Zinc in PDB 5y4h: Human SIRT3 in Complex with Halistanol Sulfate

The structure of Human SIRT3 in Complex with Halistanol Sulfate, PDB code: 5y4h was solved by N.Kudo, A.Ito, M.Yoshida, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.60
Space group	P 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	127.840, 127.840, 127.840, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 26.9

The binding sites of Zinc atom in the Human SIRT3 in Complex with Halistanol Sulfate (pdb code 5y4h). 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 in Complex with Halistanol Sulfate, PDB code: 5y4h:

Zinc binding site 1 out of 1 in the Human SIRT3 in Complex with Halistanol Sulfate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human SIRT3 in Complex with Halistanol Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:56.4 occ:1.00 SG A:CYS259 2.2 49.9 1.0 SG A:CYS280 2.2 50.2 1.0 SG A:CYS256 2.3 48.0 1.0 SG A:CYS283 2.5 67.2 1.0 CB A:CYS280 3.0 50.5 1.0 CB A:CYS256 3.2 48.6 1.0 CB A:CYS259 3.2 48.1 1.0 CB A:CYS283 3.6 61.2 1.0 N A:CYS259 3.6 49.1 1.0 CA A:CYS259 4.0 49.5 1.0 N A:CYS283 4.1 62.2 1.0 CA A:CYS283 4.3 59.3 1.0 CA A:CYS280 4.5 57.0 1.0 CA A:CYS256 4.6 47.6 1.0 C A:CYS259 4.7 51.2 1.0 N A:GLN260 4.7 53.1 1.0 C A:VAL282 4.8 63.6 1.0 C A:VAL258 4.8 48.3 1.0 CB A:VAL258 4.8 45.2 1.0 C A:CYS283 4.9 58.6 1.0 CB A:ARG261 4.9 54.8 1.0 CB A:VAL282 5.0 64.9 1.0 N A:GLY285 5.0 58.6 1.0

F.Nakamura, N.Kudo, Y.Tomachi, A.Nakata, M.Takemoto, A.Ito, H.Tabei, D.Arai, N.De Voogd, M.Yoshida, Y.Nakao, N.Fusetani. Halistanol Sulfates I and J, New SIRT1-3 Inhibitory Steroid Sulfates From A Marine Sponge of the Genus Halichondria J. Antibiot. V. 71 273 2018.
ISSN: ISSN 0021-8820
PubMed: 29184120
DOI: 10.1038/JA.2017.145