Zinc in PDB 3zgv: Structure of Human SIRT2 in Complex with Adp-Ribose

The structure of Structure of Human SIRT2 in Complex with Adp-Ribose, PDB code: 3zgv 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)	64.422 / 2.27
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.860, 77.980, 114.330, 90.00, 90.00, 90.00
R / Rfree (%)	14.95 / 18.83

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

Zinc binding site 1 out of 2 in the Structure of Human SIRT2 in Complex with Adp-Ribose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human SIRT2 in Complex with Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn400 b:47.8 occ:1.00 SG A:CYS224 2.2 43.6 1.0 SG A:CYS195 2.3 55.5 1.0 SG A:CYS200 2.3 50.8 1.0 SG A:CYS221 2.3 47.4 1.0 HB3 A:CYS221 2.8 50.6 1.0 CB A:CYS221 2.9 42.3 1.0 HB2 A:CYS221 2.9 50.6 1.0 HB3 A:CYS200 2.9 67.2 1.0 HB2 A:CYS195 3.0 58.6 1.0 CB A:CYS200 3.1 56.1 1.0 CB A:CYS195 3.1 49.0 1.0 H A:CYS224 3.2 56.1 1.0 HB3 A:CYS195 3.2 58.6 1.0 HB2 A:CYS200 3.2 67.2 1.0 HB3 A:CYS224 3.5 50.5 1.0 CB A:CYS224 3.5 42.2 1.0 HB2 A:SER226 3.7 56.0 1.0 HB2 A:ASP223 3.8 56.6 1.0 HB3 A:SER197 3.8 83.5 1.0 H A:HIS202 3.9 61.9 1.0 N A:CYS224 3.9 46.8 1.0 HB2 A:HIS202 4.0 66.9 1.0 HB3 A:HIS202 4.0 66.9 1.0 H A:SER226 4.1 65.5 1.0 H A:ARG201 4.2 70.1 1.0 CA A:CYS224 4.3 46.7 1.0 HB2 A:CYS224 4.3 50.5 1.0 CA A:CYS221 4.4 45.0 1.0 H A:ASP223 4.5 57.6 1.0 CB A:HIS202 4.5 55.9 1.0 CA A:CYS200 4.5 59.4 1.0 CA A:CYS195 4.6 45.4 1.0 H A:SER197 4.6 79.6 1.0 CB A:SER226 4.7 46.8 1.0 H A:GLN225 4.7 63.2 1.0 N A:ARG201 4.7 58.5 1.0 N A:HIS202 4.7 51.7 1.0 CB A:SER197 4.7 69.7 1.0 CB A:ASP223 4.7 47.3 1.0 HA A:CYS221 4.7 53.8 1.0 HB2 A:SER197 4.8 83.5 1.0 HA A:CYS195 4.8 54.3 1.0 C A:CYS224 4.8 45.4 1.0 N A:SER226 4.9 54.7 1.0 HA A:CYS200 4.9 71.1 1.0 N A:GLN225 4.9 52.8 1.0 C A:CYS200 5.0 57.5 1.0 H A:CYS221 5.0 53.5 1.0 C A:CYS221 5.0 50.2 1.0

Zinc binding site 2 out of 2 in the Structure of Human SIRT2 in Complex with Adp-Ribose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human SIRT2 in Complex with Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn400 b:51.5 occ:1.00 SG B:CYS221 2.2 45.8 1.0 SG B:CYS224 2.3 66.0 1.0 SG B:CYS195 2.3 50.9 1.0 SG B:CYS200 2.3 62.2 1.0 HB2 B:CYS221 2.6 49.7 1.0 CB B:CYS221 2.7 41.5 1.0 HB3 B:CYS221 2.8 49.7 1.0 HB2 B:CYS195 2.8 51.9 1.0 CB B:CYS195 3.0 43.4 1.0 H B:CYS224 3.0 86.0 1.0 HB3 B:CYS200 3.0 77.5 1.0 HB3 B:CYS195 3.1 51.9 1.0 CB B:CYS200 3.2 64.7 1.0 HB3 B:CYS224 3.4 79.0 1.0 HB2 B:CYS200 3.4 77.5 1.0 CB B:CYS224 3.4 65.9 1.0 HB2 B:ASP223 3.7 76.2 1.0 HB3 B:HIS202 3.7 73.7 1.0 HB2 B:HIS202 3.7 73.7 1.0 N B:CYS224 3.7 71.8 1.0 HB2 B:SER226 3.8 49.4 1.0 H B:HIS202 3.8 70.4 1.0 H B:SER226 4.1 59.1 1.0 CA B:CYS224 4.1 70.5 1.0 CB B:HIS202 4.2 61.6 1.0 CA B:CYS221 4.2 43.0 1.0 HB2 B:CYS224 4.2 79.0 1.0 HB3 B:SER197 4.4 60.9 1.0 H B:ASP223 4.4 73.1 1.0 CA B:CYS195 4.4 38.1 1.0 HA B:CYS221 4.5 51.4 1.0 H B:GLN225 4.5 70.8 1.0 H B:ARG201 4.5 94.9 1.0 CB B:ASP223 4.6 63.6 1.0 HE1 B:TYR204 4.6 60.8 1.0 N B:HIS202 4.6 58.8 1.0 CB B:SER226 4.6 41.3 1.0 CA B:CYS200 4.6 66.8 1.0 HA B:CYS195 4.7 45.6 1.0 OG B:SER226 4.7 49.8 1.0 C B:CYS224 4.7 67.6 1.0 HH B:TYR204 4.7 72.7 1.0 N B:GLN225 4.8 59.2 1.0 HB3 B:ASP223 4.8 76.2 1.0 C B:ASP223 4.8 63.9 1.0 H B:CYS221 4.9 49.0 1.0 N B:SER226 4.9 49.4 1.0 N B:ARG201 4.9 79.2 1.0 C B:CYS221 4.9 50.1 1.0 H B:SER197 5.0 55.9 1.0 HA B:CYS224 5.0 84.5 1.0

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