Fluorine in PDB 6nwt: Rorgamma Ligand Binding Domain

The structure of Rorgamma Ligand Binding Domain, PDB code: 6nwt 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)	29.12 / 2.35
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	99.590, 99.590, 129.600, 90.00, 90.00, 120.00
R / Rfree (%)	18.1 / 21.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Fluorine atom in the Rorgamma Ligand Binding Domain (pdb code 6nwt). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 14 binding sites of Fluorine where determined in the Rorgamma Ligand Binding Domain, PDB code: 6nwt:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 14 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:73.4 occ:1.00 F29 A:L7P601 0.0 73.4 1.0 C05 A:L7P601 1.3 77.8 1.0 C06 A:L7P601 2.3 74.7 1.0 C04 A:L7P601 2.3 81.9 1.0 H041 A:L7P601 2.5 98.4 1.0 C09 A:L7P601 2.8 69.6 1.0 H101 A:L7P601 2.9 85.6 1.0 C10 A:L7P601 3.1 71.2 1.0 NE2 A:HIS479 3.2 0.2 1.0 C07 A:L7P601 3.5 74.7 1.0 CD1 A:ILE400 3.6 39.7 1.0 C03 A:L7P601 3.6 90.5 1.0 CD2 A:HIS479 3.7 0.4 1.0 C28 A:L7P601 3.9 66.9 1.0 C08 A:L7P601 4.0 83.1 1.0 CD2 A:LEU324 4.2 49.6 1.0 CD1 A:LEU324 4.3 61.2 1.0 C11 A:L7P601 4.3 67.3 1.0 H281 A:L7P601 4.3 80.4 1.0 H071 A:L7P601 4.3 89.7 1.0 CE1 A:HIS479 4.3 0.2 1.0 CD2 A:LEU362 4.5 53.3 1.0 H011 A:L7P601 4.7 0.1 1.0 CG2 A:ILE400 4.7 26.1 1.0 H111 A:L7P601 4.8 80.9 1.0 CG A:LEU324 4.8 50.4 1.0 CG1 A:ILE400 4.8 40.5 1.0 C27 A:L7P601 4.9 71.7 1.0 C02 A:L7P601 4.9 99.6 1.0 O01 A:L7P601 4.9 0.5 1.0 CG A:HIS479 4.9 0.4 1.0 H081 A:L7P601 5.0 99.9 1.0

Fluorine binding site 2 out of 14 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:95.1 occ:1.00 F31 A:L7P601 0.0 95.1 1.0 C30 A:L7P601 1.4 97.3 1.0 F32 A:L7P601 2.1 99.0 1.0 F33 A:L7P601 2.2 96.0 1.0 C02 A:L7P601 2.5 99.6 1.0 H011 A:L7P601 2.6 0.1 1.0 O01 A:L7P601 2.9 0.5 1.0 C03 A:L7P601 3.0 90.5 1.0 H081 A:L7P601 3.5 99.9 1.0 C08 A:L7P601 3.5 83.1 1.0 CD2 A:LEU483 3.5 88.4 1.0 CZ3 A:TRP317 3.6 86.0 1.0 C34 A:L7P601 3.7 0.6 1.0 C04 A:L7P601 3.8 81.9 1.0 CE3 A:TRP317 3.9 80.4 1.0 H041 A:L7P601 4.0 98.4 1.0 CE1 A:HIS479 4.1 0.2 1.0 F35 A:L7P601 4.1 0.6 1.0 F37 A:L7P601 4.3 0.1 1.0 CD1 A:LEU324 4.3 61.2 1.0 CD2 A:PHE486 4.4 80.7 1.0 CA A:LEU483 4.5 93.3 1.0 ND1 A:HIS479 4.6 0.8 1.0 C07 A:L7P601 4.6 74.7 1.0 CG A:LEU483 4.6 90.3 1.0 NE2 A:HIS479 4.8 0.2 1.0 C05 A:L7P601 4.8 77.8 1.0 CB A:LEU483 4.8 92.6 1.0 N A:LEU483 4.8 99.8 1.0 F36 A:L7P601 4.9 0.4 1.0 CE2 A:PHE486 4.9 69.2 1.0 CH2 A:TRP317 4.9 90.6 1.0 O A:HIS479 5.0 0.7 1.0

