Zinc in PDB 3pki: Human SIRT6 Crystal Structure in Complex with Adp Ribose

The structure of Human SIRT6 Crystal Structure in Complex with Adp Ribose, PDB code: 3pki 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)	29.87 / 2.04
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	77.367, 90.200, 90.180, 118.09, 91.39, 115.80
R / Rfree (%)	18.3 / 21.3

The binding sites of Zinc atom in the Human SIRT6 Crystal Structure in Complex with Adp Ribose (pdb code 3pki). 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 Crystal Structure in Complex with Adp Ribose, PDB code: 3pki:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Human SIRT6 Crystal Structure 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 Crystal Structure in Complex with Adp Ribose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1000 b:34.4 occ:1.00 SG A:CYS142 2.2 34.6 1.0 SG A:CYS164 2.3 33.5 1.0 SG A:CYS139 2.3 33.4 1.0 SG A:CYS175 2.5 46.6 1.0 CB A:CYS164 3.0 30.0 1.0 CB A:CYS139 3.0 29.1 1.0 CB A:CYS175 3.3 43.3 1.0 CB A:CYS142 3.5 31.0 1.0 N A:CYS142 3.9 31.9 1.0 CG2 A:VAL166 4.2 45.0 1.0 CA A:CYS142 4.2 31.1 1.0 CA A:CYS164 4.4 30.3 1.0 CA A:CYS139 4.5 27.9 1.0 N A:GLY177 4.6 38.2 1.0 CA A:GLY177 4.6 37.3 1.0 CA A:CYS175 4.7 43.8 1.0 CB A:THR144 4.8 31.9 1.0 OG1 A:THR144 4.8 32.4 1.0 CB A:LYS141 4.8 36.1 1.0 C A:CYS142 4.9 34.6 1.0

Zinc binding site 2 out of 6 in the Human SIRT6 Crystal Structure 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 Crystal Structure in Complex with Adp Ribose within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1000 b:42.6 occ:1.00 SG B:CYS142 2.2 41.9 1.0 SG B:CYS139 2.3 41.2 1.0 SG B:CYS164 2.4 41.4 1.0 SG B:CYS175 2.4 49.8 1.0 CB B:CYS164 3.0 37.6 1.0 CB B:CYS139 3.1 37.0 1.0 CB B:CYS175 3.2 46.1 1.0 CB B:CYS142 3.3 38.0 1.0 N B:CYS142 3.7 38.8 1.0 CA B:CYS142 4.0 37.9 1.0 CA B:CYS164 4.5 37.5 1.0 N B:GLY177 4.6 42.9 1.0 CA B:GLY177 4.6 41.9 1.0 CA B:CYS139 4.6 36.1 1.0 CA B:CYS175 4.7 46.0 1.0 C B:CYS142 4.7 40.8 1.0 OG1 B:THR144 4.7 37.3 1.0 CB B:LYS141 4.7 42.3 1.0 CB B:THR144 4.8 39.4 1.0 C B:LYS141 4.8 43.4 1.0 N B:LYS143 4.9 36.0 1.0

Zinc binding site 3 out of 6 in the Human SIRT6 Crystal Structure 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 Crystal Structure in Complex with Adp Ribose within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1000 b:42.5 occ:1.00 SG C:CYS142 2.2 41.9 1.0 SG C:CYS139 2.2 38.9 1.0 SG C:CYS164 2.3 41.5 1.0 SG C:CYS175 2.5 47.6 1.0 CB C:CYS164 2.9 37.8 1.0 CB C:CYS139 3.0 34.9 1.0 CB C:CYS175 3.4 43.8 1.0 CB C:CYS142 3.5 38.4 1.0 N C:CYS142 3.7 39.5 1.0 OG1 C:THR144 3.9 52.8 1.0 CA C:CYS142 4.1 38.5 1.0 CA C:CYS164 4.4 38.1 1.0 CA C:CYS139 4.5 34.3 1.0 CA C:GLY177 4.6 41.3 1.0 N C:GLY177 4.6 42.3 1.0 CB C:LYS141 4.7 42.2 1.0 C C:CYS142 4.8 43.0 1.0 CA C:CYS175 4.8 43.5 1.0 C C:LYS141 4.9 43.8 1.0 CB C:VAL166 4.9 51.5 1.0 N C:LYS143 4.9 39.6 1.0

