Fluorine in PDB 3fmz: Crystal Structure of Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand

The structure of Crystal Structure of Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand, PDB code: 3fmz was solved by Z.Wang, S.Johnstone, N.P.Walker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.90
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	84.802, 84.802, 119.557, 90.00, 90.00, 120.00
R / Rfree (%)	22.3 / 28.6

The binding sites of Fluorine atom in the Crystal Structure of Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand (pdb code 3fmz). 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 Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand, PDB code: 3fmz:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand


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 Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:F184 b:37.3 occ:1.00 F1 A:2T1184 0.0 37.3 1.0 C12 A:2T1184 1.3 37.0 1.0 F2 A:2T1184 2.1 37.3 1.0 F3 A:2T1184 2.2 37.3 1.0 C4 A:2T1184 2.3 36.3 1.0 C5 A:2T1184 2.9 36.0 1.0 ND1 A:HIS104 3.0 20.1 1.0 CE1 A:HIS104 3.0 20.4 1.0 SD A:MET88 3.1 26.4 1.0 C3 A:2T1184 3.3 35.5 1.0 CE A:MET88 3.7 26.6 1.0 C7 A:2T1184 3.7 34.5 1.0 OH A:TYR133 4.0 14.7 1.0 NE2 A:HIS104 4.2 19.9 1.0 C6 A:2T1184 4.2 35.6 1.0 CG A:HIS104 4.2 20.4 1.0 CZ A:PHE77 4.4 23.8 1.0 CE2 A:PHE77 4.5 24.0 1.0 C2 A:2T1184 4.5 35.4 1.0 NE2 A:GLN117 4.7 19.1 1.0 C8 A:2T1184 4.8 34.0 1.0 C11 A:2T1184 4.8 33.8 1.0 CD2 A:HIS104 4.8 20.3 1.0 C1 A:2T1184 4.8 35.3 1.0 CG A:MET88 4.9 25.7 1.0 CZ A:PHE45 4.9 25.0 1.0 CE1 A:TYR133 4.9 14.0 1.0 CZ A:TYR133 5.0 14.6 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand


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 Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:F184 b:37.3 occ:1.00 F3 A:2T1184 0.0 37.3 1.0 C12 A:2T1184 1.3 37.0 1.0 F2 A:2T1184 2.1 37.3 1.0 F1 A:2T1184 2.2 37.3 1.0 C4 A:2T1184 2.3 36.3 1.0 C5 A:2T1184 2.8 36.0 1.0 C3 A:2T1184 3.5 35.5 1.0 CE1 A:HIS104 3.9 20.4 1.0 C7 A:2T1184 4.0 34.5 1.0 C6 A:2T1184 4.2 35.6 1.0 CZ A:PHE137 4.3 16.4 1.0 C11 A:2T1184 4.4 33.8 1.0 CZ A:PHE45 4.4 25.0 1.0 CE2 A:PHE135 4.5 14.6 1.0 ND1 A:HIS104 4.5 20.1 1.0 CE2 A:PHE45 4.6 25.1 1.0 C2 A:2T1184 4.6 35.4 1.0 CD2 A:PHE135 4.6 14.2 1.0 CB A:ALA57 4.7 28.9 1.0 CB A:ALA43 4.8 21.2 1.0 C1 A:2T1184 4.9 35.3 1.0 NE2 A:HIS104 4.9 19.9 1.0 CE2 A:PHE137 4.9 16.2 1.0 SD A:MET88 5.0 26.4 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand


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 Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:F184 b:37.3 occ:1.00 F2 A:2T1184 0.0 37.3 1.0 C12 A:2T1184 1.3 37.0 1.0 F3 A:2T1184 2.1 37.3 1.0 F1 A:2T1184 2.1 37.3 1.0 C4 A:2T1184 2.4 36.3 1.0 C7 A:2T1184 2.4 34.5 1.0 C3 A:2T1184 2.8 35.5 1.0 C11 A:2T1184 3.0 33.8 1.0 CE2 A:PHE135 3.5 14.6 1.0 C5 A:2T1184 3.6 36.0 1.0 C10 A:2T1184 3.7 33.4 1.0 OH A:TYR133 3.7 14.7 1.0 C8 A:2T1184 3.7 34.0 1.0 CE1 A:TYR133 3.8 14.0 1.0 CD2 A:PHE135 4.1 14.2 1.0 C2 A:2T1184 4.1 35.4 1.0 CZ A:TYR133 4.2 14.6 1.0 C9 A:2T1184 4.3 33.7 1.0 CE1 A:HIS104 4.5 20.4 1.0 N1 A:2T1184 4.5 33.2 1.0 CZ A:PHE135 4.6 14.7 1.0 CE A:MET88 4.6 26.6 1.0 ND1 A:HIS104 4.6 20.1 1.0 SD A:MET88 4.7 26.4 1.0 C6 A:2T1184 4.8 35.6 1.0 CD1 A:TYR133 4.9 13.7 1.0 NE2 A:GLN117 4.9 19.1 1.0 C1 A:2T1184 5.0 35.3 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand


