Zinc in PDB 3f06: Crystal Structure Analysis of Human HDAC8 D101A Variant.

All present enzymatic activity of Crystal Structure Analysis of Human HDAC8 D101A Variant.:
3.5.1.98;

The structure of Crystal Structure Analysis of Human HDAC8 D101A Variant., PDB code: 3f06 was solved by D.P.Dowling, S.L.Gantt, S.G.Gattis, C.A.Fierke, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.32 / 2.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.989, 85.875, 94.834, 90.00, 93.68, 90.00
R / Rfree (%)	22.8 / 25.9

The structure of Crystal Structure Analysis of Human HDAC8 D101A 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 D101A Variant. (pdb code 3f06). 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 D101A Variant., PDB code: 3f06:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure Analysis of Human HDAC8 D101A 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 D101A Variant. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:56.9 occ:1.00 OD2 A:ASP267 1.9 59.2 1.0 O2 A:B3N500 1.9 65.9 0.7 O2 A:B3N500 2.0 73.0 0.3 OD2 A:ASP178 2.0 55.6 1.0 O4 A:B3N500 2.1 62.3 0.7 ND1 A:HIS180 2.1 40.5 1.0 O4 A:B3N500 2.1 71.8 0.3 C1 A:B3N500 2.6 64.2 0.7 C1 A:B3N500 2.6 72.4 0.3 N3 A:B3N500 2.7 63.6 0.7 N3 A:B3N500 2.7 72.2 0.3 CE1 A:HIS180 2.8 41.2 1.0 CG A:ASP178 3.0 58.9 1.0 CG A:ASP267 3.0 62.0 1.0 CG A:HIS180 3.3 42.6 1.0 OD1 A:ASP178 3.3 63.3 1.0 OD1 A:ASP267 3.4 64.8 1.0 N A:HIS180 3.7 54.0 1.0 CB A:HIS180 3.8 47.7 1.0 NE2 A:HIS180 4.0 41.1 1.0 CA A:GLY304 4.1 59.9 1.0 C5 A:B3N500 4.1 64.5 0.7 C5 A:B3N500 4.1 72.5 0.3 N A:LEU179 4.1 56.8 1.0 CD2 A:HIS180 4.2 41.6 1.0 CB A:LEU179 4.3 54.9 1.0 CB A:ASP267 4.3 60.8 1.0 CB A:ASP178 4.4 58.3 1.0 N A:GLY304 4.4 60.2 1.0 CA A:HIS180 4.4 50.9 1.0 C A:LEU179 4.5 55.9 1.0 CA A:LEU179 4.5 55.6 1.0 C6 A:B3N500 4.6 71.7 0.3 C6 A:B3N500 4.6 62.9 0.7 OH A:TYR306 4.6 60.6 1.0 NE2 A:HIS142 4.7 63.4 1.0 C A:ASP178 4.9 58.1 1.0 CE1 A:TYR306 5.0 58.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure Analysis of Human HDAC8 D101A 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 D101A Variant. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:57.3 occ:1.00 OD2 B:ASP267 1.9 51.4 1.0 O4 B:B3N501 1.9 67.1 0.5 OD2 B:ASP178 1.9 57.7 1.0 O2 B:B3N501 2.0 55.2 0.5 O4 B:B3N501 2.0 56.8 0.5 O2 B:B3N501 2.1 65.8 0.5 ND1 B:HIS180 2.2 44.7 1.0 C1 B:B3N501 2.6 55.7 0.5 N3 B:B3N501 2.6 56.0 0.5 N3 B:B3N501 2.6 66.8 0.5 C1 B:B3N501 2.7 66.6 0.5 CE1 B:HIS180 2.9 45.0 1.0 CG B:ASP178 2.9 59.8 1.0 CG B:ASP267 3.0 56.1 1.0 OD1 B:ASP178 3.2 62.8 1.0 CG B:HIS180 3.3 46.0 1.0 OD1 B:ASP267 3.4 60.0 1.0 N B:HIS180 3.7 54.8 1.0 CB B:HIS180 3.8 48.7 1.0 CA B:GLY304 4.0 59.0 1.0 NE2 B:HIS180 4.1 44.3 1.0 C5 B:B3N501 4.1 56.9 0.5 N B:LEU179 4.1 58.0 1.0 C5 B:B3N501 4.2 67.8 0.5 CB B:LEU179 4.3 55.0 1.0 CD2 B:HIS180 4.3 45.4 1.0 CB B:ASP267 4.3 57.5 1.0 N B:GLY304 4.3 60.9 1.0 CB B:ASP178 4.3 58.3 1.0 CA B:HIS180 4.4 53.3 1.0 C B:LEU179 4.5 57.2 1.0 CA B:LEU179 4.5 56.3 1.0 C6 B:B3N501 4.6 57.9 0.5 OH B:TYR306 4.6 61.2 1.0 NE2 B:HIS142 4.7 62.5 1.0 C6 B:B3N501 4.8 69.3 0.5 C B:ASP178 4.9 58.5 1.0 CE1 B:TYR306 5.0 58.9 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