Sodium in PDB 5vb3: X-Ray Structure of Nuclear Receptor Ror-Gammat Ligand Binding Domain + SRC2 Peptide

The structure of X-Ray Structure of Nuclear Receptor Ror-Gammat Ligand Binding Domain + SRC2 Peptide, PDB code: 5vb3 was solved by X.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.33 / 1.95
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.272, 61.272, 154.226, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 23

The binding sites of Sodium atom in the X-Ray Structure of Nuclear Receptor Ror-Gammat Ligand Binding Domain + SRC2 Peptide (pdb code 5vb3). 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 Structure of Nuclear Receptor Ror-Gammat Ligand Binding Domain + SRC2 Peptide, PDB code: 5vb3:

Sodium binding site 1 out of 1 in the X-Ray Structure of Nuclear Receptor Ror-Gammat Ligand Binding Domain + 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 Structure of Nuclear Receptor Ror-Gammat Ligand Binding Domain + SRC2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:28.8 occ:1.00 O A:CYS366 2.6 23.4 1.0 O A:TYR369 2.8 27.1 1.0 OG A:SER408 2.9 33.1 1.0 O A:HOH822 2.9 35.3 1.0 O A:HOH753 2.9 39.6 1.0 O A:HOH833 2.9 34.7 1.0 O A:HOH773 3.3 38.5 1.0 CB A:SER408 3.6 25.9 1.0 C A:CYS366 3.7 22.7 1.0 NH2 A:ARG296 3.9 41.1 1.0 C A:TYR369 4.0 23.0 1.0 CA A:SER408 4.2 23.9 1.0 O A:HOH849 4.3 37.3 1.0 CA A:CYS366 4.5 27.9 1.0 N A:TYR369 4.6 21.8 1.0 CB A:TYR369 4.6 24.0 1.0 N A:ARG367 4.6 21.7 1.0 CA A:ARG367 4.6 21.9 1.0 CA A:TYR369 4.6 23.5 1.0 CB A:CYS366 4.6 25.2 1.0 O A:ARG367 4.7 26.0 1.0 CD2 A:TYR369 4.7 25.1 1.0 C A:ARG367 4.7 23.0 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