Zinc in the structure of Human SIRT6 Crystal Structure in Complex With Adp Ribose (pdb 3pki)

The binding sites of Zinc atom in the structure of Human SIRT6 Crystal Structure in Complex With Adp Ribose (pdb code 3pki). This binding sites where shown with 5.0 Angstroms radius around Zinc atom. The 3pki structure 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, brief refinement statistics is given in the table below: Resolution (A) 29.9-2.0 Space group P1 a (A) 77.367 b (A) 90.200 c (A) 90.180 alpha (°) 118.09 beta (°) 91.39 gamma (°) 115.80 Rfactor (%) 18.3 Rfree (%) 21.3 Zinc Binding Sites: Zinc binding site 1 out of 6 in 3pki Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 3pki. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Cys139, A: Lys141, A: Cys142, A: Thr144, A: Cys164, A: Val166, A: Cys175, A: Gly177, conact list: Atom Atom Distance (A) Zn CB A:Cys139 3.03 Zn SG A:Cys139 2.29 Zn CA A:Cys139 4.51 Zn CB A:Lys141 4.83 Zn N A:Cys142 3.87 Zn CB A:Cys142 3.49 Zn SG A:Cys142 2.16 Zn C A:Cys142 4.93 Zn CA A:Cys142 4.22 Zn CB A:Thr144 4.79 Zn OG1 A:Thr144 4.82 Zn CB A:Cys164 2.97 Zn SG A:Cys164 2.28 Zn CA A:Cys164 4.44 Zn CG2 A:Val166 4.16 Zn CB A:Cys175 3.27 Zn SG A:Cys175 2.48 Zn CA A:Cys175 4.72 Zn N A:Gly177 4.58 Zn CA A:Gly177 4.65 interactive model: Zinc binding site 2 out of 6 in 3pki Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 3pki. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Cys139, B: Lys141, B: Cys142, B: Lys143, B: Thr144, B: Cys164, B: Cys175, B: Gly177, conact list: Atom Atom Distance (A) Zn CB B:Cys139 3.14 Zn SG B:Cys139 2.30 Zn CA B:Cys139 4.60 Zn C B:Lys141 4.82 Zn CB B:Lys141 4.74 Zn N B:Cys142 3.66 Zn CB B:Cys142 3.31 Zn SG B:Cys142 2.18 Zn C B:Cys142 4.70 Zn CA B:Cys142 4.01 Zn N B:Lys143 4.89 Zn CB B:Thr144 4.81 Zn OG1 B:Thr144 4.72 Zn CB B:Cys164 2.98 Zn SG B:Cys164 2.36 Zn CA B:Cys164 4.48 Zn CB B:Cys175 3.22 Zn SG B:Cys175 2.40 Zn CA B:Cys175 4.67 Zn N B:Gly177 4.55 Zn CA B:Gly177 4.59 interactive model: Zinc binding site 3 out of 6 in 3pki Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Zinc in the PDB 3pki. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Cys139, C: Lys141, C: Cys142, C: Lys143, C: Thr144, C: Cys164, C: Val166, C: Cys175, C: Gly177, conact list: Atom Atom Distance (A) Zn CB C:Cys139 3.02 Zn SG C:Cys139 2.21 Zn CA C:Cys139 4.49 Zn C C:Lys141 4.85 Zn CB C:Lys141 4.71 Zn N C:Cys142 3.72 Zn CB C:Cys142 3.47 Zn SG C:Cys142 2.16 Zn C C:Cys142 4.78 Zn CA C:Cys142 4.11 Zn N C:Lys143 4.93 Zn OG1 C:Thr144 3.90 Zn CB C:Cys164 2.93 Zn SG C:Cys164 2.30 Zn CA C:Cys164 4.42 Zn CB C:Val166 4.92 Zn CB C:Cys175 3.35 Zn SG C:Cys175 2.50 Zn CA C:Cys175 4.79 Zn N C:Gly177 4.59 Zn CA C:Gly177 4.58 interactive model: Zinc binding site 4 out of 6 in 3pki Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Zinc in the PDB 3pki. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Cys139, D: Lys141, D: Cys142, D: Lys143, D: Thr144, D: Cys164, D: Cys175, D: Gly177, conact list: Atom Atom Distance (A) Zn CB D:Cys139 3.02 Zn SG D:Cys139 2.18 Zn CA D:Cys139 4.48 Zn C D:Lys141 4.75 Zn CB D:Lys141 4.66 Zn N D:Cys142 3.65 Zn CB D:Cys142 3.36 Zn SG D:Cys142 2.16 Zn C D:Cys142 4.74 Zn CA D:Cys142 4.03 Zn N D:Lys143 4.94 Zn CB D:Thr144 4.87 Zn OG1 D:Thr144 4.58 Zn CB D:Cys164 3.00 Zn SG D:Cys164 2.45 Zn CA D:Cys164 4.50 Zn CB D:Cys175 3.27 Zn SG D:Cys175 2.41 Zn CA D:Cys175 4.68 Zn N D:Gly177 4.56 Zn CA D:Gly177 4.66 interactive model: Zinc binding site 5 out of 6 in 3pki Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Zinc in the PDB 3pki. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: E: Cys139, E: Lys141, E: Cys142, E: Thr144, E: Cys164, E: Val166, E: Cys175, E: Gly177, conact list: Atom Atom Distance (A) Zn CB E:Cys139 3.12 Zn SG E:Cys139 2.27 Zn CA E:Cys139 4.58 Zn CB E:Lys141 4.43 Zn C E:Lys141 4.85 Zn N E:Cys142 3.76 Zn CB E:Cys142 3.48 Zn SG E:Cys142 2.18 Zn C E:Cys142 4.92 Zn CA E:Cys142 4.17 Zn CB E:Thr144 4.88 Zn OG1 E:Thr144 4.90 Zn CB E:Cys164 2.95 Zn SG E:Cys164 2.33 Zn CA E:Cys164 4.44 Zn CB E:Val166 4.82 Zn CG2 E:Val166 4.97 Zn CB E:Cys175 3.39 Zn SG E:Cys175 2.36 Zn CA E:Cys175 4.77 Zn N E:Gly177 4.39 Zn CA E:Gly177 4.50 interactive model: Zinc binding site 6 out of 6 in 3pki Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Zinc in the PDB 3pki. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: F: Cys139, F: Lys141, F: Cys142, F: Lys143, F: Thr144, F: Cys164, F: Cys175, F: Gly177, conact list: Atom Atom Distance (A) Zn CB F:Cys139 3.16 Zn SG F:Cys139 2.23 Zn CA F:Cys139 4.61 Zn C F:Lys141 4.84 Zn CB F:Lys141 4.73 Zn N F:Cys142 3.72 Zn CB F:Cys142 3.40 Zn SG F:Cys142 2.16 Zn C F:Cys142 4.82 Zn CA F:Cys142 4.10 Zn N F:Lys143 4.93 Zn OG1 F:Thr144 3.86 Zn CB F:Cys164 2.99 Zn SG F:Cys164 2.43 Zn CA F:Cys164 4.49 Zn CB F:Cys175 3.52 Zn SG F:Cys175 2.42 Zn CA F:Cys175 4.91 Zn N F:Gly177 4.51 Zn CA F:Gly177 4.54 interactive model: