Fluorine in PDB 5krm: Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the A-Cd Ring Estrogen, (1S,7AS)-5-(2,5-Difluoro-4- Hydroxyphenyl)-7A-Methyl-2,3,3A,4,7,7A-Hexahydro-1H-Inden-1-Ol

The structure of Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the A-Cd Ring Estrogen, (1S,7AS)-5-(2,5-Difluoro-4- Hydroxyphenyl)-7A-Methyl-2,3,3A,4,7,7A-Hexahydro-1H-Inden-1-Ol, PDB code: 5krm was solved by J.C.Nwachukwu, S.Srinivasan, N.E.Bruno, J.Nowak, D.J.Kojetin, O.Elemento, 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)	46.52 / 2.24
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.127, 84.327, 58.504, 90.00, 108.65, 90.00
R / Rfree (%)	17.1 / 21.3

The binding sites of Fluorine atom in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the A-Cd Ring Estrogen, (1S,7AS)-5-(2,5-Difluoro-4- Hydroxyphenyl)-7A-Methyl-2,3,3A,4,7,7A-Hexahydro-1H-Inden-1-Ol (pdb code 5krm). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the A-Cd Ring Estrogen, (1S,7AS)-5-(2,5-Difluoro-4- Hydroxyphenyl)-7A-Methyl-2,3,3A,4,7,7A-Hexahydro-1H-Inden-1-Ol, PDB code: 5krm:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the A-Cd Ring Estrogen, (1S,7AS)-5-(2,5-Difluoro-4- Hydroxyphenyl)-7A-Methyl-2,3,3A,4,7,7A-Hexahydro-1H-Inden-1-Ol


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 (Y537S) in Complex with the A-Cd Ring Estrogen, (1S,7AS)-5-(2,5-Difluoro-4- Hydroxyphenyl)-7A-Methyl-2,3,3A,4,7,7A-Hexahydro-1H-Inden-1-Ol within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:18.5 occ:1.00 F01 A:6WU601 0.0 18.5 1.0 C02 A:6WU601 1.3 16.6 1.0 C01 A:6WU601 2.2 16.8 1.0 C05 A:6WU601 2.4 16.8 1.0 C07 A:6WU601 2.8 21.6 1.0 C12 A:6WU601 3.2 26.2 1.0 CG A:MET388 3.5 13.7 1.0 C04 A:6WU601 3.5 18.5 1.0 C06 A:6WU601 3.5 17.4 1.0 CD2 A:LEU391 3.8 18.9 1.0 C03 A:6WU601 4.0 19.7 1.0 C08 A:6WU601 4.0 24.6 1.0 CA A:MET388 4.2 17.3 1.0 CE1 A:PHE404 4.3 17.4 1.0 CE A:MET388 4.4 14.0 1.0 CB A:MET388 4.4 15.2 1.0 N A:MET388 4.4 14.8 1.0 C11 A:6WU601 4.5 28.0 1.0 CD1 A:LEU384 4.5 16.9 1.0 C A:LEU387 4.6 15.2 1.0 CD1 A:LEU428 4.6 9.9 1.0 O A:LEU387 4.6 14.8 1.0 O01 A:6WU601 4.6 15.0 1.0 CB A:LEU391 4.7 13.6 1.0 SD A:MET388 4.8 10.0 1.0 CB A:LEU387 4.8 11.5 1.0 CG A:LEU391 4.9 17.2 1.0 CD2 A:LEU428 4.9 8.6 1.0 C09 A:6WU601 5.0 28.6 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the A-Cd Ring Estrogen, (1S,7AS)-5-(2,5-Difluoro-4- Hydroxyphenyl)-7A-Methyl-2,3,3A,4,7,7A-Hexahydro-1H-Inden-1-Ol


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 (Y537S) in Complex with the A-Cd Ring Estrogen, (1S,7AS)-5-(2,5-Difluoro-4- Hydroxyphenyl)-7A-Methyl-2,3,3A,4,7,7A-Hexahydro-1H-Inden-1-Ol within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:20.3 occ:1.00 F02 A:6WU601 0.0 20.3 1.0 C03 A:6WU601 1.3 19.7 1.0 C04 A:6WU601 2.3 18.5 1.0 C06 A:6WU601 2.3 17.4 1.0 OE1 A:GLU353 2.7 22.3 1.0 O01 A:6WU601 2.7 15.0 1.0 N A:ALA350 3.3 17.1 1.0 CA A:ALA350 3.4 19.5 1.0 O A:LEU346 3.5 19.4 1.0 C01 A:6WU601 3.5 16.8 1.0 CG A:LEU349 3.5 15.3 1.0 CB A:ALA350 3.5 11.0 1.0 C05 A:6WU601 3.6 16.8 1.0 CD2 A:LEU349 3.6 12.4 1.0 CB A:LEU349 3.8 16.5 1.0 C A:LEU349 3.8 18.7 1.0 CD A:GLU353 3.9 21.8 1.0 C02 A:6WU601 4.0 16.6 1.0 O A:LEU349 4.4 17.4 1.0 CA A:LEU349 4.4 18.9 1.0 C A:LEU346 4.6 16.3 1.0 CD1 A:PHE404 4.6 18.6 1.0 OE2 A:GLU353 4.7 24.7 1.0 C07 A:6WU601 4.7 21.6 1.0 C A:ALA350 4.8 20.2 1.0 CD1 A:LEU349 4.9 15.3 1.0 CD1 A:LEU387 4.9 17.3 1.0 CG A:GLU353 4.9 16.4 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the A-Cd Ring Estrogen, (1S,7AS)-5-(2,5-Difluoro-4- Hydroxyphenyl)-7A-Methyl-2,3,3A,4,7,7A-Hexahydro-1H-Inden-1-Ol


