Fluorine in PDB 5td7: Crystal Structure of Histone Deacetylase 10

The structure of Crystal Structure of Histone Deacetylase 10, PDB code: 5td7 was solved by Y.Hai, S.A.Shinsky, N.J.Porter, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.51 / 2.85
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	80.449, 80.449, 243.037, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 22.7

The structure of Crystal Structure of Histone Deacetylase 10 also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Zinc	(Zn)	1 atom

The binding sites of Fluorine atom in the Crystal Structure of Histone Deacetylase 10 (pdb code 5td7). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Histone Deacetylase 10, PDB code: 5td7:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Histone Deacetylase 10


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Histone Deacetylase 10 within 5.0Å range: probe atom residue distance (Å) B Occ A:F711 b:59.0 occ:1.00 F15 A:FKS711 0.0 59.0 1.0 C12 A:FKS711 1.4 60.2 1.0 F16 A:FKS711 2.2 60.0 1.0 F17 A:FKS711 2.2 78.2 1.0 C11 A:FKS711 2.5 58.5 1.0 O13 A:FKS711 2.7 50.3 1.0 O14 A:FKS711 2.9 50.5 1.0 N A:GLY305 3.0 59.1 1.0 CA A:GLY305 3.3 44.8 1.0 C A:GLU304 3.3 51.6 1.0 ZN A:ZN701 3.3 58.5 1.0 OD1 A:ASP174 3.3 46.8 1.0 NE2 A:HIS136 3.4 41.2 1.0 CB A:GLU304 3.6 41.9 1.0 CB A:PRO134 3.8 48.5 1.0 C10 A:FKS711 3.8 58.5 1.0 CA A:GLU304 3.9 44.2 1.0 O A:GLU304 3.9 48.7 1.0 CG A:ASP174 3.9 36.1 1.0 CD2 A:HIS136 4.0 52.8 1.0 OE1 A:GLU304 4.0 49.1 1.0 OD2 A:ASP174 4.0 43.0 1.0 CG A:PRO134 4.2 41.0 1.0 CE1 A:HIS136 4.3 41.6 1.0 NE2 A:HIS137 4.8 52.0 1.0 C A:GLY305 4.8 49.9 1.0 CG A:GLU304 4.8 52.0 1.0 OD2 A:ASP267 4.8 56.5 1.0 CD A:GLU304 4.8 55.4 1.0 CD2 A:HIS137 4.9 52.7 1.0 CZ A:PHE307 5.0 54.7 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Histone Deacetylase 10


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Histone Deacetylase 10 within 5.0Å range: probe atom residue distance (Å) B Occ A:F711 b:60.0 occ:1.00 F16 A:FKS711 0.0 60.0 1.0 C12 A:FKS711 1.3 60.2 1.0 F15 A:FKS711 2.2 59.0 1.0 F17 A:FKS711 2.2 78.2 1.0 C11 A:FKS711 2.5 58.5 1.0 O13 A:FKS711 2.8 50.3 1.0 C10 A:FKS711 2.9 58.5 1.0 CB A:PRO134 3.3 48.5 1.0 O A:GLY145 3.4 52.5 1.0 CD2 A:HIS137 3.4 52.7 1.0 SG A:CYS147 3.4 46.2 1.0 CG A:PRO134 3.6 41.0 1.0 NE2 A:HIS136 3.7 41.2 1.0 O14 A:FKS711 3.7 50.5 1.0 CD2 A:HIS136 3.8 52.8 1.0 NE2 A:HIS137 3.8 52.0 1.0 C9 A:FKS711 4.4 46.6 1.0 CG A:HIS137 4.4 45.1 1.0 OE1 A:GLU304 4.4 49.1 1.0 C A:GLY145 4.5 56.0 1.0 ZN A:ZN701 4.6 58.5 1.0 CB A:PHE146 4.7 46.0 1.0 CD A:PRO134 4.7 43.4 1.0 CA A:PRO134 4.7 46.6 1.0 CD2 A:PHE146 4.8 45.6 1.0 CE1 A:HIS137 4.9 48.5 1.0 N A:GLY135 4.9 54.2 1.0 CE1 A:HIS136 4.9 41.6 1.0 N A:GLY305 5.0 59.1 1.0 C A:GLU304 5.0 51.6 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Histone Deacetylase 10


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Histone Deacetylase 10 within 5.0Å range: probe atom residue distance (Å) B Occ A:F711 b:78.2 occ:1.00 F17 A:FKS711 0.0 78.2 1.0 C12 A:FKS711 1.3 60.2 1.0 F16 A:FKS711 2.2 60.0 1.0 F15 A:FKS711 2.2 59.0 1.0 C11 A:FKS711 2.5 58.5 1.0 O14 A:FKS711 2.9 50.5 1.0 C10 A:FKS711 3.1 58.5 1.0 CG A:PRO134 3.2 41.0 1.0 O13 A:FKS711 3.6 50.3 1.0 CZ A:PHE307 3.6 54.7 1.0 CB A:PRO134 3.6 48.5 1.0 CA A:GLY305 3.7 44.8 1.0 CD2 A:PHE146 3.8 45.6 1.0 N A:GLY305 4.0 59.1 1.0 O A:GLU304 4.0 48.7 1.0 C A:GLU304 4.1 51.6 1.0 CE1 A:PHE307 4.3 59.7 1.0 CB A:PHE146 4.4 46.0 1.0 ZN A:ZN701 4.4 58.5 1.0 CD A:PRO134 4.5 43.4 1.0 O A:GLY145 4.5 52.5 1.0 C9 A:FKS711 4.5 46.6 1.0 CE2 A:PHE307 4.5 52.6 1.0 CG A:PHE146 4.6 49.7 1.0 CE2 A:PHE146 4.7 46.1 1.0 NH2 A:ARG32 4.9 42.6 1.0

Y.Hai, S.A.Shinsky, N.J.Porter, D.W.Christianson. Histone Deacetylase 10 Structure and Molecular Function As A Polyamine Deacetylase. Nat Commun V. 8 15368 2017.
ISSN: ESSN 2041-1723
PubMed: 28516954
DOI: 10.1038/NCOMMS15368