Fluorine in PDB 8fm3: Hiv-1 GP120 Complex with Cjf-III-288

The structure of Hiv-1 GP120 Complex with Cjf-III-288, PDB code: 8fm3 was solved by Z.Gong, W.A.Hendrickson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.80 / 2.11
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.464, 121.718, 195.183, 90, 90, 90
R / Rfree (%)	24.7 / 27.3

The structure of Hiv-1 GP120 Complex with Cjf-III-288 also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Fluorine atom in the Hiv-1 GP120 Complex with Cjf-III-288 (pdb code 8fm3). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Hiv-1 GP120 Complex with Cjf-III-288, PDB code: 8fm3:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Hiv-1 GP120 Complex with Cjf-III-288


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Hiv-1 GP120 Complex with Cjf-III-288 within 5.0Å range: probe atom residue distance (Å) B Occ A:F507 b:35.4 occ:1.00 F22 A:Y26507 0.0 35.4 1.0 C21 A:Y26507 1.4 27.6 1.0 C20 A:Y26507 2.3 24.6 1.0 C23 A:Y26507 2.4 21.0 1.0 CL24 A:Y26507 3.0 102.0 1.0 OG A:SER375 3.0 28.7 1.0 O A:SER375 3.1 27.9 1.0 CA A:SER256 3.3 25.3 1.0 C A:SER256 3.5 24.5 1.0 C19 A:Y26507 3.6 20.8 1.0 C25 A:Y26507 3.6 27.8 1.0 C A:SER375 3.6 25.2 1.0 N A:SER256 3.7 26.8 1.0 N A:THR257 3.8 24.8 1.0 CG2 A:THR257 3.8 23.2 1.0 CG1 A:VAL255 3.8 23.5 1.0 CE A:MET475 4.0 21.8 1.0 C A:VAL255 4.0 24.5 1.0 O A:VAL255 4.0 30.7 1.0 C26 A:Y26507 4.1 25.0 1.0 CB A:SER375 4.1 21.8 1.0 N A:PHE376 4.1 26.6 1.0 O A:SER256 4.2 27.8 1.0 CA A:PHE376 4.2 27.4 1.0 CA A:SER375 4.4 24.4 1.0 CB A:SER256 4.5 24.9 1.0 O27 A:Y26507 4.6 27.6 1.0 CB A:THR257 4.7 25.3 1.0 CA A:THR257 4.8 23.9 1.0 N18 A:Y26507 4.8 26.4 1.0 OG1 A:THR257 4.8 29.8 1.0 CB A:VAL255 4.9 21.2 1.0 SD A:MET475 5.0 25.7 1.0

Fluorine binding site 2 out of 4 in the Hiv-1 GP120 Complex with Cjf-III-288


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Hiv-1 GP120 Complex with Cjf-III-288 within 5.0Å range: probe atom residue distance (Å) B Occ C:F507 b:32.3 occ:1.00 F22 C:Y26507 0.0 32.3 1.0 C21 C:Y26507 1.4 26.2 1.0 C20 C:Y26507 2.3 24.1 1.0 C23 C:Y26507 2.4 18.9 1.0 CL24 C:Y26507 3.0 46.1 1.0 OG C:SER375 3.0 26.2 1.0 O C:SER375 3.1 26.4 1.0 CA C:SER256 3.3 22.3 1.0 C C:SER256 3.5 23.0 1.0 C19 C:Y26507 3.6 22.2 1.0 C25 C:Y26507 3.6 23.6 1.0 C C:SER375 3.6 23.2 1.0 N C:SER256 3.7 24.4 1.0 N C:THR257 3.8 19.6 1.0 CG2 C:THR257 3.8 20.3 1.0 CG1 C:VAL255 3.8 24.8 1.0 CE C:MET475 4.0 25.3 1.0 C C:VAL255 4.0 26.4 1.0 O C:VAL255 4.0 29.3 1.0 C26 C:Y26507 4.1 22.6 1.0 CB C:SER375 4.1 21.5 1.0 N C:PHE376 4.1 25.9 1.0 O C:SER256 4.2 27.7 1.0 CA C:PHE376 4.2 24.5 1.0 CA C:SER375 4.4 22.5 1.0 CB C:SER256 4.5 23.4 1.0 O27 C:Y26507 4.6 21.7 1.0 CB C:THR257 4.7 20.0 1.0 CA C:THR257 4.8 23.0 1.0 OG1 C:THR257 4.8 26.4 1.0 N18 C:Y26507 4.8 25.2 1.0 CB C:VAL255 4.9 20.9 1.0 SD C:MET475 5.0 25.4 1.0

