Fluorine in PDB 8fm2: Hiv-1 GP120 Complex with Cjf-III-289

The structure of Hiv-1 GP120 Complex with Cjf-III-289, PDB code: 8fm2 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)	48.66 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.223, 121.179, 194.626, 90, 90, 90
R / Rfree (%)	21.9 / 26.2

The structure of Hiv-1 GP120 Complex with Cjf-III-289 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-289 (pdb code 8fm2). 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-289, PDB code: 8fm2:
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-289


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-289 within 5.0Å range: probe atom residue distance (Å) B Occ D:F507 b:29.9 occ:1.00 F25 D:Y1X507 0.0 29.9 1.0 C24 D:Y1X507 1.3 25.1 1.0 C22 D:Y1X507 2.3 23.1 1.0 C26 D:Y1X507 2.3 25.0 1.0 CL23 D:Y1X507 2.8 34.8 1.0 OG D:SER375 3.2 29.9 1.0 O D:SER375 3.4 23.0 1.0 CG1 D:VAL255 3.5 27.5 1.0 CA D:SER256 3.5 20.2 1.0 C19 D:Y1X507 3.6 23.7 1.0 C21 D:Y1X507 3.6 18.2 1.0 CE D:MET475 3.8 12.9 1.0 C D:SER256 3.8 22.5 1.0 C D:SER375 3.8 26.2 1.0 CG2 D:THR257 3.8 22.5 1.0 N D:SER256 3.9 18.5 1.0 N D:THR257 4.0 20.8 1.0 C20 D:Y1X507 4.0 28.2 1.0 C D:VAL255 4.1 21.6 1.0 N D:PHE376 4.1 25.5 1.0 O D:VAL255 4.2 25.7 1.0 CA D:PHE376 4.2 15.6 1.0 CB D:SER375 4.2 24.9 1.0 O D:SER256 4.4 27.5 1.0 O27 D:Y1X507 4.6 25.5 1.0 CA D:SER375 4.6 21.2 1.0 CB D:VAL255 4.7 11.0 1.0 N18 D:Y1X507 4.8 19.4 1.0 CB D:SER256 4.8 20.9 1.0 CB D:THR257 4.8 22.5 1.0 OG1 D:THR257 5.0 17.9 1.0 CA D:THR257 5.0 26.9 1.0 CA D:VAL255 5.0 14.0 1.0

Fluorine binding site 2 out of 4 in the Hiv-1 GP120 Complex with Cjf-III-289


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-289 within 5.0Å range: probe atom residue distance (Å) B Occ B:F507 b:33.0 occ:1.00 F25 B:Y1X507 0.0 33.0 1.0 C24 B:Y1X507 1.3 17.6 1.0 C22 B:Y1X507 2.3 17.7 1.0 C26 B:Y1X507 2.3 21.0 1.0 CL23 B:Y1X507 2.8 34.8 1.0 OG B:SER375 3.2 18.9 1.0 O B:SER375 3.4 29.4 1.0 CG1 B:VAL255 3.5 25.4 1.0 CA B:SER256 3.5 13.9 1.0 C19 B:Y1X507 3.6 17.4 1.0 C21 B:Y1X507 3.6 23.0 1.0 CE B:MET475 3.8 16.5 1.0 C B:SER256 3.8 22.1 1.0 C B:SER375 3.8 21.3 1.0 CG2 B:THR257 3.8 22.2 1.0 N B:SER256 3.9 18.6 1.0 N B:THR257 4.0 19.2 1.0 C20 B:Y1X507 4.0 14.2 1.0 C B:VAL255 4.1 20.3 1.0 N B:PHE376 4.1 22.9 1.0 O B:VAL255 4.2 19.5 1.0 CA B:PHE376 4.2 18.3 1.0 CB B:SER375 4.2 17.3 1.0 O B:SER256 4.4 23.5 1.0 O27 B:Y1X507 4.6 20.7 1.0 CA B:SER375 4.6 16.4 1.0 CB B:VAL255 4.7 27.4 1.0 N18 B:Y1X507 4.8 20.8 1.0 CB B:SER256 4.8 20.9 1.0 CB B:THR257 4.8 21.3 1.0 OG1 B:THR257 5.0 17.3 1.0 CA B:THR257 5.0 22.4 1.0 CA B:VAL255 5.0 15.8 1.0

