Fluorine in PDB 7zgd: Structure of Yeast SEC14P with NPPM244

The structure of Structure of Yeast SEC14P with NPPM244, PDB code: 7zgd was solved by Z.Hong, P.Johnen, G.Schaaf, F.Bono, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.27 / 2.08
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	86.728, 86.728, 109.61, 90, 90, 120
R / Rfree (%)	19.8 / 23.2

The structure of Structure of Yeast SEC14P with NPPM244 also contains other interesting chemical elements:

Bromine

(Br)

1 atom

The binding sites of Fluorine atom in the Structure of Yeast SEC14P with NPPM244 (pdb code 7zgd). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Structure of Yeast SEC14P with NPPM244, PDB code: 7zgd:

Fluorine binding site 1 out of 1 in the Structure of Yeast SEC14P with NPPM244


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Yeast SEC14P with NPPM244 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:47.7 occ:1.00 F25 A:IUC401 0.0 47.7 1.0 C24 A:IUC401 1.3 44.9 1.0 C23 A:IUC401 2.3 41.1 1.0 C19 A:IUC401 2.4 45.1 1.0 N18 A:IUC401 3.0 44.3 1.0 C17 A:IUC401 3.0 43.5 1.0 CE2 A:TYR122 3.5 49.9 1.0 C22 A:IUC401 3.6 45.0 1.0 OE1 A:GLU124 3.6 56.9 1.0 C20 A:IUC401 3.7 45.5 1.0 CD A:GLU124 3.9 58.0 1.0 CG2 A:THR175 3.9 42.6 1.0 OE2 A:GLU124 4.0 60.1 1.0 CE A:MET177 4.0 49.7 1.0 CD2 A:TYR122 4.1 47.3 1.0 C15 A:IUC401 4.1 42.0 1.0 C21 A:IUC401 4.1 43.1 1.0 CE2 A:PHE212 4.1 43.8 1.0 C16 A:IUC401 4.2 42.5 1.0 CZ A:PHE212 4.5 47.2 1.0 CZ A:TYR122 4.7 40.8 1.0 CB A:GLU124 4.7 45.3 1.0 CG A:GLU124 4.8 60.1 1.0 OH A:TYR122 4.8 40.2 1.0 OG1 A:THR175 4.8 45.1 1.0 CB A:THR175 5.0 45.0 1.0

X.R.Chen, L.Poudel, Z.Hong, P.Johnen, S.Katti, A.Tripathi, A.H.Nile, S.M.Green, D.Khan, G.Schaaf, F.Bono, V.A.Bankaitis, T.I.Igumenova. Mechanisms By Which Small Molecules of Diverse Chemotypes Arrest SEC14 Lipid Transfer Activity. J.Biol.Chem. 02861 2023.
ISSN: ESSN 1083-351X
PubMed: 36603766
DOI: 10.1016/J.JBC.2022.102861