Yttrium in PDB 5u5t: Crystal Structure of Eed in Complex with H3K27ME3 Peptide and 3- (Benzo[D][1,3]Dioxol-4-Ylmethyl)Piperidine-1-Carboximidamide

All present enzymatic activity of Crystal Structure of Eed in Complex with H3K27ME3 Peptide and 3- (Benzo[D][1,3]Dioxol-4-Ylmethyl)Piperidine-1-Carboximidamide:
2.1.1.43;

The structure of Crystal Structure of Eed in Complex with H3K27ME3 Peptide and 3- (Benzo[D][1,3]Dioxol-4-Ylmethyl)Piperidine-1-Carboximidamide, PDB code: 5u5t was solved by D.Bussiere, W.Shu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.22 / 1.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	92.810, 177.909, 50.340, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 20

The binding sites of Yttrium atom in the Crystal Structure of Eed in Complex with H3K27ME3 Peptide and 3- (Benzo[D][1,3]Dioxol-4-Ylmethyl)Piperidine-1-Carboximidamide (pdb code 5u5t). This binding sites where shown within 5.0 Angstroms radius around Yttrium atom.
In total 2 binding sites of Yttrium where determined in the Crystal Structure of Eed in Complex with H3K27ME3 Peptide and 3- (Benzo[D][1,3]Dioxol-4-Ylmethyl)Piperidine-1-Carboximidamide, PDB code: 5u5t:
Jump to Yttrium binding site number: 1; 2;

Yttrium binding site 1 out of 2 in the Crystal Structure of Eed in Complex with H3K27ME3 Peptide and 3- (Benzo[D][1,3]Dioxol-4-Ylmethyl)Piperidine-1-Carboximidamide


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 1 of Crystal Structure of Eed in Complex with H3K27ME3 Peptide and 3- (Benzo[D][1,3]Dioxol-4-Ylmethyl)Piperidine-1-Carboximidamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Y501 b:18.8 occ:0.89 NH1 B:ARG269 3.4 22.4 1.0 O B:HOH998 3.6 34.8 1.0 N B:HIS295 3.6 14.6 1.0 O B:LYS293 3.7 19.2 1.0 CD2 B:PHE296 3.8 20.1 1.0 NH2 B:ARG269 3.9 27.8 1.0 O B:HOH636 3.9 32.3 1.0 CZ B:ARG269 4.1 28.4 1.0 CB B:HIS295 4.2 15.6 1.0 CE2 B:PHE296 4.2 22.5 1.0 CD2 B:HIS295 4.3 21.6 1.0 CA B:ILE294 4.3 16.6 1.0 CA B:HIS295 4.5 13.6 1.0 C B:ILE294 4.5 18.1 1.0 CG B:HIS295 4.6 19.3 1.0 N B:PHE296 4.6 16.0 1.0 C B:LYS293 4.7 20.6 1.0 N B:ILE294 5.0 18.3 1.0 CG B:PHE296 5.0 15.4 1.0

Yttrium binding site 2 out of 2 in the Crystal Structure of Eed in Complex with H3K27ME3 Peptide and 3- (Benzo[D][1,3]Dioxol-4-Ylmethyl)Piperidine-1-Carboximidamide


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 2 of Crystal Structure of Eed in Complex with H3K27ME3 Peptide and 3- (Benzo[D][1,3]Dioxol-4-Ylmethyl)Piperidine-1-Carboximidamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Y502 b:19.3 occ:1.00 O B:HOH767 3.6 28.3 1.0 CG B:ARG269 3.8 18.0 1.0 CB B:ARG269 3.8 18.8 1.0 CA B:ARG269 3.9 18.6 1.0 N B:ARG269 4.6 19.2 1.0 CD B:ARG269 4.7 20.1 1.0

A.Lingel, M.Sendzik, Y.Huang, M.D.Shultz, J.Cantwell, M.P.Dillon, X.Fu, J.Fuller, T.Gabriel, J.Gu, X.Jiang, L.Li, F.Liang, M.Mckenna, W.Qi, W.Rao, X.Sheng, W.Shu, J.Sutton, B.Taft, L.Wang, J.Zeng, H.Zhang, M.Zhang, K.Zhao, M.Lindvall, D.E.Bussiere. Structure-Guided Design of Eed Binders Allosterically Inhibiting the Epigenetic Polycomb Repressive Complex 2 (PRC2) Methyltransferase. J. Med. Chem. V. 60 415 2017.
ISSN: ISSN 1520-4804
PubMed: 27992714
DOI: 10.1021/ACS.JMEDCHEM.6B01473