Sodium in PDB 5ni5: Ligand Complex of Rorg Lbd

The structure of Ligand Complex of Rorg Lbd, PDB code: 5ni5 was solved by Y.Xue, A.Aagaard, F.Narjes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.85 / 2.30
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	62.310, 62.310, 158.640, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 26.5

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

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Ligand Complex of Rorg Lbd (pdb code 5ni5). 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: 5ni5:

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:66.4 occ:1.00 O A:TYR369 2.4 49.8 1.0 O A:CYS366 2.4 49.6 1.0 OG A:SER408 2.7 57.9 1.0 O A:HOH734 2.8 53.4 1.0 O A:HOH749 2.8 49.4 1.0 C A:TYR369 3.6 49.0 1.0 CB A:SER408 3.6 49.1 1.0 C A:CYS366 3.6 48.3 1.0 NH2 A:ARG296 3.8 74.6 1.0 N A:TYR369 4.3 46.2 1.0 CA A:TYR369 4.3 44.1 1.0 CA A:SER408 4.3 46.8 1.0 CB A:TYR369 4.5 43.4 1.0 CA A:ARG367 4.5 41.7 1.0 N A:ARG367 4.5 41.9 1.0 CD2 A:TYR369 4.5 42.9 1.0 C A:ARG367 4.5 46.9 1.0 N A:ASN370 4.6 46.9 1.0 CA A:CYS366 4.6 45.2 1.0 O A:ARG367 4.6 45.7 1.0 O A:HOH728 4.7 44.2 1.0 CA A:ASN370 4.8 47.8 1.0 N A:ALA371 4.9 50.6 1.0 O A:HOH776 4.9 53.1 1.0 CB A:CYS366 4.9 45.9 1.0

F.Narjes, Y.Xue, S.Von Berg, J.Malmberg, A.Llinas, R.I.Olsson, J.Jirholt, H.Grindebacke, A.Leffler, N.Hossain, M.Lepisto, L.Thunberg, H.Leek, A.Aagaard, J.Mcpheat, E.L.Hansson, E.Back, S.Tangefjord, R.Chen, Y.Xiong, G.Hongbin, T.G.Hansson. Potent and Orally Bioavailable Inverse Agonists of Ror Gamma T Resulting From Structure-Based Design. J. Med. Chem. V. 61 7796 2018.
ISSN: ISSN 1520-4804
PubMed: 30095900
DOI: 10.1021/ACS.JMEDCHEM.8B00783