Chlorine in PDB 6csp: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclohexenylhydroxamate

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclohexenylhydroxamate, PDB code: 6csp 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)	48.28 / 1.24
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.700, 91.830, 96.549, 90.00, 90.00, 90.00
R / Rfree (%)	12.7 / 15.3

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclohexenylhydroxamate 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 Cyclohexenylhydroxamate (pdb code 6csp). 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 Cyclohexenylhydroxamate, PDB code: 6csp:
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 Cyclohexenylhydroxamate


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 Cyclohexenylhydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl804 b:13.2 occ:1.00 HE2 A:HIS614 2.3 7.8 1.0 O A:HOH1124 3.1 10.8 1.0 H11 A:FBM807 3.2 12.7 1.0 NE2 A:HIS614 3.2 6.5 1.0 O A:HOH1026 3.2 10.8 1.0 HB3 A:PHE643 3.5 8.4 1.0 HB3 A:LEU712 3.5 8.9 1.0 HB2 A:PHE643 3.7 8.4 1.0 HZ A:PHE642 3.7 10.7 1.0 H9 A:FBM807 3.8 12.2 1.0 H1 A:FBM807 3.8 12.1 1.0 CZ A:PHE642 3.8 8.9 1.0 H21 A:EDO811 3.8 38.2 0.9 HD22 A:LEU712 3.9 13.8 1.0 C09 A:FBM807 4.0 10.6 1.0 HD13 A:LEU712 4.0 13.2 1.0 CB A:PHE643 4.0 7.0 1.0 CD2 A:HIS614 4.1 5.7 1.0 CE2 A:PHE642 4.1 8.5 1.0 HD2 A:HIS614 4.1 6.8 1.0 CE1 A:HIS614 4.1 5.1 1.0 HE2 A:PHE642 4.1 10.2 1.0 H A:PHE643 4.2 9.1 1.0 HE1 A:HIS614 4.2 6.1 1.0 C08 A:FBM807 4.3 10.2 1.0 CE1 A:PHE642 4.4 9.4 1.0 C10 A:FBM807 4.4 10.1 1.0 CB A:LEU712 4.4 7.4 1.0 HE1 A:PHE642 4.6 11.3 1.0 H8 A:FBM807 4.6 12.2 1.0 H10 A:FBM807 4.7 12.7 1.0 O A:LEU712 4.7 8.0 1.0 CD2 A:LEU712 4.8 11.5 1.0 CD2 A:PHE642 4.8 7.5 1.0 C2 A:EDO811 4.8 31.8 0.9 CD1 A:LEU712 4.9 11.0 1.0 HB2 A:LEU712 4.9 8.9 1.0 H22 A:EDO811 4.9 38.2 0.9 N A:PHE643 4.9 7.6 1.0 CG A:LEU712 4.9 9.0 1.0 CG A:PHE643 4.9 7.6 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 Cyclohexenylhydroxamate


