Sodium in PDB 6r7k: Ligand Complex of Rorg Lbd

The structure of Ligand Complex of Rorg Lbd, PDB code: 6r7k was solved by Y.Xue, A.Aagaard, F.Narjes, S.Von Berg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.81 / 1.54
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.790, 61.790, 159.170, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 21.4

The structure of Ligand Complex of Rorg Lbd also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Sodium atom in the Ligand Complex of Rorg Lbd (pdb code 6r7k). 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 Ligand Complex of Rorg Lbd, PDB code: 6r7k:

Sodium binding site 1 out of 1 in the Ligand Complex of Rorg Lbd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ligand Complex of Rorg Lbd within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:33.8 occ:1.00 O A:CYS366 2.3 25.3 1.0 O A:TYR369 2.4 27.5 1.0 OG A:SER408 2.6 35.2 1.0 O A:HOH848 2.7 40.4 1.0 O A:HOH772 2.8 37.8 1.0 O A:HOH931 3.0 60.2 1.0 C A:CYS366 3.5 24.7 1.0 C A:TYR369 3.5 27.7 1.0 CB A:SER408 3.6 29.1 1.0 NH2 A:ARG296 3.7 33.2 1.0 N A:TYR369 4.1 23.9 1.0 CA A:TYR369 4.2 23.2 1.0 CB A:TYR369 4.2 22.5 1.0 CA A:SER408 4.3 27.0 1.0 CD2 A:TYR369 4.4 23.7 1.0 O A:HOH761 4.4 42.0 1.0 N A:ARG367 4.4 22.0 1.0 CA A:CYS366 4.4 22.8 1.0 CA A:ARG367 4.4 22.3 1.0 C A:ARG367 4.4 26.7 1.0 O A:HOH964 4.5 41.5 1.0 O A:ARG367 4.5 27.1 1.0 N A:ASN370 4.6 25.2 1.0 CB A:CYS366 4.6 23.8 1.0 CG A:TYR369 4.8 22.9 1.0 O A:HOH966 4.9 63.5 1.0 CA A:ASN370 4.9 24.0 1.0 O A:HOH795 4.9 34.0 1.0 N A:ALA371 4.9 28.3 1.0 CZ A:ARG296 5.0 53.6 1.0

S.Von Berg, Y.Xue, M.Collins, A.Llinas, R.I.Olsson, T.Halvarsson, M.Lindskog, J.Malmberg, J.Jirholt, N.Krutrok, M.Ramnegard, M.Brannstrom, A.Lundqvist, M.Lepisto, A.Aagaard, J.Mcpheat, E.L.Hansson, R.Chen, Y.Xiong, T.G.Hansson, F.Narjes. Discovery of Potent and Orally Bioavailable Inverse Agonists of the Retinoic Acid Receptor-Related Orphan Receptor C2. Acs Med.Chem.Lett. V. 10 972 2019.
ISSN: ISSN 1948-5875
PubMed: 31223457
DOI: 10.1021/ACSMEDCHEMLETT.9B00158