Zinc in PDB 5mar: Structure of Human SIRT2 in Complex with 1,2,4-Oxadiazole Inhibitor and Adp Ribose.

The structure of Structure of Human SIRT2 in Complex with 1,2,4-Oxadiazole Inhibitor and Adp Ribose., PDB code: 5mar 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)	48.93 / 1.89
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.557, 76.709, 113.827, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 19.4

The structure of Structure of Human SIRT2 in Complex with 1,2,4-Oxadiazole Inhibitor and Adp Ribose. also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Structure of Human SIRT2 in Complex with 1,2,4-Oxadiazole Inhibitor and Adp Ribose. (pdb code 5mar). 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 1,2,4-Oxadiazole Inhibitor and Adp Ribose., PDB code: 5mar:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Human SIRT2 in Complex with 1,2,4-Oxadiazole Inhibitor and 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 1,2,4-Oxadiazole Inhibitor and Adp Ribose. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:47.8 occ:1.00 SG A:CYS200 2.3 52.5 1.0 SG A:CYS221 2.3 51.2 1.0 SG A:CYS224 2.4 52.0 1.0 SG A:CYS195 2.4 47.1 1.0 HB3 A:CYS200 2.7 63.5 1.0 CB A:CYS200 2.9 52.9 1.0 HB2 A:CYS195 2.9 56.1 1.0 HB3 A:CYS221 3.0 63.2 1.0 HB2 A:CYS200 3.0 63.5 1.0 CB A:CYS221 3.1 52.6 1.0 HB2 A:CYS221 3.1 63.2 1.0 CB A:CYS195 3.1 46.8 1.0 HB3 A:CYS195 3.2 56.1 1.0 H A:CYS224 3.3 73.0 1.0 HB3 A:CYS224 3.4 68.1 1.0 CB A:CYS224 3.5 56.7 1.0 HB2 A:ASP223 3.6 81.5 1.0 HB3 A:SER197 3.8 71.7 1.0 HB2 A:SER226 3.8 60.4 1.0 H A:HIS202 3.9 61.7 1.0 N A:CYS224 3.9 60.8 1.0 HB2 A:HIS202 4.0 70.6 1.0 HB3 A:HIS202 4.1 70.6 1.0 H A:SER226 4.2 58.5 1.0 H A:ARG201 4.2 65.5 1.0 H A:ASP223 4.2 80.6 1.0 CA A:CYS224 4.3 60.7 1.0 HB2 A:CYS224 4.3 68.1 1.0 CA A:CYS200 4.3 55.1 1.0 CB A:ASP223 4.5 67.9 1.0 CB A:HIS202 4.5 58.8 1.0 CA A:CYS221 4.5 54.0 1.0 H A:SER197 4.6 64.2 1.0 HH A:TYR204 4.6 70.8 1.0 CA A:CYS195 4.6 44.1 1.0 N A:ARG201 4.6 54.5 1.0 HG A:SER226 4.6 63.2 1.0 N A:HIS202 4.7 51.4 1.0 H A:GLN225 4.7 74.4 1.0 CB A:SER197 4.7 59.7 1.0 HB3 A:ASP223 4.7 81.5 1.0 CB A:SER226 4.7 50.3 1.0 C A:ASP223 4.8 68.7 1.0 HA A:CYS200 4.8 66.2 1.0 C A:CYS200 4.8 53.6 1.0 HB2 A:SER197 4.8 71.7 1.0 HA A:CYS195 4.8 53.0 1.0 C A:CYS224 4.9 62.0 1.0 HA A:CYS221 4.9 64.8 1.0 N A:ASP223 4.9 67.1 1.0 N A:SER226 4.9 48.9 1.0 CA A:ASP223 5.0 69.1 1.0 HE1 A:TYR204 5.0 64.7 1.0 N A:GLN225 5.0 62.0 1.0 OG A:SER226 5.0 52.7 1.0

Zinc binding site 2 out of 2 in the Structure of Human SIRT2 in Complex with 1,2,4-Oxadiazole Inhibitor and 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 1,2,4-Oxadiazole Inhibitor and Adp Ribose. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:36.9 occ:1.00 SG B:CYS200 2.3 49.3 1.0 SG B:CYS224 2.3 41.0 1.0 SG B:CYS195 2.4 36.5 1.0 SG B:CYS221 2.4 41.8 1.0 HB3 B:CYS200 2.8 58.7 1.0 CB B:CYS200 3.0 48.9 1.0 HB3 B:CYS221 3.0 48.1 1.0 HB2 B:CYS195 3.0 46.0 1.0 CB B:CYS221 3.1 40.3 1.0 HB2 B:CYS221 3.1 48.1 1.0 CB B:CYS195 3.2 38.3 1.0 HB2 B:CYS200 3.2 58.7 1.0 H B:CYS224 3.3 57.0 1.0 HB3 B:CYS195 3.3 46.0 1.0 HB3 B:CYS224 3.5 52.2 1.0 HB2 B:ASP223 3.6 59.7 1.0 CB B:CYS224 3.6 43.5 1.0 HB3 B:SER197 3.8 55.0 1.0 HB2 B:SER226 3.8 40.7 1.0 H B:HIS202 3.8 53.4 1.0 N B:CYS224 3.9 47.5 1.0 HB2 B:HIS202 3.9 55.2 1.0 HB3 B:HIS202 4.0 55.2 1.0 H B:SER226 4.1 44.6 1.0 H B:ARG201 4.2 58.5 1.0 CA B:CYS224 4.3 46.7 1.0 H B:ASP223 4.3 56.7 1.0 HB2 B:CYS224 4.3 52.2 1.0 HG B:SER226 4.3 41.0 1.0 CB B:HIS202 4.4 46.0 1.0 CA B:CYS200 4.4 49.8 1.0 HH B:TYR204 4.5 54.3 1.0 CB B:ASP223 4.5 49.7 1.0 CA B:CYS221 4.5 41.9 1.0 H B:GLN225 4.6 53.3 1.0 N B:HIS202 4.6 44.5 1.0 N B:ARG201 4.6 48.7 1.0 CA B:CYS195 4.6 34.9 1.0 CB B:SER226 4.6 34.0 1.0 CB B:SER197 4.7 45.8 1.0 H B:SER197 4.7 46.7 1.0 OG B:SER226 4.8 34.3 1.0 HB3 B:ASP223 4.8 59.7 1.0 C B:CYS224 4.8 45.9 1.0 N B:SER226 4.8 37.3 1.0 C B:CYS200 4.8 49.6 1.0 HA B:CYS200 4.8 59.8 1.0 C B:ASP223 4.9 46.7 1.0 HA B:CYS195 4.9 41.9 1.0 HA B:CYS221 4.9 50.1 1.0 HE1 B:TYR204 4.9 50.5 1.0 N B:GLN225 4.9 44.4 1.0 HB2 B:SER197 4.9 55.0 1.0 N B:ASP223 5.0 47.4 1.0

S.Moniot, M.Forgione, A.Lucidi, G.S.Hailu, A.Nebbioso, V.Carafa, F.Baratta, L.Altucci, N.Giacche, D.Passeri, R.Pellicciari, A.Mai, C.Steegborn, D.Rotili. Development of 1,2,4-Oxadiazoles As Potent and Selective Inhibitors of the Human Deacetylase Sirtuin 2: Structure-Activity Relationship, X-Ray Crystal Structure, and Anticancer Activity. J. Med. Chem. V. 60 2344 2017.
ISSN: ISSN 1520-4804
PubMed: 28240897
DOI: 10.1021/ACS.JMEDCHEM.6B01609