Fluorine in PDB 5v56: 2.9A Xfel Structure of the Multi-Domain Human Smoothened Receptor (with E194M Mutation) in Complex with TC114

The structure of 2.9A Xfel Structure of the Multi-Domain Human Smoothened Receptor (with E194M Mutation) in Complex with TC114, PDB code: 5v56 was solved by X.Zhang, F.Zhao, Y.Wu, J.Yang, G.W.Han, S.Zhao, A.Ishchenko, L.Ye, X.Lin, K.Ding, V.Dharmarajan, P.R.Griffin, C.Gati, G.Nelson, M.S.Hunter, M.A.Hanson, V.Cherezov, R.C.Stevens, W.Tan, H.Tao, F.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.90 / 2.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.590, 349.540, 61.760, 90.00, 101.10, 90.00
R / Rfree (%)	21.8 / 23.9

The binding sites of Fluorine atom in the 2.9A Xfel Structure of the Multi-Domain Human Smoothened Receptor (with E194M Mutation) in Complex with TC114 (pdb code 5v56). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the 2.9A Xfel Structure of the Multi-Domain Human Smoothened Receptor (with E194M Mutation) in Complex with TC114, PDB code: 5v56:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the 2.9A Xfel Structure of the Multi-Domain Human Smoothened Receptor (with E194M Mutation) in Complex with TC114


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of 2.9A Xfel Structure of the Multi-Domain Human Smoothened Receptor (with E194M Mutation) in Complex with TC114 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1201 b:0.3 occ:1.00 F2 A:8361201 0.0 0.3 1.0 C4 A:8361201 1.4 0.8 1.0 F3 A:8361201 2.2 0.8 1.0 F4 A:8361201 2.2 99.0 1.0 C3 A:8361201 2.4 98.7 1.0 C8 A:8361201 3.1 92.0 1.0 C5 A:8361201 3.2 94.0 1.0 N01 A:8361201 3.2 87.9 1.0 CG A:GLN477 3.2 0.6 1.0 C9 A:8361201 3.3 85.2 1.0 C2 A:8361201 3.4 0.1 1.0 CD A:GLN477 3.4 0.5 1.0 NE2 A:GLN477 3.7 0.0 1.0 O1 A:8361201 3.8 91.5 1.0 CG A:PRO513 3.9 0.0 1.0 C10 A:8361201 4.0 85.2 1.0 OE1 A:GLN477 4.1 0.0 1.0 C14 A:8361201 4.1 85.4 1.0 CB A:TRP480 4.2 0.9 1.0 O A:TYR394 4.3 0.7 1.0 C6 A:8361201 4.4 93.5 1.0 CE3 A:TRP480 4.5 0.4 1.0 CD A:PRO513 4.7 0.6 1.0 C1 A:8361201 4.7 99.8 1.0 CB A:GLN477 4.7 0.2 1.0 CG A:GLU481 4.8 0.8 1.0

Fluorine binding site 2 out of 6 in the 2.9A Xfel Structure of the Multi-Domain Human Smoothened Receptor (with E194M Mutation) in Complex with TC114


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of 2.9A Xfel Structure of the Multi-Domain Human Smoothened Receptor (with E194M Mutation) in Complex with TC114 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1201 b:0.8 occ:1.00 F3 A:8361201 0.0 0.8 1.0 C4 A:8361201 1.4 0.8 1.0 F2 A:8361201 2.2 0.3 1.0 F4 A:8361201 2.2 99.0 1.0 C3 A:8361201 2.4 98.7 1.0 C2 A:8361201 2.7 0.1 1.0 N A:GLU481 3.2 0.6 1.0 CA A:GLU481 3.3 1.0 1.0 C A:TRP480 3.3 0.1 1.0 CG A:GLU481 3.4 0.8 1.0 O A:TRP480 3.5 0.8 1.0 CB A:TRP480 3.7 0.9 1.0 C5 A:8361201 3.8 94.0 1.0 CB A:GLU481 3.9 0.7 1.0 CG A:GLN477 4.0 0.6 1.0 CA A:TRP480 4.2 1.0 1.0 C1 A:8361201 4.2 99.8 1.0 O A:GLN477 4.2 0.8 1.0 NE2 A:GLN477 4.3 0.0 1.0 CB A:PHE484 4.3 0.9 1.0 C8 A:8361201 4.5 92.0 1.0 CD A:GLN477 4.5 0.5 1.0 CD A:GLU481 4.6 0.4 1.0 C A:GLU481 4.6 0.9 1.0 O2 A:8361201 4.8 0.8 1.0 CG A:PHE484 4.8 0.4 1.0 OE2 A:GLU481 4.9 0.2 1.0 C6 A:8361201 4.9 93.5 1.0 O1 A:8361201 4.9 91.5 1.0

