Zinc in PDB 5fyq: SIRT2 in Complex with A 13-Mer Trifluoroacetylated Ran Peptide

The structure of SIRT2 in Complex with A 13-Mer Trifluoroacetylated Ran Peptide, PDB code: 5fyq was solved by P.Knyphausen, S.De Boor, L.Scislowski, A.Extra, L.Baldus, M.Schacherl, U.Baumann, I.Neundorf, M.Lammers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.61 / 3.00
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	114.948, 114.948, 206.476, 90.00, 90.00, 120.00
R / Rfree (%)	23.2 / 27.1

The structure of SIRT2 in Complex with A 13-Mer Trifluoroacetylated Ran Peptide also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Zinc atom in the SIRT2 in Complex with A 13-Mer Trifluoroacetylated Ran Peptide (pdb code 5fyq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the SIRT2 in Complex with A 13-Mer Trifluoroacetylated Ran Peptide, PDB code: 5fyq:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the SIRT2 in Complex with A 13-Mer Trifluoroacetylated Ran Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of SIRT2 in Complex with A 13-Mer Trifluoroacetylated Ran Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1358 b:0.3 occ:1.00 SG A:CYS221 2.1 81.7 1.0 SG A:CYS195 2.3 80.5 1.0 CB A:CYS224 2.8 97.1 1.0 CB A:CYS195 3.5 74.1 1.0 N A:CYS224 3.7 0.9 1.0 CB A:CYS221 3.7 83.0 1.0 CA A:CYS224 3.9 99.9 1.0 SG A:CYS224 3.9 0.8 1.0 CB A:ASP223 4.2 0.9 1.0 OG A:SER197 4.4 78.5 1.0 C A:ASP223 4.7 0.5 1.0 CB A:SER197 4.7 80.5 1.0 CB A:SER199 4.9 0.3 1.0 O A:SER197 4.9 84.3 1.0 CA A:ASP223 4.9 0.4 1.0 OD2 A:ASP223 4.9 0.0 1.0 CA A:CYS195 4.9 70.4 1.0 CG A:ASP223 5.0 0.8 1.0 N A:ASP223 5.0 99.3 1.0

Zinc binding site 2 out of 2 in the SIRT2 in Complex with A 13-Mer Trifluoroacetylated Ran Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of SIRT2 in Complex with A 13-Mer Trifluoroacetylated Ran Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1358 b:86.6 occ:1.00 SG B:CYS195 2.8 0.1 1.0 O B:HOH2041 3.0 50.6 1.0 CB B:CYS200 3.3 0.3 1.0 N B:VAL217 3.4 0.7 1.0 CA B:VAL217 3.7 0.9 1.0 N B:GLU216 4.0 0.6 1.0 CA B:SER215 4.2 0.5 1.0 C B:SER215 4.3 0.6 1.0 CB B:VAL217 4.5 0.5 1.0 C B:GLU216 4.5 0.4 1.0 CA B:CYS200 4.5 0.6 1.0 O B:SER199 4.6 1.0 1.0 CB B:CYS195 4.6 0.5 1.0 CA B:GLU216 4.7 0.6 1.0 CB B:SER215 4.7 0.1 1.0 C B:VAL217 5.0 0.1 1.0 O B:PHE214 5.0 93.6 1.0

P.Knyphausen, S.De Boor, N.Kuhlmann, L.Scislowski, A.Extra, L.Baldus, M.Schacherl, U.Baumann, I.Neundorf, M.Lammers. Insights Into Lysine-Deacetylation of Natively Folded Substrate Proteins By Sirtuins. J.Biol.Chem. V. 291 14677 2016.
ISSN: ISSN 0021-9258
PubMed: 27226597
DOI: 10.1074/JBC.M116.726307