.6 49.8 1.0 CE1 B:TYR306 4.7 67.6 1.0 C B:ASP178 4.8 54.9 1.0 CE1 B:HIS142 4.9 58.1 1.0 C6 B:B3N500 4.9 61.2 0.5 CA B:ASP178 5.0 56.0 1.0

D.P.Dowling, S.L.Gantt, S.G.Gattis, C.A.Fierke, D.W.Christianson. Structural Studies of Human Histone Deacetylase 8 and Its Site-Specific Variants Complexed with Substrate and Inhibitors. Biochemistry V. 47 13554 2008.
ISSN: ISSN 0006-2960
PubMed: 19053282
DOI: 10.1021/BI801610C