Fluorine in PDB 6nws: Rorgamma Ligand Binding Domain

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

Resolution Low / High (Å)	56.87 / 2.44
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	60.805, 60.805, 160.650, 90.00, 90.00, 90.00
R / Rfree (%)	25 / 29.7

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

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Rorgamma Ligand Binding Domain (pdb code 6nws). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Rorgamma Ligand Binding Domain, PDB code: 6nws:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 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:54.1 occ:1.00 F1 A:L77601 0.0 54.1 1.0 C14 A:L77601 1.4 57.8 1.0 C21 A:L77601 2.4 63.3 1.0 C5 A:L77601 2.4 59.2 1.0 C13 A:L77601 2.8 62.5 1.0 O1 A:L77601 3.3 59.9 1.0 N1 A:L77601 3.6 66.3 1.0 C15 A:L77601 3.6 67.8 1.0 C3 A:L77601 3.6 61.5 1.0 C A:CYS320 3.7 52.0 1.0 N A:ALA321 3.7 47.5 1.0 O A:CYS320 3.7 52.2 1.0 CA A:ALA321 3.8 46.5 1.0 CB A:CYS320 3.8 52.1 1.0 CD2 A:LEU324 4.0 55.0 1.0 CE1 A:HIS479 4.1 75.8 1.0 C6 A:L77601 4.1 63.6 1.0 CA A:CYS320 4.4 53.2 1.0 CB A:ALA321 4.4 45.7 1.0 CB A:LEU324 4.4 59.6 1.0 O A:TRP317 4.6 58.6 1.0 CE1 A:TYR502 4.7 59.3 1.0 C16 A:L77601 4.7 70.7 1.0 CG A:LEU324 4.8 57.2 1.0 NE2 A:HIS479 4.9 74.0 1.0 C11 A:L77601 4.9 72.0 1.0 CD2 A:LEU483 5.0 85.9 1.0

Fluorine binding site 2 out of 4 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:57.3 occ:1.00 F2 A:L77601 0.0 57.3 1.0 C22 A:L77601 1.4 58.5 1.0 F3 A:L77601 2.2 57.5 1.0 F4 A:L77601 2.2 57.6 1.0 C18 A:L77601 2.4 60.3 1.0 C7 A:L77601 2.7 61.5 1.0 CE1 A:PHE388 3.4 48.1 1.0 CZ A:PHE388 3.5 47.6 1.0 CE1 A:PHE401 3.5 48.2 1.0 C12 A:L77601 3.6 64.0 1.0 CD1 A:ILE397 3.7 53.9 1.0 CD1 A:PHE388 3.7 47.6 1.0 CE2 A:PHE388 4.0 46.6 1.0 C4 A:L77601 4.1 60.5 1.0 CG A:PHE388 4.2 46.5 1.0 CD1 A:PHE401 4.3 48.6 1.0 CD2 A:PHE388 4.3 46.2 1.0 CZ A:PHE401 4.4 49.0 1.0 CL1 A:L77601 4.4 78.3 1.0 CG2 A:ILE400 4.5 47.4 1.0 CG2 A:ILE397 4.5 57.9 1.0 C20 A:L77601 4.7 65.9 1.0 CG1 A:VAL376 4.9 51.8 1.0 C9 A:L77601 5.0 64.9 1.0 CG1 A:ILE397 5.0 57.7 1.0

Fluorine binding site 3 out of 4 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:57.5 occ:1.00 F3 A:L77601 0.0 57.5 1.0 C22 A:L77601 1.4 58.5 1.0 F4 A:L77601 2.2 57.6 1.0 F2 A:L77601 2.2 57.3 1.0 C18 A:L77601 2.3 60.3 1.0 C12 A:L77601 3.1 64.0 1.0 C7 A:L77601 3.2 61.5 1.0 CL1 A:L77601 3.4 78.3 1.0 CE A:MET365 3.6 68.1 1.0 CD1 A:ILE400 3.8 47.1 1.0 CG2 A:ILE400 3.8 47.4 1.0 C16 A:L77601 3.9 70.7 1.0 N1 A:L77601 4.0 66.3 1.0 O1 A:L77601 4.0 59.9 1.0 C13 A:L77601 4.1 62.5 1.0 C8 A:L77601 4.1 73.2 1.0 C11 A:L77601 4.3 72.0 1.0 C20 A:L77601 4.4 65.9 1.0 C4 A:L77601 4.4 60.5 1.0 CD1 A:ILE397 4.5 53.9 1.0 SD A:MET365 4.5 70.3 1.0 CB A:ILE400 4.5 47.8 1.0 CG1 A:ILE400 4.6 47.7 1.0 C10 A:L77601 4.7 75.0 1.0 C15 A:L77601 4.8 67.8 1.0 C19 A:L77601 4.8 71.2 1.0 C9 A:L77601 4.9 64.9 1.0

Fluorine binding site 4 out of 4 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 4 of Rorgamma Ligand Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:57.6 occ:1.00 F4 A:L77601 0.0 57.6 1.0 C22 A:L77601 1.4 58.5 1.0 F3 A:L77601 2.2 57.5 1.0 F2 A:L77601 2.2 57.3 1.0 C18 A:L77601 2.4 60.3 1.0 C12 A:L77601 2.8 64.0 1.0 O1 A:L77601 3.1 59.9 1.0 CL1 A:L77601 3.2 78.3 1.0 CE2 A:PHE388 3.4 46.6 1.0 C7 A:L77601 3.6 61.5 1.0 CD2 A:PHE388 3.6 46.2 1.0 CZ A:PHE388 3.7 47.6 1.0 CD1 A:ILE397 3.7 53.9 1.0 C13 A:L77601 3.7 62.5 1.0 CG A:PHE388 4.1 46.5 1.0 C20 A:L77601 4.1 65.9 1.0 CE1 A:PHE388 4.1 48.1 1.0 C15 A:L77601 4.3 67.8 1.0 CD1 A:PHE388 4.3 47.6 1.0 N1 A:L77601 4.4 66.3 1.0 C21 A:L77601 4.5 63.3 1.0 C11 A:L77601 4.5 72.0 1.0 C16 A:L77601 4.5 70.7 1.0 SG A:CYS320 4.7 53.9 1.0 C4 A:L77601 4.7 60.5 1.0 CD1 A:LEU391 4.8 45.7 1.0 C9 A:L77601 4.9 64.9 1.0 O3 A:L77601 5.0 67.5 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