Zinc in PDB 3zgo: Re-Refined Structure of the Human SIRT2 Apoform

The structure of Re-Refined Structure of the Human SIRT2 Apoform, PDB code: 3zgo was solved by S.Moniot, C.Steegborn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.84 / 1.63
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	78.940, 119.070, 218.220, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 19.5

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

Zinc binding site 1 out of 3 in the Re-Refined Structure of the Human SIRT2 Apoform


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Re-Refined Structure of the Human SIRT2 Apoform within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn400 b:26.0 occ:1.00 SG A:CYS221 2.3 24.6 1.0 SG A:CYS195 2.3 23.8 1.0 SG A:CYS224 2.3 27.1 1.0 SG A:CYS200 2.4 29.7 1.0 CB A:CYS221 3.2 24.9 1.0 CB A:CYS195 3.2 21.8 1.0 CB A:CYS200 3.3 30.6 1.0 CB A:CYS224 3.5 28.7 1.0 N A:CYS224 3.9 31.2 1.0 CA A:CYS224 4.2 30.6 1.0 CB A:HIS202 4.5 32.7 1.0 CA A:CYS195 4.6 19.7 1.0 CB A:ASP223 4.6 36.3 1.0 CA A:CYS221 4.6 24.4 1.0 CB A:SER226 4.6 25.8 1.0 N A:ARG201 4.6 28.9 1.0 O A:HOH2227 4.6 25.8 1.0 CA A:CYS200 4.6 29.7 1.0 N A:HIS202 4.7 27.7 1.0 OG A:SER226 4.8 28.8 1.0 C A:CYS224 4.9 31.2 1.0 C A:ASP223 4.9 35.2 1.0 C A:CYS200 4.9 31.4 1.0 CB A:SER197 4.9 25.2 1.0 N A:SER226 4.9 27.4 1.0 N A:GLN225 4.9 32.8 1.0

Zinc binding site 2 out of 3 in the Re-Refined Structure of the Human SIRT2 Apoform


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Re-Refined Structure of the Human SIRT2 Apoform within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn400 b:39.5 occ:1.00 SG B:CYS221 2.2 28.1 1.0 SG B:CYS200 2.3 36.3 1.0 SG B:CYS224 2.3 37.0 1.0 SG B:CYS195 2.3 34.2 1.0 CB B:CYS221 3.1 31.0 1.0 CB B:CYS200 3.2 37.2 1.0 CB B:CYS195 3.2 29.6 1.0 CB B:CYS224 3.4 38.1 1.0 N B:CYS224 3.9 36.8 1.0 CA B:CYS224 4.2 38.2 1.0 O B:HOH2180 4.4 37.5 1.0 CB B:HIS202 4.4 39.0 1.0 CA B:CYS221 4.5 31.9 1.0 CA B:CYS200 4.5 36.5 1.0 N B:HIS202 4.6 34.1 1.0 CB B:SER197 4.6 33.9 1.0 N B:ARG201 4.6 37.8 1.0 CB B:SER226 4.6 33.6 1.0 CA B:CYS195 4.6 27.0 1.0 C B:CYS224 4.7 39.3 1.0 C B:CYS200 4.8 37.2 1.0 N B:SER226 4.8 37.8 1.0 OG B:SER226 4.9 34.5 1.0 C B:ASP223 4.9 42.8 1.0 N B:GLN225 5.0 40.9 1.0 CB B:ASP223 5.0 48.1 1.0

Zinc binding site 3 out of 3 in the Re-Refined Structure of the Human SIRT2 Apoform


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Re-Refined Structure of the Human SIRT2 Apoform within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn400 b:12.8 occ:1.00 SG C:CYS200 2.3 15.4 1.0 SG C:CYS195 2.3 13.2 1.0 SG C:CYS224 2.3 15.3 1.0 SG C:CYS221 2.3 11.8 1.0 CB C:CYS200 3.1 15.3 1.0 CB C:CYS195 3.2 12.0 1.0 CB C:CYS221 3.2 11.5 1.0 CB C:CYS224 3.5 16.6 1.0 N C:CYS224 4.0 16.7 1.0 CA C:CYS224 4.2 16.1 1.0 CB C:HIS202 4.3 16.1 0.6 CA C:CYS200 4.5 16.4 1.0 O C:HOH2221 4.5 34.2 1.0 CA C:CYS195 4.6 11.6 1.0 CA C:CYS221 4.6 11.7 1.0 CB C:SER197 4.6 16.1 1.0 CB C:ASP223 4.7 23.2 1.0 N C:HIS202 4.7 15.1 0.6 CB C:SER226 4.7 13.6 1.0 N C:HIS202 4.8 15.2 0.4 O C:HOH2216 4.8 30.8 1.0 N C:ARG201 4.8 15.4 1.0 C C:CYS224 4.9 15.8 1.0 CB C:HIS202 4.9 16.3 0.4 C C:CYS200 4.9 16.0 1.0 C C:ASP223 4.9 19.6 1.0 OG C:SER226 5.0 15.9 1.0 N C:SER226 5.0 14.2 1.0 N C:GLN225 5.0 15.7 0.5

S.Moniot, M.Schutkowski, C.Steegborn. Crystal Structure Analysis of Human SIRT2 and Its Adp-Ribose Complex J.Struct.Biol. V. 182 136 2013.
ISSN: ISSN 1047-8477
PubMed: 23454361
DOI: 10.1016/J.JSB.2013.02.012