Zinc in PDB 8v15: Human SIRT3 Bound to P53-Amc Peptide, Carba-Nad, and Honokiol

The structure of Human SIRT3 Bound to P53-Amc Peptide, Carba-Nad, and Honokiol, PDB code: 8v15 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)	44.16 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	34.683, 159.432, 53.047, 90, 90.61, 90
R / Rfree (%)	19.4 / 30.3

The binding sites of Zinc atom in the Human SIRT3 Bound to P53-Amc Peptide, Carba-Nad, and Honokiol (pdb code 8v15). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human SIRT3 Bound to P53-Amc Peptide, Carba-Nad, and Honokiol, PDB code: 8v15:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human SIRT3 Bound to P53-Amc Peptide, Carba-Nad, 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, Carba-Nad, and Honokiol within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:61.5 occ:1.00 SG A:CYS259 2.1 54.2 1.0 SG A:CYS280 2.2 53.9 1.0 SG A:CYS283 2.4 72.3 1.0 CB A:CYS259 2.5 59.0 1.0 SG A:CYS256 2.6 46.8 1.0 CB A:CYS280 3.0 51.0 1.0 CB A:CYS256 3.4 32.6 1.0 N A:CYS259 3.5 86.3 1.0 CB A:CYS283 3.5 77.5 1.0 CA A:CYS259 3.6 74.4 1.0 N A:CYS283 3.8 78.4 1.0 CA A:CYS283 4.1 88.2 1.0 CB A:VAL282 4.2 68.2 1.0 C A:CYS259 4.4 67.2 1.0 CG1 A:VAL282 4.5 92.5 1.0 CA A:CYS280 4.5 58.8 1.0 N A:GLY285 4.7 67.7 1.0 C A:VAL258 4.7 91.2 1.0 N A:GLN260 4.7 72.4 1.0 C A:CYS283 4.7 73.1 1.0 C A:VAL282 4.8 85.5 1.0 N A:THR284 4.8 61.7 1.0 CA A:CYS256 4.8 39.8 1.0 CB A:VAL258 4.8 72.2 1.0 CA A:VAL282 4.9 66.6 1.0

Zinc binding site 2 out of 2 in the Human SIRT3 Bound to P53-Amc Peptide, Carba-Nad, and Honokiol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human SIRT3 Bound to P53-Amc Peptide, Carba-Nad, and Honokiol within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:52.8 occ:1.00 SG C:CYS280 2.0 43.4 1.0 SG C:CYS283 2.2 70.9 1.0 SG C:CYS259 2.3 47.2 1.0 SG C:CYS256 2.4 59.4 1.0 CB C:CYS259 2.9 39.9 1.0 CB C:CYS280 2.9 46.5 1.0 CB C:CYS256 3.2 43.2 1.0 CB C:CYS283 3.4 59.8 1.0 N C:CYS259 3.6 60.3 1.0 N C:CYS283 3.7 49.0 1.0 CA C:CYS259 3.8 60.0 1.0 CB C:VAL282 4.0 90.1 1.0 CA C:CYS283 4.0 50.6 1.0 CA C:CYS280 4.4 59.8 1.0 CG1 C:VAL282 4.6 94.1 1.0 C C:CYS283 4.6 55.1 1.0 N C:GLY285 4.6 82.6 1.0 C C:CYS259 4.6 53.8 1.0 C C:VAL282 4.6 76.0 1.0 CA C:CYS256 4.7 41.3 1.0 CA C:VAL282 4.7 79.3 1.0 CG2 C:VAL282 4.8 83.5 1.0 N C:THR284 4.8 58.1 1.0 C C:VAL258 4.8 63.3 1.0 N C:VAL282 4.9 73.3 1.0 N C:GLN260 4.9 64.0 1.0 CB C:VAL258 4.9 65.4 1.0 CA C:GLY285 5.0 59.1 1.0

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. Computationally Driven Discovery and Characterization of SIRT3 Activating Compounds That Fully Recover Catalytic Activity Under Nad+ Depletion Biorxiv 2023.
ISSN: ISSN 2692-8205
DOI: 10.1101/2023.11.09.566481