Chlorine 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:

Zinc	(Zn)	1 atom
Sodium	(Na)	2 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Danio Rerio HDAC6 CD1 in Complex with Trichostatin A, PDB code: 5g0g:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Crystal Structure of Danio Rerio HDAC6 CD1 in Complex with Trichostatin A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl1422 b:37.1 occ:1.00 NE1 A:TRP78 3.1 41.9 1.0 O A:HOH2017 3.1 33.0 1.0 O A:HOH2081 3.3 45.7 1.0 O A:HOH2018 3.3 45.1 1.0 N A:LEU153 3.3 31.3 1.0 CD1 A:TRP78 3.6 42.5 1.0 CA A:LYS142 3.7 43.5 1.0 CB A:ALA145 3.7 33.8 1.0 CA A:TYR152 3.7 29.0 1.0 CB A:TYR152 3.9 29.3 1.0 O A:LEU153 3.9 36.9 1.0 C A:TYR152 4.1 28.0 1.0 O A:LEU141 4.1 39.1 1.0 N A:LYS142 4.2 42.0 1.0 CB A:LYS142 4.2 46.3 1.0 CA A:LEU153 4.3 32.8 1.0 CE2 A:TRP78 4.3 43.6 1.0 C A:LEU141 4.3 40.9 1.0 CG A:LYS142 4.4 50.2 1.0 C A:LEU153 4.5 35.6 1.0 CB A:LEU153 4.5 34.0 1.0 C A:LYS142 4.8 42.5 1.0 O A:VAL151 4.9 30.5 1.0 O A:LYS142 4.9 41.8 1.0 CG A:TRP78 4.9 42.5 1.0 CZ2 A:TRP78 5.0 44.1 1.0

Chlorine binding site 2 out of 5 in the Crystal Structure of Danio Rerio HDAC6 CD1 in Complex with Trichostatin A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl1423 b:32.4 occ:1.00 O A:HOH2215 2.9 26.5 1.0 O A:HOH2116 3.1 23.5 1.0 NH1 A:ARG181 3.2 35.0 1.0 O A:HOH2217 3.5 44.6 1.0 CD A:ARG181 3.6 33.3 1.0 CG A:ARG181 3.9 29.3 1.0 CD A:LYS348 4.0 29.4 1.0 CZ A:ARG181 4.2 36.1 1.0 CB A:LYS348 4.2 21.8 1.0 CA A:GLY353 4.2 20.8 1.0 NE A:ARG181 4.3 33.6 1.0 CE A:LYS348 4.5 30.4 1.0 CG A:LYS348 4.5 23.4 1.0 NZ A:LYS348 4.6 27.7 1.0 O A:LYS348 4.7 23.3 1.0 O A:GLY353 4.9 20.3 1.0

Chlorine binding site 3 out of 5 in the Crystal Structure of Danio Rerio HDAC6 CD1 in Complex with Trichostatin A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 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:Cl1424 b:57.6 occ:1.00 OG A:SER293 2.8 28.0 0.7 OG A:SER293 3.0 24.8 0.3 OG A:SER336 3.1 33.4 1.0 O A:HOH2194 3.3 29.8 1.0 C A:SER389 3.4 70.8 1.0 N A:SER389 3.5 69.0 1.0 CB A:SER293 3.5 24.2 0.3 CB A:SER293 3.6 25.0 0.7 N A:SER390 3.6 67.5 1.0 CB A:SER336 3.6 27.7 1.0 O A:SER389 3.7 72.9 1.0 CD A:PRO388 3.7 57.8 1.0 CB A:LEU387 3.8 41.4 1.0 CA A:SER389 3.8 71.5 1.0 N A:PRO388 3.9 56.3 1.0 CG A:PRO388 4.0 59.0 1.0 CB A:SER389 4.1 73.7 1.0 CA A:SER390 4.1 65.4 1.0 C A:LEU387 4.1 48.9 1.0 CD1 A:LEU387 4.2 44.7 1.0 C A:PRO388 4.2 65.0 1.0 CD2 A:LEU387 4.3 42.4 1.0 CA A:LEU387 4.3 42.4 1.0 CG A:LEU387 4.3 42.9 1.0 CA A:PRO388 4.5 60.6 1.0 CB A:SER390 4.7 69.0 1.0 N A:SER336 4.8 24.4 1.0 O A:LEU387 4.8 47.6 1.0 CA A:SER336 4.8 24.6 1.0 CA A:SER293 4.8 23.8 0.3 CA A:SER293 4.9 23.6 0.7 CB A:PRO388 4.9 59.7 1.0 N A:SER293 4.9 24.7 0.3 N A:SER293 4.9 24.9 0.7

Chlorine binding site 4 out of 5 in the Crystal Structure of Danio Rerio HDAC6 CD1 in Complex with Trichostatin A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 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:Cl1425 b:92.5 occ:1.00 NZ A:LYS174 2.9 44.3 1.0 NE2 A:GLN179 2.9 30.0 1.0 O A:HOH2061 3.2 53.5 1.0 O A:HOH2104 3.7 41.0 1.0 CD A:GLN179 3.8 30.1 1.0 CE A:LYS174 3.8 39.8 1.0 OE1 A:GLN179 3.8 32.4 1.0 CD A:LYS174 3.9 35.8 1.0 CB A:ASP173 4.7 25.1 1.0 OG1 A:THR177 5.0 28.6 1.0

Chlorine binding site 5 out of 5 in the Crystal Structure of Danio Rerio HDAC6 CD1 in Complex with Trichostatin A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 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:Cl1426 b:72.3 occ:1.00 N A:GLU395 3.1 26.9 1.0 CG A:GLU395 3.4 50.2 1.0 O A:HOH2187 3.4 26.9 1.0 CB A:CYS394 3.6 27.1 1.0 CA A:CYS394 3.7 26.8 1.0 O A:HOH2241 3.8 59.2 1.0 CB A:GLU395 3.8 39.1 1.0 C A:CYS394 3.9 26.2 1.0 CA A:GLU395 4.0 31.1 1.0 CD A:GLU395 4.5 61.3 1.0 OE2 A:GLU395 4.6 64.2 1.0 O A:HOH2240 4.9 52.5 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