Fluorine in PDB 5dz3: Crystal Structure of the Er-Alpha Ligand-Binding Domain in Complex with the Cyclofenil Derivative 4,4'-{[4-(Fluoromethyl) Cyclohexylidene]Methanediyl}Diphenol

The structure of Crystal Structure of the Er-Alpha Ligand-Binding Domain in Complex with the Cyclofenil Derivative 4,4'-{[4-(Fluoromethyl) Cyclohexylidene]Methanediyl}Diphenol, PDB code: 5dz3 was solved by J.C.Nwachukwu, S.Srinivasan, Y.Zheng, S.Wang, J.Min, C.Dong, Z.Liao, V.Cavett, J.Nowak, R.Houtman, K.E.Carlson, J.S.Josan, O.Elemento, J.A.Katzenellenbogen, H.B.Zhou, K.W.Nettles, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.76 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.986, 80.804, 58.073, 90.00, 109.96, 90.00
R / Rfree (%)	20.2 / 23.4

The binding sites of Fluorine atom in the Crystal Structure of the Er-Alpha Ligand-Binding Domain in Complex with the Cyclofenil Derivative 4,4'-{[4-(Fluoromethyl) Cyclohexylidene]Methanediyl}Diphenol (pdb code 5dz3). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of the Er-Alpha Ligand-Binding Domain in Complex with the Cyclofenil Derivative 4,4'-{[4-(Fluoromethyl) Cyclohexylidene]Methanediyl}Diphenol, PDB code: 5dz3:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain in Complex with the Cyclofenil Derivative 4,4'-{[4-(Fluoromethyl) Cyclohexylidene]Methanediyl}Diphenol


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 Er-Alpha Ligand-Binding Domain in Complex with the Cyclofenil Derivative 4,4'-{[4-(Fluoromethyl) Cyclohexylidene]Methanediyl}Diphenol within 5.0Å range: probe atom residue distance (Å) B Occ A:F900 b:49.3 occ:1.00 F19 A:5JX900 0.0 49.3 1.0 C18 A:5JX900 1.3 43.9 1.0 C17 A:5JX900 2.3 40.3 1.0 SD A:MET421 2.4 1.0 1.0 C20 A:5JX900 2.9 38.3 1.0 C16 A:5JX900 3.0 39.2 1.0 CE2 A:PHE425 3.4 44.6 1.0 CG A:MET421 3.6 57.3 1.0 CD2 A:PHE425 3.7 44.1 1.0 CE A:MET421 4.0 49.4 1.0 C21 A:5JX900 4.3 38.3 1.0 O A:MET421 4.4 51.5 1.0 C15 A:5JX900 4.4 38.8 1.0 CB A:MET421 4.4 58.9 1.0 CE1 A:HIS524 4.5 65.3 1.0 ND1 A:HIS524 4.5 61.9 1.0 CB A:ILE424 4.5 40.5 1.0 CA A:MET421 4.6 58.6 1.0 CZ A:PHE425 4.6 46.0 1.0 CG2 A:ILE424 4.7 38.2 1.0 CD1 A:ILE424 4.7 42.2 1.0 C14 A:5JX900 4.8 38.1 1.0 C A:MET421 4.9 54.9 1.0 NE2 A:HIS524 4.9 67.8 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain in Complex with the Cyclofenil Derivative 4,4'-{[4-(Fluoromethyl) Cyclohexylidene]Methanediyl}Diphenol


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 Er-Alpha Ligand-Binding Domain in Complex with the Cyclofenil Derivative 4,4'-{[4-(Fluoromethyl) Cyclohexylidene]Methanediyl}Diphenol within 5.0Å range: probe atom residue distance (Å) B Occ B:F901 b:53.2 occ:1.00 F19 B:5JX901 0.0 53.2 1.0 C18 B:5JX901 1.3 47.6 1.0 C17 B:5JX901 2.3 44.9 1.0 C20 B:5JX901 2.7 43.6 1.0 CB B:MET421 3.2 62.8 1.0 C16 B:5JX901 3.3 44.0 1.0 O B:MET421 3.9 57.2 1.0 CD1 B:PHE425 3.9 53.7 1.0 CA B:MET421 4.0 63.3 1.0 CE1 B:PHE425 4.0 56.1 1.0 C21 B:5JX901 4.1 42.6 1.0 C B:MET421 4.3 60.5 1.0 CB B:ILE424 4.3 41.2 1.0 CG2 B:ILE424 4.5 38.8 1.0 ND1 B:HIS524 4.5 68.9 1.0 CE1 B:HIS524 4.5 72.8 1.0 CD1 B:ILE424 4.5 45.5 1.0 C15 B:5JX901 4.6 43.3 1.0 C14 B:5JX901 4.8 42.2 1.0 CG1 B:ILE424 5.0 42.9 1.0

J.C.Nwachukwu, S.Srinivasan, Y.Zheng, S.Wang, J.Min, C.Dong, Z.Liao, J.Nowak, N.J.Wright, R.Houtman, K.E.Carlson, J.S.Josan, O.Elemento, J.A.Katzenellenbogen, H.B.Zhou, K.W.Nettles. Predictive Features of Ligand-Specific Signaling Through the Estrogen Receptor. Mol.Syst.Biol. V. 12 864 2016.
ISSN: ESSN 1744-4292
PubMed: 27107013
DOI: 10.15252/MSB.20156701