Fluorine in PDB 1p93: Crystal Structure of the Agonist Form of Glucocorticoid Receptor

The structure of Crystal Structure of the Agonist Form of Glucocorticoid Receptor, PDB code: 1p93 was solved by B.Kauppi, C.Jakob, M.Farnegardh, J.Yang, H.Ahola, M.Alarcon, K.Calles, O.Engstrom, J.Harlan, S.Muchmore, A.-K.Ramqvist, S.Thorell, L.Ohman, J.Greer, J.-A.Gustafsson, J.Carlstedt-Duke, M.Carlquist, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.17 / 2.70
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	127.400, 127.400, 91.800, 90.00, 90.00, 120.00
R / Rfree (%)	n/a / n/a

The binding sites of Fluorine atom in the Crystal Structure of the Agonist Form of Glucocorticoid Receptor (pdb code 1p93). 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 Agonist Form of Glucocorticoid Receptor, PDB code: 1p93:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of the Agonist Form of Glucocorticoid Receptor


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 Agonist Form of Glucocorticoid Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:F1999 b:72.5 occ:1.00 F1 A:DEX1999 0.0 72.5 1.0 C9 A:DEX1999 1.4 67.0 1.0 C10 A:DEX1999 2.4 67.3 1.0 C11 A:DEX1999 2.4 67.0 1.0 C8 A:DEX1999 2.4 65.7 1.0 C5 A:DEX1999 3.0 67.6 1.0 C14 A:DEX1999 3.0 68.5 1.0 C7 A:DEX1999 3.0 63.5 1.0 C12 A:DEX1999 3.0 66.2 1.0 C1 A:DEX1999 3.0 67.8 1.0 C6 A:DEX1999 3.6 65.8 1.0 CE1 A:PHE623 3.6 61.4 1.0 C13 A:DEX1999 3.6 69.0 1.0 O2 A:DEX1999 3.6 69.7 1.0 CE A:MET646 3.7 72.2 1.0 C19 A:DEX1999 3.8 66.2 1.0 C4 A:DEX1999 3.8 68.5 1.0 C2 A:DEX1999 3.9 68.6 1.0 CD1 A:LEU563 4.1 66.6 1.0 CB A:LEU563 4.1 62.6 1.0 CD1 A:PHE623 4.1 62.3 1.0 C3 A:DEX1999 4.2 70.2 1.0 C15 A:DEX1999 4.5 64.3 1.0 CZ A:PHE623 4.5 62.6 1.0 O3 A:DEX1999 4.6 72.3 1.0 C17 A:DEX1999 4.7 67.9 1.0 CG A:LEU563 4.7 65.6 1.0 C18 A:DEX1999 4.8 66.1 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of the Agonist Form of Glucocorticoid Receptor


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 Agonist Form of Glucocorticoid Receptor within 5.0Å range: probe atom residue distance (Å) B Occ B:F2999 b:68.2 occ:1.00 F1 B:DEX2999 0.0 68.2 1.0 C9 B:DEX2999 1.3 65.9 1.0 C11 B:DEX2999 2.4 65.7 1.0 C10 B:DEX2999 2.4 67.4 1.0 C8 B:DEX2999 2.4 65.8 1.0 C12 B:DEX2999 3.0 63.7 1.0 C5 B:DEX2999 3.0 68.5 1.0 C14 B:DEX2999 3.0 67.4 1.0 C1 B:DEX2999 3.0 66.9 1.0 C7 B:DEX2999 3.0 67.3 1.0 CE1 B:PHE623 3.2 62.3 1.0 O2 B:DEX2999 3.6 65.6 1.0 C13 B:DEX2999 3.6 66.7 1.0 C6 B:DEX2999 3.6 66.6 1.0 CD1 B:PHE623 3.7 60.4 1.0 C19 B:DEX2999 3.8 67.8 1.0 C4 B:DEX2999 3.8 68.9 1.0 C2 B:DEX2999 3.9 69.0 1.0 CE B:MET646 3.9 70.6 1.0 C3 B:DEX2999 4.2 68.7 1.0 CZ B:PHE623 4.3 62.0 1.0 CB B:LEU563 4.4 63.1 1.0 CD1 B:LEU563 4.5 63.9 1.0 C15 B:DEX2999 4.5 65.0 1.0 O3 B:DEX2999 4.6 72.9 1.0 C17 B:DEX2999 4.7 69.7 1.0 C18 B:DEX2999 4.8 67.0 1.0 CG B:LEU563 4.9 63.2 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of the Agonist Form of Glucocorticoid Receptor


