Sodium in PDB 5g0g: Crystal Structure of Danio Rerio HDAC6 CD1 in Complex with Trichostatin A

The structure of Crystal Structure of Danio Rerio HDAC6 CD1 in Complex with Trichostatin A, PDB code: 5g0g was solved by Y.Miyake, J.J.Keusch, L.Wang, M.Saito, D.Hess, X.Wang, B.J.Melancon, P.Helquist, H.Gut, P.Matthias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.505 / 1.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	68.470, 93.010, 118.470, 90.00, 90.00, 90.00
R / Rfree (%)	13.89 / 16.96

The structure of Crystal Structure of Danio Rerio HDAC6 CD1 in Complex with Trichostatin A also contains other interesting chemical elements:

Chlorine	(Cl)	5 atoms
Zinc	(Zn)	1 atom

The binding sites of Sodium atom in the Crystal Structure of Danio Rerio HDAC6 CD1 in Complex with Trichostatin A (pdb code 5g0g). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Danio Rerio HDAC6 CD1 in Complex with Trichostatin A, PDB code: 5g0g:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Danio Rerio HDAC6 CD1 in Complex with Trichostatin A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Danio Rerio HDAC6 CD1 in Complex with Trichostatin A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1420 b:22.4 occ:1.00 O A:ASP244 2.3 26.7 1.0 O A:HOH2150 2.3 21.8 1.0 O A:VAL247 2.3 23.4 1.0 O A:HOH2149 2.3 24.2 1.0 O A:PHE241 2.5 22.5 1.0 C A:ASP244 3.4 27.0 1.0 C A:VAL247 3.6 21.6 1.0 C A:PHE241 3.6 22.2 1.0 CB A:TYR280 3.6 21.6 1.0 O A:TYR280 3.6 19.3 1.0 CB A:PHE241 3.7 21.6 1.0 N A:ASP244 4.0 27.6 1.0 CA A:ASP244 4.1 26.8 1.0 CB A:ASP244 4.1 28.4 1.0 C A:TYR280 4.2 20.6 1.0 CA A:PHE241 4.2 22.0 1.0 O A:HOH2143 4.3 23.6 1.0 CA A:VAL247 4.4 20.4 1.0 N A:VAL247 4.4 19.5 1.0 N A:PRO245 4.4 28.0 1.0 CB A:VAL247 4.5 23.0 1.0 CA A:TYR280 4.5 20.8 1.0 N A:LEU248 4.5 20.5 0.5 N A:LEU248 4.5 20.1 0.5 CA A:PRO245 4.6 28.1 1.0 O A:GLU242 4.6 26.9 1.0 CA A:LEU248 4.6 19.1 0.5 N A:GLU242 4.7 24.0 1.0 CA A:LEU248 4.7 18.4 0.5 O A:GLY277 4.7 26.5 1.0 C A:GLU242 4.7 26.7 1.0 CG A:TYR280 4.7 21.3 1.0 CA A:GLY277 4.9 30.4 1.0 CG A:PHE241 4.9 20.9 1.0 CA A:GLU242 4.9 27.1 1.0 N A:TYR249 5.0 19.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Danio Rerio HDAC6 CD1 in Complex with Trichostatin A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Danio Rerio HDAC6 CD1 in Complex with Trichostatin A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1421 b:19.6 occ:1.00 O A:ASP230 2.3 20.2 1.0 OD1 A:ASP228 2.5 18.8 1.0 O A:VAL252 2.6 19.6 1.0 O A:HIS232 2.6 19.6 1.0 OG A:SER251 2.6 18.8 1.0 O A:ASP228 2.7 18.8 1.0 CG A:ASP228 3.2 17.9 1.0 C A:ASP230 3.4 18.5 1.0 C A:ASP228 3.4 17.3 1.0 C A:VAL252 3.6 17.6 1.0 C A:HIS232 3.7 19.9 1.0 CB A:ASP228 3.7 17.7 1.0 N A:ASP230 3.7 17.9 1.0 N A:VAL252 3.8 16.7 1.0 CB A:SER251 3.8 18.2 1.0 OD2 A:ASP228 3.9 21.3 1.0 CB A:HIS253 4.0 19.3 1.0 CA A:ASP230 4.0 18.9 1.0 C A:TRP229 4.1 17.1 1.0 N A:TRP229 4.1 16.8 1.0 CA A:ASP228 4.2 17.0 1.0 CA A:SER251 4.2 17.4 1.0 CA A:TRP229 4.2 16.8 1.0 N A:HIS232 4.3 20.1 1.0 CB A:ASP230 4.3 19.1 1.0 ND1 A:HIS253 4.3 19.7 1.0 C A:SER251 4.4 17.8 1.0 CA A:VAL252 4.4 17.0 1.0 CA A:HIS253 4.4 19.2 1.0 N A:HIS253 4.4 19.3 1.0 O A:HOH2139 4.4 21.3 1.0 N A:HIS233 4.5 20.6 1.0 CA A:HIS233 4.5 18.8 1.0 N A:VAL231 4.5 18.8 1.0 C A:VAL231 4.6 20.3 1.0 CA A:HIS232 4.6 20.5 1.0 CG A:HIS253 4.6 18.6 1.0 O A:TRP229 4.7 19.1 1.0 N A:GLY234 4.8 18.9 1.0 CA A:VAL231 4.8 19.1 1.0 CE1 A:HIS192 4.9 19.2 1.0 CG1 A:VAL252 5.0 19.8 1.0 OD1 A:ASP230 5.0 20.7 1.0

Y.Miyake, J.J.Keusch, L.Wang, M.Saito, D.Hess, X.Wang, B.J.Melancon, P.Helquist, H.Gut, P.Matthias. Structural Insights Into HDAC6 Tubulin Deacetylation and Its Selective Inhibition Nat.Chem.Biol. V. 12 748 2016.
ISSN: ISSN 1552-4450
PubMed: 27454931
DOI: 10.1038/NCHEMBIO.2140