Zinc in PDB 3k35: Crystal Structure of Human SIRT6

The structure of Crystal Structure of Human SIRT6, PDB code: 3k35 was solved by P.W.Pan, A.Dong, W.Qiu, P.Loppnau, J.Wang, M.Ravichandran, A.Bochkarev, C.Bountra, J.Weigelt, C.H.Arrowsmith, J.Min, A.M.Edwards, Structuralgenomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.95 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.388, 136.266, 89.260, 90.00, 119.87, 90.00
R / Rfree (%)	20.2 / 26.7

The binding sites of Zinc atom in the Crystal Structure of Human SIRT6 (pdb code 3k35). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Human SIRT6, PDB code: 3k35:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Human SIRT6


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 SIRT6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn317 b:50.1 occ:1.00 SG A:CYS142 1.9 38.9 1.0 SG A:CYS139 2.3 41.3 1.0 SG A:CYS175 2.4 50.3 1.0 SG A:CYS164 2.5 46.5 1.0 CB A:CYS139 3.1 38.1 1.0 CB A:CYS164 3.2 47.1 1.0 CB A:CYS142 3.3 41.6 1.0 CB A:CYS175 3.4 48.5 1.0 N A:CYS142 3.6 41.8 1.0 CA A:CYS142 4.0 41.3 1.0 CB A:LYS141 4.5 41.8 1.0 N A:GLY177 4.5 45.0 1.0 OG1 A:THR144 4.6 42.0 1.0 CA A:CYS139 4.6 38.3 1.0 CA A:CYS164 4.7 47.2 1.0 CA A:GLY177 4.7 44.2 1.0 C A:LYS141 4.7 41.7 1.0 CA A:CYS175 4.8 48.6 1.0 C A:CYS142 4.8 41.7 1.0 N A:LYS143 4.9 41.8 1.0 CB A:VAL166 5.0 50.9 1.0 CA A:LYS141 5.0 41.6 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Human SIRT6


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 SIRT6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn317 b:46.2 occ:1.00 SG B:CYS142 1.9 43.4 1.0 SG B:CYS164 2.3 42.2 1.0 SG B:CYS175 2.4 44.7 1.0 SG B:CYS139 2.4 39.5 1.0 CB B:CYS164 3.0 44.5 1.0 CB B:CYS175 3.2 46.1 1.0 CB B:CYS139 3.2 35.3 1.0 CB B:CYS142 3.3 40.3 1.0 N B:CYS142 3.8 40.6 1.0 CA B:CYS142 4.1 41.0 1.0 CG2 B:VAL166 4.3 50.8 1.0 CA B:CYS164 4.5 44.7 1.0 N B:GLY177 4.6 42.9 1.0 CA B:CYS175 4.6 46.3 1.0 CA B:GLY177 4.6 41.9 1.0 CA B:CYS139 4.7 34.8 1.0 CB B:LYS141 4.7 38.5 1.0 OG1 B:THR144 4.7 37.0 1.0 C B:CYS142 4.8 40.6 1.0 N B:LYS143 4.9 40.3 1.0 CB B:THR144 4.9 36.1 1.0 C B:LYS141 5.0 39.8 1.0 C B:CYS175 5.0 46.0 1.0 OH B:TYR146 5.0 38.0 1.0 C B:CYS164 5.0 45.7 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Human SIRT6


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 Human SIRT6 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn317 b:40.8 occ:1.00 SG C:CYS142 2.2 39.8 1.0 SG C:CYS139 2.2 33.3 1.0 SG C:CYS164 2.4 39.9 1.0 SG C:CYS175 2.5 43.1 1.0 CB C:CYS164 3.1 38.8 1.0 CB C:CYS139 3.1 30.7 1.0 CB C:CYS175 3.4 45.2 1.0 CB C:CYS142 3.4 37.5 1.0 N C:CYS142 3.8 38.0 1.0 OG1 C:THR144 3.8 40.1 1.0 CA C:CYS142 4.2 37.5 1.0 N C:GLY177 4.4 42.1 1.0 CA C:CYS164 4.6 38.8 1.0 CA C:CYS139 4.6 31.6 1.0 CA C:GLY177 4.6 41.2 1.0 CB C:LYS141 4.6 37.8 1.0 CA C:CYS175 4.8 45.2 1.0 CG2 C:VAL166 4.8 44.7 1.0 C C:CYS142 4.9 36.4 1.0 C C:LYS141 4.9 38.0 1.0 N C:LYS143 5.0 36.7 1.0 C C:CYS175 5.0 44.9 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Human SIRT6