Fluorine binding site 3 out of 14 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:99.0 occ:1.00 F32 A:L7P601 0.0 99.0 1.0 C30 A:L7P601 1.4 97.3 1.0 F31 A:L7P601 2.1 95.1 1.0 F33 A:L7P601 2.2 96.0 1.0 C02 A:L7P601 2.5 99.6 1.0 F35 A:L7P601 2.6 0.6 1.0 O01 A:L7P601 2.8 0.5 1.0 C34 A:L7P601 3.0 0.6 1.0 H011 A:L7P601 3.0 0.1 1.0 CD2 A:PHE486 3.2 80.7 1.0 CE2 A:PHE486 3.5 69.2 1.0 CB A:ARG482 3.6 90.7 1.0 F37 A:L7P601 3.6 0.1 1.0 C A:ARG482 3.7 98.1 1.0 O A:ARG482 3.7 92.7 1.0 N A:LEU483 3.8 99.8 1.0 C03 A:L7P601 3.8 90.5 1.0 CG A:ARG482 3.8 90.0 0.0 CA A:LEU483 4.0 93.3 1.0 F36 A:L7P601 4.2 0.4 1.0 H081 A:L7P601 4.2 99.9 1.0 CA A:ARG482 4.3 96.2 1.0 CG A:PHE486 4.4 85.6 1.0 O A:HIS479 4.5 0.7 1.0 C08 A:L7P601 4.5 83.1 1.0 CZ3 A:TRP317 4.5 86.0 1.0 CE3 A:TRP317 4.5 80.4 1.0 CD2 A:LEU483 4.7 88.4 1.0 CB A:PHE486 4.8 89.4 1.0 CB A:LEU483 4.9 92.6 1.0 C04 A:L7P601 4.9 81.9 1.0 CZ A:PHE486 4.9 59.2 1.0 H041 A:L7P601 4.9 98.4 1.0

Fluorine binding site 4 out of 14 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:96.0 occ:1.00 F33 A:L7P601 0.0 96.0 1.0 C30 A:L7P601 1.4 97.3 1.0 F32 A:L7P601 2.2 99.0 1.0 F31 A:L7P601 2.2 95.1 1.0 C02 A:L7P601 2.5 99.6 1.0 H081 A:L7P601 2.5 99.9 1.0 F37 A:L7P601 2.8 0.1 1.0 C34 A:L7P601 2.9 0.6 1.0 C08 A:L7P601 3.0 83.1 1.0 C03 A:L7P601 3.1 90.5 1.0 F35 A:L7P601 3.2 0.6 1.0 CE2 A:PHE486 3.3 69.2 1.0 CD2 A:PHE486 3.5 80.7 1.0 O01 A:L7P601 3.6 0.5 1.0 CD1 A:LEU391 3.8 40.1 1.0 H011 A:L7P601 3.8 0.1 1.0 CE3 A:TRP317 4.1 80.4 1.0 CD2 A:LEU391 4.2 38.4 1.0 F36 A:L7P601 4.2 0.4 1.0 C07 A:L7P601 4.4 74.7 1.0 C04 A:L7P601 4.4 81.9 1.0 CZ A:PHE486 4.5 59.2 1.0 CZ3 A:TRP317 4.5 86.0 1.0 CG A:LEU391 4.5 34.2 1.0 H071 A:L7P601 4.7 89.7 1.0 CG A:PHE486 4.8 85.6 1.0 H041 A:L7P601 4.9 98.4 1.0 CB A:CYS320 4.9 31.8 1.0

Fluorine binding site 5 out of 14 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 5 of Rorgamma Ligand Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:0.6 occ:1.00 F35 A:L7P601 0.0 0.6 1.0 C34 A:L7P601 1.4 0.6 1.0 F37 A:L7P601 2.1 0.1 1.0 F36 A:L7P601 2.1 0.4 1.0 C02 A:L7P601 2.5 99.6 1.0 F32 A:L7P601 2.6 99.0 1.0 C30 A:L7P601 2.8 97.3 1.0 O01 A:L7P601 2.9 0.5 1.0 CG A:ARG482 3.1 90.0 0.0 SG A:CYS393 3.1 60.5 1.0 F33 A:L7P601 3.2 96.0 1.0 CB A:ARG482 3.4 90.7 1.0 H011 A:L7P601 3.7 0.1 1.0 CB A:CYS393 3.7 49.0 1.0 C03 A:L7P601 3.8 90.5 1.0 CD2 A:LEU396 3.9 56.9 1.0 F31 A:L7P601 4.1 95.1 1.0 CE2 A:PHE486 4.3 69.2 1.0 CD A:ARG482 4.3 89.7 0.0 H081 A:L7P601 4.3 99.9 1.0 C08 A:L7P601 4.5 83.1 1.0 NE A:ARG482 4.7 90.1 0.0 CD2 A:PHE486 4.7 80.7 1.0 CA A:ARG482 4.8 96.2 1.0 CG A:LEU396 4.8 57.2 1.0 C04 A:L7P601 4.9 81.9 1.0 H041 A:L7P601 4.9 98.4 1.0