Fluorine binding site 3 out of 4 in the Hiv-1 GP120 Complex with Cjf-III-288


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Hiv-1 GP120 Complex with Cjf-III-288 within 5.0Å range: probe atom residue distance (Å) B Occ D:F507 b:36.2 occ:1.00 F22 D:Y26507 0.0 36.2 1.0 C21 D:Y26507 1.4 26.9 1.0 C20 D:Y26507 2.3 29.0 1.0 C23 D:Y26507 2.4 21.6 1.0 CL24 D:Y26507 3.0 69.3 1.0 OG D:SER375 3.0 30.0 1.0 O D:SER375 3.1 29.3 1.0 CA D:SER256 3.3 22.7 1.0 C D:SER256 3.5 27.3 1.0 C19 D:Y26507 3.6 27.3 1.0 C25 D:Y26507 3.6 29.0 1.0 C D:SER375 3.6 29.1 1.0 N D:SER256 3.7 24.6 1.0 N D:THR257 3.8 28.5 1.0 CG2 D:THR257 3.8 27.4 1.0 CG1 D:VAL255 3.8 25.5 1.0 CE D:MET475 4.0 24.1 1.0 C D:VAL255 4.0 26.7 1.0 O D:VAL255 4.0 31.3 1.0 C26 D:Y26507 4.1 28.7 1.0 CB D:SER375 4.1 27.8 1.0 N D:PHE376 4.1 29.3 1.0 O D:SER256 4.2 29.8 1.0 CA D:PHE376 4.2 28.0 1.0 CA D:SER375 4.4 29.2 1.0 CB D:SER256 4.5 23.9 1.0 O27 D:Y26507 4.6 31.2 1.0 CB D:THR257 4.7 24.5 1.0 CA D:THR257 4.8 27.5 1.0 N18 D:Y26507 4.8 25.1 1.0 OG1 D:THR257 4.8 24.9 1.0 CB D:VAL255 4.9 25.3 1.0 SD D:MET475 5.0 29.7 1.0

Fluorine binding site 4 out of 4 in the Hiv-1 GP120 Complex with Cjf-III-288


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Hiv-1 GP120 Complex with Cjf-III-288 within 5.0Å range: probe atom residue distance (Å) B Occ B:F507 b:33.9 occ:1.00 F22 B:Y26507 0.0 33.9 1.0 C21 B:Y26507 1.4 27.5 1.0 C20 B:Y26507 2.3 27.7 1.0 C23 B:Y26507 2.4 24.0 1.0 CL24 B:Y26507 3.0 84.1 1.0 OG B:SER375 3.0 24.8 1.0 O B:SER375 3.1 28.2 1.0 CA B:SER256 3.3 25.2 1.0 C B:SER256 3.6 26.3 1.0 C19 B:Y26507 3.6 23.6 1.0 C25 B:Y26507 3.6 31.9 1.0 C B:SER375 3.6 28.8 1.0 N B:SER256 3.7 27.6 1.0 N B:THR257 3.8 25.5 1.0 CG2 B:THR257 3.8 23.4 1.0 CG1 B:VAL255 3.8 27.9 1.0 CE B:MET475 4.0 27.9 1.0 C B:VAL255 4.0 26.9 1.0 O B:VAL255 4.0 28.5 1.0 C26 B:Y26507 4.1 22.5 1.0 CB B:SER375 4.1 24.6 1.0 N B:PHE376 4.1 29.0 1.0 O B:SER256 4.2 24.6 1.0 CA B:PHE376 4.2 28.7 1.0 CA B:SER375 4.4 24.3 1.0 CB B:SER256 4.5 27.8 1.0 O27 B:Y26507 4.6 28.5 1.0 CB B:THR257 4.7 22.6 1.0 CA B:THR257 4.8 25.8 1.0 N18 B:Y26507 4.8 27.7 1.0 OG1 B:THR257 4.8 25.1 1.0 CB B:VAL255 4.9 27.6 1.0 SD B:MET475 5.0 24.4 1.0

C.J.Fritschi, S.Anang, Z.Gong, M.Mohammadi, J.Richard, C.Bourassa, K.T.Severino, H.Richter, D.Yang, H.C.Chen, T.J.Chiu, M.S.Seaman, N.Madani, C.Abrams, A.Finzi, W.A.Hendrickson, J.G.Sodroski, A.B.Smith Iii. Indoline CD4-Mimetic Compounds Mediate Potent and Broad Hiv-1 Inhibition and Sensitization to Antibody-Dependent Cellular Cytotoxicity. Proc.Natl.Acad.Sci.Usa V. 120 73120 2023.
ISSN: ESSN 1091-6490
PubMed: 36961924
DOI: 10.1073/PNAS.2222073120