Zinc in PDB 4y6o: Human SIRT2 in Complex with Myristoylated Peptide (Tnf-ALPHAK20MYR)

The structure of Human SIRT2 in Complex with Myristoylated Peptide (Tnf-ALPHAK20MYR), PDB code: 4y6o 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 (°)	37.136, 48.785, 96.960, 101.07, 91.33, 112.27
R / Rfree (%)	20.6 / 23.5

The binding sites of Zinc atom in the Human SIRT2 in Complex with Myristoylated Peptide (Tnf-ALPHAK20MYR) (pdb code 4y6o). 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 (Tnf-ALPHAK20MYR), PDB code: 4y6o:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human SIRT2 in Complex with Myristoylated Peptide (Tnf-ALPHAK20MYR)


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 (Tnf-ALPHAK20MYR) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:7.7 occ:1.00 SG A:CYS200 2.3 9.1 1.0 SG A:CYS224 2.3 7.7 1.0 SG A:CYS195 2.3 8.1 1.0 SG A:CYS221 2.3 7.8 1.0 CB A:CYS221 3.1 8.5 1.0 CB A:CYS200 3.2 9.8 1.0 CB A:CYS195 3.2 7.7 1.0 CB A:CYS224 3.4 7.9 1.0 N A:CYS224 3.8 8.3 1.0 CA A:CYS224 4.1 8.1 1.0 CB A:HIS202 4.5 8.4 1.0 N A:HIS202 4.6 9.2 1.0 CA A:CYS200 4.6 10.7 1.0 CA A:CYS221 4.6 8.9 1.0 CB A:SER197 4.6 10.8 1.0 N A:ARG201 4.6 11.2 1.0 CA A:CYS195 4.6 7.8 1.0 CB A:SER226 4.7 7.7 1.0 C A:CYS224 4.7 8.3 1.0 CB A:ASP223 4.7 8.7 1.0 C A:CYS200 4.8 10.9 1.0 N A:GLN225 4.9 8.4 1.0 OG A:SER226 4.9 7.7 1.0 N A:SER226 4.9 7.8 1.0 C A:ASP223 4.9 8.6 1.0

Zinc binding site 2 out of 2 in the Human SIRT2 in Complex with Myristoylated Peptide (Tnf-ALPHAK20MYR)


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 (Tnf-ALPHAK20MYR) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:20.7 occ:1.00 SG B:CYS200 2.3 23.4 1.0 SG B:CYS195 2.3 18.8 1.0 SG B:CYS221 2.3 20.5 1.0 SG B:CYS224 2.3 21.6 1.0 CB B:CYS221 3.2 21.4 1.0 CB B:CYS200 3.2 22.7 1.0 CB B:CYS195 3.2 17.5 1.0 CB B:CYS224 3.4 21.9 1.0 N B:CYS224 3.9 22.9 1.0 CA B:CYS224 4.2 22.4 1.0 CB B:HIS202 4.3 22.9 1.0 N B:HIS202 4.6 22.1 1.0 CA B:CYS200 4.6 23.0 1.0 CA B:CYS195 4.6 16.5 1.0 CA B:CYS221 4.7 22.4 1.0 CB B:ASP223 4.7 24.6 1.0 CB B:SER226 4.7 19.8 1.0 N B:ARG201 4.7 22.9 1.0 CB B:SER197 4.7 19.5 1.0 C B:CYS224 4.8 22.1 1.0 C B:CYS200 4.9 22.9 1.0 OG B:SER226 4.9 20.2 1.0 C B:ASP223 5.0 24.0 1.0 N B:SER226 5.0 20.4 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