Fluorine in PDB 2zk6: Human Peroxisome Proliferator-Activated Receptor Gamma Ligand Binding Domain Complexed with C8-Bodipy

The structure of Human Peroxisome Proliferator-Activated Receptor Gamma Ligand Binding Domain Complexed with C8-Bodipy, PDB code: 2zk6 was solved by T.Waku, T.Shiraki, T.Oyama, Y.Fujimoto, K.Morikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.76 / 2.41
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	93.425, 61.149, 118.433, 90.00, 102.91, 90.00
R / Rfree (%)	25 / 29.9

The binding sites of Fluorine atom in the Human Peroxisome Proliferator-Activated Receptor Gamma Ligand Binding Domain Complexed with C8-Bodipy (pdb code 2zk6). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Human Peroxisome Proliferator-Activated Receptor Gamma Ligand Binding Domain Complexed with C8-Bodipy, PDB code: 2zk6:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Human Peroxisome Proliferator-Activated Receptor Gamma Ligand Binding Domain Complexed with C8-Bodipy


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Peroxisome Proliferator-Activated Receptor Gamma Ligand Binding Domain Complexed with C8-Bodipy within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:77.2 occ:1.00 F01 A:C081 0.0 77.2 1.0 B A:C081 1.3 76.3 1.0 F02 A:C081 2.1 76.4 1.0 N02 A:C081 2.3 76.2 1.0 N01 A:C081 2.3 75.9 1.0 C05 A:C081 2.8 74.9 1.0 C02 A:C081 3.0 75.5 1.0 C14 A:C081 3.0 76.2 1.0 CA A:CYS285 3.3 57.3 1.0 C22 A:C081 3.3 76.4 1.0 C06 A:C081 3.3 72.8 1.0 C15 A:C081 3.4 77.4 1.0 CB A:CYS285 3.5 58.7 1.0 C04 A:C081 3.6 74.5 1.0 C01 A:C081 3.6 75.7 1.0 C03 A:C081 3.7 75.1 1.0 CB A:ARG288 3.9 51.9 1.0 C16 A:C081 4.0 76.8 1.0 N A:CYS285 4.2 56.7 1.0 O A:CYS285 4.2 57.4 1.0 C A:CYS285 4.2 57.1 1.0 SG A:CYS285 4.3 62.1 1.0 CG A:ARG288 4.3 51.6 1.0 C20 A:C081 4.3 76.1 1.0 C21 A:C081 4.4 76.7 1.0 C07 A:C081 4.5 70.5 1.0 O A:GLY284 4.7 56.4 1.0 C17 A:C081 4.8 78.0 1.0 C A:GLY284 4.8 56.5 1.0

Fluorine binding site 2 out of 4 in the Human Peroxisome Proliferator-Activated Receptor Gamma Ligand Binding Domain Complexed with C8-Bodipy


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Peroxisome Proliferator-Activated Receptor Gamma Ligand Binding Domain Complexed with C8-Bodipy within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:76.4 occ:1.00 F02 A:C081 0.0 76.4 1.0 B A:C081 1.3 76.3 1.0 F01 A:C081 2.1 77.2 1.0 N01 A:C081 2.2 75.9 1.0 N02 A:C081 2.3 76.2 1.0 C14 A:C081 2.9 76.2 1.0 C05 A:C081 3.0 74.9 1.0 C15 A:C081 3.0 77.4 1.0 C06 A:C081 3.1 72.8 1.0 C22 A:C081 3.5 76.4 1.0 C02 A:C081 3.5 75.5 1.0 C01 A:C081 4.0 75.7 1.0 C16 A:C081 4.2 76.8 1.0 C04 A:C081 4.2 74.5 1.0 C20 A:C081 4.3 76.1 1.0 C03 A:C081 4.5 75.1 1.0 C21 A:C081 4.5 76.7 1.0 O A:LEU340 4.5 39.1 1.0 CD1 A:LEU330 4.5 34.5 1.0 C07 A:C081 4.6 70.5 1.0 CG2 A:ILE341 4.7 42.1 1.0 C17 A:C081 4.8 78.0 1.0 CG2 A:VAL339 4.9 28.0 1.0 CG A:ARG288 5.0 51.6 1.0

