Zinc in PDB 4l3o: Crystal Structure of SIRT2 in Complex with the Macrocyclic Peptide S2IL5

The structure of Crystal Structure of SIRT2 in Complex with the Macrocyclic Peptide S2IL5, PDB code: 4l3o was solved by K.Yamagata, H.Nishimasu, R.Ishitani, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.59 / 2.52
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	91.180, 135.613, 148.830, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 26.3

The structure of Crystal Structure of SIRT2 in Complex with the Macrocyclic Peptide S2IL5 also contains other interesting chemical elements:

Fluorine

(F)

12 atoms

The binding sites of Zinc atom in the Crystal Structure of SIRT2 in Complex with the Macrocyclic Peptide S2IL5 (pdb code 4l3o). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of SIRT2 in Complex with the Macrocyclic Peptide S2IL5, PDB code: 4l3o:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of SIRT2 in Complex with the Macrocyclic Peptide S2IL5


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 SIRT2 in Complex with the Macrocyclic Peptide S2IL5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:66.4 occ:1.00 SG A:CYS224 2.4 60.1 1.0 SG A:CYS221 2.4 49.5 1.0 SG A:CYS200 2.4 70.1 1.0 SG A:CYS195 2.4 63.9 1.0 CB A:CYS200 3.0 49.7 1.0 CB A:CYS195 3.2 44.5 1.0 CB A:CYS221 3.3 48.8 1.0 CB A:CYS224 3.7 69.8 1.0 N A:CYS224 3.9 67.3 1.0 CA A:CYS224 4.3 69.6 1.0 CA A:CYS200 4.5 64.1 1.0 CB A:HIS202 4.5 66.2 1.0 CB A:SER197 4.6 65.7 1.0 CB A:SER226 4.6 54.2 1.0 N A:ARG201 4.6 69.0 1.0 CB A:ASP223 4.6 69.7 1.0 N A:HIS202 4.7 56.6 1.0 CA A:CYS195 4.7 47.6 1.0 CA A:CYS221 4.7 57.7 1.0 C A:CYS224 4.8 74.6 1.0 N A:SER226 4.8 54.8 1.0 C A:CYS200 4.9 67.7 1.0 OH A:TYR204 4.9 59.6 1.0 N A:GLN225 4.9 71.2 1.0 OG A:SER226 4.9 55.9 1.0 C A:ASP223 5.0 72.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of SIRT2 in Complex with the Macrocyclic Peptide S2IL5


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 SIRT2 in Complex with the Macrocyclic Peptide S2IL5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:58.5 occ:1.00 SG B:CYS200 2.3 65.8 1.0 SG B:CYS224 2.4 81.8 1.0 SG B:CYS221 2.4 56.1 1.0 SG B:CYS195 2.4 82.3 1.0 CB B:CYS200 2.8 52.5 1.0 CB B:CYS221 3.0 57.3 1.0 CB B:CYS195 3.4 58.7 1.0 N B:CYS224 3.9 78.5 1.0 CB B:CYS224 3.9 77.7 1.0 CB B:SER226 4.2 59.4 1.0 OG B:SER197 4.3 72.7 1.0 CA B:CYS200 4.3 56.8 1.0 CA B:CYS224 4.3 84.0 1.0 CA B:CYS221 4.5 58.1 1.0 N B:SER226 4.5 76.3 1.0 CB B:ASP223 4.6 70.8 1.0 C B:CYS224 4.7 73.6 1.0 CA B:CYS195 4.8 55.1 1.0 CB B:HIS202 4.8 70.2 1.0 N B:GLN225 4.8 75.5 1.0 CA B:SER226 4.9 64.5 1.0 N B:ASP223 4.9 75.1 1.0 C B:ASP223 4.9 73.4 1.0 C B:CYS200 4.9 69.1 1.0 N B:ARG201 5.0 59.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of SIRT2 in Complex with the Macrocyclic Peptide S2IL5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of SIRT2 in Complex with the Macrocyclic Peptide S2IL5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:70.9 occ:1.00 SG C:CYS221 2.3 60.5 1.0 SG C:CYS224 2.4 0.9 1.0 SG C:CYS200 2.5 97.7 1.0 SG C:CYS195 2.5 86.3 1.0 CB C:CYS221 3.1 67.4 1.0 CB C:CYS195 3.3 72.1 1.0 CB C:CYS200 3.4 62.5 1.0 N C:CYS224 3.7 87.6 1.0 CB C:CYS224 3.7 97.8 1.0 CA C:CYS224 4.2 82.8 1.0 CB C:ASP223 4.4 90.4 1.0 CA C:CYS221 4.5 64.3 1.0 N C:GLN225 4.6 75.5 1.0 CB C:HIS202 4.6 75.5 1.0 N C:HIS202 4.6 77.4 1.0 C C:CYS224 4.7 80.5 1.0 N C:ARG201 4.7 87.3 1.0 N C:SER226 4.7 75.3 1.0 C C:ASP223 4.7 96.5 1.0 CA C:CYS200 4.8 77.1 1.0 CA C:CYS195 4.8 59.1 1.0 N C:ASP223 4.8 80.1 1.0 OH C:TYR204 4.8 75.0 1.0 CB C:SER226 4.8 59.8 1.0 CA C:ASP223 4.9 86.1 1.0 C C:CYS200 4.9 88.5 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of SIRT2 in Complex with the Macrocyclic Peptide S2IL5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of SIRT2 in Complex with the Macrocyclic Peptide S2IL5 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:59.0 occ:1.00 SG D:CYS221 2.4 63.9 1.0 SG D:CYS200 2.4 73.8 1.0 SG D:CYS224 2.4 82.7 1.0 SG D:CYS195 2.4 55.7 1.0 CB D:CYS221 3.1 57.6 1.0 CB D:CYS200 3.2 53.6 1.0 CB D:CYS195 3.3 55.2 1.0 N D:CYS224 3.7 80.0 1.0 CB D:CYS224 3.8 73.5 1.0 CB D:ASP223 4.2 69.2 1.0 CA D:CYS224 4.2 81.9 1.0 CA D:CYS221 4.6 67.7 1.0 CB D:HIS202 4.6 61.1 1.0 CB D:SER226 4.6 52.7 1.0 C D:CYS224 4.7 83.5 1.0 N D:SER226 4.7 71.6 1.0 N D:GLN225 4.7 73.7 1.0 CA D:CYS200 4.7 62.0 1.0 CA D:CYS195 4.7 52.4 1.0 C D:ASP223 4.8 80.5 1.0 CA D:ASP223 4.8 76.0 1.0 CB D:SER197 4.8 59.8 1.0 N D:ASP223 4.9 72.2 1.0 N D:HIS202 4.9 55.2 1.0 N D:ARG201 5.0 62.4 1.0

K.Yamagata, Y.Goto, H.Nishimasu, J.Morimoto, R.Ishitani, N.Dohmae, N.Takeda, R.Nagai, I.Komuro, H.Suga, O.Nureki. Structural Basis For Potent Inhibition of SIRT2 Deacetylase By A Macrocyclic Peptide Inducing Dynamic Structural Change Structure V. 22 345 2013.
ISSN: ISSN 0969-2126
PubMed: 24389023
DOI: 10.1016/J.STR.2013.12.001