Fluorine binding site 3 out of 6 in the 2.9A Xfel Structure of the Multi-Domain Human Smoothened Receptor (with E194M Mutation) in Complex with TC114


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of 2.9A Xfel Structure of the Multi-Domain Human Smoothened Receptor (with E194M Mutation) in Complex with TC114 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1201 b:99.0 occ:1.00 F4 A:8361201 0.0 99.0 1.0 C4 A:8361201 1.4 0.8 1.0 F2 A:8361201 2.2 0.3 1.0 F3 A:8361201 2.2 0.8 1.0 C3 A:8361201 2.4 98.7 1.0 C5 A:8361201 3.1 94.0 1.0 C8 A:8361201 3.1 92.0 1.0 O1 A:8361201 3.2 91.5 1.0 CD1 A:LEU221 3.4 0.7 1.0 C2 A:8361201 3.4 0.1 1.0 CG A:PRO513 3.4 0.0 1.0 CD A:PRO513 3.6 0.6 1.0 CB A:TRP480 3.8 0.9 1.0 N01 A:8361201 4.0 87.9 1.0 O A:TRP480 4.0 0.8 1.0 C A:TRP480 4.2 0.1 1.0 C6 A:8361201 4.3 93.5 1.0 CD1 A:PHE484 4.6 0.2 1.0 CA A:TRP480 4.6 1.0 1.0 CB A:PHE484 4.6 0.9 1.0 CG A:LEU221 4.7 0.8 1.0 C9 A:8361201 4.7 85.2 1.0 N A:GLU481 4.7 0.6 1.0 C1 A:8361201 4.7 99.8 1.0 C10 A:8361201 4.7 85.2 1.0 CG A:TRP480 4.8 1.0 1.0 N A:PRO513 4.9 1.0 1.0 CG A:PHE484 4.9 0.4 1.0 CB A:PRO513 4.9 0.6 1.0

Fluorine binding site 4 out of 6 in the 2.9A Xfel Structure of the Multi-Domain Human Smoothened Receptor (with E194M Mutation) in Complex with TC114


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of 2.9A Xfel Structure of the Multi-Domain Human Smoothened Receptor (with E194M Mutation) in Complex with TC114 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1201 b:0.8 occ:1.00 F2 B:8361201 0.0 0.8 1.0 C4 B:8361201 1.4 0.9 1.0 F3 B:8361201 2.2 0.9 1.0 F4 B:8361201 2.2 0.0 1.0 C3 B:8361201 2.4 0.1 1.0 C8 B:8361201 2.9 0.5 1.0 C5 B:8361201 3.0 0.4 1.0 N01 B:8361201 3.1 98.3 1.0 CG B:GLN477 3.2 0.9 1.0 C9 B:8361201 3.3 96.8 1.0 O1 B:8361201 3.5 99.0 1.0 CD B:GLN477 3.5 1.0 1.0 C2 B:8361201 3.5 0.7 1.0 CG B:PRO513 3.7 0.4 1.0 NE2 B:GLN477 3.8 0.0 1.0 C10 B:8361201 4.0 96.5 1.0 CB B:TRP480 4.1 0.5 1.0 OE1 B:GLN477 4.1 0.5 1.0 C11 B:8361201 4.3 96.5 1.0 C6 B:8361201 4.3 0.1 1.0 CE3 B:TRP480 4.3 0.3 1.0 O B:TYR394 4.5 0.1 1.0 CD B:PRO513 4.6 0.3 1.0 CB B:GLN477 4.7 0.5 1.0 C1 B:8361201 4.8 0.4 1.0 CG B:TRP480 4.9 0.8 1.0 CD2 B:TRP480 4.9 0.3 1.0 C B:TRP480 4.9 0.5 1.0 CB B:PRO513 4.9 0.7 1.0 CG B:GLU481 4.9 0.8 1.0 N B:GLU481 5.0 0.1 1.0

Fluorine binding site 5 out of 6 in the 2.9A Xfel Structure of the Multi-Domain Human Smoothened Receptor (with E194M Mutation) in Complex with TC114


