Chlorine in PDB 5q16: Ligand Binding to Farnesoid-X-Receptor

The structure of Ligand Binding to Farnesoid-X-Receptor, PDB code: 5q16 was solved by M.G.Rudolph, J.Benz, D.Burger, R.Thoma, A.Ruf, C.Joseph, B.Kuhn, C.Shao, H.Yang, S.K.Burley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	12.65 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	71.949, 84.566, 190.701, 90.00, 90.00, 90.00
R / Rfree (%)	26.3 / 28.4

The structure of Ligand Binding to Farnesoid-X-Receptor also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Chlorine atom in the Ligand Binding to Farnesoid-X-Receptor (pdb code 5q16). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Ligand Binding to Farnesoid-X-Receptor, PDB code: 5q16:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Ligand Binding to Farnesoid-X-Receptor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ligand Binding to Farnesoid-X-Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl501 b:77.4 occ:1.00 CL35 A:9MS501 0.0 77.4 1.0 C34 A:9MS501 1.7 74.0 1.0 C32 A:9MS501 2.7 72.3 1.0 C31 A:9MS501 2.7 71.6 1.0 CG A:LEU455 3.4 43.1 1.0 SD A:MET454 3.6 53.6 0.5 CD2 A:LEU455 3.7 44.7 1.0 O A:HIS451 3.8 46.5 1.0 CG A:MET454 3.9 51.2 0.5 CG A:MET454 3.9 51.0 0.5 CB A:MET454 4.0 47.5 0.5 CB A:MET454 4.0 47.8 0.5 C28 A:9MS501 4.0 70.1 1.0 C29 A:9MS501 4.0 70.4 1.0 SD A:MET454 4.0 54.6 0.5 CD1 A:LEU455 4.1 42.6 1.0 CZ A:PHE333 4.3 46.5 1.0 N A:LEU455 4.3 43.1 1.0 C14 A:9MS501 4.5 67.6 1.0 CA A:HIS451 4.5 46.7 1.0 CE A:MET454 4.5 51.2 0.5 C A:HIS451 4.6 48.4 1.0 CB A:LEU455 4.6 40.5 1.0 CB A:HIS451 4.6 45.6 1.0 CA A:LEU455 4.7 41.4 1.0 C A:MET454 4.7 48.9 1.0 CE2 A:PHE333 4.7 47.5 1.0 CA A:MET454 5.0 46.6 0.5 CA A:MET454 5.0 46.8 0.5

Chlorine binding site 2 out of 2 in the Ligand Binding to Farnesoid-X-Receptor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ligand Binding to Farnesoid-X-Receptor within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl501 b:75.2 occ:1.00 CL35 C:9MS501 0.0 75.2 1.0 C34 C:9MS501 1.7 72.6 1.0 C32 C:9MS501 2.7 71.0 1.0 C31 C:9MS501 2.7 71.7 1.0 CB C:MET454 3.6 51.7 1.0 CG C:MET454 3.6 55.9 1.0 CG C:LEU455 3.7 51.5 1.0 CD2 C:LEU455 3.8 54.0 1.0 SD C:MET454 3.8 59.5 1.0 N C:LEU455 4.0 48.1 1.0 C28 C:9MS501 4.0 70.2 1.0 C29 C:9MS501 4.0 69.8 1.0 C C:MET454 4.1 52.2 1.0 O C:HIS451 4.2 51.3 1.0 CA C:LEU455 4.3 48.7 1.0 C14 C:9MS501 4.5 67.5 1.0 CA C:MET454 4.5 50.2 1.0 O C:MET454 4.6 52.1 1.0 CB C:LEU455 4.6 48.4 1.0 CD2 C:LEU291 4.6 50.2 1.0 CD1 C:LEU455 4.6 51.1 1.0 CZ C:PHE333 4.6 45.1 1.0 CZ3 C:TRP458 4.8 46.8 1.0

Z.Gaieb, S.Liu, S.Gathiaka, M.Chiu, H.Yang, C.Shao, V.A.Feher, W.P.Walters, B.Kuhn, M.G.Rudolph, S.K.Burley, M.K.Gilson, R.E.Amaro. D3R Grand Challenge 2: Blind Prediction of Protein-Ligand Poses, Affinity Rankings, and Relative Binding Free Energies. J. Comput. Aided Mol. Des. V. 32 1 2018.
ISSN: ISSN 1573-4951
PubMed: 29204945
DOI: 10.1007/S10822-017-0088-4