Sodium in PDB 7yxd: Crystal Structure of Wt ANCGR2-Lbd Bound to Dexamethasone and Shp Coregulator Fragment

The structure of Crystal Structure of Wt ANCGR2-Lbd Bound to Dexamethasone and Shp Coregulator Fragment, PDB code: 7yxd was solved by A.Jimenez-Panizo, E.Estebanez-Perpina, P.Fuentes-Prior, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	76.81 / 2.30
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	107.599, 107.599, 135.641, 90, 90, 120
R / Rfree (%)	17.7 / 22.1

The structure of Crystal Structure of Wt ANCGR2-Lbd Bound to Dexamethasone and Shp Coregulator Fragment also contains other interesting chemical elements:

Fluorine

(F)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of Wt ANCGR2-Lbd Bound to Dexamethasone and Shp Coregulator Fragment (pdb code 7yxd). 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 Crystal Structure of Wt ANCGR2-Lbd Bound to Dexamethasone and Shp Coregulator Fragment, PDB code: 7yxd:

Sodium binding site 1 out of 1 in the Crystal Structure of Wt ANCGR2-Lbd Bound to Dexamethasone and Shp Coregulator Fragment


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Wt ANCGR2-Lbd Bound to Dexamethasone and Shp Coregulator Fragment within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1002 b:23.1 occ:1.00 OG1 H:THR555 2.2 66.0 1.0 CB H:THR555 3.4 57.1 1.0 N H:ARG558 3.6 40.2 1.0 CB H:THR557 3.8 41.9 1.0 CB H:ARG558 3.8 43.0 1.0 CG2 H:THR555 3.9 57.9 1.0 CA H:ARG558 4.3 41.7 1.0 CG2 H:THR557 4.4 34.9 1.0 C H:THR557 4.5 37.9 1.0 CA H:THR557 4.5 30.5 1.0 N H:THR557 4.6 33.0 1.0 CA H:THR555 4.6 50.7 1.0 OG1 H:THR557 4.6 50.4 1.0 C H:THR555 4.9 42.9 1.0

A.Jimenez-Panizo, A.Alegre-Marti, T.T.Tettey, G.Fettweis, M.Abella, R.Anton, T.A.Johnson, S.Kim, R.L.Schiltz, I.Nunez-Barrios, J.Font-Diaz, C.Caelles, A.F.Valledor, P.Perez, A.M.Rojas, J.Fernandez-Recio, D.M.Presman, G.L.Hager, P.Fuentes-Prior, E.Estebanez-Perpina. The Multivalency of the Glucocorticoid Receptor Ligand-Binding Domain Explains Its Manifold Physiological Activities. Nucleic Acids Res. 2022.
ISSN: ESSN 1362-4962
PubMed: 36464162
DOI: 10.1093/NAR/GKAC1119