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Zinc in PDB 8v2n: Human SIRT3 Co-Crystallized with Ligands, Including P53-Amc Peptide and Carba-Nad

Protein crystallography data

The structure of Human SIRT3 Co-Crystallized with Ligands, Including P53-Amc Peptide and Carba-Nad, PDB code: 8v2n 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) 42.04 / 1.74
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 34.339, 53.178, 68.539, 90, 91.75, 90
R / Rfree (%) 24.2 / 28.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Human SIRT3 Co-Crystallized with Ligands, Including P53-Amc Peptide and Carba-Nad (pdb code 8v2n). 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 Co-Crystallized with Ligands, Including P53-Amc Peptide and Carba-Nad, PDB code: 8v2n:

Zinc binding site 1 out of 1 in 8v2n

Go back to Zinc Binding Sites List in 8v2n
Zinc binding site 1 out of 1 in the Human SIRT3 Co-Crystallized with Ligands, Including P53-Amc Peptide and Carba-Nad


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human SIRT3 Co-Crystallized with Ligands, Including P53-Amc Peptide and Carba-Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:27.1
occ:1.00
SG A:CYS280 2.3 27.4 1.0
SG A:CYS259 2.3 31.9 1.0
SG A:CYS256 2.3 24.7 1.0
SG A:CYS283 2.3 28.3 1.0
CB A:CYS280 3.1 25.5 1.0
CB A:CYS256 3.1 22.5 1.0
CB A:CYS259 3.3 30.6 1.0
CB A:CYS283 3.4 30.9 1.0
N A:CYS259 3.7 30.5 1.0
N A:CYS283 3.8 32.8 1.0
CA A:CYS259 4.0 29.2 1.0
CA A:CYS283 4.1 32.6 1.0
CB A:VAL282 4.3 37.0 1.0
CA A:CYS280 4.5 24.9 1.0
O A:HOH550 4.5 33.5 1.0
CA A:CYS256 4.6 21.4 1.0
CG1 A:VAL282 4.6 36.7 1.0
CB A:VAL258 4.6 27.8 1.0
C A:VAL282 4.7 36.4 1.0
N A:GLY285 4.7 34.7 1.0
C A:CYS283 4.7 32.1 1.0
CB A:ARG261 4.7 32.4 1.0
N A:VAL282 4.8 38.6 1.0
C A:CYS259 4.8 31.5 1.0
N A:GLN260 4.8 32.1 1.0
CA A:VAL282 4.8 37.1 1.0
N A:THR284 4.8 31.5 1.0
C A:VAL258 4.8 29.6 1.0
N A:VAL258 4.9 28.0 1.0

Reference:

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
Page generated: Thu Dec 28 13:45:27 2023

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