Fluorine in PDB 4iwf: Crystal Structure of the Estrogen Receptor Alpha Ligand-Binding Domain in Complex with A Dynamic Oxime-Derivative

The structure of Crystal Structure of the Estrogen Receptor Alpha Ligand-Binding Domain in Complex with A Dynamic Oxime-Derivative, PDB code: 4iwf was solved by J.C.Nwachukwu, S.Srinivasan, A.A.Parent, V.Cavett, J.Nowak, T.S.Hughes, D.J.Kojetin, J.A.Katzenellenbogen, K.W.Nettles, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.42 / 1.93
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.897, 83.036, 58.191, 90.00, 108.54, 90.00
R / Rfree (%)	17.3 / 20.9

The structure of Crystal Structure of the Estrogen Receptor Alpha Ligand-Binding Domain in Complex with A Dynamic Oxime-Derivative also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Fluorine atom in the Crystal Structure of the Estrogen Receptor Alpha Ligand-Binding Domain in Complex with A Dynamic Oxime-Derivative (pdb code 4iwf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of the Estrogen Receptor Alpha Ligand-Binding Domain in Complex with A Dynamic Oxime-Derivative, PDB code: 4iwf:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of the Estrogen Receptor Alpha Ligand-Binding Domain in Complex with A Dynamic Oxime-Derivative


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the Estrogen Receptor Alpha Ligand-Binding Domain in Complex with A Dynamic Oxime-Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:24.6 occ:0.23 FAD A:15Q601 0.0 24.6 0.2 H3 A:15Q601 0.5 34.5 0.7 CAG A:15Q601 1.2 28.7 0.7 CAO A:15Q601 1.3 27.1 0.2 CAI A:15Q601 2.1 27.5 0.7 H4 A:15Q601 2.2 33.0 0.7 CAK A:15Q601 2.3 28.7 0.2 CAM A:15Q601 2.4 27.4 0.2 CAM A:15Q601 2.4 25.6 0.7 H1 A:15Q601 2.5 34.4 0.2 O A:LEU387 2.7 26.4 1.0 OAB A:15Q601 2.8 26.6 0.2 OAB A:15Q601 2.9 27.6 0.7 CB A:LEU391 3.1 24.9 1.0 C A:LEU387 3.1 23.7 1.0 H2 A:15Q601 3.1 31.9 0.2 CA A:MET388 3.4 24.7 1.0 CAR A:15Q601 3.4 26.5 0.7 N A:MET388 3.4 24.0 1.0 CD2 A:LEU391 3.5 31.1 1.0 H2 A:15Q601 3.5 33.1 0.7 CAO A:15Q601 3.6 28.5 0.7 CAR A:15Q601 3.6 28.3 0.2 CAG A:15Q601 3.6 27.9 0.2 CG A:LEU391 3.8 31.2 1.0 CB A:LEU387 3.9 30.2 1.0 H5 A:15Q601 3.9 35.9 0.7 CAK A:15Q601 4.0 26.4 0.7 CG A:MET388 4.0 29.2 1.0 CA A:LEU387 4.0 30.3 1.0 CAI A:15Q601 4.1 27.1 0.2 CA A:LEU391 4.2 28.1 1.0 N A:LEU391 4.3 31.0 1.0 O A:HOH706 4.3 33.7 1.0 CB A:MET388 4.3 27.8 1.0 C A:MET388 4.4 25.6 1.0 H3 A:15Q601 4.4 33.5 0.2 CAS A:15Q601 4.4 29.5 0.7 CAJ A:15Q601 4.5 29.9 0.7 O A:MET388 4.5 28.8 1.0 NH2 A:ARG394 4.5 32.5 1.0 CD1 A:LEU391 4.6 28.0 1.0 FAD A:15Q601 4.7 29.9 0.7 CAS A:15Q601 4.7 32.6 0.2 CE1 A:PHE404 4.8 28.1 1.0 H1 A:15Q601 4.9 31.7 0.7

Fluorine binding site 2 out of 3 in the Crystal Structure of the Estrogen Receptor Alpha Ligand-Binding Domain in Complex with A Dynamic Oxime-Derivative


