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Fluorine in PDB 5die: Crystal Structure of the Er-Alpha Ligand-Binding Domain in Complex with A Trifluoro-Substituted A-Cd Ring Estrogen Derivative (1S,3AR, 5S,7AS)-7A-Methyl-5-(2,3,5-Trifluoro-4-Hydroxyphenyl)Octahydro-1H- Inden-1-Ol

Protein crystallography data

The structure of Crystal Structure of the Er-Alpha Ligand-Binding Domain in Complex with A Trifluoro-Substituted A-Cd Ring Estrogen Derivative (1S,3AR, 5S,7AS)-7A-Methyl-5-(2,3,5-Trifluoro-4-Hydroxyphenyl)Octahydro-1H- Inden-1-Ol, PDB code: 5die 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) 46.45 / 2.24
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.137, 84.053, 58.536, 90.00, 108.35, 90.00
R / Rfree (%) 20.4 / 24.7

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Er-Alpha Ligand-Binding Domain in Complex with A Trifluoro-Substituted A-Cd Ring Estrogen Derivative (1S,3AR, 5S,7AS)-7A-Methyl-5-(2,3,5-Trifluoro-4-Hydroxyphenyl)Octahydro-1H- Inden-1-Ol (pdb code 5die). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of the Er-Alpha Ligand-Binding Domain in Complex with A Trifluoro-Substituted A-Cd Ring Estrogen Derivative (1S,3AR, 5S,7AS)-7A-Methyl-5-(2,3,5-Trifluoro-4-Hydroxyphenyl)Octahydro-1H- Inden-1-Ol, PDB code: 5die:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5die

Go back to Fluorine Binding Sites List in 5die
Fluorine binding site 1 out of 6 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain in Complex with A Trifluoro-Substituted A-Cd Ring Estrogen Derivative (1S,3AR, 5S,7AS)-7A-Methyl-5-(2,3,5-Trifluoro-4-Hydroxyphenyl)Octahydro-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 in Complex with A Trifluoro-Substituted A-Cd Ring Estrogen Derivative (1S,3AR, 5S,7AS)-7A-Methyl-5-(2,3,5-Trifluoro-4-Hydroxyphenyl)Octahydro-1H- Inden-1-Ol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:38.3
occ:1.00
 F01 A:5CJ601 0.0 38.3 1.0
C09 A:5CJ601 1.3 43.8 1.0
C02 A:5CJ601 2.3 42.7 1.0
C10 A:5CJ601 2.3 44.0 1.0
F02 A:5CJ601 2.6 46.2 1.0
O01 A:5CJ601 2.7 43.8 1.0
O A:LEU387 2.8 29.2 1.0
CB A:LEU391 3.1 26.9 1.0
C A:LEU387 3.2 27.7 1.0
O A:HOH718 3.5 41.2 1.0
C01 A:5CJ601 3.5 41.8 1.0
CD2 A:LEU391 3.6 29.1 1.0
C12 A:5CJ601 3.6 43.5 1.0
N A:MET388 3.6 27.3 1.0
CA A:MET388 3.7 26.7 1.0
CB A:LEU387 3.7 31.5 1.0
CG A:LEU391 3.9 27.9 1.0
CA A:LEU387 4.0 30.1 1.0
C03 A:5CJ601 4.0 39.8 1.0
CA A:LEU391 4.3 27.7 1.0
N A:LEU391 4.4 28.7 1.0
CG A:MET388 4.4 29.3 1.0
CD1 A:LEU391 4.5 29.1 1.0
F A:5CJ601 4.6 40.5 1.0
C A:MET388 4.6 29.5 1.0
CB A:MET388 4.7 29.9 1.0
NH2 A:ARG394 4.7 31.4 1.0
CE1 A:PHE404 4.7 28.6 1.0
C04 A:5CJ601 4.8 39.0 1.0
CG A:LEU387 4.8 32.5 1.0
O A:MET388 4.8 31.5 1.0
CD1 A:PHE404 4.8 29.9 1.0
OE1 A:GLU353 5.0 34.0 1.0

Fluorine binding site 2 out of 6 in 5die

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Fluorine binding site 2 out of 6 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain in Complex with A Trifluoro-Substituted A-Cd Ring Estrogen Derivative (1S,3AR, 5S,7AS)-7A-Methyl-5-(2,3,5-Trifluoro-4-Hydroxyphenyl)Octahydro-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 in Complex with A Trifluoro-Substituted A-Cd Ring Estrogen Derivative (1S,3AR, 5S,7AS)-7A-Methyl-5-(2,3,5-Trifluoro-4-Hydroxyphenyl)Octahydro-1H- Inden-1-Ol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:46.2
occ:1.00
 F02 A:5CJ601 0.0 46.2 1.0
C10 A:5CJ601 1.3 44.0 1.0
C09 A:5CJ601 2.3 43.8 1.0
C12 A:5CJ601 2.3 43.5 1.0
F01 A:5CJ601 2.6 38.3 1.0
C04 A:5CJ601 2.8 39.0 1.0
CG A:MET388 3.2 29.3 1.0
C03 A:5CJ601 3.5 39.8 1.0
C02 A:5CJ601 3.5 42.7 1.0
C14 A:5CJ601 3.6 37.9 1.0
CD2 A:LEU391 3.9 29.1 1.0
CE A:MET388 3.9 26.3 1.0
C01 A:5CJ601 4.0 41.8 1.0
C05 A:5CJ601 4.0 38.3 1.0
CA A:MET388 4.2 26.7 1.0
CD1 A:LEU384 4.2 28.5 1.0
CB A:MET388 4.3 29.9 1.0
N A:MET388 4.4 27.3 1.0
CE1 A:PHE404 4.4 28.6 1.0
SD A:MET388 4.4 29.3 1.0
CD1 A:LEU428 4.6 27.0 1.0
O01 A:5CJ601 4.6 43.8 1.0
C A:LEU387 4.7 27.7 1.0
CB A:LEU387 4.7 31.5 1.0
CB A:LEU391 4.9 26.9 1.0
O A:LEU387 4.9 29.2 1.0
CD2 A:LEU428 5.0 22.6 1.0