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 Cyclohexenylhydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl805 b:13.2 occ:1.00 HE2 B:HIS614 2.3 7.9 1.0 HZ2 A:LYS658 2.4 23.3 1.0 HD3 A:LYS658 2.9 19.9 1.0 H10 B:FBM805 3.1 11.5 1.0 O B:HOH1126 3.1 11.2 1.0 NE2 B:HIS614 3.1 6.6 1.0 O B:HOH1010 3.2 12.3 1.0 NZ A:LYS658 3.3 19.4 1.0 HB3 B:PHE643 3.5 8.5 1.0 HB3 B:LEU712 3.5 9.3 1.0 HB2 B:PHE643 3.7 8.5 1.0 HZ B:PHE642 3.7 11.2 1.0 HZ1 A:LYS658 3.7 23.3 1.0 CD A:LYS658 3.7 16.6 1.0 H9 B:FBM805 3.8 11.7 1.0 HE2 A:LYS658 3.8 22.1 1.0 CZ B:PHE642 3.8 9.3 1.0 HZ3 A:LYS658 3.8 23.3 1.0 H1 B:FBM805 3.8 11.6 1.0 CE A:LYS658 3.8 18.4 1.0 C09 B:FBM805 3.9 9.6 1.0 HD22 B:LEU712 4.0 14.3 1.0 CD2 B:HIS614 4.0 5.7 1.0 CE2 B:PHE642 4.0 8.5 1.0 HD2 B:HIS614 4.0 6.8 1.0 CB B:PHE643 4.0 7.1 1.0 HE2 B:PHE642 4.1 10.2 1.0 HD13 B:LEU712 4.1 12.4 1.0 HD2 A:LYS658 4.1 19.9 1.0 CE1 B:HIS614 4.1 6.3 1.0 H B:PHE643 4.2 8.7 1.0 HE1 B:HIS614 4.2 7.5 1.0 C08 B:FBM805 4.3 9.7 1.0 CE1 B:PHE642 4.4 9.6 1.0 C10 B:FBM805 4.4 9.7 1.0 CB B:LEU712 4.5 7.7 1.0 H8 B:FBM805 4.6 11.7 1.0 H11 B:FBM805 4.6 11.5 1.0 HE1 B:PHE642 4.6 11.5 1.0 O B:LEU712 4.7 8.6 1.0 CD2 B:PHE642 4.8 8.6 1.0 HE3 A:LYS658 4.8 22.1 1.0 CD2 B:LEU712 4.8 11.9 1.0 HB2 A:LYS658 4.8 13.7 1.0 N B:PHE643 4.9 7.3 1.0 CD1 B:LEU712 4.9 10.3 1.0 HG2 A:LYS658 4.9 18.0 1.0 CG A:LYS658 5.0 15.0 1.0 HB2 B:LEU712 5.0 9.3 1.0 CG B:PHE643 5.0 6.6 1.0 CG B:LEU712 5.0 9.6 1.0 H2 B:FBM805 5.0 11.6 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 Cyclohexenylhydroxamate


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 Cyclohexenylhydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl806 b:22.9 occ:1.00 O A:HOH1252 2.8 18.4 1.0 O A:HOH1179 4.7 18.2 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 Cyclohexenylhydroxamate


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 Cyclohexenylhydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl804 b:24.3 occ:0.80 H B:ARG488 2.0 7.9 1.0 N B:ARG488 2.8 6.6 1.0 HB3 B:ARG488 2.9 9.4 1.0 HA B:HIS487 3.1 8.4 1.0 HB2 B:ARG488 3.2 9.4 1.0 CB B:ARG488 3.4 7.9 1.0 ND1 B:HIS487 3.6 12.3 1.0 CA B:ARG488 3.6 6.9 1.0 C B:HIS487 3.8 6.5 1.0 CA B:HIS487 3.8 7.0 1.0 CE1 B:HIS487 4.0 14.2 1.0 HE1 B:HIS487 4.1 17.1 1.0 O B:ARG488 4.2 10.7 1.0 O B:HOH1024 4.2 39.9 1.0 O B:CYS486 4.2 11.1 1.0 CG B:HIS487 4.2 10.2 1.0 C B:ARG488 4.4 7.9 1.0 HA B:ARG488 4.4 8.3 1.0 CB B:HIS487 4.6 8.3 1.0 NE2 B:HIS487 4.8 14.9 1.0 CG B:ARG488 4.8 8.8 1.0 CD2 B:HIS487 4.9 12.9 1.0 N B:HIS487 4.9 7.3 1.0 HB2 B:HIS487 4.9 10.0 1.0 HG2 B:ARG488 5.0 10.6 1.0 O B:HIS487 5.0 8.4 1.0 O B:HOH1190 5.0 14.6 1.0

N.J.Porter, F.F.Wagner, D.W.Christianson. Entropy As A Driver of Selectivity For Inhibitor Binding to Histone Deacetylase 6. Biochemistry V. 57 3916 2018.
ISSN: ISSN 1520-4995
PubMed: 29775292
DOI: 10.1021/ACS.BIOCHEM.8B00367