Zinc in PDB 6xv6: Human SIRT6 3-318 in Complex with Adp-Ribose

All present enzymatic activity of Human SIRT6 3-318 in Complex with Adp-Ribose:
2.3.1.286;

The structure of Human SIRT6 3-318 in Complex with Adp-Ribose, PDB code: 6xv6 was solved by W.You, C.Steegborn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.72 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.689, 136.310, 90.096, 90.00, 117.37, 90.00
R / Rfree (%)	20 / 22.5

The binding sites of Zinc atom in the Human SIRT6 3-318 in Complex with Adp-Ribose (pdb code 6xv6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Human SIRT6 3-318 in Complex with Adp-Ribose, PDB code: 6xv6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Human SIRT6 3-318 in Complex with Adp-Ribose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human SIRT6 3-318 in Complex with Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:38.4 occ:1.00 SG A:CYS144 2.0 35.6 1.0 SG A:CYS141 2.3 35.9 1.0 SG A:CYS166 2.4 35.6 1.0 SG A:CYS177 2.4 43.0 1.0 CB A:CYS166 3.0 31.8 1.0 CB A:CYS141 3.1 35.8 1.0 CB A:CYS177 3.3 47.6 1.0 CB A:CYS144 3.4 42.3 1.0 N A:CYS144 3.8 42.0 1.0 CA A:CYS144 4.1 40.0 1.0 N A:GLY179 4.4 42.6 1.0 CA A:CYS166 4.5 34.5 1.0 CA A:GLY179 4.5 41.1 1.0 CA A:CYS141 4.6 33.1 1.0 CB A:LYS143 4.7 47.2 1.0 CA A:CYS177 4.7 43.8 1.0 OG1 A:THR146 4.8 36.0 1.0 C A:CYS144 4.8 41.5 1.0 C A:LYS143 4.8 44.4 1.0 CB A:THR146 4.9 36.7 1.0 CB A:VAL168 4.9 51.6 1.0 N A:LYS145 5.0 42.9 1.0

Zinc binding site 2 out of 6 in the Human SIRT6 3-318 in Complex with Adp-Ribose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human SIRT6 3-318 in Complex with Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:45.0 occ:1.00 SG B:CYS144 2.0 42.4 1.0 SG B:CYS166 2.3 47.1 1.0 SG B:CYS141 2.3 42.0 1.0 SG B:CYS177 2.4 50.3 1.0 CB B:CYS166 3.0 45.4 1.0 CB B:CYS141 3.1 42.0 1.0 CB B:CYS177 3.3 56.0 1.0 CB B:CYS144 3.3 46.9 1.0 N B:CYS144 3.8 49.2 1.0 CA B:CYS144 4.1 42.2 1.0 CA B:CYS166 4.5 45.6 1.0 N B:GLY179 4.5 47.0 1.0 CA B:CYS141 4.6 40.4 1.0 CA B:GLY179 4.6 45.5 1.0 CA B:CYS177 4.7 56.3 1.0 OG1 B:THR146 4.7 36.8 1.0 CB B:LYS143 4.8 58.3 1.0 C B:CYS144 4.8 51.7 1.0 CB B:THR146 4.8 37.9 1.0 C B:LYS143 4.9 53.7 1.0 N B:LYS145 5.0 48.5 1.0 CB B:VAL168 5.0 59.9 1.0

Zinc binding site 3 out of 6 in the Human SIRT6 3-318 in Complex with Adp-Ribose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human SIRT6 3-318 in Complex with Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:37.0 occ:1.00 SG C:CYS144 1.9 34.0 1.0 SG C:CYS141 2.3 35.2 1.0 SG C:CYS177 2.4 42.5 1.0 SG C:CYS166 2.4 35.6 1.0 CB C:CYS166 3.0 33.1 1.0 CB C:CYS141 3.1 34.6 1.0 CB C:CYS177 3.2 44.4 1.0 CB C:CYS144 3.3 39.9 1.0 N C:CYS144 3.7 41.8 1.0 CA C:CYS144 4.0 37.5 1.0 N C:GLY179 4.4 37.2 1.0 CA C:CYS166 4.5 33.4 1.0 CA C:CYS141 4.5 30.6 1.0 CA C:GLY179 4.5 35.9 1.0 CA C:CYS177 4.7 44.3 1.0 CB C:LYS143 4.7 41.5 1.0 C C:CYS144 4.8 36.1 1.0 C C:LYS143 4.8 41.0 1.0 OG1 C:THR146 4.8 34.8 1.0 CB C:THR146 4.9 34.3 1.0 N C:LYS145 4.9 35.2 1.0 C C:CYS177 5.0 39.0 1.0