Fluorine binding site 3 out of 6 in 5die

Go back to Fluorine Binding Sites List in 5die
Fluorine binding site 3 out of 6 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain in Complex with A Trifluoro-Substituted A-Cd Ring Estrogen Derivative (1S,3AR, 5S,7AS)-7A-Methyl-5-(2,3,5-Trifluoro-4-Hydroxyphenyl)Octahydro-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 in Complex with A Trifluoro-Substituted A-Cd Ring Estrogen Derivative (1S,3AR, 5S,7AS)-7A-Methyl-5-(2,3,5-Trifluoro-4-Hydroxyphenyl)Octahydro-1H- Inden-1-Ol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:40.5
occ:1.00
 F A:5CJ601 0.0 40.5 1.0
C01 A:5CJ601 1.3 41.8 1.0
C03 A:5CJ601 2.3 39.8 1.0
C02 A:5CJ601 2.3 42.7 1.0
O01 A:5CJ601 2.7 43.8 1.0
OE1 A:GLU353 3.1 34.0 1.0
O A:LEU346 3.3 34.4 1.0
N A:ALA350 3.3 31.2 1.0
C09 A:5CJ601 3.5 43.8 1.0
CA A:ALA350 3.5 34.0 1.0
C12 A:5CJ601 3.6 43.5 1.0
CB A:ALA350 3.6 25.9 1.0
CG A:LEU349 3.6 26.7 1.0
CD2 A:LEU349 3.8 28.8 1.0
CB A:LEU349 3.8 27.2 1.0
C A:LEU349 4.0 31.7 1.0
C10 A:5CJ601 4.0 44.0 1.0
CD A:GLU353 4.3 34.8 1.0
CD1 A:PHE404 4.3 29.9 1.0
C A:LEU346 4.4 34.7 1.0
CA A:LEU349 4.5 32.5 1.0
F01 A:5CJ601 4.6 38.3 1.0
O A:LEU349 4.7 32.0 1.0
CE1 A:PHE404 4.8 28.6 1.0
CA A:LEU346 4.8 34.2 1.0
C04 A:5CJ601 4.8 39.0 1.0
OE2 A:GLU353 4.9 38.7 1.0

Fluorine binding site 4 out of 6 in 5die

Go back to Fluorine Binding Sites List in 5die
Fluorine binding site 4 out of 6 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain in Complex with A Trifluoro-Substituted A-Cd Ring Estrogen Derivative (1S,3AR, 5S,7AS)-7A-Methyl-5-(2,3,5-Trifluoro-4-Hydroxyphenyl)Octahydro-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 in Complex with A Trifluoro-Substituted A-Cd Ring Estrogen Derivative (1S,3AR, 5S,7AS)-7A-Methyl-5-(2,3,5-Trifluoro-4-Hydroxyphenyl)Octahydro-1H- Inden-1-Ol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:56.5
occ:1.00
 F01 B:5CJ601 0.0 56.5 1.0
C09 B:5CJ601 1.3 53.3 1.0
C02 B:5CJ601 2.3 49.5 1.0
C10 B:5CJ601 2.3 50.6 1.0
O B:LEU387 2.6 33.7 1.0
F02 B:5CJ601 2.6 49.4 1.0
O01 B:5CJ601 2.7 39.7 1.0
C B:LEU387 3.0 31.9 1.0
CB B:LEU391 3.1 32.2 1.0
O B:HOH707 3.2 36.1 1.0
N B:MET388 3.4 32.8 1.0
C01 B:5CJ601 3.5 50.7 1.0
CA B:MET388 3.5 28.9 1.0
C12 B:5CJ601 3.5 50.5 1.0
CB B:LEU387 3.6 33.2 1.0
CD2 B:LEU391 3.7 35.8 1.0
CA B:LEU387 3.8 32.7 1.0
CG B:LEU391 4.0 35.2 1.0
C03 B:5CJ601 4.0 50.1 1.0
N B:LEU391 4.2 31.5 1.0
CA B:LEU391 4.2 33.2 1.0
C B:MET388 4.4 29.8 1.0
CG B:MET388 4.5 29.2 1.0
CB B:MET388 4.6 27.5 1.0
F B:5CJ601 4.6 50.3 1.0
O B:MET388 4.6 31.2 1.0
CD1 B:LEU391 4.6 37.6 1.0
NH2 B:ARG394 4.8 39.6 1.0
C04 B:5CJ601 4.8 45.5 1.0
CG B:LEU387 4.8 35.1 1.0
CE1 B:PHE404 5.0 39.8 1.0