Zinc binding site 4 out of 6 in the Human SIRT6 Crystal Structure 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 Crystal Structure in Complex with Adp Ribose within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1000 b:41.2 occ:1.00 SG D:CYS142 2.2 40.1 1.0 SG D:CYS139 2.2 37.0 1.0 SG D:CYS175 2.4 50.3 1.0 SG D:CYS164 2.5 39.3 1.0 CB D:CYS164 3.0 35.6 1.0 CB D:CYS139 3.0 32.9 1.0 CB D:CYS175 3.3 46.6 1.0 CB D:CYS142 3.4 36.3 1.0 N D:CYS142 3.7 36.4 1.0 CA D:CYS142 4.0 36.1 1.0 CA D:CYS139 4.5 32.4 1.0 CA D:CYS164 4.5 35.7 1.0 N D:GLY177 4.6 41.9 1.0 OG1 D:THR144 4.6 44.0 1.0 CB D:LYS141 4.7 38.6 1.0 CA D:GLY177 4.7 40.8 1.0 CA D:CYS175 4.7 46.8 1.0 C D:CYS142 4.7 39.9 1.0 C D:LYS141 4.8 40.3 1.0 CB D:THR144 4.9 41.7 1.0 N D:LYS143 4.9 36.8 1.0

Zinc binding site 5 out of 6 in the Human SIRT6 Crystal Structure 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 Crystal Structure in Complex with Adp Ribose within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1000 b:37.7 occ:1.00 SG E:CYS142 2.2 40.9 1.0 SG E:CYS139 2.3 37.4 1.0 SG E:CYS164 2.3 41.3 1.0 SG E:CYS175 2.4 44.8 1.0 CB E:CYS164 3.0 37.5 1.0 CB E:CYS139 3.1 33.2 1.0 CB E:CYS175 3.4 41.2 1.0 CB E:CYS142 3.5 37.1 1.0 N E:CYS142 3.8 36.9 1.0 CA E:CYS142 4.2 36.7 1.0 N E:GLY177 4.4 40.4 1.0 CB E:LYS141 4.4 37.4 1.0 CA E:CYS164 4.4 37.2 1.0 CA E:GLY177 4.5 39.6 1.0 CA E:CYS139 4.6 32.5 1.0 CA E:CYS175 4.8 41.2 1.0 CB E:VAL166 4.8 63.5 1.0 C E:LYS141 4.9 40.4 1.0 CB E:THR144 4.9 39.4 1.0 OG1 E:THR144 4.9 38.3 1.0 C E:CYS142 4.9 39.7 1.0 CG2 E:VAL166 5.0 63.2 1.0

Zinc binding site 6 out of 6 in the Human SIRT6 Crystal Structure 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 Crystal Structure in Complex with Adp Ribose within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn1000 b:51.3 occ:1.00 SG F:CYS142 2.2 43.8 1.0 SG F:CYS139 2.2 43.4 1.0 SG F:CYS175 2.4 61.4 1.0 SG F:CYS164 2.4 48.6 1.0 CB F:CYS164 3.0 44.6 1.0 CB F:CYS139 3.2 39.4 1.0 CB F:CYS142 3.4 40.5 1.0 CB F:CYS175 3.5 57.5 1.0 N F:CYS142 3.7 41.6 1.0 OG1 F:THR144 3.9 55.3 1.0 CA F:CYS142 4.1 40.7 1.0 CA F:CYS164 4.5 44.5 1.0 N F:GLY177 4.5 54.6 1.0 CA F:GLY177 4.5 53.9 1.0 CA F:CYS139 4.6 38.7 1.0 CB F:LYS141 4.7 45.2 1.0 C F:CYS142 4.8 45.2 1.0 C F:LYS141 4.8 45.9 1.0 CA F:CYS175 4.9 57.1 1.0 N F:LYS143 4.9 42.1 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