Fluorine in PDB 8gd0: Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Tfh-I-070-A6

The structure of Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Tfh-I-070-A6, PDB code: 8gd0 was solved by W.D.Tolbert, D.N.Nguyen, M.Pazgier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.88 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.577, 66.275, 91.388, 90, 90, 90
R / Rfree (%)	21.8 / 27.4

The structure of Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Tfh-I-070-A6 also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Fluorine atom in the Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Tfh-I-070-A6 (pdb code 8gd0). 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 Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Tfh-I-070-A6, PDB code: 8gd0:

Fluorine binding site 1 out of 1 in the Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Tfh-I-070-A6


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 Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Tfh-I-070-A6 within 5.0Å range: probe atom residue distance (Å) B Occ A:F513 b:39.5 occ:1.00 F16 A:Z3F513 0.0 39.5 1.0 C15 A:Z3F513 1.3 37.9 1.0 C17 A:Z3F513 2.3 38.6 1.0 C14 A:Z3F513 2.4 35.3 1.0 CL1 A:Z3F513 2.9 41.4 1.0 O A:THR375 3.1 42.4 1.0 CE A:MET475 3.4 34.4 1.0 CG1 A:VAL255 3.5 31.6 1.0 CG2 A:THR257 3.5 38.7 1.0 C19 A:Z3F513 3.6 36.2 1.0 CA A:SER256 3.6 40.1 1.0 C13 A:Z3F513 3.6 37.8 1.0 C A:SER256 3.7 38.5 1.0 N A:SER256 3.8 34.9 1.0 C A:THR375 3.9 40.1 1.0 N A:THR257 3.9 35.1 1.0 CG2 A:THR375 4.0 38.4 1.0 CB A:THR375 4.1 37.5 1.0 C20 A:Z3F513 4.1 38.1 1.0 C A:VAL255 4.1 38.5 1.0 O A:SER256 4.2 39.0 1.0 O A:VAL255 4.3 34.9 1.0 N A:PHE376 4.6 37.5 1.0 CA A:THR375 4.6 40.6 1.0 CA A:PHE376 4.6 41.6 1.0 CB A:THR257 4.7 36.4 1.0 CB A:VAL255 4.7 35.8 1.0 SD A:MET475 4.8 38.7 1.0 N12 A:Z3F513 4.8 38.2 1.0 O11 A:Z3F513 4.8 42.9 1.0 CA A:THR257 4.8 34.9 1.0 OG1 A:THR257 4.9 37.8 1.0 CA A:VAL255 5.0 31.6 1.0

S.Ding, W.D.Tolbert, H.Zhu, D.Lee, L.Marchitto, T.Higgins, X.Zhao, D.Nguyen, R.Sherburn, J.Richard, G.Gendron-Lepage, H.Medjahed, M.Mohammadi, C.Abrams, M.Pazgier, A.B.Smith Iii, A.Finzi. Piperidine CD4-Mimetic Compounds Expose Vulnerable Env Epitopes Sensitizing Hiv-1-Infected Cells to Adcc. Viruses V. 15 2023.
ISSN: ESSN 1999-4915
PubMed: 37243271
DOI: 10.3390/V15051185