Zinc in PDB 4y6l: Human SIRT2 in Complex with Myristoylated Peptide (H3K9MYR)

The structure of Human SIRT2 in Complex with Myristoylated Peptide (H3K9MYR), PDB code: 4y6l 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 / 1.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	37.102, 48.824, 97.147, 101.05, 91.53, 112.07
R / Rfree (%)	20.7 / 23.2

The binding sites of Zinc atom in the Human SIRT2 in Complex with Myristoylated Peptide (H3K9MYR) (pdb code 4y6l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human SIRT2 in Complex with Myristoylated Peptide (H3K9MYR), PDB code: 4y6l:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human SIRT2 in Complex with Myristoylated Peptide (H3K9MYR)


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 Myristoylated Peptide (H3K9MYR) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:7.1 occ:1.00 SG A:CYS224 2.3 7.2 1.0 SG A:CYS200 2.3 8.2 1.0 SG A:CYS195 2.3 7.1 1.0 SG A:CYS221 2.3 7.0 1.0 CB A:CYS221 3.2 7.7 1.0 CB A:CYS200 3.2 8.9 1.0 CB A:CYS195 3.2 6.9 1.0 CB A:CYS224 3.4 7.6 1.0 N A:CYS224 3.8 8.1 1.0 CA A:CYS224 4.1 7.8 1.0 CB A:HIS202 4.5 7.5 1.0 CA A:CYS200 4.6 9.7 1.0 N A:HIS202 4.6 8.2 1.0 CA A:CYS221 4.6 8.1 1.0 N A:ARG201 4.6 10.0 1.0 CB A:ASP223 4.7 8.6 1.0 CA A:CYS195 4.7 6.8 1.0 CB A:SER197 4.7 10.2 1.0 C A:CYS224 4.7 8.0 1.0 CB A:SER226 4.7 7.1 1.0 C A:CYS200 4.8 9.7 1.0 C A:ASP223 4.9 8.3 1.0 N A:SER226 4.9 7.4 1.0 N A:GLN225 4.9 8.1 1.0 OG A:SER226 4.9 7.0 1.0

Zinc binding site 2 out of 2 in the Human SIRT2 in Complex with Myristoylated Peptide (H3K9MYR)


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 Myristoylated Peptide (H3K9MYR) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:20.6 occ:1.00 SG B:CYS200 2.3 22.2 1.0 SG B:CYS224 2.3 20.6 1.0 SG B:CYS221 2.3 21.6 1.0 SG B:CYS195 2.3 18.6 1.0 CB B:CYS221 3.2 22.2 1.0 CB B:CYS200 3.2 22.1 1.0 CB B:CYS195 3.3 17.8 1.0 CB B:CYS224 3.4 21.6 1.0 N B:CYS224 3.8 23.2 1.0 CA B:CYS224 4.1 22.3 1.0 CB B:HIS202 4.3 24.2 1.0 CA B:CYS200 4.6 22.4 1.0 CB B:ASP223 4.6 25.6 1.0 N B:HIS202 4.6 23.2 1.0 CA B:CYS195 4.7 17.2 1.0 CB B:SER226 4.7 19.7 1.0 CA B:CYS221 4.7 23.3 1.0 C B:CYS224 4.7 22.2 1.0 N B:ARG201 4.7 23.2 1.0 CB B:SER197 4.8 19.6 1.0 OG B:SER226 4.9 19.9 1.0 C B:CYS200 4.9 22.9 1.0 C B:ASP223 4.9 24.4 1.0 N B:SER226 5.0 20.2 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