Zinc in PDB 4y6q: Human SIRT2 in Complex with 2-O-Myristoyl-Adp-Ribose

The structure of Human SIRT2 in Complex with 2-O-Myristoyl-Adp-Ribose, PDB code: 4y6q was solved by N.Kudo, A.Ito, M.Yoshida, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.186, 142.369, 62.626, 90.00, 94.41, 90.00
R / Rfree (%)	23.1 / 26.7

The binding sites of Zinc atom in the Human SIRT2 in Complex with 2-O-Myristoyl-Adp-Ribose (pdb code 4y6q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Human SIRT2 in Complex with 2-O-Myristoyl-Adp-Ribose, PDB code: 4y6q:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Human SIRT2 in Complex with 2-O-Myristoyl-Adp-Ribose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human SIRT2 in Complex with 2-O-Myristoyl-Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:21.7 occ:1.00 SG A:CYS200 2.3 21.4 1.0 SG A:CYS224 2.3 21.5 1.0 SG A:CYS195 2.3 19.9 1.0 SG A:CYS221 2.3 19.1 1.0 CB A:CYS195 3.2 18.4 1.0 CB A:CYS200 3.2 23.5 1.0 CB A:CYS221 3.2 19.9 1.0 CB A:CYS224 3.5 22.3 1.0 N A:CYS224 3.9 22.8 1.0 CA A:CYS224 4.3 21.5 1.0 CB A:ASP223 4.5 25.1 1.0 CB A:HIS202 4.5 25.4 1.0 N A:ARG201 4.6 24.8 1.0 CA A:CYS200 4.6 24.9 1.0 CA A:CYS195 4.6 17.6 1.0 CA A:CYS221 4.7 19.6 1.0 N A:HIS202 4.7 24.6 1.0 CB A:SER226 4.8 19.9 1.0 C A:CYS200 4.8 24.7 1.0 CB A:SER197 4.9 24.2 1.0 C A:ASP223 4.9 24.3 1.0 C A:CYS224 4.9 21.3 1.0 OG A:SER226 5.0 22.3 1.0

Zinc binding site 2 out of 4 in the Human SIRT2 in Complex with 2-O-Myristoyl-Adp-Ribose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human SIRT2 in Complex with 2-O-Myristoyl-Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:34.3 occ:1.00 SG B:CYS224 2.3 27.9 1.0 SG B:CYS200 2.3 39.2 1.0 SG B:CYS221 2.3 35.6 1.0 SG B:CYS195 2.3 32.3 1.0 CB B:CYS195 3.2 31.0 1.0 CB B:CYS200 3.2 38.7 1.0 CB B:CYS221 3.3 35.0 1.0 CB B:CYS224 3.4 34.6 1.0 N B:CYS224 3.9 38.1 1.0 OG B:SER226 4.2 38.2 1.0 CA B:CYS224 4.3 35.9 1.0 CB B:HIS202 4.4 40.6 1.0 N B:HIS202 4.5 40.6 1.0 CB B:ASP223 4.5 43.1 1.0 N B:ARG201 4.6 41.8 1.0 CA B:CYS200 4.6 39.5 1.0 CA B:CYS195 4.7 30.0 1.0 CA B:CYS221 4.7 34.4 1.0 CB B:SER197 4.8 38.3 1.0 C B:CYS200 4.8 40.5 1.0 C B:ASP223 4.9 40.7 1.0

Zinc binding site 3 out of 4 in the Human SIRT2 in Complex with 2-O-Myristoyl-Adp-Ribose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human SIRT2 in Complex with 2-O-Myristoyl-Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:26.9 occ:1.00 SG C:CYS224 2.3 27.0 1.0 SG C:CYS195 2.3 23.0 1.0 SG C:CYS200 2.3 30.1 1.0 SG C:CYS221 2.3 24.4 1.0 CB C:CYS221 3.2 26.7 1.0 CB C:CYS195 3.2 21.8 1.0 CB C:CYS200 3.2 29.7 1.0 CB C:CYS224 3.5 30.6 1.0 N C:CYS224 4.0 33.9 1.0 CA C:CYS224 4.3 31.6 1.0 CB C:HIS202 4.5 28.6 1.0 CB C:ASP223 4.5 37.9 1.0 N C:ARG201 4.6 28.6 1.0 CA C:CYS200 4.6 29.4 1.0 N C:HIS202 4.6 26.7 1.0 CA C:CYS195 4.7 20.7 1.0 CA C:CYS221 4.7 27.6 1.0 CB C:SER226 4.8 26.5 1.0 C C:CYS200 4.9 30.0 1.0 OG C:SER226 4.9 27.7 1.0 CB C:SER197 4.9 28.0 1.0 C C:CYS224 4.9 32.7 1.0

Zinc binding site 4 out of 4 in the Human SIRT2 in Complex with 2-O-Myristoyl-Adp-Ribose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human SIRT2 in Complex with 2-O-Myristoyl-Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:57.7 occ:1.00 SG D:CYS200 2.3 58.8 1.0 SG D:CYS195 2.3 59.0 1.0 SG D:CYS221 2.3 57.1 1.0 SG D:CYS224 2.3 49.0 1.0 CB D:CYS221 3.3 55.8 1.0 CB D:CYS195 3.3 55.6 1.0 CB D:CYS200 3.3 61.3 1.0 CB D:CYS224 3.4 53.6 1.0 N D:CYS224 3.9 56.4 1.0 CA D:CYS224 4.2 53.2 1.0 CB D:HIS202 4.5 72.4 1.0 CB D:ASP223 4.6 60.8 1.0 N D:HIS202 4.7 71.0 1.0 CB D:SER197 4.7 59.7 1.0 CA D:CYS200 4.7 62.5 1.0 CA D:CYS221 4.7 53.9 1.0 CA D:CYS195 4.8 53.9 1.0 N D:ARG201 4.8 65.4 1.0 C D:ASP223 4.9 58.2 1.0 C D:CYS224 4.9 52.4 1.0 C D:CYS200 5.0 63.5 1.0

J.L.Feldman, K.E.Dittenhafer-Reed, N.Kudo, J.N.Thelen, A.Ito, M.Yoshida, J.M.Denu. Kinetic and Structural Basis For Acyl-Group Selectivity and Nad(+) Dependence in Sirtuin-Catalyzed Deacylation. Biochemistry V. 54 3037 2015.
ISSN: ISSN 0006-2960
PubMed: 25897714
DOI: 10.1021/ACS.BIOCHEM.5B00150