Fluorine binding site 3 out of 4 in the Human Peroxisome Proliferator-Activated Receptor Gamma Ligand Binding Domain Complexed with C8-Bodipy


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Peroxisome Proliferator-Activated Receptor Gamma Ligand Binding Domain Complexed with C8-Bodipy within 5.0Å range: probe atom residue distance (Å) B Occ B:F2 b:74.6 occ:1.00 F01 B:C082 0.0 74.6 1.0 B B:C082 1.3 74.0 1.0 F02 B:C082 2.1 74.8 1.0 N02 B:C082 2.3 74.2 1.0 N01 B:C082 2.3 73.9 1.0 CA B:CYS285 2.8 60.2 1.0 C05 B:C082 2.8 71.9 1.0 C02 B:C082 2.9 73.7 1.0 C14 B:C082 3.1 73.5 1.0 C22 B:C082 3.2 74.3 1.0 C16 B:C082 3.3 72.6 1.0 CB B:CYS285 3.4 62.4 1.0 O B:CYS285 3.4 57.3 1.0 C01 B:C082 3.5 74.1 1.0 C04 B:C082 3.5 72.4 1.0 C06 B:C082 3.5 68.4 1.0 C B:CYS285 3.5 57.7 1.0 C03 B:C082 3.5 72.9 1.0 C15 B:C082 3.7 72.9 1.0 N B:CYS285 3.8 60.1 1.0 O B:GLY284 3.8 61.7 1.0 SG B:CYS285 4.1 68.2 1.0 C B:GLY284 4.2 60.6 1.0 C21 B:C082 4.4 73.3 1.0 C20 B:C082 4.4 73.4 1.0 CB B:ARG288 4.5 45.8 1.0 C17 B:C082 4.6 72.6 1.0 C07 B:C082 4.7 65.3 1.0 N B:GLN286 4.8 55.9 1.0 O02 B:C082 4.8 69.5 1.0 CG B:ARG288 4.8 45.1 1.0 C18 B:C082 4.9 71.9 1.0 C19 B:C082 5.0 71.6 1.0

Fluorine binding site 4 out of 4 in the Human Peroxisome Proliferator-Activated Receptor Gamma Ligand Binding Domain Complexed with C8-Bodipy


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human Peroxisome Proliferator-Activated Receptor Gamma Ligand Binding Domain Complexed with C8-Bodipy within 5.0Å range: probe atom residue distance (Å) B Occ B:F2 b:74.8 occ:1.00 F02 B:C082 0.0 74.8 1.0 B B:C082 1.3 74.0 1.0 F01 B:C082 2.1 74.6 1.0 N01 B:C082 2.2 73.9 1.0 N02 B:C082 2.3 74.2 1.0 C16 B:C082 2.8 72.6 1.0 C14 B:C082 2.9 73.5 1.0 C05 B:C082 3.0 71.9 1.0 O02 B:C082 3.1 69.5 1.0 C06 B:C082 3.2 68.4 1.0 C15 B:C082 3.3 72.9 1.0 C02 B:C082 3.5 73.7 1.0 C22 B:C082 3.5 74.3 1.0 C19 B:C082 3.7 71.6 1.0 C17 B:C082 3.7 72.6 1.0 C01 B:C082 4.0 74.1 1.0 CG2 B:ILE341 4.1 49.6 1.0 C18 B:C082 4.1 71.9 1.0 C04 B:C082 4.2 72.4 1.0 C20 B:C082 4.3 73.4 1.0 C03 B:C082 4.4 72.9 1.0 CG B:ARG288 4.5 45.1 1.0 C21 B:C082 4.5 73.3 1.0 CB B:ARG288 4.7 45.8 1.0 C07 B:C082 4.7 65.3 1.0 O01 B:C082 4.7 72.2 1.0 CA B:CYS285 4.7 60.2 1.0 CB B:ILE341 4.9 49.1 1.0 O B:GLY284 4.9 61.7 1.0 CD1 B:LEU330 5.0 43.5 1.0

T.Waku, T.Shiraki, T.Oyama, K.Maebara, R.Nakamori, K.Morikawa. The Nuclear Receptor Ppargamma Individually Responds to Serotonin- and Fatty Acid-Metabolites Embo J. V. 29 3395 2010.
ISSN: ISSN 0261-4189
PubMed: 20717101
DOI: 10.1038/EMBOJ.2010.197