Fluorine in PDB 6nwu: Rorgamma Ligand Binding Domain

The structure of Rorgamma Ligand Binding Domain, PDB code: 6nwu was solved by T.S.Strutzenberg, H.Park, P.R.Griffin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.19 / 3.20
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	59.880, 59.880, 162.550, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 27.6

The structure of Rorgamma Ligand Binding Domain also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Rorgamma Ligand Binding Domain (pdb code 6nwu). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Rorgamma Ligand Binding Domain, PDB code: 6nwu:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Rorgamma Ligand Binding Domain


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Rorgamma Ligand Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:58.4 occ:1.00 FAJ A:L7J601 0.0 58.4 1.0 CAI A:L7J601 1.4 55.3 1.0 FAL A:L7J601 2.2 56.0 1.0 FAK A:L7J601 2.2 57.6 1.0 CAH A:L7J601 2.4 50.8 1.0 CAG A:L7J601 3.1 50.0 1.0 CAM A:L7J601 3.3 51.5 1.0 CG2 A:ILE400 3.8 33.2 1.0 CLB A:L7J601 3.8 69.8 1.0 CD1 A:ILE397 3.8 34.0 1.0 CD1 A:ILE400 3.9 29.7 1.0 CAF A:L7J601 4.3 51.8 1.0 CB A:ILE400 4.3 32.5 1.0 SD A:MET365 4.5 46.4 1.0 CE A:MET365 4.5 45.7 1.0 CAD A:L7J601 4.5 54.6 1.0 CAS A:L7J601 4.6 61.5 1.0 CG1 A:ILE400 4.7 28.4 1.0 CAT A:L7J601 4.7 61.2 1.0 CAR A:L7J601 4.8 61.4 1.0 CE1 A:PHE401 4.9 34.8 1.0 CBC A:L7J601 4.9 65.8 1.0 CAE A:L7J601 4.9 52.1 1.0

Fluorine binding site 2 out of 3 in the Rorgamma Ligand Binding Domain


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Rorgamma Ligand Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:57.6 occ:1.00 FAK A:L7J601 0.0 57.6 1.0 CAI A:L7J601 1.4 55.3 1.0 FAL A:L7J601 2.2 56.0 1.0 FAJ A:L7J601 2.2 58.4 1.0 CAH A:L7J601 2.4 50.8 1.0 CAG A:L7J601 2.8 50.0 1.0 CD2 A:PHE388 3.4 34.6 1.0 CE2 A:PHE388 3.4 35.2 1.0 CD1 A:ILE397 3.5 34.0 1.0 CG A:PHE388 3.5 34.2 1.0 CAM A:L7J601 3.5 51.5 1.0 CZ A:PHE388 3.5 34.5 1.0 CD1 A:PHE388 3.7 33.6 1.0 CE1 A:PHE388 3.7 34.0 1.0 CE1 A:PHE401 3.7 34.8 1.0 CG2 A:ILE397 4.0 38.8 1.0 CAF A:L7J601 4.2 51.8 1.0 CZ A:PHE401 4.2 34.6 1.0 CB A:PHE388 4.4 35.8 1.0 CG1 A:ILE397 4.5 34.6 1.0 CAD A:L7J601 4.7 54.6 1.0 CB A:ILE397 4.7 36.9 1.0 CD1 A:PHE401 4.7 35.1 1.0 CAE A:L7J601 4.9 52.1 1.0

Fluorine binding site 3 out of 3 in the Rorgamma Ligand Binding Domain


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Rorgamma Ligand Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:56.0 occ:1.00 FAL A:L7J601 0.0 56.0 1.0 CAI A:L7J601 1.4 55.3 1.0 FAK A:L7J601 2.2 57.6 1.0 FAJ A:L7J601 2.2 58.4 1.0 CAH A:L7J601 2.4 50.8 1.0 CAM A:L7J601 2.7 51.5 1.0 CD1 A:ILE397 3.5 34.0 1.0 CAG A:L7J601 3.6 50.0 1.0 CD1 A:PHE388 3.8 33.6 1.0 CE1 A:PHE388 3.9 34.0 1.0 CLB A:L7J601 4.0 69.8 1.0 CAD A:L7J601 4.1 54.6 1.0 CBC A:L7J601 4.2 65.8 1.0 CAT A:L7J601 4.3 61.2 1.0 OAU A:L7J601 4.3 62.2 1.0 CG A:PHE388 4.3 34.2 1.0 CD1 A:LEU391 4.3 28.6 1.0 CBE A:L7J601 4.4 61.1 1.0 CZ A:PHE388 4.4 34.5 1.0 SG A:CYS320 4.4 37.9 1.0 CAW A:L7J601 4.6 63.7 1.0 CBB A:L7J601 4.7 65.3 1.0 CAF A:L7J601 4.8 51.8 1.0 CAS A:L7J601 4.8 61.5 1.0 CD2 A:PHE388 4.8 34.6 1.0 CAV A:L7J601 4.8 62.9 1.0 CE2 A:PHE388 4.8 35.2 1.0 CG1 A:ILE397 4.9 34.6 1.0 CB A:PHE388 4.9 35.8 1.0 CAE A:L7J601 5.0 52.1 1.0

T.S.Strutzenberg, R.D.Garcia-Ordonez, S.J.Novick, H.Park, M.R.Chang, C.Doebellin, Y.He, R.Patouret, T.M.Kamenecka, P.R.Griffin. Hdx-Ms Reveals Structural Determinants For Ror Gamma Hyperactivation By Synthetic Agonists. Elife V. 8 2019.
ISSN: ESSN 2050-084X
PubMed: 31172947
DOI: 10.7554/ELIFE.47172