Fluorine binding site 6 out of 14 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 6 of Rorgamma Ligand Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:0.4 occ:1.00 F36 A:L7P601 0.0 0.4 1.0 C34 A:L7P601 1.4 0.6 1.0 F35 A:L7P601 2.1 0.6 1.0 F37 A:L7P601 2.2 0.1 1.0 C02 A:L7P601 2.4 99.6 1.0 O01 A:L7P601 2.8 0.5 1.0 CD2 A:LEU396 3.1 56.9 1.0 C03 A:L7P601 3.1 90.5 1.0 CG A:LEU396 3.4 57.2 1.0 H011 A:L7P601 3.6 0.1 1.0 CB A:CYS393 3.6 49.0 1.0 CB A:LEU396 3.7 46.4 1.0 C30 A:L7P601 3.7 97.3 1.0 C04 A:L7P601 3.8 81.9 1.0 H041 A:L7P601 3.8 98.4 1.0 CD1 A:ILE397 3.9 34.6 1.0 C08 A:L7P601 3.9 83.1 1.0 H081 A:L7P601 4.0 99.9 1.0 SG A:CYS393 4.1 60.5 1.0 F32 A:L7P601 4.2 99.0 1.0 F33 A:L7P601 4.2 96.0 1.0 CG1 A:ILE397 4.2 46.9 1.0 N A:ILE397 4.6 39.1 1.0 O A:CYS393 4.6 36.3 1.0 C A:LEU396 4.8 37.8 1.0 CD1 A:LEU396 4.8 56.4 1.0 F31 A:L7P601 4.9 95.1 1.0 CA A:LEU396 4.9 42.2 1.0 C05 A:L7P601 4.9 77.8 1.0 CG A:ARG482 4.9 90.0 0.0 CB A:ARG482 5.0 90.7 1.0 CD1 A:ILE400 5.0 39.7 1.0

Fluorine binding site 7 out of 14 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 7 of Rorgamma Ligand Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:0.1 occ:1.00 F37 A:L7P601 0.0 0.1 1.0 C34 A:L7P601 1.4 0.6 1.0 F35 A:L7P601 2.1 0.6 1.0 F36 A:L7P601 2.2 0.4 1.0 C02 A:L7P601 2.5 99.6 1.0 H081 A:L7P601 2.7 99.9 1.0 F33 A:L7P601 2.8 96.0 1.0 C30 A:L7P601 3.0 97.3 1.0 C03 A:L7P601 3.0 90.5 1.0 C08 A:L7P601 3.1 83.1 1.0 CB A:CYS393 3.4 49.0 1.0 CD1 A:LEU391 3.4 40.1 1.0 SG A:CYS393 3.5 60.5 1.0 F32 A:L7P601 3.6 99.0 1.0 O01 A:L7P601 3.6 0.5 1.0 CD1 A:ILE397 3.9 34.6 1.0 CB A:LEU391 4.0 31.3 1.0 CG A:LEU391 4.2 34.2 1.0 C04 A:L7P601 4.2 81.9 1.0 F31 A:L7P601 4.3 95.1 1.0 H011 A:L7P601 4.3 0.1 1.0 CG1 A:ILE397 4.3 46.9 1.0 C07 A:L7P601 4.4 74.7 1.0 CE2 A:PHE486 4.6 69.2 1.0 H041 A:L7P601 4.7 98.4 1.0 CD2 A:LEU391 4.7 38.4 1.0 H071 A:L7P601 4.7 89.7 1.0 CA A:CYS393 4.9 41.8 1.0

