Zinc in PDB 8v5u: Human SIRT3 Bound to P53-Amc Peptide and Honokiol

The structure of Human SIRT3 Bound to P53-Amc Peptide and Honokiol, PDB code: 8v5u was solved by R.Chakrabarti, A.Ghosh, X.Guan, A.Upadhyay, R.K.Dumpati, S.Munshi, S.Roy, S.Chall, A.Rahnamoun, C.Reverdy, G.Errasti, T.Delacroix, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	68.69 / 1.48
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	34.452, 52.901, 68.753, 90, 92.52, 90
R / Rfree (%)	22.6 / 24.6

The binding sites of Zinc atom in the Human SIRT3 Bound to P53-Amc Peptide and Honokiol (pdb code 8v5u). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Human SIRT3 Bound to P53-Amc Peptide and Honokiol, PDB code: 8v5u:

Zinc binding site 1 out of 1 in the Human SIRT3 Bound to P53-Amc Peptide and Honokiol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human SIRT3 Bound to P53-Amc Peptide and Honokiol within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:21.8 occ:1.00 SG A:CYS259 2.3 24.2 1.0 SG A:CYS256 2.3 19.6 1.0 SG A:CYS280 2.3 24.8 1.0 SG A:CYS283 2.3 21.4 1.0 CB A:CYS280 3.1 22.9 1.0 CB A:CYS256 3.2 18.8 1.0 CB A:CYS259 3.2 27.5 1.0 N A:CYS259 3.6 22.4 1.0 CB A:CYS283 3.6 20.5 1.0 N A:CYS283 3.8 22.4 1.0 CA A:CYS259 3.9 25.6 1.0 CA A:CYS283 4.2 21.3 1.0 CB A:VAL282 4.4 28.5 1.0 CA A:CYS280 4.5 23.3 1.0 CA A:CYS256 4.6 18.3 1.0 C A:CYS259 4.6 24.3 1.0 N A:GLY285 4.6 27.0 1.0 N A:GLN260 4.8 25.8 1.0 C A:VAL258 4.8 23.4 1.0 C A:CYS283 4.8 22.6 1.0 C A:VAL282 4.8 26.4 1.0 N A:THR284 4.8 25.9 1.0 CB A:ARG261 4.8 23.9 1.0 CB A:VAL258 4.9 20.9 1.0 N A:VAL282 4.9 26.6 1.0 CA A:VAL282 4.9 28.0 1.0 CA A:GLY285 4.9 26.4 1.0

X.Guan, R.K.Dumpati, S.Munshi, S.Chall, R.Bose, A.Rahnamoun, C.Reverdy, G.Errasti, T.Delacroix, A.Ghosh, R.Chakrabarti. Computationally Driven Discovery and Characterization of SIRT3-Activating Compounds That Fully Recover Catalytic Activity Under ${\Mathrm{Nad}}^{+}$ Depletion Phys. Rev. X V. 14 2024.
DOI: 10.1103/PHYSREVX.14.041019