Zinc in PDB 1j8f: Human SIRT2 Histone Deacetylase

The structure of Human SIRT2 Histone Deacetylase, PDB code: 1j8f was solved by N.P.Pavletich, M.S.Finnin, J.R.Donigian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 1.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	78.943, 119.070, 218.220, 90.00, 90.00, 90.00
R / Rfree (%)	23.5 / 26

The binding sites of Zinc atom in the Human SIRT2 Histone Deacetylase (pdb code 1j8f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Human SIRT2 Histone Deacetylase, PDB code: 1j8f:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Human SIRT2 Histone Deacetylase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human SIRT2 Histone Deacetylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:27.3 occ:1.00 SG A:CYS224 2.2 27.0 1.0 SG A:CYS221 2.2 26.1 1.0 SG A:CYS195 2.3 22.8 1.0 SG A:CYS200 2.3 30.1 1.0 CB A:CYS221 3.1 27.6 1.0 CB A:CYS200 3.1 30.3 1.0 CB A:CYS195 3.2 19.8 1.0 H A:CYS224 3.2 0.0 1.0 CB A:CYS224 3.4 29.6 1.0 H A:HIS202 3.7 0.0 1.0 N A:CYS224 3.8 34.6 1.0 H A:SER226 3.9 0.0 1.0 CA A:CYS224 4.2 30.6 1.0 H A:ARG201 4.3 0.0 1.0 H A:ASP223 4.4 0.0 1.0 CB A:HIS202 4.4 34.9 1.0 HG A:SER226 4.5 0.0 1.0 H A:GLN225 4.5 0.0 1.0 CA A:CYS221 4.6 27.1 1.0 CA A:CYS200 4.6 30.6 1.0 CA A:CYS195 4.6 20.2 1.0 H A:SER197 4.6 0.0 1.0 N A:HIS202 4.7 32.5 1.0 CB A:SER226 4.7 26.3 1.0 CB A:ASP223 4.7 39.1 1.0 O A:HOH1072 4.7 24.4 1.0 C A:CYS224 4.7 31.1 1.0 N A:ARG201 4.7 31.6 1.0 C A:ASP223 4.8 36.9 1.0 N A:SER226 4.8 26.3 1.0 N A:GLN225 4.9 31.6 1.0 CB A:SER197 4.9 30.6 1.0 H1 A:HOH1072 4.9 0.0 1.0 C A:CYS200 5.0 32.1 1.0 OG A:SER226 5.0 27.3 1.0

Zinc binding site 2 out of 3 in the Human SIRT2 Histone Deacetylase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human SIRT2 Histone Deacetylase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2001 b:33.4 occ:1.00 SG B:CYS221 2.1 30.6 1.0 SG B:CYS224 2.2 37.0 1.0 SG B:CYS195 2.3 30.7 1.0 SG B:CYS200 2.3 35.0 1.0 CB B:CYS221 3.0 33.6 1.0 CB B:CYS195 3.2 29.5 1.0 CB B:CYS200 3.2 34.3 1.0 H B:CYS224 3.3 0.0 1.0 CB B:CYS224 3.3 38.9 1.0 H B:HIS202 3.6 0.0 1.0 OG B:SER197 3.7 36.7 1.0 H1 B:HOH2277 3.8 0.0 1.0 N B:CYS224 3.9 40.1 1.0 H B:SER226 3.9 0.0 1.0 HG B:SER197 4.1 0.0 1.0 CA B:CYS224 4.1 38.2 1.0 O B:HOH2277 4.2 30.5 1.0 CB B:HIS202 4.3 35.9 1.0 H B:ASP223 4.4 0.0 1.0 CA B:CYS221 4.5 35.3 1.0 N B:HIS202 4.5 32.8 1.0 CA B:CYS200 4.5 35.2 1.0 CB B:SER226 4.6 31.5 1.0 CA B:CYS195 4.6 27.7 1.0 HG B:SER226 4.6 0.0 1.0 H B:GLN225 4.6 0.0 1.0 H B:SER197 4.6 0.0 1.0 H B:ARG201 4.6 0.0 1.0 C B:CYS224 4.7 38.6 1.0 N B:ARG201 4.7 36.6 1.0 C B:CYS200 4.7 36.1 1.0 N B:SER226 4.8 33.7 1.0 HD1 B:HIS202 4.9 0.0 1.0 N B:GLN225 4.9 38.3 1.0 C B:ASP223 4.9 41.6 1.0 CB B:SER197 5.0 31.0 1.0

Zinc binding site 3 out of 3 in the Human SIRT2 Histone Deacetylase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human SIRT2 Histone Deacetylase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn3001 b:14.1 occ:1.00 SG C:CYS224 2.3 25.9 1.0 SG C:CYS200 2.3 15.6 1.0 SG C:CYS221 2.3 16.3 1.0 SG C:CYS195 2.3 12.4 1.0 CB C:CYS224 3.0 26.7 1.0 CB C:CYS200 3.1 18.8 1.0 CB C:CYS221 3.2 17.4 1.0 CB C:CYS195 3.2 19.1 1.0 N C:CYS224 3.9 24.2 1.0 H C:HIS202 3.9 0.0 1.0 H C:CYS224 3.9 0.0 1.0 CA C:CYS224 4.0 21.9 1.0 H C:SER226 4.1 0.0 1.0 H C:GLN225 4.2 0.0 1.0 HH C:TYR204 4.2 0.0 1.0 H C:ASP223 4.4 0.0 1.0 CB C:HIS202 4.4 22.5 1.0 H C:ARG201 4.4 0.0 1.0 CA C:CYS200 4.5 20.8 1.0 CA C:CYS221 4.6 15.6 1.0 CA C:CYS195 4.6 14.7 1.0 HG C:SER226 4.6 0.0 1.0 H C:SER197 4.6 0.0 1.0 CB C:SER197 4.7 14.6 1.0 C C:CYS224 4.7 23.2 1.0 N C:HIS202 4.7 14.9 1.0 CB C:SER226 4.8 16.4 1.0 H2 C:HOH3175 4.8 0.0 1.0 CB C:ASP223 4.8 32.5 1.0 H2 C:HOH3291 4.8 0.0 1.0 N C:ARG201 4.8 17.5 1.0 HD1 C:HIS202 4.9 0.0 1.0 C C:ASP223 4.9 28.4 1.0 C C:CYS200 4.9 20.1 1.0 OG C:SER226 4.9 15.9 1.0 H1 C:HOH3291 5.0 0.0 1.0 N C:GLN225 5.0 20.4 1.0 N C:SER226 5.0 16.9 1.0

M.S.Finnin, J.R.Donigian, N.P.Pavletich. Structure of the Histone Deacetylase SIRT2. Nat.Struct.Biol. V. 8 621 2001.
ISSN: ISSN 1072-8368
PubMed: 11427894
DOI: 10.1038/89668