Chlorine in PDB 8fm8: Hiv-1 GP120 Complex with Cjf-IV-046

The structure of Hiv-1 GP120 Complex with Cjf-IV-046, PDB code: 8fm8 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)	48.65 / 2.47
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.534, 121.79, 194.603, 90, 90, 90
R / Rfree (%)	21.7 / 26.3

The structure of Hiv-1 GP120 Complex with Cjf-IV-046 also contains other interesting chemical elements:

Fluorine

(F)

24 atoms

The binding sites of Chlorine atom in the Hiv-1 GP120 Complex with Cjf-IV-046 (pdb code 8fm8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Hiv-1 GP120 Complex with Cjf-IV-046, PDB code: 8fm8:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Hiv-1 GP120 Complex with Cjf-IV-046


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Hiv-1 GP120 Complex with Cjf-IV-046 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl507 b:24.2 occ:1.00 CL09 C:Y1T507 0.0 24.2 1.0 C08 C:Y1T507 1.8 16.6 1.0 C10 C:Y1T507 2.7 23.4 1.0 C07 C:Y1T507 2.8 17.8 1.0 F11 C:Y1T507 2.8 34.5 1.0 C C:PHE376 3.5 21.1 1.0 CA C:PHE376 3.5 19.4 1.0 N C:ASN377 3.6 20.1 1.0 CD1 C:PHE382 3.7 28.4 1.0 CG1 C:VAL255 3.8 21.5 1.0 N C:PHE376 3.9 19.5 1.0 CE1 C:PHE382 4.0 23.2 1.0 C12 C:Y1T507 4.0 18.2 1.0 C06 C:Y1T507 4.0 23.5 1.0 O C:VAL255 4.1 28.5 1.0 O C:PHE376 4.1 20.1 1.0 CH2 C:TRP112 4.3 14.4 1.0 CB C:ASN377 4.4 21.5 1.0 C C:SER375 4.4 21.4 1.0 CA C:ASN377 4.4 24.4 1.0 C05 C:Y1T507 4.5 19.6 1.0 O C:SER375 4.6 21.0 1.0 CB C:VAL255 4.6 17.1 1.0 C C:VAL255 4.7 26.8 1.0 OG C:SER375 4.7 21.2 1.0 CB C:PHE376 4.9 14.7 1.0 CZ3 C:TRP112 5.0 17.3 1.0 CG C:PHE382 5.0 31.1 1.0

Chlorine binding site 2 out of 4 in the Hiv-1 GP120 Complex with Cjf-IV-046


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Hiv-1 GP120 Complex with Cjf-IV-046 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl507 b:33.1 occ:1.00 CL09 D:Y1T507 0.0 33.1 1.0 C08 D:Y1T507 1.8 21.0 1.0 C10 D:Y1T507 2.7 27.3 1.0 C07 D:Y1T507 2.8 20.4 1.0 F11 D:Y1T507 2.8 31.2 1.0 C D:PHE376 3.5 32.1 1.0 CA D:PHE376 3.5 23.2 1.0 N D:ASN377 3.6 33.6 1.0 CD1 D:PHE382 3.7 30.9 1.0 CG1 D:VAL255 3.8 24.9 1.0 N D:PHE376 3.9 31.0 1.0 CE1 D:PHE382 4.0 25.7 1.0 C12 D:Y1T507 4.0 35.0 1.0 C06 D:Y1T507 4.0 28.9 1.0 O D:VAL255 4.1 26.9 1.0 O D:PHE376 4.1 31.2 1.0 CH2 D:TRP112 4.3 25.6 1.0 CB D:ASN377 4.4 26.9 1.0 C D:SER375 4.4 32.8 1.0 CA D:ASN377 4.4 33.9 1.0 C05 D:Y1T507 4.5 30.4 1.0 O D:SER375 4.6 24.8 1.0 CB D:VAL255 4.6 21.2 1.0 C D:VAL255 4.7 24.4 1.0 OG D:SER375 4.7 27.3 1.0 CB D:PHE376 4.9 30.5 1.0 CZ3 D:TRP112 5.0 32.2 1.0 CG D:PHE382 5.0 29.8 1.0

Chlorine binding site 3 out of 4 in the Hiv-1 GP120 Complex with Cjf-IV-046


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Hiv-1 GP120 Complex with Cjf-IV-046 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl507 b:18.6 occ:1.00 CL09 A:Y1T507 0.0 18.6 1.0 C08 A:Y1T507 1.8 26.8 1.0 C10 A:Y1T507 2.7 30.5 1.0 C07 A:Y1T507 2.8 26.3 1.0 F11 A:Y1T507 2.8 32.9 1.0 C A:PHE376 3.5 24.4 1.0 CA A:PHE376 3.5 19.1 1.0 N A:ASN377 3.6 22.8 1.0 CD1 A:PHE382 3.7 28.0 1.0 CG1 A:VAL255 3.8 14.9 1.0 N A:PHE376 3.9 17.9 1.0 CE1 A:PHE382 4.0 30.8 1.0 C12 A:Y1T507 4.0 25.2 1.0 C06 A:Y1T507 4.0 25.8 1.0 O A:VAL255 4.1 26.5 1.0 O A:PHE376 4.1 21.9 1.0 CH2 A:TRP112 4.3 17.2 1.0 CB A:ASN377 4.4 22.4 1.0 C A:SER375 4.4 16.4 1.0 CA A:ASN377 4.4 19.1 1.0 C05 A:Y1T507 4.5 21.6 1.0 O A:SER375 4.6 20.6 1.0 CB A:VAL255 4.6 17.1 1.0 C A:VAL255 4.7 15.7 1.0 OG A:SER375 4.7 21.2 1.0 CB A:PHE376 4.9 21.6 1.0 CZ3 A:TRP112 5.0 19.1 1.0 CG A:PHE382 5.0 21.1 1.0

Chlorine binding site 4 out of 4 in the Hiv-1 GP120 Complex with Cjf-IV-046


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Hiv-1 GP120 Complex with Cjf-IV-046 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl507 b:33.3 occ:1.00 CL09 B:Y1T507 0.0 33.3 1.0 C08 B:Y1T507 1.8 17.5 1.0 C10 B:Y1T507 2.7 23.4 1.0 C07 B:Y1T507 2.8 26.4 1.0 F11 B:Y1T507 2.8 36.2 1.0 C B:PHE376 3.5 24.9 1.0 CA B:PHE376 3.5 25.8 1.0 N B:ASN377 3.6 23.9 1.0 CD1 B:PHE382 3.7 20.2 1.0 CG1 B:VAL255 3.8 28.7 1.0 N B:PHE376 3.9 23.4 1.0 CE1 B:PHE382 4.0 21.7 1.0 C12 B:Y1T507 4.0 24.7 1.0 C06 B:Y1T507 4.0 18.9 1.0 O B:VAL255 4.1 26.0 1.0 O B:PHE376 4.1 23.1 1.0 CH2 B:TRP112 4.3 27.6 1.0 CB B:ASN377 4.4 20.4 1.0 C B:SER375 4.4 29.2 1.0 CA B:ASN377 4.4 17.1 1.0 C05 B:Y1T507 4.5 21.7 1.0 O B:SER375 4.6 27.0 1.0 CB B:VAL255 4.6 32.5 1.0 C B:VAL255 4.7 26.1 1.0 OG B:SER375 4.7 21.6 1.0 CB B:PHE376 4.9 28.0 1.0 CZ3 B:TRP112 5.0 20.5 1.0 CG B:PHE382 5.0 26.0 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