Chlorine 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:

Fluorine

(F)

4 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Hiv-1 GP120 Complex with Cjf-III-288, PDB code: 8fm3:
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-III-288


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-III-288 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl507 b:102.0 occ:1.00 CL24 A:Y26507 0.0 102.0 1.0 C23 A:Y26507 1.8 21.0 1.0 C25 A:Y26507 2.7 27.8 1.0 C21 A:Y26507 2.7 27.6 1.0 F22 A:Y26507 3.0 35.4 1.0 C A:PHE376 3.4 31.2 1.0 CA A:PHE376 3.4 27.4 1.0 N A:ASN377 3.5 30.5 1.0 CD1 A:PHE382 3.7 29.2 1.0 N A:PHE376 3.7 26.6 1.0 O A:PHE376 3.9 31.0 1.0 CE1 A:PHE382 3.9 27.8 1.0 CG1 A:VAL255 4.0 23.5 1.0 C26 A:Y26507 4.0 25.0 1.0 C20 A:Y26507 4.0 24.6 1.0 O A:VAL255 4.1 30.7 1.0 C A:SER375 4.3 25.2 1.0 CH2 A:TRP112 4.3 24.4 1.0 CA A:ASN377 4.3 27.2 1.0 CB A:ASN377 4.4 31.1 1.0 O A:SER375 4.4 27.9 1.0 C19 A:Y26507 4.5 20.8 1.0 C A:VAL255 4.6 24.5 1.0 CB A:VAL255 4.7 21.2 1.0 OG A:SER375 4.7 28.7 1.0 CB A:PHE376 4.8 24.5 1.0 CG A:PHE382 4.9 28.8 1.0 CZ3 A:TRP112 4.9 25.2 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl507 b:46.1 occ:1.00 CL24 C:Y26507 0.0 46.1 1.0 C23 C:Y26507 1.8 18.9 1.0 C25 C:Y26507 2.7 23.6 1.0 C21 C:Y26507 2.7 26.2 1.0 F22 C:Y26507 3.0 32.3 1.0 C C:PHE376 3.4 25.6 1.0 CA C:PHE376 3.4 24.5 1.0 N C:ASN377 3.5 24.8 1.0 CD1 C:PHE382 3.7 24.6 1.0 N C:PHE376 3.7 25.9 1.0 O C:PHE376 3.9 24.2 1.0 CE1 C:PHE382 3.9 27.2 1.0 CG1 C:VAL255 4.0 24.8 1.0 C26 C:Y26507 4.0 22.6 1.0 C20 C:Y26507 4.0 24.1 1.0 O C:VAL255 4.1 29.3 1.0 C C:SER375 4.3 23.2 1.0 CH2 C:TRP112 4.3 22.4 1.0 CA C:ASN377 4.3 24.7 1.0 CB C:ASN377 4.4 24.6 1.0 O C:SER375 4.4 26.4 1.0 C19 C:Y26507 4.5 22.2 1.0 C C:VAL255 4.6 26.4 1.0 CB C:VAL255 4.7 20.9 1.0 OG C:SER375 4.7 26.2 1.0 CB C:PHE376 4.8 22.4 1.0 CG C:PHE382 4.9 27.8 1.0 CZ3 C:TRP112 4.9 22.2 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl507 b:69.3 occ:1.00 CL24 D:Y26507 0.0 69.3 1.0 C23 D:Y26507 1.8 21.6 1.0 C25 D:Y26507 2.7 29.0 1.0 C21 D:Y26507 2.7 26.9 1.0 F22 D:Y26507 3.0 36.2 1.0 C D:PHE376 3.4 31.0 1.0 CA D:PHE376 3.4 28.0 1.0 N D:ASN377 3.5 33.4 1.0 CD1 D:PHE382 3.7 27.4 1.0 N D:PHE376 3.7 29.3 1.0 O D:PHE376 3.9 32.6 1.0 CE1 D:PHE382 3.9 28.4 1.0 CG1 D:VAL255 4.0 25.5 1.0 C26 D:Y26507 4.0 28.7 1.0 C20 D:Y26507 4.0 29.0 1.0 O D:VAL255 4.1 31.3 1.0 C D:SER375 4.3 29.1 1.0 CH2 D:TRP112 4.3 27.9 1.0 CA D:ASN377 4.3 30.7 1.0 CB D:ASN377 4.4 29.1 1.0 O D:SER375 4.4 29.3 1.0 C19 D:Y26507 4.5 27.3 1.0 C D:VAL255 4.6 26.7 1.0 CB D:VAL255 4.7 25.3 1.0 OG D:SER375 4.7 30.0 1.0 O D:HOH616 4.8 31.8 1.0 CB D:PHE376 4.8 31.0 1.0 CG D:PHE382 4.9 28.7 1.0 CZ3 D:TRP112 4.9 29.0 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl507 b:84.1 occ:1.00 CL24 B:Y26507 0.0 84.1 1.0 C23 B:Y26507 1.8 24.0 1.0 C25 B:Y26507 2.7 31.9 1.0 C21 B:Y26507 2.7 27.5 1.0 F22 B:Y26507 3.0 33.9 1.0 C B:PHE376 3.4 27.6 1.0 CA B:PHE376 3.4 28.7 1.0 N B:ASN377 3.5 25.2 1.0 CD1 B:PHE382 3.7 26.3 1.0 N B:PHE376 3.7 29.0 1.0 O B:PHE376 3.9 27.2 1.0 CE1 B:PHE382 3.9 27.6 1.0 CG1 B:VAL255 4.0 27.9 1.0 C26 B:Y26507 4.0 22.5 1.0 C20 B:Y26507 4.0 27.7 1.0 O B:VAL255 4.1 28.5 1.0 C B:SER375 4.3 28.8 1.0 CH2 B:TRP112 4.3 31.8 1.0 CA B:ASN377 4.3 24.8 1.0 CB B:ASN377 4.4 27.9 1.0 O B:SER375 4.4 28.2 1.0 C19 B:Y26507 4.5 23.6 1.0 C B:VAL255 4.6 26.9 1.0 CB B:VAL255 4.7 27.6 1.0 OG B:SER375 4.7 24.8 1.0 CB B:PHE376 4.8 29.9 1.0 CG B:PHE382 4.9 29.8 1.0 CZ3 B:TRP112 4.9 26.5 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