Zinc in PDB 4rn1: Crystal Structure of S39D HDAC8 in Complex with A Largazole Analogue.

All present enzymatic activity of Crystal Structure of S39D HDAC8 in Complex with A Largazole Analogue.:
3.5.1.98;

The structure of Crystal Structure of S39D HDAC8 in Complex with A Largazole Analogue., PDB code: 4rn1 was solved by C.Decroos, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.11 / 2.18
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.051, 85.124, 95.354, 90.00, 100.21, 90.00
R / Rfree (%)	18.2 / 21.2

The structure of Crystal Structure of S39D HDAC8 in Complex with A Largazole Analogue. also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of S39D HDAC8 in Complex with A Largazole Analogue. (pdb code 4rn1). 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 S39D HDAC8 in Complex with A Largazole Analogue., PDB code: 4rn1:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of S39D HDAC8 in Complex with A Largazole Analogue.


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 S39D HDAC8 in Complex with A Largazole Analogue. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:25.9 occ:1.00 OD1 A:ASP178 2.0 19.9 1.0 OD2 A:ASP267 2.0 25.5 1.0 ND1 A:HIS180 2.1 21.6 1.0 S1 A:L8G404 2.4 24.9 1.0 CE1 A:HIS180 2.9 27.2 1.0 CG A:ASP178 2.9 30.2 1.0 C1 A:L8G404 3.1 29.6 1.0 CG A:ASP267 3.1 23.2 1.0 OD2 A:ASP178 3.1 22.5 1.0 CG A:HIS180 3.2 26.0 1.0 OD1 A:ASP267 3.5 22.3 1.0 CB A:HIS180 3.7 19.4 1.0 N A:HIS180 3.8 20.9 1.0 NE2 A:HIS180 4.0 23.5 1.0 C2 A:L8G404 4.0 34.0 1.0 N A:LEU179 4.1 22.6 1.0 CA A:GLY304 4.2 26.4 1.0 CD2 A:HIS180 4.2 23.4 1.0 CB A:ASP178 4.3 21.2 1.0 CB A:LEU179 4.4 23.6 1.0 CA A:HIS180 4.4 25.2 1.0 CB A:ASP267 4.4 21.6 1.0 NE2 A:HIS143 4.6 28.6 1.0 NE2 A:HIS142 4.6 34.6 1.0 CA A:LEU179 4.6 20.2 1.0 C A:LEU179 4.6 27.1 1.0 N A:GLY304 4.7 22.1 1.0 CE1 A:TYR306 4.7 26.7 1.0 OH A:TYR306 4.7 37.2 1.0 C A:ASP178 4.9 24.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of S39D HDAC8 in Complex with A Largazole Analogue.


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 S39D HDAC8 in Complex with A Largazole Analogue. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:26.9 occ:1.00 OD2 B:ASP178 2.0 19.8 1.0 OD2 B:ASP267 2.0 24.2 1.0 ND1 B:HIS180 2.1 27.0 1.0 S1 B:L8G404 2.4 27.6 1.0 CE1 B:HIS180 2.9 33.5 1.0 CG B:ASP178 2.9 29.0 1.0 CG B:ASP267 3.1 29.8 1.0 OD1 B:ASP178 3.1 25.5 1.0 C1 B:L8G404 3.1 26.2 1.0 CG B:HIS180 3.2 31.5 1.0 OD1 B:ASP267 3.5 27.9 1.0 CB B:HIS180 3.7 25.0 1.0 N B:HIS180 3.8 20.4 1.0 NE2 B:HIS180 4.1 31.4 1.0 C2 B:L8G404 4.1 30.5 1.0 N B:LEU179 4.2 26.1 1.0 CA B:GLY304 4.2 30.1 1.0 CD2 B:HIS180 4.3 25.9 1.0 CB B:ASP178 4.3 25.0 1.0 CB B:ASP267 4.4 22.6 1.0 NE2 B:HIS143 4.4 34.3 1.0 CA B:HIS180 4.4 27.6 1.0 CB B:LEU179 4.5 18.6 1.0 NE2 B:HIS142 4.6 26.6 1.0 C B:LEU179 4.7 32.0 1.0 CA B:LEU179 4.7 28.6 1.0 OH B:TYR306 4.7 34.6 1.0 N B:GLY304 4.7 27.4 1.0 CE1 B:TYR306 4.8 25.4 1.0 C B:ASP178 4.9 28.6 1.0

C.Decroos, D.J.Clausen, B.E.Haines, O.Wiest, R.M.Williams, D.W.Christianson. Variable Active Site Loop Conformations Accommodate the Binding of Macrocyclic Largazole Analogues to HDAC8. Biochemistry 2015.
ISSN: ISSN 0006-2960
PubMed: 25793284
DOI: 10.1021/ACS.BIOCHEM.5B00010