Sodium in PDB 6w7g: Structure of Eed Bound to Inhibitor 1056

The structure of Structure of Eed Bound to Inhibitor 1056, PDB code: 6w7g was solved by E.M.Petrunak, J.A.Stuckey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.21 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.780, 85.091, 91.734, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 19.1

The structure of Structure of Eed Bound to Inhibitor 1056 also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Sodium atom in the Structure of Eed Bound to Inhibitor 1056 (pdb code 6w7g). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structure of Eed Bound to Inhibitor 1056, PDB code: 6w7g:

Sodium binding site 1 out of 1 in the Structure of Eed Bound to Inhibitor 1056


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Eed Bound to Inhibitor 1056 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:17.5 occ:1.00 O A:HOH921 2.2 42.2 1.0 O A:HOH906 2.2 46.5 1.0 SG A:CYS182 2.4 24.4 1.0 ND1 A:HIS185 2.9 39.1 1.0 CB A:CYS182 3.3 19.7 1.0 O A:CYS182 3.7 24.3 1.0 CG A:HIS185 3.8 36.0 1.0 C A:CYS182 3.9 24.8 1.0 CE1 A:HIS185 3.9 39.1 1.0 CB A:HIS185 3.9 29.9 1.0 C A:LYS184 3.9 24.7 1.0 N A:HIS185 4.0 23.8 1.0 NH1 A:ARG173 4.0 34.1 1.0 N A:LYS184 4.1 23.1 1.0 CA A:LYS184 4.1 23.2 1.0 CA A:CYS182 4.2 18.3 1.0 O A:LYS184 4.3 20.2 1.0 N A:ILE183 4.5 22.1 1.0 C A:ILE183 4.6 28.3 1.0 CA A:HIS185 4.6 27.2 1.0 O A:HOH876 4.7 46.1 1.0

R.K.Rej, C.Wang, J.Lu, M.Wang, E.Petrunak, K.P.Zawacki, D.Mceachern, E.Fernandez-Salas, C.Y.Yang, L.Wang, R.Li, K.Chinnaswamy, B.Wen, D.Sun, J.Stuckey, Y.Zhou, J.Chen, G.Tang, S.Wang. Eedi-5285: An Exceptionally Potent, Efficacious, and Orally Active Small-Molecule Inhibitor of Embryonic Ectoderm Development. J.Med.Chem. V. 63 7252 2020.
ISSN: ISSN 0022-2623
PubMed: 32580550
DOI: 10.1021/ACS.JMEDCHEM.0C00479