Sodium in PDB 4ymq: X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist

The structure of X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist, PDB code: 4ymq was solved by X.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.96 / 2.00
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.909, 61.909, 156.965, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 23.9

The structure of X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Sodium atom in the X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist (pdb code 4ymq). 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 + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist, PDB code: 4ymq:

Sodium binding site 1 out of 1 in the X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist


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 + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:54.0 occ:1.00 OG A:SER408 2.4 50.5 1.0 O A:CYS366 2.5 36.1 1.0 O A:HOH775 2.8 52.4 1.0 O A:TYR369 2.9 41.9 1.0 O A:HOH776 2.9 45.5 1.0 O A:HOH791 3.0 54.7 1.0 CB A:SER408 3.5 44.6 1.0 C A:CYS366 3.7 37.9 1.0 C A:TYR369 3.9 41.1 1.0 CA A:SER408 4.0 39.6 1.0 O A:HOH772 4.2 50.7 1.0 CB A:TYR369 4.3 36.7 1.0 O A:HOH765 4.3 49.1 1.0 N A:TYR369 4.5 36.1 1.0 CA A:TYR369 4.5 32.5 1.0 CA A:CYS366 4.5 40.6 1.0 CD2 A:TYR369 4.5 38.5 1.0 NH2 A:ARG296 4.5 59.2 1.0 CB A:CYS366 4.5 42.2 1.0 N A:ARG367 4.5 35.8 1.0 CA A:ARG367 4.6 38.0 1.0 O A:ARG367 4.7 44.2 1.0 C A:ARG367 4.7 39.0 1.0 N A:SER408 4.8 33.7 1.0 CG A:TYR369 4.9 38.0 1.0 O A:HOH752 4.9 44.1 1.0 SG A:CYS366 5.0 38.7 1.0

I.Muegge, D.Collin, B.Cook, M.Hill-Drzewi, J.Horan, S.Kugler, M.Labadia, X.Li, L.Smith, Y.Zhang. Discovery of 1,3-Dihydro-2,1,3-Benzothiadiazole 2,2-Dioxide Analogs As New Rorc Modulators. Bioorg.Med.Chem.Lett. V. 25 1892 2015.
ISSN: ESSN 1464-3405
PubMed: 25840886
DOI: 10.1016/J.BMCL.2015.03.042