Chlorine in PDB 6mr5: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor, PDB code: 6mr5 was solved by 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)	47.76 / 1.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	159.010, 46.460, 96.400, 90.00, 119.19, 90.00
R / Rfree (%)	19 / 22.6

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor also contains other interesting chemical elements:

Potassium	(K)	4 atoms
Zinc	(Zn)	2 atoms

The binding sites of Chlorine atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor (pdb code 6mr5). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor, PDB code: 6mr5:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor


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 Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl804 b:47.4 occ:1.00 CL2 A:W45804 0.0 47.4 1.0 C16 A:W45804 1.7 29.3 1.0 O A:HOH982 2.6 26.0 1.0 C15 A:W45804 2.7 27.8 1.0 C18 A:W45804 2.7 34.6 1.0 CL1 A:W45804 3.1 47.1 1.0 CD A:PRO464 3.5 29.5 1.0 O B:HOH1044 3.7 25.1 1.0 CG A:PRO464 3.9 25.0 1.0 C14 A:W45804 3.9 28.7 1.0 C20 A:W45804 4.0 32.3 1.0 CD1 B:PHE642 4.2 22.7 1.0 O B:ALA641 4.2 24.1 1.0 C21 A:W45804 4.4 26.4 1.0 CE1 B:PHE642 4.5 21.9 1.0 CA B:PHE642 4.8 22.7 1.0 N A:PRO464 4.8 26.9 1.0 C B:ALA641 4.9 26.2 1.0 CB A:PRO464 4.9 25.9 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor


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 Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl804 b:47.1 occ:1.00 CL1 A:W45804 0.0 47.1 1.0 C18 A:W45804 1.7 34.6 1.0 O A:HOH982 2.4 26.0 1.0 C20 A:W45804 2.7 32.3 1.0 C16 A:W45804 2.7 29.3 1.0 CL2 A:W45804 3.1 47.4 1.0 CD2 A:HIS463 3.7 30.5 1.0 NE2 A:HIS463 3.9 30.4 1.0 C21 A:W45804 3.9 26.4 1.0 O A:HOH1001 4.0 28.0 1.0 C15 A:W45804 4.0 27.8 1.0 CE1 B:PHE642 4.2 21.9 1.0 O B:HOH1051 4.2 34.2 1.0 O B:HOH1073 4.2 35.5 1.0 CD A:PRO464 4.3 29.5 1.0 C14 A:W45804 4.5 28.7 1.0 CG A:HIS463 4.6 27.9 1.0 CD1 B:PHE642 4.6 22.7 1.0 NH2 B:ARG636 4.6 26.2 1.0 NH1 B:ARG636 4.7 21.5 1.0 OD2 A:ASP460 4.7 34.2 1.0 CE1 A:HIS463 4.8 31.1 1.0 CZ B:ARG636 4.8 23.4 1.0 CG A:PRO464 5.0 25.0 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor


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 Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl804 b:57.6 occ:1.00 CL2 B:W45804 0.0 57.6 1.0 C16 B:W45804 1.7 46.2 1.0 C15 B:W45804 2.7 41.4 1.0 C18 B:W45804 2.7 44.4 1.0 CL1 B:W45804 3.1 60.8 1.0 OG A:SER461 3.9 43.9 1.0 C14 B:W45804 3.9 44.8 1.0 O A:TRP459 4.0 39.4 1.0 CG B:PRO464 4.0 24.4 1.0 C20 B:W45804 4.0 41.3 1.0 CD B:PRO464 4.0 22.1 1.0 N A:SER461 4.1 36.3 1.0 O A:HOH933 4.3 37.1 1.0 CD1 B:LEU712 4.3 31.2 1.0 CD2 A:HIS462 4.4 43.4 1.0 C21 B:W45804 4.5 44.7 1.0 CA A:ASP460 4.6 36.8 1.0 CB A:SER461 4.7 40.0 1.0 OD1 A:ASP460 4.7 32.9 1.0 C A:ASP460 4.8 40.7 1.0 CA A:SER461 4.9 38.2 1.0 C A:TRP459 5.0 39.1 1.0 NE2 A:HIS462 5.0 43.1 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor


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 Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl804 b:60.8 occ:1.00 CL1 B:W45804 0.0 60.8 1.0 C18 B:W45804 1.7 44.4 1.0 C20 B:W45804 2.7 41.3 1.0 C16 B:W45804 2.7 46.2 1.0 O A:HOH1007 2.9 44.0 1.0 CL2 B:W45804 3.1 57.6 1.0 NE2 B:HIS463 3.7 28.4 1.0 CD2 B:HIS463 3.8 30.7 1.0 NE2 A:HIS462 3.9 43.1 1.0 C21 B:W45804 3.9 44.7 1.0 C15 B:W45804 4.0 41.4 1.0 CD B:PRO464 4.1 22.1 1.0 CD2 A:HIS462 4.1 43.4 1.0 CG B:PRO464 4.4 24.4 1.0 CE1 B:HIS463 4.4 24.0 1.0 C14 B:W45804 4.5 44.8 1.0 CZ B:PHE583 4.6 27.8 1.0 CG B:HIS463 4.6 24.3 1.0 CE1 A:HIS462 4.7 43.4 1.0 CE1 B:PHE583 4.9 24.1 1.0 ND1 B:HIS463 4.9 23.4 1.0

N.J.Porter, S.Shen, C.Barinka, A.P.Kozikowski, D.W.Christianson. Molecular Basis For the Selective Inhibition of Histone Deacetylase 6 By A Mercaptoacetamide Inhibitor. Acs Med Chem Lett V. 9 1301 2018.
ISSN: ISSN 1948-5875
PubMed: 30613344
DOI: 10.1021/ACSMEDCHEMLETT.8B00487