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of 2.9A Xfel Structure of the Multi-Domain Human Smoothened Receptor (with E194M Mutation) in Complex with TC114 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1201 b:0.9 occ:1.00 F3 B:8361201 0.0 0.9 1.0 C4 B:8361201 1.4 0.9 1.0 F2 B:8361201 2.2 0.8 1.0 F4 B:8361201 2.2 0.0 1.0 C3 B:8361201 2.4 0.1 1.0 C2 B:8361201 2.8 0.7 1.0 N B:GLU481 3.0 0.1 1.0 C B:TRP480 3.1 0.5 1.0 CA B:GLU481 3.3 0.3 1.0 CG B:GLU481 3.4 0.8 1.0 CB B:TRP480 3.4 0.5 1.0 O B:TRP480 3.4 0.9 1.0 CG B:GLN477 3.8 0.9 1.0 C5 B:8361201 3.8 0.4 1.0 CA B:TRP480 3.9 0.6 1.0 CB B:GLU481 3.9 0.6 1.0 O B:GLN477 4.0 0.8 1.0 NE2 B:GLN477 4.3 0.0 1.0 C1 B:8361201 4.3 0.4 1.0 C8 B:8361201 4.4 0.5 1.0 CD B:GLN477 4.4 1.0 1.0 CB B:PHE484 4.4 0.3 1.0 C B:GLU481 4.6 0.6 1.0 CD B:GLU481 4.7 0.2 1.0 CG B:TRP480 4.8 0.8 1.0 O1 B:8361201 4.8 99.0 1.0 OE2 B:GLU481 4.8 0.0 1.0 N B:TRP480 4.9 0.5 1.0 C6 B:8361201 4.9 0.1 1.0 C B:GLN477 4.9 1.0 1.0 CB B:GLN477 5.0 0.5 1.0 CG B:PHE484 5.0 0.9 1.0

Fluorine binding site 6 out of 6 in the 2.9A Xfel Structure of the Multi-Domain Human Smoothened Receptor (with E194M Mutation) in Complex with TC114


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of 2.9A Xfel Structure of the Multi-Domain Human Smoothened Receptor (with E194M Mutation) in Complex with TC114 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1201 b:0.0 occ:1.00 F4 B:8361201 0.0 0.0 1.0 C4 B:8361201 1.4 0.9 1.0 F2 B:8361201 2.2 0.8 1.0 F3 B:8361201 2.2 0.9 1.0 C3 B:8361201 2.3 0.1 1.0 O1 B:8361201 3.0 99.0 1.0 C5 B:8361201 3.0 0.4 1.0 C8 B:8361201 3.1 0.5 1.0 CD1 B:LEU221 3.3 0.6 1.0 C2 B:8361201 3.3 0.7 1.0 CG B:PRO513 3.7 0.4 1.0 CD B:PRO513 3.8 0.3 1.0 CB B:TRP480 3.9 0.5 1.0 O B:TRP480 4.0 0.9 1.0 N01 B:8361201 4.1 98.3 1.0 C6 B:8361201 4.2 0.1 1.0 C B:TRP480 4.2 0.5 1.0 CD1 B:PHE484 4.3 0.3 1.0 CB B:PHE484 4.5 0.3 1.0 CG B:LEU221 4.5 0.1 1.0 C1 B:8361201 4.6 0.4 1.0 CG B:PHE484 4.7 0.9 1.0 CA B:TRP480 4.7 0.6 1.0 N B:GLU481 4.7 0.1 1.0 C10 B:8361201 4.8 96.5 1.0 C9 B:8361201 4.8 96.8 1.0 C7 B:8361201 4.9 0.8 1.0 CG B:TRP480 4.9 0.8 1.0

X.Zhang, F.Zhao, Y.Wu, J.Yang, G.W.Han, S.Zhao, A.Ishchenko, L.Ye, X.Lin, K.Ding, V.Dharmarajan, P.R.Griffin, C.Gati, G.Nelson, M.S.Hunter, M.A.Hanson, V.Cherezov, R.C.Stevens, W.Tan, H.Tao, F.Xu. Crystal Structure of A Multi-Domain Human Smoothened Receptor in Complex with A Super Stabilizing Ligand. Nat Commun V. 8 15383 2017.
ISSN: ESSN 2041-1723
PubMed: 28513578
DOI: 10.1038/NCOMMS15383