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 Human SIRT6 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn317 b:58.9 occ:1.00 SG D:CYS142 2.1 45.1 1.0 SG D:CYS139 2.2 43.2 1.0 SG D:CYS164 2.4 48.1 1.0 SG D:CYS175 2.4 49.1 1.0 CB D:CYS164 2.9 48.3 1.0 CB D:CYS139 3.1 41.7 1.0 CB D:CYS142 3.3 44.9 1.0 CB D:CYS175 3.5 48.6 1.0 N D:CYS142 3.7 45.0 1.0 OG1 D:THR144 3.9 45.2 1.0 CA D:CYS142 4.0 44.5 1.0 N D:GLY177 4.4 47.1 1.0 CA D:CYS164 4.4 48.4 1.0 CA D:CYS139 4.6 41.9 1.0 C D:CYS142 4.7 44.1 1.0 CA D:GLY177 4.7 45.6 1.0 CB D:LYS141 4.7 45.1 1.0 CA D:CYS175 4.8 48.6 1.0 N D:LYS143 4.9 43.7 1.0 C D:LYS141 4.9 45.1 1.0 C D:CYS175 4.9 48.6 1.0 N D:ARG176 5.0 48.2 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Human SIRT6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Human SIRT6 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn317 b:45.1 occ:1.00 SG E:CYS142 2.3 29.7 1.0 SG E:CYS164 2.4 42.1 1.0 SG E:CYS139 2.4 34.7 1.0 SG E:CYS175 2.5 45.2 1.0 CB E:CYS139 3.2 34.3 1.0 CB E:CYS164 3.2 41.9 1.0 CB E:CYS175 3.2 48.3 1.0 CB E:CYS142 3.2 37.0 1.0 N E:CYS142 3.6 38.5 1.0 CA E:CYS142 3.9 37.3 1.0 OG1 E:THR144 4.0 41.8 1.0 C E:CYS142 4.6 38.3 1.0 N E:LYS143 4.6 39.1 1.0 N E:GLY177 4.6 45.9 1.0 CA E:CYS175 4.7 48.4 1.0 CA E:CYS164 4.7 41.9 1.0 CA E:CYS139 4.7 34.2 1.0 C E:LYS141 4.7 39.0 1.0 CA E:GLY177 4.8 44.8 1.0 CB E:LYS141 4.8 39.5 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Human SIRT6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Human SIRT6 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn317 b:46.8 occ:1.00 SG F:CYS139 2.2 39.1 1.0 SG F:CYS164 2.2 44.4 1.0 SG F:CYS142 2.2 46.0 1.0 SG F:CYS175 2.3 43.1 1.0 CB F:CYS164 2.9 45.1 1.0 CB F:CYS139 3.1 37.3 1.0 CB F:CYS175 3.1 45.0 1.0 CB F:CYS142 3.4 41.4 1.0 N F:CYS142 3.8 41.6 1.0 CA F:CYS142 4.2 41.7 1.0 N F:GLY177 4.3 43.7 1.0 CA F:CYS164 4.4 45.2 1.0 CB F:LYS141 4.4 41.6 1.0 CA F:GLY177 4.5 43.3 1.0 CA F:CYS175 4.5 45.4 1.0 CA F:CYS139 4.5 37.7 1.0 CB F:THR144 4.7 33.8 1.0 C F:CYS142 4.8 40.9 1.0 C F:LYS141 4.8 41.8 1.0 C F:CYS175 4.8 45.2 1.0 OG1 F:THR144 4.8 35.7 1.0 CG2 F:VAL166 4.9 47.5 1.0 CA F:LYS141 5.0 41.6 1.0

P.W.Pan, J.L.Feldman, M.K.Devries, A.Dong, A.M.Edwards, J.M.Denu. Structure and Biochemical Functions of SIRT6. J.Biol.Chem. V. 286 14575 2011.
ISSN: ISSN 0021-9258
PubMed: 21362626
DOI: 10.1074/JBC.M111.218990