Fluorine binding site 8 out of 14 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 8 of Rorgamma Ligand Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:F601 b:75.8 occ:1.00 F29 C:L7P601 0.0 75.8 1.0 C05 C:L7P601 1.3 86.4 1.0 C04 C:L7P601 2.3 93.7 1.0 C06 C:L7P601 2.3 89.7 1.0 H041 C:L7P601 2.5 0.6 1.0 H101 C:L7P601 2.9 94.0 1.0 C09 C:L7P601 2.9 84.8 1.0 C10 C:L7P601 3.2 78.3 1.0 C07 C:L7P601 3.5 95.3 1.0 CD1 C:ILE400 3.6 40.3 1.0 C03 C:L7P601 3.6 0.5 1.0 C28 C:L7P601 4.0 80.1 1.0 C08 C:L7P601 4.0 0.4 1.0 CD2 C:LEU324 4.2 65.2 1.0 CD1 C:LEU324 4.2 67.7 1.0 H071 C:L7P601 4.3 0.5 1.0 C11 C:L7P601 4.4 77.2 1.0 H281 C:L7P601 4.4 96.2 1.0 CE C:MET358 4.4 78.7 1.0 H011 C:L7P601 4.5 0.7 1.0 CG C:LEU324 4.5 57.5 1.0 CG2 C:ILE400 4.7 31.6 1.0 H111 C:L7P601 4.9 92.7 1.0 C02 C:L7P601 4.9 0.3 1.0 O01 C:L7P601 4.9 0.8 1.0 H081 C:L7P601 5.0 0.6 1.0 CG1 C:ILE400 5.0 40.4 1.0

Fluorine binding site 9 out of 14 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 9 of Rorgamma Ligand Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:F601 b:0.0 occ:1.00 F31 C:L7P601 0.0 0.0 1.0 C30 C:L7P601 1.4 0.9 1.0 F32 C:L7P601 2.1 0.7 1.0 F33 C:L7P601 2.2 0.4 1.0 C02 C:L7P601 2.5 0.3 1.0 H011 C:L7P601 2.8 0.7 1.0 O01 C:L7P601 2.9 0.8 1.0 C03 C:L7P601 3.0 0.5 1.0 H081 C:L7P601 3.3 0.6 1.0 C08 C:L7P601 3.4 0.4 1.0 CZ3 C:TRP317 3.7 86.7 1.0 CE3 C:TRP317 3.8 84.8 1.0 C34 C:L7P601 3.8 0.8 1.0 C04 C:L7P601 3.9 93.7 1.0 H041 C:L7P601 4.1 0.6 1.0 F36 C:L7P601 4.2 0.2 1.0 F35 C:L7P601 4.2 0.1 1.0 ND1 C:HIS479 4.3 1.0 1.0 CE1 C:HIS479 4.3 0.2 1.0 O C:ARG482 4.4 99.9 1.0 C07 C:L7P601 4.5 95.3 1.0 CD2 C:LEU324 4.6 65.2 1.0 CB C:CYS320 4.7 24.7 1.0 C05 C:L7P601 4.9 86.4 1.0 F37 C:L7P601 4.9 0.9 1.0 CH2 C:TRP317 4.9 90.2 1.0

Fluorine binding site 10 out of 14 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 10 of Rorgamma Ligand Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:F601 b:0.7 occ:1.00 F32 C:L7P601 0.0 0.7 1.0 C30 C:L7P601 1.4 0.9 1.0 F31 C:L7P601 2.1 0.0 1.0 F33 C:L7P601 2.2 0.4 1.0 C02 C:L7P601 2.5 0.3 1.0 F36 C:L7P601 2.8 0.2 1.0 O01 C:L7P601 2.8 0.8 1.0 C34 C:L7P601 3.0 0.8 1.0 O C:ARG482 3.1 99.9 1.0 H011 C:L7P601 3.2 0.7 1.0 F35 C:L7P601 3.5 0.1 1.0 CB C:ARG482 3.5 0.9 1.0 C03 C:L7P601 3.8 0.5 1.0 CZ3 C:TRP317 4.0 86.7 1.0 C C:ARG482 4.0 0.2 1.0 CE3 C:TRP317 4.0 84.8 1.0 H081 C:L7P601 4.2 0.6 1.0 F37 C:L7P601 4.3 0.9 1.0 CA C:ARG482 4.4 0.2 1.0 C08 C:L7P601 4.5 0.4 1.0 ND1 C:HIS479 4.5 1.0 1.0 CG C:ARG482 4.6 0.1 1.0 O C:HIS479 4.8 0.5 1.0 C04 C:L7P601 4.9 93.7 1.0 CD2 C:LEU483 5.0 96.1 1.0 CE1 C:HIS479 5.0 0.2 1.0 H041 C:L7P601 5.0 0.6 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