Sodium in PDB 5vb6: X-Ray Co-Structure of Nuclear Receptor Ror-Gammat Ligand Binding Domain with An Inverse Agonist and SRC2 Peptide

The structure of X-Ray Co-Structure of Nuclear Receptor Ror-Gammat Ligand Binding Domain with An Inverse Agonist and SRC2 Peptide, PDB code: 5vb6 was solved by X.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.65 / 2.04
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	62.305, 62.305, 154.178, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 20.8

The binding sites of Sodium atom in the X-Ray Co-Structure of Nuclear Receptor Ror-Gammat Ligand Binding Domain with An Inverse Agonist and SRC2 Peptide (pdb code 5vb6). 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 X-Ray Co-Structure of Nuclear Receptor Ror-Gammat Ligand Binding Domain with An Inverse Agonist and SRC2 Peptide, PDB code: 5vb6:

Sodium binding site 1 out of 1 in the X-Ray Co-Structure of Nuclear Receptor Ror-Gammat Ligand Binding Domain with An Inverse Agonist and SRC2 Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Co-Structure of Nuclear Receptor Ror-Gammat Ligand Binding Domain with An Inverse Agonist and SRC2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:30.4 occ:1.00 OG A:SER408 2.6 42.9 1.0 O A:CYS366 2.6 22.6 1.0 O A:TYR369 2.7 25.7 1.0 O A:HOH828 2.9 34.6 1.0 O A:HOH794 3.0 44.6 1.0 O A:HOH801 3.2 38.9 1.0 O A:HOH875 3.5 43.6 1.0 CB A:SER408 3.6 24.0 1.0 C A:CYS366 3.8 14.9 1.0 C A:TYR369 3.8 27.7 1.0 NH2 A:ARG296 3.8 40.0 1.0 CA A:SER408 4.2 26.3 1.0 O A:HOH879 4.4 40.0 1.0 N A:TYR369 4.4 21.4 1.0 CB A:TYR369 4.5 21.9 1.0 CA A:TYR369 4.5 23.6 1.0 O A:ARG367 4.5 22.7 1.0 CA A:ARG367 4.5 24.6 1.0 N A:ARG367 4.6 20.9 1.0 C A:ARG367 4.6 22.9 1.0 CA A:CYS366 4.7 20.1 1.0 CD2 A:TYR369 4.7 22.1 1.0 CB A:CYS366 4.8 22.4 1.0 N A:ASN370 4.9 28.8 1.0

X.Li, M.Anderson, D.Collin, I.Muegge, J.Wan, D.Brennan, S.Kugler, D.Terenzio, C.Kennedy, S.Lin, M.E.Labadia, B.Cook, R.Hughes, N.A.Farrow. Structural Studies Unravel the Active Conformation of Apo Ror Gamma T Nuclear Receptor and A Common Inverse Agonism of Two Diverse Classes of Ror Gamma T Inhibitors. J. Biol. Chem. V. 292 11618 2017.
ISSN: ESSN 1083-351X
PubMed: 28546429
DOI: 10.1074/JBC.M117.789024