Fluorine binding site 5 out of 6 in 5die

Go back to Fluorine Binding Sites List in 5die
Fluorine binding site 5 out of 6 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain in Complex with A Trifluoro-Substituted A-Cd Ring Estrogen Derivative (1S,3AR, 5S,7AS)-7A-Methyl-5-(2,3,5-Trifluoro-4-Hydroxyphenyl)Octahydro-1H- Inden-1-Ol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of the Er-Alpha Ligand-Binding Domain in Complex with A Trifluoro-Substituted A-Cd Ring Estrogen Derivative (1S,3AR, 5S,7AS)-7A-Methyl-5-(2,3,5-Trifluoro-4-Hydroxyphenyl)Octahydro-1H- Inden-1-Ol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:49.4
occ:1.00
 F02 B:5CJ601 0.0 49.4 1.0
C10 B:5CJ601 1.3 50.6 1.0
C09 B:5CJ601 2.3 53.3 1.0
C12 B:5CJ601 2.3 50.5 1.0
F01 B:5CJ601 2.6 56.5 1.0
C04 B:5CJ601 2.8 45.5 1.0
CG B:MET388 3.2 29.2 1.0
C03 B:5CJ601 3.5 50.1 1.0
C02 B:5CJ601 3.5 49.5 1.0
C14 B:5CJ601 3.7 48.9 1.0
CD2 B:LEU391 3.9 35.8 1.0
C05 B:5CJ601 4.0 44.1 1.0
CA B:MET388 4.0 28.9 1.0
C01 B:5CJ601 4.0 50.7 1.0
CE B:MET388 4.1 28.2 1.0
CB B:MET388 4.2 27.5 1.0
CD1 B:LEU384 4.2 33.1 1.0
N B:MET388 4.2 32.8 1.0
SD B:MET388 4.5 33.8 1.0
C B:LEU387 4.5 31.9 1.0
O01 B:5CJ601 4.6 39.7 1.0
CB B:LEU387 4.7 33.2 1.0
CD1 B:LEU428 4.7 30.3 1.0
CE1 B:PHE404 4.7 39.8 1.0
O B:LEU387 4.7 33.7 1.0
CB B:LEU391 4.7 32.2 1.0
CG B:LEU391 5.0 35.2 1.0

Fluorine binding site 6 out of 6 in 5die

Go back to Fluorine Binding Sites List in 5die
Fluorine binding site 6 out of 6 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain in Complex with A Trifluoro-Substituted A-Cd Ring Estrogen Derivative (1S,3AR, 5S,7AS)-7A-Methyl-5-(2,3,5-Trifluoro-4-Hydroxyphenyl)Octahydro-1H- Inden-1-Ol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of the Er-Alpha Ligand-Binding Domain in Complex with A Trifluoro-Substituted A-Cd Ring Estrogen Derivative (1S,3AR, 5S,7AS)-7A-Methyl-5-(2,3,5-Trifluoro-4-Hydroxyphenyl)Octahydro-1H- Inden-1-Ol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:50.3
occ:1.00
 F B:5CJ601 0.0 50.3 1.0
C01 B:5CJ601 1.3 50.7 1.0
C03 B:5CJ601 2.3 50.1 1.0
C02 B:5CJ601 2.3 49.5 1.0
O01 B:5CJ601 2.7 39.7 1.0
OE1 B:GLU353 3.0 40.6 1.0
N B:ALA350 3.3 37.3 1.0
O B:LEU346 3.4 44.2 1.0
CG B:LEU349 3.4 37.6 1.0
CD2 B:LEU349 3.4 38.0 1.0
CA B:ALA350 3.5 35.9 1.0
C09 B:5CJ601 3.5 53.3 1.0
C12 B:5CJ601 3.6 50.5 1.0
CB B:ALA350 3.6 33.6 1.0
CB B:LEU349 3.6 36.5 1.0
C B:LEU349 3.8 37.8 1.0
C10 B:5CJ601 4.0 50.6 1.0
CD B:GLU353 4.2 37.6 1.0
CD1 B:PHE404 4.3 38.9 1.0
CA B:LEU349 4.4 38.8 1.0
C B:LEU346 4.4 43.0 1.0
O B:LEU349 4.5 36.2 1.0
F01 B:5CJ601 4.6 56.5 1.0
CE1 B:PHE404 4.7 39.8 1.0
CD1 B:LEU349 4.8 40.4 1.0
OE2 B:GLU353 4.8 37.0 1.0
CA B:LEU346 4.8 42.9 1.0
C04 B:5CJ601 4.8 45.5 1.0
C B:ALA350 5.0 35.5 1.0

Reference:

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
Page generated: Thu Aug 1 08:44:54 2024

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