Magnesium in PDB 7p3j: Eed in Complex with Compound 4

The structure of Eed in Complex with Compound 4, PDB code: 7p3j was solved by J.A.Read, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.26 / 1.93
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.1, 86.6, 97.29, 90, 90, 90
R / Rfree (%)	18.2 / 20.4

The structure of Eed in Complex with Compound 4 also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Magnesium atom in the Eed in Complex with Compound 4 (pdb code 7p3j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Eed in Complex with Compound 4, PDB code: 7p3j:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Eed in Complex with Compound 4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Eed in Complex with Compound 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:31.4 occ:1.00 OD2 A:ASP341 2.1 44.9 1.0 O A:HOH870 2.2 43.1 1.0 O A:HOH716 2.4 39.7 1.0 O A:HOH777 2.6 37.0 1.0 O A:HOH690 2.6 46.2 1.0 O A:HOH839 2.8 51.7 1.0 O A:HOH804 2.9 53.1 1.0 CG A:ASP341 3.2 39.2 1.0 CB A:ASP341 3.8 30.6 1.0 OD1 A:ASP341 4.1 38.4 1.0 OD1 A:ASP339 4.4 38.0 1.0 O A:HOH734 4.6 33.4 1.0 O A:HOH877 4.7 56.3 1.0 OE1 A:GLU249 4.9 35.7 1.0 OD2 A:ASP317 5.0 58.0 1.0

Magnesium binding site 2 out of 3 in the Eed in Complex with Compound 4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Eed in Complex with Compound 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:38.3 occ:1.00 OE2 A:GLU337 2.6 44.8 1.0 O A:HOH837 2.8 56.1 1.0 OE1 A:GLU337 3.3 60.5 1.0 CD A:GLU337 3.3 55.5 1.0 CG A:MET336 4.5 37.7 1.0 CG A:GLU337 4.8 43.3 1.0 O A:HOH865 5.0 59.1 1.0 SD A:MET336 5.0 41.2 1.0

Magnesium binding site 3 out of 3 in the Eed in Complex with Compound 4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Eed in Complex with Compound 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:55.2 occ:1.00 O A:VAL350 2.3 27.5 1.0 O A:HOH838 2.7 54.2 1.0 O A:HOH826 2.7 44.7 1.0 O A:HOH800 2.8 50.8 1.0 C A:VAL350 3.5 27.9 1.0 N A:VAL350 4.1 26.9 1.0 O A:HOH760 4.2 34.6 1.0 N A:THR351 4.4 22.6 1.0 CA A:VAL350 4.5 25.9 1.0 CA A:THR351 4.5 23.9 1.0 CG2 A:VAL350 4.7 29.2 1.0 ND2 A:ASN349 4.9 46.2 1.0 OG1 A:THR351 4.9 27.5 1.0 CB A:ASN349 4.9 33.8 1.0

S.K.Bagal, C.Gregson, D.H.O' Donovan, K.G.Pike, A.Bloecher, P.Barton, A.Borodovsky, E.Code, S.M.Fillery, J.H.Hsu, S.P.Kawatkar, C.Li, D.Longmire, Y.Nai, S.C.Nash, A.Pike, J.Robinson, J.A.Read, P.B.Rawlins, M.Shen, J.Tang, P.Wang, H.Woods, B.Williamson. Diverse, Potent, and Efficacious Inhibitors That Target the Eed Subunit of the Polycomb Repressive Complex 2 Methyltransferase. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 34807608
DOI: 10.1021/ACS.JMEDCHEM.1C01161