Zinc in PDB 5d7p: Crystal Structure of Human SIRT2 in Complex with Adpr and Ex-243

The structure of Crystal Structure of Human SIRT2 in Complex with Adpr and Ex-243, PDB code: 5d7p was solved by T.Rumpf, S.Gerhardt, O.Einsle, M.Jung, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.41 / 1.76
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.496, 77.578, 114.206, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 22.4

The structure of Crystal Structure of Human SIRT2 in Complex with Adpr and Ex-243 also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of Human SIRT2 in Complex with Adpr and Ex-243 (pdb code 5d7p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Human SIRT2 in Complex with Adpr and Ex-243, PDB code: 5d7p:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Human SIRT2 in Complex with Adpr and Ex-243


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 SIRT2 in Complex with Adpr and Ex-243 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:54.5 occ:1.00 SG A:CYS221 2.3 52.6 1.0 SG A:CYS200 2.3 54.7 1.0 SG A:CYS224 2.3 54.0 1.0 SG A:CYS195 2.4 50.6 1.0 CB A:CYS221 3.2 52.3 1.0 CB A:CYS200 3.2 57.8 1.0 CB A:CYS195 3.3 48.3 1.0 CB A:CYS224 3.4 53.8 1.0 N A:CYS224 3.8 56.9 1.0 CA A:CYS224 4.2 53.5 1.0 CB A:ASP223 4.4 62.3 1.0 C A:ASP223 4.5 60.4 1.0 CA A:CYS200 4.6 60.5 1.0 CB A:HIS202 4.6 68.7 1.0 CA A:CYS221 4.6 50.6 1.0 N A:HIS202 4.7 65.7 1.0 N A:ARG201 4.7 64.1 1.0 CB A:SER197 4.7 52.5 1.0 CA A:CYS195 4.7 47.0 1.0 N A:ASP223 4.8 60.1 1.0 C A:CYS224 4.8 50.5 1.0 CA A:ASP223 4.8 61.3 1.0 CB A:SER226 4.9 41.4 1.0 C A:CYS200 5.0 63.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human SIRT2 in Complex with Adpr and Ex-243


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human SIRT2 in Complex with Adpr and Ex-243 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:35.7 occ:1.00 SG B:CYS200 2.3 39.4 1.0 SG B:CYS221 2.3 38.8 1.0 SG B:CYS195 2.3 34.2 1.0 SG B:CYS224 2.3 35.1 1.0 CB B:CYS221 3.2 38.3 1.0 CB B:CYS200 3.2 40.1 1.0 CB B:CYS195 3.2 33.9 1.0 CB B:CYS224 3.4 36.7 1.0 N B:CYS224 3.9 40.4 1.0 CA B:CYS224 4.2 37.2 1.0 CB B:HIS202 4.4 43.4 1.0 CB B:ASP223 4.5 45.2 1.0 N B:HIS202 4.6 40.1 1.0 CA B:CYS200 4.6 40.6 1.0 N B:ARG201 4.6 40.4 1.0 CA B:CYS221 4.7 39.0 1.0 CA B:CYS195 4.7 33.4 1.0 CB B:SER197 4.7 39.0 1.0 CB B:SER226 4.7 35.1 1.0 C B:CYS224 4.8 37.6 1.0 C B:CYS200 4.9 41.9 1.0 C B:ASP223 4.9 42.4 1.0 OG B:SER226 4.9 35.5 1.0 N B:GLN225 5.0 37.0 1.0 N B:SER226 5.0 35.2 1.0

T.Rumpf, S.Gerhardt, O.Einsle, M.Jung. Seeding For Sirtuins: Microseed Matrix Seeding to Obtain Crystals of Human SIRT3 and SIRT2 Suitable For Soaking. Acta Crystallogr.,Sect.F V. 71 1498 2015.
ISSN: ESSN 2053-230X
PubMed: 26625292
DOI: 10.1107/S2053230X15019986