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the Estrogen Receptor Alpha Ligand-Binding Domain in Complex with A Dynamic Oxime-Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:29.9 occ:0.73 FAD A:15Q601 0.0 29.9 0.7 H3 A:15Q601 0.5 33.5 0.2 CAO A:15Q601 1.3 28.5 0.7 CAG A:15Q601 1.4 27.9 0.2 CAI A:15Q601 2.3 27.1 0.2 CAM A:15Q601 2.3 25.6 0.7 CAK A:15Q601 2.4 26.4 0.7 CAM A:15Q601 2.4 27.4 0.2 H4 A:15Q601 2.5 32.5 0.2 H1 A:15Q601 2.5 31.7 0.7 OE1 A:GLU353 2.7 35.9 1.0 OAB A:15Q601 2.8 27.6 0.7 H2 A:15Q601 2.8 33.1 0.7 OAB A:15Q601 2.8 26.6 0.2 H2 A:15Q601 2.9 31.9 0.2 N A:ALA350 3.4 31.7 1.0 CG A:LEU349 3.4 34.4 1.0 CD2 A:LEU349 3.4 32.3 1.0 O A:LEU346 3.5 33.2 1.0 CA A:ALA350 3.5 33.9 1.0 CAG A:15Q601 3.6 28.7 0.7 CAR A:15Q601 3.6 28.3 0.2 CAR A:15Q601 3.6 26.5 0.7 CAO A:15Q601 3.6 27.1 0.2 CB A:LEU349 3.7 34.3 1.0 CB A:ALA350 3.8 26.5 1.0 C A:LEU349 3.8 33.6 1.0 CD A:GLU353 3.9 38.0 1.0 CAI A:15Q601 4.1 27.5 0.7 CAK A:15Q601 4.1 28.7 0.2 H5 A:15Q601 4.3 42.3 0.2 O A:LEU349 4.3 33.6 1.0 H3 A:15Q601 4.4 34.5 0.7 CA A:LEU349 4.4 35.1 1.0 C A:LEU346 4.5 36.8 1.0 CD1 A:PHE404 4.5 28.5 1.0 CAS A:15Q601 4.7 32.6 0.2 FAD A:15Q601 4.7 24.6 0.2 OE2 A:GLU353 4.7 35.0 1.0 CA A:LEU346 4.8 36.9 1.0 CD1 A:LEU349 4.8 37.5 1.0 CG A:GLU353 4.8 35.3 1.0 CAJ A:15Q601 4.8 35.2 0.2 CAS A:15Q601 4.9 29.5 0.7 CD1 A:LEU387 4.9 34.3 1.0 CL A:15Q601 4.9 33.2 0.7

Fluorine binding site 3 out of 3 in the Crystal Structure of the Estrogen Receptor Alpha Ligand-Binding Domain in Complex with A Dynamic Oxime-Derivative


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the Estrogen Receptor Alpha Ligand-Binding Domain in Complex with A Dynamic Oxime-Derivative within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:45.7 occ:1.00 FAD B:15Q601 0.0 45.7 1.0 CAO B:15Q601 1.4 42.8 1.0 H2 B:15Q601 1.8 43.8 1.0 CAM B:15Q601 2.1 40.4 1.0 OAB B:15Q601 2.2 36.5 1.0 CAK B:15Q601 2.5 39.9 1.0 OE1 B:GLU353 2.6 36.4 1.0 H1 B:15Q601 2.8 47.9 1.0 CAG B:15Q601 3.5 38.4 1.0 CG B:LEU349 3.5 46.6 1.0 N B:ALA350 3.6 40.6 1.0 CD2 B:LEU349 3.6 44.4 1.0 CAR B:15Q601 3.6 41.7 1.0 O B:LEU346 3.7 43.2 1.0 CA B:ALA350 3.7 34.0 1.0 CD B:GLU353 3.8 43.5 1.0 CB B:LEU349 3.8 40.1 1.0 CB B:ALA350 3.9 31.7 1.0 CAI B:15Q601 4.0 34.5 1.0 C B:LEU349 4.1 39.8 1.0 H3 B:15Q601 4.2 46.1 1.0 CD1 B:PHE404 4.5 40.1 1.0 OE2 B:GLU353 4.5 37.7 1.0 O B:LEU349 4.6 36.9 1.0 CA B:LEU349 4.6 43.1 1.0 C B:LEU346 4.7 43.3 1.0 CD1 B:LEU387 4.8 31.4 1.0 CD1 B:LEU349 4.8 48.7 1.0 CG B:GLU353 4.8 39.4 1.0 CAS B:15Q601 4.9 35.7 1.0 NH2 B:ARG394 4.9 41.7 1.0 H4 B:15Q601 5.0 41.4 1.0

S.Srinivasan, J.C.Nwachukwu, A.A.Parent, V.Cavett, J.Nowak, T.S.Hughes, D.J.Kojetin, J.A.Katzenellenbogen, K.W.Nettles. Ligand Binding Dynamics Rewire Cellular Signaling Via Estrogen Receptor-Alpha Nat.Chem.Biol. V. 9 326 2013.
ISSN: ISSN 1552-4450
PubMed: 23524984
DOI: 10.1038/NCHEMBIO.1214