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Yttrium in PDB 5u62: Crystal Structure of Eed in Complex with H3K27ME3 Peptide and 6- (Benzo[D][1,3]Dioxol-4-Ylmethyl)-5,6,7,8-Tetrahydroimidazo[1,5- A]Pyridin-3-Amine

Enzymatic activity of Crystal Structure of Eed in Complex with H3K27ME3 Peptide and 6- (Benzo[D][1,3]Dioxol-4-Ylmethyl)-5,6,7,8-Tetrahydroimidazo[1,5- A]Pyridin-3-Amine

All present enzymatic activity of Crystal Structure of Eed in Complex with H3K27ME3 Peptide and 6- (Benzo[D][1,3]Dioxol-4-Ylmethyl)-5,6,7,8-Tetrahydroimidazo[1,5- A]Pyridin-3-Amine:
2.1.1.43;

Protein crystallography data

The structure of Crystal Structure of Eed in Complex with H3K27ME3 Peptide and 6- (Benzo[D][1,3]Dioxol-4-Ylmethyl)-5,6,7,8-Tetrahydroimidazo[1,5- A]Pyridin-3-Amine, PDB code: 5u62 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) 44.94 / 1.90
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 92.881, 178.113, 50.480, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 20.8

Yttrium Binding Sites:

The binding sites of Yttrium atom in the Crystal Structure of Eed in Complex with H3K27ME3 Peptide and 6- (Benzo[D][1,3]Dioxol-4-Ylmethyl)-5,6,7,8-Tetrahydroimidazo[1,5- A]Pyridin-3-Amine (pdb code 5u62). 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 6- (Benzo[D][1,3]Dioxol-4-Ylmethyl)-5,6,7,8-Tetrahydroimidazo[1,5- A]Pyridin-3-Amine, PDB code: 5u62:
Jump to Yttrium binding site number: 1; 2;

Yttrium binding site 1 out of 2 in 5u62

Go back to Yttrium Binding Sites List in 5u62
Yttrium binding site 1 out of 2 in the Crystal Structure of Eed in Complex with H3K27ME3 Peptide and 6- (Benzo[D][1,3]Dioxol-4-Ylmethyl)-5,6,7,8-Tetrahydroimidazo[1,5- A]Pyridin-3-Amine


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 6- (Benzo[D][1,3]Dioxol-4-Ylmethyl)-5,6,7,8-Tetrahydroimidazo[1,5- A]Pyridin-3-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y502

b:23.0
occ:0.89
 O A:HOH637 3.5 27.9 1.0
O A:HOH933 3.7 45.7 1.0
CB A:ARG269 3.7 21.7 1.0
CG A:ARG269 3.8 21.5 1.0
CA A:ARG269 3.9 21.1 1.0
CD A:ARG269 4.6 26.8 1.0
N A:ARG269 4.7 19.4 1.0
O A:ARG269 4.9 21.5 1.0
C A:ARG269 4.9 23.2 1.0

Yttrium binding site 2 out of 2 in 5u62

Go back to Yttrium Binding Sites List in 5u62
Yttrium binding site 2 out of 2 in the Crystal Structure of Eed in Complex with H3K27ME3 Peptide and 6- (Benzo[D][1,3]Dioxol-4-Ylmethyl)-5,6,7,8-Tetrahydroimidazo[1,5- A]Pyridin-3-Amine


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 6- (Benzo[D][1,3]Dioxol-4-Ylmethyl)-5,6,7,8-Tetrahydroimidazo[1,5- A]Pyridin-3-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y503

b:23.2
occ:0.98
 NH1 A:ARG269 3.4 27.1 1.0
N A:HIS295 3.6 19.6 1.0
O A:HOH945 3.7 47.8 1.0
O A:LYS293 3.7 24.0 1.0
CD2 A:PHE296 3.8 22.6 1.0
O A:HOH647 3.9 28.5 1.0
NH2 A:ARG269 3.9 29.2 1.0
CZ A:ARG269 4.1 37.8 1.0
CD2 A:HIS295 4.2 26.7 1.0
CE2 A:PHE296 4.3 25.2 1.0
CB A:HIS295 4.3 21.4 1.0
CA A:ILE294 4.3 20.9 1.0
C A:ILE294 4.5 21.9 1.0
CA A:HIS295 4.5 19.8 1.0
N A:PHE296 4.6 19.9 1.0
CG A:HIS295 4.7 25.0 1.0
C A:LYS293 4.7 25.5 1.0
CG A:PHE296 5.0 22.1 1.0

Reference:

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
Page generated: Sat Oct 12 20:47:03 2024

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