Zinc in PDB 5y5n: Crystal Structure of Human Sirtuin 2 in Complex with A Selective Inhibitor

The structure of Crystal Structure of Human Sirtuin 2 in Complex with A Selective Inhibitor, PDB code: 5y5n was solved by P.Mellini, Y.Itoh, H.Tsumoto, Y.Li, M.Suzuki, N.Tokuda, T.Kakizawa, Y.Miura, J.Takeuchi, M.Lahtela-Kakkonen, T.Suzuki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.43 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.850, 57.980, 124.532, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Zinc atom in the Crystal Structure of Human Sirtuin 2 in Complex with A Selective Inhibitor (pdb code 5y5n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Human Sirtuin 2 in Complex with A Selective Inhibitor, PDB code: 5y5n:

Zinc binding site 1 out of 1 in the Crystal Structure of Human Sirtuin 2 in Complex with A Selective Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human Sirtuin 2 in Complex with A Selective Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:47.4 occ:1.00 SG A:CYS200 2.0 52.5 1.0 SG A:CYS221 2.1 41.8 1.0 SG A:CYS195 2.2 36.8 1.0 SG A:CYS224 2.3 61.0 1.0 CB A:CYS200 3.0 49.2 1.0 CB A:CYS221 3.1 39.8 1.0 CB A:CYS224 3.2 48.6 1.0 CB A:CYS195 3.2 27.2 1.0 N A:CYS224 3.4 51.3 1.0 CA A:CYS224 3.8 51.1 1.0 CA A:CYS200 4.4 46.9 1.0 CB A:HIS202 4.4 42.4 1.0 N A:HIS202 4.5 41.0 1.0 CA A:CYS221 4.5 34.2 1.0 CA A:CYS195 4.5 27.7 1.0 C A:CYS224 4.5 49.5 1.0 N A:ARG201 4.6 36.4 1.0 CB A:ASP223 4.6 51.8 1.0 C A:ASP223 4.6 51.8 1.0 C A:CYS200 4.6 46.6 1.0 OG A:SER197 4.7 58.0 1.0 CB A:SER197 4.8 52.8 1.0 CB A:SER226 4.8 54.8 1.0 N A:GLN225 4.9 41.9 1.0 N A:SER226 5.0 31.1 1.0 C A:CYS221 5.0 36.2 1.0

P.Mellini, Y.Itoh, H.Tsumoto, Y.Li, M.Suzuki, M.Tokuda, T.Kakizawa, Y.Miura, J.Takeuchi, M.Lahtela-Kakkonen, T.Suzuki. Potent Mechanism-Based Sirtuin-2-Selective Inhibition By An in-Situ-Generated Occupant of the "Selectivity Pocket", Substrate Binding Site, and Nad+ Binding Pocket Chem Sci V. 8 6400 2017.
ISSN: ISSN 2041-6520
DOI: 10.1039/C7SC02738A