Fluorine in PDB 8flz: Hiv-1 GP120 Complex with Cjf-III-049-S

The structure of Hiv-1 GP120 Complex with Cjf-III-049-S, PDB code: 8flz 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)	48.98 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.082, 121.925, 195.931, 90, 90, 90
R / Rfree (%)	26.3 / 28.3

The structure of Hiv-1 GP120 Complex with Cjf-III-049-S 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-049-S (pdb code 8flz). 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-049-S, PDB code: 8flz:
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-049-S


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-049-S within 5.0Å range: probe atom residue distance (Å) B Occ A:F507 b:41.5 occ:1.00 F23 A:7IT507 0.0 41.5 1.0 C22 A:7IT507 1.4 28.4 1.0 C24 A:7IT507 2.3 21.2 1.0 C21 A:7IT507 2.4 29.9 1.0 CL25 A:7IT507 2.8 26.0 1.0 OG A:SER375 3.1 28.9 1.0 O A:SER375 3.2 26.8 1.0 CA A:SER256 3.4 20.6 1.0 C26 A:7IT507 3.6 25.1 1.0 C20 A:7IT507 3.6 22.7 1.0 C A:SER375 3.7 22.7 1.0 C A:SER256 3.7 22.1 1.0 N A:SER256 3.7 25.1 1.0 CG1 A:VAL255 3.7 22.8 1.0 CG2 A:THR257 3.8 21.5 1.0 N A:THR257 3.9 23.8 1.0 CE A:MET475 4.0 20.7 1.0 C27 A:7IT507 4.1 23.1 1.0 C A:VAL255 4.1 25.4 1.0 CB A:SER375 4.1 23.4 1.0 O A:VAL255 4.1 31.4 1.0 N A:PHE376 4.1 28.9 1.0 CA A:PHE376 4.3 25.6 1.0 O A:SER256 4.5 35.6 1.0 CA A:SER375 4.5 26.8 1.0 CB A:SER256 4.7 22.5 1.0 CB A:THR257 4.7 25.9 1.0 O18 A:7IT507 4.7 30.1 1.0 OG1 A:THR257 4.7 34.7 1.0 N19 A:7IT507 4.9 25.6 1.0 CA A:THR257 4.9 21.4 1.0 CB A:VAL255 4.9 26.8 1.0 SD A:MET475 4.9 23.1 1.0

Fluorine binding site 2 out of 4 in the Hiv-1 GP120 Complex with Cjf-III-049-S


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-049-S within 5.0Å range: probe atom residue distance (Å) B Occ D:F507 b:41.5 occ:1.00 F23 D:7IT507 0.0 41.5 1.0 C22 D:7IT507 1.4 28.4 1.0 C24 D:7IT507 2.3 21.2 1.0 C21 D:7IT507 2.4 29.9 1.0 CL25 D:7IT507 2.8 26.0 1.0 OG D:SER375 3.1 28.9 1.0 O D:SER375 3.2 26.8 1.0 CA D:SER256 3.4 20.6 1.0 C26 D:7IT507 3.6 25.1 1.0 C20 D:7IT507 3.6 22.7 1.0 C D:SER375 3.7 22.7 1.0 C D:SER256 3.7 22.1 1.0 N D:SER256 3.7 25.1 1.0 CG1 D:VAL255 3.7 22.8 1.0 CG2 D:THR257 3.8 21.5 1.0 N D:THR257 3.9 23.8 1.0 CE D:MET475 4.0 20.7 1.0 C27 D:7IT507 4.1 23.1 1.0 C D:VAL255 4.1 25.4 1.0 CB D:SER375 4.1 23.4 1.0 O D:VAL255 4.1 31.4 1.0 N D:PHE376 4.1 28.9 1.0 CA D:PHE376 4.3 25.6 1.0 O D:SER256 4.5 35.6 1.0 CA D:SER375 4.5 26.8 1.0 CB D:SER256 4.7 22.5 1.0 CB D:THR257 4.7 25.9 1.0 O18 D:7IT507 4.7 30.1 1.0 OG1 D:THR257 4.7 34.7 1.0 N19 D:7IT507 4.9 25.6 1.0 CA D:THR257 4.9 21.4 1.0 CB D:VAL255 4.9 26.8 1.0 SD D:MET475 4.9 23.1 1.0

