Zinc in PDB 5yvx: Crystal Structure of SDG8 Cw Domain in Complex with H3K4ME1 Peptide

All present enzymatic activity of Crystal Structure of SDG8 Cw Domain in Complex with H3K4ME1 Peptide:
2.1.1.43;

The structure of Crystal Structure of SDG8 Cw Domain in Complex with H3K4ME1 Peptide, PDB code: 5yvx was solved by Y.Liu, Y.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.76 / 1.59
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	66.421, 66.421, 29.241, 90.00, 90.00, 120.00
R / Rfree (%)	16.8 / 18.5

The binding sites of Zinc atom in the Crystal Structure of SDG8 Cw Domain in Complex with H3K4ME1 Peptide (pdb code 5yvx). 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 Crystal Structure of SDG8 Cw Domain in Complex with H3K4ME1 Peptide, PDB code: 5yvx:

Zinc binding site 1 out of 1 in the Crystal Structure of SDG8 Cw Domain in Complex with H3K4ME1 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of SDG8 Cw Domain in Complex with H3K4ME1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:21.7 occ:0.88 SG A:CYS904 2.3 18.5 1.0 SG A:CYS871 2.3 18.3 1.0 SG A:CYS893 2.3 18.2 1.0 SG A:CYS868 2.4 16.7 1.0 CB A:CYS868 3.1 16.1 1.0 CB A:CYS871 3.2 18.4 1.0 CB A:CYS904 3.3 20.4 1.0 CB A:CYS893 3.4 17.2 1.0 CA A:CYS904 3.5 19.3 1.0 N A:CYS871 3.7 16.0 1.0 N A:CYS893 3.9 17.5 1.0 CA A:CYS871 4.0 19.1 1.0 N A:CYS904 4.1 20.1 1.0 CA A:CYS893 4.3 18.9 1.0 CA A:CYS868 4.6 17.2 1.0 CB A:ASP870 4.6 18.8 1.0 C A:ASP870 4.7 17.8 1.0 C A:CYS904 4.7 22.7 1.0 C A:CYS871 4.7 19.8 1.0 C A:ASP903 4.8 21.2 1.0 N A:PHE872 4.8 17.4 1.0 NH2 A:ARG875 4.8 19.1 1.0 O A:CYS904 4.8 23.0 1.0 O A:ASP903 5.0 18.8 1.0

Y.Liu, Y.Huang. Uncovering the Mechanistic Basis For Specific Recognition of Monomethylated H3K4 By the Cw Domain Ofarabidopsishistone Methyltransferase SDG8. J. Biol. Chem. V. 293 6470 2018.
ISSN: ESSN 1083-351X
PubMed: 29496997
DOI: 10.1074/JBC.RA117.001390