Zinc binding site 4 out of 6 in the Human SIRT6 3-318 in Complex with Adp-Ribose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human SIRT6 3-318 in Complex with Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn402 b:39.2 occ:1.00 SG D:CYS144 2.0 31.9 1.0 SG D:CYS141 2.3 35.3 1.0 SG D:CYS177 2.4 40.4 1.0 SG D:CYS166 2.4 37.2 1.0 CB D:CYS166 3.0 34.9 1.0 CB D:CYS141 3.1 40.6 1.0 CB D:CYS177 3.3 43.1 1.0 CB D:CYS144 3.4 40.0 1.0 N D:CYS144 3.8 47.9 1.0 CA D:CYS144 4.1 41.5 1.0 N D:GLY179 4.4 45.2 1.0 CA D:CYS166 4.5 34.6 1.0 CA D:GLY179 4.5 40.9 1.0 CA D:CYS141 4.5 36.4 1.0 CB D:LYS143 4.7 42.7 1.0 CA D:CYS177 4.7 44.0 1.0 OG1 D:THR146 4.8 42.4 1.0 C D:CYS144 4.8 44.5 1.0 C D:LYS143 4.9 43.1 1.0 CB D:THR146 4.9 41.4 1.0 N D:LYS145 5.0 44.2 1.0

Zinc binding site 5 out of 6 in the Human SIRT6 3-318 in Complex with Adp-Ribose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human SIRT6 3-318 in Complex with Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn402 b:43.8 occ:1.00 SG E:CYS144 2.0 38.0 1.0 SG E:CYS141 2.3 43.4 1.0 SG E:CYS166 2.4 42.8 1.0 SG E:CYS177 2.4 50.8 1.0 CB E:CYS166 3.0 42.9 1.0 CB E:CYS141 3.0 44.8 1.0 CB E:CYS144 3.3 43.6 1.0 CB E:CYS177 3.4 51.4 1.0 N E:CYS144 3.7 49.6 1.0 CA E:CYS144 4.1 44.2 1.0 CG2 E:VAL168 4.3 58.0 1.0 N E:GLY179 4.4 45.2 1.0 CA E:CYS166 4.5 44.8 1.0 CA E:CYS141 4.5 43.2 1.0 CA E:GLY179 4.5 46.8 1.0 CB E:LYS143 4.7 58.5 1.0 CG1 E:VAL168 4.7 57.4 1.0 CA E:CYS177 4.8 49.3 1.0 C E:CYS144 4.8 42.9 1.0 OG1 E:THR146 4.8 42.9 1.0 C E:LYS143 4.8 54.4 1.0 CB E:THR146 4.9 41.0 1.0 N E:LYS145 4.9 43.2 1.0

Zinc binding site 6 out of 6 in the Human SIRT6 3-318 in Complex with Adp-Ribose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Human SIRT6 3-318 in Complex with Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn402 b:38.5 occ:1.00 SG F:CYS144 2.0 41.2 1.0 SG F:CYS166 2.3 37.3 1.0 SG F:CYS141 2.3 33.9 1.0 SG F:CYS177 2.4 41.5 1.0 CB F:CYS166 3.0 36.6 1.0 CB F:CYS141 3.1 33.2 1.0 CB F:CYS177 3.3 41.6 1.0 CB F:CYS144 3.4 41.3 1.0 N F:CYS144 3.8 43.6 1.0 CA F:CYS144 4.1 41.2 1.0 CA F:CYS166 4.4 39.6 1.0 N F:GLY179 4.5 36.7 1.0 CA F:CYS141 4.6 34.1 1.0 CA F:GLY179 4.6 39.7 1.0 CA F:CYS177 4.7 45.7 1.0 CB F:LYS143 4.8 44.8 1.0 OG1 F:THR146 4.8 44.8 1.0 C F:CYS144 4.8 43.8 1.0 C F:LYS143 4.9 43.0 1.0 CB F:THR146 4.9 39.9 1.0 CB F:VAL168 4.9 51.7 1.0 N F:LYS145 5.0 39.8 1.0

W.You, C.Steegborn. Crystal Structures of SIRT6 Complexes with the Allosteric Activator Mdl-801 Reveal Binding Site and Interaction Details To Be Published.