Zinc in PDB 4rn0: 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: 4rn0 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)	42.91 / 1.76
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.921, 85.006, 94.665, 90.00, 100.33, 90.00
R / Rfree (%)	13.7 / 16.2

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 4rn0). 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: 4rn0:
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:Zn502 b:12.2 occ:1.00 OD2 A:ASP178 2.0 9.6 1.0 OD2 A:ASP267 2.0 10.8 1.0 ND1 A:HIS180 2.1 10.8 1.0 S1 A:L6G501 2.3 13.3 1.0 CG A:ASP178 2.8 11.0 1.0 CE1 A:HIS180 2.9 13.3 1.0 CG A:ASP267 3.0 12.7 1.0 OD1 A:ASP178 3.0 10.7 1.0 C1 A:L6G501 3.1 11.4 1.0 CG A:HIS180 3.2 9.7 1.0 OD1 A:ASP267 3.3 10.2 1.0 CB A:HIS180 3.7 8.9 1.0 N A:HIS180 3.8 9.7 1.0 C2 A:L6G501 3.8 15.3 1.0 NE2 A:HIS180 4.1 12.5 1.0 CA A:GLY304 4.2 10.9 1.0 NE2 A:HIS142 4.3 15.2 1.0 CD2 A:HIS180 4.3 12.3 1.0 N A:LEU179 4.3 8.6 1.0 CB A:ASP178 4.3 9.3 1.0 CB A:ASP267 4.3 8.2 1.0 CA A:HIS180 4.4 9.3 1.0 CB A:LEU179 4.4 11.2 1.0 NE2 A:HIS143 4.5 13.3 1.0 CE1 A:TYR306 4.6 11.6 1.0 N A:GLY304 4.6 10.8 1.0 CE1 A:HIS142 4.7 12.4 1.0 CA A:LEU179 4.7 10.6 1.0 C A:LEU179 4.7 11.2 1.0 OH A:TYR306 4.7 15.5 1.0 C3 A:L6G501 4.9 16.9 1.0 C A:ASP178 4.9 8.8 1.0 O A:HOH966 4.9 29.9 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:Zn502 b:12.5 occ:1.00 OD2 B:ASP267 2.0 10.5 1.0 OD2 B:ASP178 2.0 11.2 1.0 ND1 B:HIS180 2.1 12.9 1.0 S1 B:L6G501 2.3 14.3 1.0 CG B:ASP178 2.9 12.1 1.0 CE1 B:HIS180 3.0 14.8 1.0 CG B:ASP267 3.0 11.0 1.0 OD1 B:ASP178 3.1 11.0 1.0 CG B:HIS180 3.2 12.0 1.0 C1 B:L6G501 3.2 14.0 1.0 OD1 B:ASP267 3.3 11.2 1.0 CB B:HIS180 3.7 12.3 1.0 N B:HIS180 3.8 10.2 1.0 C2 B:L6G501 4.0 15.9 1.0 NE2 B:HIS180 4.1 13.1 1.0 CA B:GLY304 4.2 10.0 1.0 N B:LEU179 4.3 8.8 1.0 CB B:ASP178 4.3 10.2 1.0 NE2 B:HIS142 4.3 16.7 1.0 CD2 B:HIS180 4.3 12.1 1.0 CB B:ASP267 4.4 11.1 1.0 CA B:HIS180 4.4 11.0 1.0 CB B:LEU179 4.4 10.2 1.0 NE2 B:HIS143 4.5 14.9 1.0 CE1 B:TYR306 4.6 11.0 1.0 N B:GLY304 4.6 9.3 1.0 CE1 B:HIS142 4.7 14.0 1.0 OH B:TYR306 4.7 13.7 1.0 CA B:LEU179 4.7 10.3 1.0 C B:LEU179 4.7 11.5 1.0 O B:HOH910 4.8 24.6 1.0 C B:ASP178 4.9 11.8 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