Fluorine binding site 3 out of 4 in the Hiv-1 GP120 Complex with Cjf-III-289


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-289 within 5.0Å range: probe atom residue distance (Å) B Occ A:F507 b:32.9 occ:1.00 F25 A:Y1X507 0.0 32.9 1.0 C24 A:Y1X507 1.3 20.1 1.0 C22 A:Y1X507 2.3 19.2 1.0 C26 A:Y1X507 2.3 19.3 1.0 CL23 A:Y1X507 2.8 34.8 1.0 OG A:SER375 3.2 19.0 1.0 O A:SER375 3.4 15.4 1.0 CG1 A:VAL255 3.5 11.3 1.0 CA A:SER256 3.5 14.8 1.0 C19 A:Y1X507 3.6 22.8 1.0 C21 A:Y1X507 3.6 22.3 1.0 CE A:MET475 3.8 9.2 1.0 C A:SER256 3.8 13.5 1.0 C A:SER375 3.8 10.7 1.0 CG2 A:THR257 3.8 23.4 1.0 N A:SER256 3.9 18.7 1.0 N A:THR257 4.0 11.4 1.0 C20 A:Y1X507 4.0 23.1 1.0 C A:VAL255 4.1 13.6 1.0 N A:PHE376 4.1 13.5 1.0 O A:VAL255 4.2 24.9 1.0 CA A:PHE376 4.2 21.8 1.0 CB A:SER375 4.2 19.4 1.0 O A:SER256 4.4 17.7 1.0 O27 A:Y1X507 4.6 20.2 1.0 CA A:SER375 4.6 15.4 1.0 CB A:VAL255 4.7 9.0 1.0 N18 A:Y1X507 4.8 18.0 1.0 CB A:SER256 4.8 16.6 1.0 CB A:THR257 4.8 14.5 1.0 OG1 A:THR257 5.0 19.3 1.0 CA A:THR257 5.0 13.1 1.0 CA A:VAL255 5.0 8.3 1.0

Fluorine binding site 4 out of 4 in the Hiv-1 GP120 Complex with Cjf-III-289


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-289 within 5.0Å range: probe atom residue distance (Å) B Occ C:F507 b:26.6 occ:1.00 F25 C:Y1X507 0.0 26.6 1.0 C24 C:Y1X507 1.3 15.6 1.0 C22 C:Y1X507 2.3 8.2 1.0 C26 C:Y1X507 2.3 13.6 1.0 CL23 C:Y1X507 2.8 34.8 1.0 OG C:SER375 3.2 19.6 1.0 O C:SER375 3.4 17.0 1.0 CG1 C:VAL255 3.5 18.6 1.0 CA C:SER256 3.5 15.1 1.0 C19 C:Y1X507 3.6 14.2 1.0 C21 C:Y1X507 3.6 15.6 1.0 CE C:MET475 3.8 14.9 1.0 C C:SER256 3.8 18.5 1.0 C C:SER375 3.8 22.0 1.0 CG2 C:THR257 3.8 9.9 1.0 N C:SER256 3.9 23.3 1.0 N C:THR257 4.0 17.6 1.0 C20 C:Y1X507 4.0 17.7 1.0 C C:VAL255 4.1 24.5 1.0 N C:PHE376 4.1 20.4 1.0 O C:VAL255 4.2 29.9 1.0 CA C:PHE376 4.2 15.7 1.0 CB C:SER375 4.2 13.9 1.0 O C:SER256 4.4 23.4 1.0 O27 C:Y1X507 4.6 15.3 1.0 CA C:SER375 4.6 16.9 1.0 CB C:VAL255 4.7 16.5 1.0 N18 C:Y1X507 4.8 23.5 1.0 CB C:SER256 4.8 25.6 1.0 CB C:THR257 4.8 12.1 1.0 OG1 C:THR257 5.0 15.9 1.0 CA C:THR257 5.0 20.9 1.0 CA C:VAL255 5.0 17.2 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