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 Agonist Form of Glucocorticoid Receptor within 5.0Å range: probe atom residue distance (Å) B Occ C:F3999 b:64.2 occ:1.00 F1 C:DEX3999 0.0 64.2 1.0 C9 C:DEX3999 1.4 65.3 1.0 C10 C:DEX3999 2.4 63.3 1.0 C11 C:DEX3999 2.4 66.0 1.0 C8 C:DEX3999 2.4 67.1 1.0 C12 C:DEX3999 3.0 65.1 1.0 C14 C:DEX3999 3.0 67.1 1.0 C5 C:DEX3999 3.0 66.2 1.0 C7 C:DEX3999 3.0 65.4 1.0 C1 C:DEX3999 3.0 65.7 1.0 CE1 C:PHE623 3.5 58.7 1.0 CE C:MET646 3.5 70.3 1.0 O2 C:DEX3999 3.6 74.6 1.0 C13 C:DEX3999 3.6 68.1 1.0 C6 C:DEX3999 3.6 66.6 1.0 C19 C:DEX3999 3.8 69.1 1.0 C4 C:DEX3999 3.9 68.5 1.0 C2 C:DEX3999 3.9 67.5 1.0 CD1 C:PHE623 3.9 59.7 1.0 C3 C:DEX3999 4.3 66.1 1.0 CB C:LEU563 4.4 61.1 1.0 C15 C:DEX3999 4.5 70.8 1.0 CZ C:PHE623 4.6 58.4 1.0 O3 C:DEX3999 4.6 73.7 1.0 C17 C:DEX3999 4.7 71.7 1.0 CD1 C:LEU563 4.7 58.5 1.0 C18 C:DEX3999 4.8 68.5 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of the Agonist Form of Glucocorticoid Receptor


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 Agonist Form of Glucocorticoid Receptor within 5.0Å range: probe atom residue distance (Å) B Occ D:F4999 b:63.6 occ:1.00 F1 D:DEX4999 0.0 63.6 1.0 C9 D:DEX4999 1.4 67.3 1.0 C10 D:DEX4999 2.4 65.4 1.0 C11 D:DEX4999 2.4 63.6 1.0 C8 D:DEX4999 2.4 66.1 1.0 C12 D:DEX4999 3.0 65.3 1.0 C14 D:DEX4999 3.0 64.6 1.0 C5 D:DEX4999 3.0 67.4 1.0 C7 D:DEX4999 3.0 63.5 1.0 C1 D:DEX4999 3.0 66.6 1.0 CE1 D:PHE623 3.1 55.5 1.0 O2 D:DEX4999 3.6 68.4 1.0 C6 D:DEX4999 3.6 63.6 1.0 C13 D:DEX4999 3.6 65.9 1.0 C19 D:DEX4999 3.8 65.6 1.0 C4 D:DEX4999 3.8 69.0 1.0 CD1 D:PHE623 3.9 61.2 1.0 C2 D:DEX4999 3.9 65.8 1.0 CE D:MET646 3.9 68.2 1.0 CZ D:PHE623 3.9 61.5 1.0 C3 D:DEX4999 4.3 68.5 1.0 CB D:LEU563 4.5 60.8 1.0 C15 D:DEX4999 4.5 65.7 1.0 O3 D:DEX4999 4.7 63.8 1.0 C17 D:DEX4999 4.7 68.8 1.0 C18 D:DEX4999 4.8 68.8 1.0 CD1 D:LEU563 4.8 62.6 1.0 SD D:MET646 5.0 69.7 1.0

B.Kauppi, C.Jakob, M.Farnegardh, J.Yang, H.Ahola, M.Alarcon, K.Calles, O.Engstrom, J.Harlan, S.Muchmore, A.-K.Ramqvist, S.Thorell, L.Ohman, J.Greer, J.-A.Gustafsson, J.Carlstedt-Duke, M.Carlquist. The Three-Dimensional Structures of Antagonistic and Agonistic Forms of the Glucocorticoid Receptor Ligand-Binding Domain: Ru-486 Induces A Transconformation That Leads to Active Antagonism. J.Biol.Chem. V. 278 22748 2003.
ISSN: ISSN 0021-9258
PubMed: 12686538
DOI: 10.1074/JBC.M212711200