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 Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:F184 b:35.6 occ:1.00 F1 B:2T1184 0.0 35.6 1.0 C12 B:2T1184 1.3 35.2 1.0 F3 B:2T1184 2.2 35.3 1.0 F2 B:2T1184 2.2 35.0 1.0 C4 B:2T1184 2.3 34.5 1.0 C3 B:2T1184 3.2 33.9 1.0 C5 B:2T1184 3.2 33.8 1.0 ND1 B:HIS104 3.4 23.1 1.0 C7 B:2T1184 3.4 33.0 1.0 CE1 B:HIS104 3.4 22.8 1.0 NE2 B:GLN117 3.6 17.1 1.0 CE B:MET88 3.7 26.3 1.0 SD B:MET88 3.9 27.1 1.0 OH B:TYR133 4.2 11.9 1.0 C11 B:2T1184 4.3 32.7 1.0 C2 B:2T1184 4.4 33.6 1.0 C6 B:2T1184 4.4 33.6 1.0 C8 B:2T1184 4.5 32.3 1.0 CG B:HIS104 4.6 22.8 1.0 NE2 B:HIS104 4.6 22.8 1.0 CD B:GLN117 4.7 17.1 1.0 CE2 B:PHE135 4.7 13.2 1.0 CE1 B:TYR133 4.8 11.8 1.0 C1 B:2T1184 4.9 33.5 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand


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 Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:F184 b:35.3 occ:1.00 F3 B:2T1184 0.0 35.3 1.0 C12 B:2T1184 1.3 35.2 1.0 F2 B:2T1184 2.1 35.0 1.0 F1 B:2T1184 2.2 35.6 1.0 C4 B:2T1184 2.3 34.5 1.0 C5 B:2T1184 2.7 33.8 1.0 C3 B:2T1184 3.6 33.9 1.0 C6 B:2T1184 4.1 33.6 1.0 CE1 B:HIS104 4.1 22.8 1.0 C7 B:2T1184 4.2 33.0 1.0 CZ B:PHE45 4.3 28.4 1.0 CZ B:PHE137 4.4 14.9 1.0 CB B:ALA43 4.4 24.6 1.0 C11 B:2T1184 4.6 32.7 1.0 CE2 B:PHE45 4.6 28.4 1.0 ND1 B:HIS104 4.7 23.1 1.0 C2 B:2T1184 4.7 33.6 1.0 CB B:ALA57 4.8 33.9 1.0 CE2 B:PHE135 4.9 13.2 1.0 C1 B:2T1184 4.9 33.5 1.0 CE2 B:PHE137 4.9 14.4 1.0 NE2 B:GLN117 5.0 17.1 1.0 NE2 B:HIS104 5.0 22.8 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand


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 Retinol-Binding Protein 4 (RBP4) in Complex with Non-Retinoid Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:F184 b:35.0 occ:1.00 F2 B:2T1184 0.0 35.0 1.0 C12 B:2T1184 1.3 35.2 1.0 F3 B:2T1184 2.1 35.3 1.0 F1 B:2T1184 2.2 35.6 1.0 C4 B:2T1184 2.3 34.5 1.0 C7 B:2T1184 2.6 33.0 1.0 C11 B:2T1184 2.7 32.7 1.0 C3 B:2T1184 2.8 33.9 1.0 CE2 B:PHE135 3.4 13.2 1.0 C10 B:2T1184 3.5 32.3 1.0 C5 B:2T1184 3.5 33.8 1.0 CZ B:PHE135 4.0 13.3 1.0 C8 B:2T1184 4.1 32.3 1.0 CD2 B:PHE135 4.1 13.0 1.0 C2 B:2T1184 4.2 33.6 1.0 CB B:ALA57 4.5 33.9 1.0 N1 B:2T1184 4.6 32.2 1.0 C6 B:2T1184 4.7 33.6 1.0 C9 B:2T1184 4.7 32.0 1.0 CE1 B:TYR133 4.7 11.8 1.0 NE2 B:GLN117 4.8 17.1 1.0 OH B:TYR133 4.9 11.9 1.0 C1 B:2T1184 4.9 33.5 1.0

A.Motani, Z.Wang, M.Conn, K.Siegler, Y.Zhang, Q.Liu, S.Johnstone, H.Xu, S.Thibault, Y.Wang, P.Fan, R.Connors, H.Le, G.Xu, N.Walker, B.Shan, P.Coward. Identification and Characterization of A Non-Retinoid Ligand For Retinol-Binding Protein 4 Which Lowers Serum Retinol-Binding Protein 4 Levels in Vivo. J.Biol.Chem. V. 284 7673 2009.
ISSN: ISSN 0021-9258
PubMed: 19147488
DOI: 10.1074/JBC.M809654200