Zinc in PDB 6j6t: Crystal Structure of HDA15 Hd Domain

All present enzymatic activity of Crystal Structure of HDA15 Hd Domain:
3.5.1.98;

The structure of Crystal Structure of HDA15 Hd Domain, PDB code: 6j6t was solved by Y.S.Cheng, J.C.Hsu, H.C.Hung, T.C.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.52 / 2.36
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.809, 78.833, 176.794, 90.00, 94.22, 90.00
R / Rfree (%)	16.7 / 21.8

The structure of Crystal Structure of HDA15 Hd Domain also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of HDA15 Hd Domain (pdb code 6j6t). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of HDA15 Hd Domain, PDB code: 6j6t:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of HDA15 Hd Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of HDA15 Hd Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:36.6 occ:1.00 OD1 A:ASP313 2.2 15.8 1.0 ND1 A:HIS315 2.2 13.6 1.0 OD2 A:ASP404 2.2 16.1 1.0 OD2 A:ASP313 2.7 15.1 1.0 CG A:ASP313 2.8 14.0 1.0 CE1 A:HIS315 3.0 10.8 1.0 CG A:ASP404 3.2 15.5 1.0 CG A:HIS315 3.3 13.8 1.0 OD1 A:ASP404 3.6 15.9 1.0 CB A:HIS315 3.7 11.0 1.0 N A:HIS315 4.1 12.7 1.0 NE2 A:HIS276 4.1 15.9 1.0 CA A:GLY442 4.2 16.4 1.0 NE2 A:HIS315 4.2 14.3 1.0 OH A:TYR444 4.2 14.7 1.0 CB A:ASP313 4.3 11.6 1.0 CD2 A:HIS315 4.3 14.8 1.0 CG1 A:VAL314 4.4 11.2 1.0 CA A:HIS315 4.5 13.1 1.0 CB A:ASP404 4.5 13.1 1.0 N A:GLY442 4.5 17.0 1.0 CE2 A:TYR444 4.6 15.1 1.0 CE1 A:HIS276 4.6 13.8 1.0 N A:VAL314 4.6 13.1 1.0 NE2 A:HIS277 4.7 21.9 1.0 CZ A:TYR444 4.9 15.7 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of HDA15 Hd Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of HDA15 Hd Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:36.6 occ:1.00 OD2 B:ASP404 2.1 18.9 1.0 OD1 B:ASP313 2.1 16.3 1.0 ND1 B:HIS315 2.3 10.6 1.0 OD2 B:ASP313 2.7 13.1 1.0 CG B:ASP313 2.8 14.5 1.0 CG B:ASP404 3.2 14.3 1.0 CE1 B:HIS315 3.2 15.1 1.0 CG B:HIS315 3.3 14.5 1.0 OD1 B:ASP404 3.6 12.0 1.0 CB B:HIS315 3.7 10.5 1.0 N B:HIS315 4.1 13.5 1.0 NE2 B:HIS276 4.2 16.4 1.0 CA B:GLY442 4.2 16.2 1.0 CB B:ASP313 4.2 12.8 1.0 NE2 B:HIS315 4.4 17.3 1.0 CB B:ASP404 4.4 16.0 1.0 CD2 B:HIS315 4.4 12.1 1.0 OH B:TYR444 4.5 15.4 1.0 CG1 B:VAL314 4.5 10.5 1.0 CA B:HIS315 4.6 14.1 1.0 CE2 B:TYR444 4.6 16.1 1.0 N B:GLY442 4.6 19.3 1.0 N B:VAL314 4.6 12.9 1.0 CE1 B:HIS276 4.6 20.1 1.0 NE2 B:HIS277 4.7 18.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of HDA15 Hd Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of HDA15 Hd Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn601 b:45.2 occ:1.00 OD2 C:ASP404 2.1 37.7 1.0 OD1 C:ASP313 2.1 29.9 1.0 ND1 C:HIS315 2.1 25.4 1.0 OD2 C:ASP313 2.7 24.8 1.0 CG C:ASP313 2.7 28.3 1.0 CE1 C:HIS315 2.8 24.4 1.0 CG C:ASP404 3.2 34.5 1.0 CG C:HIS315 3.3 27.9 1.0 OD1 C:ASP404 3.6 35.7 1.0 NE2 C:HIS276 3.9 27.6 1.0 CB C:HIS315 3.9 26.7 1.0 NE2 C:HIS315 4.0 24.0 1.0 N C:HIS315 4.1 28.8 1.0 CB C:ASP313 4.2 29.8 1.0 CA C:GLY442 4.2 34.4 1.0 CE1 C:HIS276 4.2 32.5 1.0 OH C:TYR444 4.3 30.1 1.0 CD2 C:HIS315 4.3 23.1 1.0 CG1 C:VAL314 4.4 28.8 1.0 N C:VAL314 4.4 30.8 1.0 CB C:ASP404 4.4 39.6 1.0 N C:GLY442 4.6 30.4 1.0 CA C:HIS315 4.6 29.7 1.0 CE2 C:TYR444 4.6 35.3 1.0 NE2 C:HIS277 4.6 29.8 1.0 CZ C:TYR444 4.9 32.2 1.0 C C:ASP313 4.9 28.7 1.0 C C:VAL314 5.0 29.7 1.0 CA C:ASP313 5.0 31.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of HDA15 Hd Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of HDA15 Hd Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:36.4 occ:1.00 OD2 D:ASP404 2.0 19.0 1.0 OD1 D:ASP313 2.1 19.5 1.0 ND1 D:HIS315 2.2 15.3 1.0 OD2 D:ASP313 2.7 13.3 1.0 CG D:ASP313 2.8 17.8 1.0 CE1 D:HIS315 3.1 15.4 1.0 CG D:ASP404 3.1 20.8 1.0 CG D:HIS315 3.3 15.9 1.0 OD1 D:ASP404 3.7 18.6 1.0 CB D:HIS315 3.7 15.6 1.0 N D:HIS315 4.0 16.3 1.0 CA D:GLY442 4.2 17.6 1.0 NE2 D:HIS276 4.2 16.8 1.0 CB D:ASP313 4.2 16.3 1.0 NE2 D:HIS315 4.3 22.9 1.0 CB D:ASP404 4.3 18.7 1.0 OH D:TYR444 4.4 20.9 1.0 CD2 D:HIS315 4.4 20.0 1.0 CA D:HIS315 4.5 15.5 1.0 N D:VAL314 4.5 16.9 1.0 N D:GLY442 4.5 14.9 1.0 CG1 D:VAL314 4.6 13.9 1.0 CE2 D:TYR444 4.6 18.6 1.0 CE1 D:HIS276 4.7 17.9 1.0 NE2 D:HIS277 4.8 20.8 1.0 C D:VAL314 5.0 18.8 1.0

Y.S.Cheng, Y.S.Cheng, J.C.Hsu, H.C.Hung, T.C.Liu. N/A N/A.