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 Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the A-Cd Ring Estrogen, (1S,7AS)-5-(2,5-Difluoro-4- Hydroxyphenyl)-7A-Methyl-2,3,3A,4,7,7A-Hexahydro-1H-Inden-1-Ol within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:23.4 occ:1.00 F01 B:6WU601 0.0 23.4 1.0 C02 B:6WU601 1.3 23.6 1.0 C01 B:6WU601 2.2 22.1 1.0 C05 B:6WU601 2.4 25.2 1.0 C07 B:6WU601 2.8 26.9 1.0 C12 B:6WU601 3.1 30.1 1.0 CG B:MET388 3.4 16.2 1.0 C04 B:6WU601 3.5 21.8 1.0 C06 B:6WU601 3.5 23.6 1.0 CD2 B:LEU391 3.8 12.5 1.0 C03 B:6WU601 4.0 22.9 1.0 C08 B:6WU601 4.0 28.3 1.0 CA B:MET388 4.0 16.5 1.0 CB B:MET388 4.3 16.2 1.0 N B:MET388 4.3 19.0 1.0 CE B:MET388 4.3 11.0 1.0 C11 B:6WU601 4.4 33.5 1.0 C B:LEU387 4.5 22.4 1.0 CD1 B:LEU384 4.5 15.6 1.0 O B:LEU387 4.5 23.0 1.0 CD1 B:LEU428 4.5 21.1 1.0 CE1 B:PHE404 4.6 19.7 1.0 O01 B:6WU601 4.6 20.7 1.0 CB B:LEU391 4.6 14.3 1.0 CB B:LEU387 4.7 18.4 1.0 SD B:MET388 4.7 20.9 1.0 CG B:LEU391 4.9 16.1 1.0 C13 B:6WU601 4.9 32.8 1.0 CD2 B:LEU428 4.9 13.8 1.0 C09 B:6WU601 4.9 31.2 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the A-Cd Ring Estrogen, (1S,7AS)-5-(2,5-Difluoro-4- Hydroxyphenyl)-7A-Methyl-2,3,3A,4,7,7A-Hexahydro-1H-Inden-1-Ol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with the A-Cd Ring Estrogen, (1S,7AS)-5-(2,5-Difluoro-4- Hydroxyphenyl)-7A-Methyl-2,3,3A,4,7,7A-Hexahydro-1H-Inden-1-Ol within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:20.1 occ:1.00 F02 B:6WU601 0.0 20.1 1.0 C03 B:6WU601 1.3 22.9 1.0 C04 B:6WU601 2.3 21.8 1.0 C06 B:6WU601 2.3 23.6 1.0 OE1 B:GLU353 2.7 24.7 1.0 O01 B:6WU601 2.7 20.7 1.0 CD2 B:LEU349 3.3 28.9 1.0 CG B:LEU349 3.3 28.3 1.0 N B:ALA350 3.4 18.8 1.0 C01 B:6WU601 3.5 22.1 1.0 CA B:ALA350 3.5 19.6 1.0 C05 B:6WU601 3.6 25.2 1.0 O B:LEU346 3.6 18.6 1.0 CB B:ALA350 3.7 18.9 1.0 CB B:LEU349 3.8 23.4 1.0 C B:LEU349 3.9 22.0 1.0 CD B:GLU353 3.9 24.0 1.0 C02 B:6WU601 4.0 23.6 1.0 CD1 B:PHE404 4.3 19.5 1.0 O B:LEU349 4.5 20.6 1.0 CA B:LEU349 4.5 23.0 1.0 CD1 B:LEU349 4.7 31.9 1.0 OE2 B:GLU353 4.7 27.5 1.0 C B:LEU346 4.7 20.4 1.0 C07 B:6WU601 4.7 26.9 1.0 NH2 B:ARG394 4.8 20.3 1.0 CE1 B:PHE404 4.9 19.7 1.0 CG B:GLU353 4.9 20.5 1.0

J.C.Nwachukwu, S.Srinivasan, N.E.Bruno, J.Nowak, N.J.Wright, F.Minutolo, E.S.Rangarajan, T.Izard, X.Q.Yao, B.J.Grant, D.J.Kojetin, O.Elemento, J.A.Katzenellenbogen, K.W.Nettles. Systems Structural Biology Analysis of Ligand Effects on Er Alpha Predicts Cellular Response to Environmental Estrogens and Anti-Hormone Therapies. Cell Chem Biol V. 24 35 2017.
ISSN: ESSN 2451-9456
PubMed: 28042045
DOI: 10.1016/J.CHEMBIOL.2016.11.014