Fluorine binding site 3 out of 4 in the Hiv-1 GP120 Complex with Cjf-III-049-S


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-049-S within 5.0Å range: probe atom residue distance (Å) B Occ B:F507 b:41.5 occ:1.00 F23 B:7IT507 0.0 41.5 1.0 C22 B:7IT507 1.3 28.4 1.0 C24 B:7IT507 2.3 21.2 1.0 C21 B:7IT507 2.4 29.9 1.0 CL25 B:7IT507 2.8 26.0 1.0 OG B:SER375 3.1 28.9 1.0 O B:SER375 3.2 26.8 1.0 CA B:SER256 3.4 20.6 1.0 C26 B:7IT507 3.6 25.1 1.0 C20 B:7IT507 3.6 22.7 1.0 C B:SER375 3.7 22.7 1.0 C B:SER256 3.7 22.1 1.0 N B:SER256 3.7 25.1 1.0 CG1 B:VAL255 3.7 22.8 1.0 CG2 B:THR257 3.8 21.5 1.0 N B:THR257 3.9 23.8 1.0 CE B:MET475 4.0 20.7 1.0 C27 B:7IT507 4.1 23.1 1.0 C B:VAL255 4.1 25.4 1.0 CB B:SER375 4.1 23.4 1.0 O B:VAL255 4.1 31.4 1.0 N B:PHE376 4.1 28.9 1.0 CA B:PHE376 4.3 25.6 1.0 O B:SER256 4.5 35.6 1.0 CA B:SER375 4.5 26.8 1.0 CB B:SER256 4.7 22.5 1.0 CB B:THR257 4.7 25.9 1.0 O18 B:7IT507 4.7 30.1 1.0 OG1 B:THR257 4.7 34.7 1.0 N19 B:7IT507 4.9 25.6 1.0 CA B:THR257 4.9 21.4 1.0 CB B:VAL255 4.9 26.8 1.0 SD B:MET475 4.9 23.1 1.0

Fluorine binding site 4 out of 4 in the Hiv-1 GP120 Complex with Cjf-III-049-S


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-049-S within 5.0Å range: probe atom residue distance (Å) B Occ C:F507 b:41.5 occ:1.00 F23 C:7IT507 0.0 41.5 1.0 C22 C:7IT507 1.3 28.4 1.0 C24 C:7IT507 2.3 21.2 1.0 C21 C:7IT507 2.4 29.9 1.0 CL25 C:7IT507 2.8 26.0 1.0 OG C:SER375 3.1 28.9 1.0 O C:SER375 3.2 26.8 1.0 CA C:SER256 3.4 20.6 1.0 C26 C:7IT507 3.6 25.1 1.0 C20 C:7IT507 3.6 22.7 1.0 C C:SER375 3.7 22.7 1.0 C C:SER256 3.7 22.1 1.0 N C:SER256 3.7 25.1 1.0 CG1 C:VAL255 3.7 22.8 1.0 CG2 C:THR257 3.8 21.5 1.0 N C:THR257 3.9 23.8 1.0 CE C:MET475 4.0 20.7 1.0 C27 C:7IT507 4.1 23.1 1.0 C C:VAL255 4.1 25.4 1.0 CB C:SER375 4.1 23.4 1.0 O C:VAL255 4.1 31.4 1.0 N C:PHE376 4.1 28.9 1.0 CA C:PHE376 4.3 25.6 1.0 O C:SER256 4.5 35.6 1.0 CA C:SER375 4.5 26.8 1.0 CB C:SER256 4.7 22.5 1.0 CB C:THR257 4.7 25.9 1.0 O18 C:7IT507 4.7 30.1 1.0 OG1 C:THR257 4.7 34.7 1.0 N19 C:7IT507 4.9 25.6 1.0 CA C:THR257 4.9 21.4 1.0 CB C:VAL255 4.9 26.8 1.0 SD C:MET475 4.9 23.1 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