Chlorine 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:

Fluorine

(F)

4 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Hiv-1 GP120 Complex with Cjf-III-289, PDB code: 8fm2:
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-289


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-289 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl507 b:34.8 occ:1.00 CL23 D:Y1X507 0.0 34.8 1.0 C22 D:Y1X507 1.8 23.1 1.0 C24 D:Y1X507 2.7 25.1 1.0 C21 D:Y1X507 2.8 18.2 1.0 F25 D:Y1X507 2.8 29.9 1.0 CA D:PHE376 3.5 15.6 1.0 C D:PHE376 3.5 21.1 1.0 CD1 D:PHE382 3.6 21.9 1.0 N D:ASN377 3.8 19.9 1.0 CG1 D:VAL255 3.9 27.5 1.0 CE1 D:PHE382 3.9 18.6 1.0 N D:PHE376 3.9 25.5 1.0 O D:PHE376 4.0 32.0 1.0 C26 D:Y1X507 4.0 25.0 1.0 C20 D:Y1X507 4.0 28.2 1.0 O D:VAL255 4.3 25.7 1.0 CB D:ASN377 4.3 18.5 1.0 CH2 D:TRP112 4.3 20.2 1.0 C D:SER375 4.4 26.2 1.0 CA D:ASN377 4.5 23.2 1.0 C19 D:Y1X507 4.5 23.7 1.0 O D:SER375 4.6 23.0 1.0 CB D:VAL255 4.7 11.0 1.0 CG D:PHE382 4.8 25.4 1.0 OG D:SER375 4.8 29.9 1.0 C D:VAL255 4.8 21.6 1.0 CB D:PHE376 4.9 18.4 1.0 CZ3 D:TRP112 4.9 27.9 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl507 b:34.8 occ:1.00 CL23 B:Y1X507 0.0 34.8 1.0 C22 B:Y1X507 1.8 17.7 1.0 C24 B:Y1X507 2.7 17.6 1.0 C21 B:Y1X507 2.8 23.0 1.0 F25 B:Y1X507 2.8 33.0 1.0 CA B:PHE376 3.5 18.3 1.0 C B:PHE376 3.5 18.6 1.0 CD1 B:PHE382 3.6 15.9 1.0 N B:ASN377 3.8 13.7 1.0 CG1 B:VAL255 3.9 25.4 1.0 CE1 B:PHE382 3.9 14.6 1.0 N B:PHE376 3.9 22.9 1.0 O B:PHE376 4.0 22.4 1.0 C26 B:Y1X507 4.0 21.0 1.0 C20 B:Y1X507 4.0 14.2 1.0 O B:VAL255 4.3 19.5 1.0 CB B:ASN377 4.3 12.0 1.0 CH2 B:TRP112 4.3 21.7 1.0 C B:SER375 4.4 21.3 1.0 CA B:ASN377 4.5 12.0 1.0 C19 B:Y1X507 4.5 17.4 1.0 O B:SER375 4.6 29.4 1.0 CB B:VAL255 4.7 27.4 1.0 CG B:PHE382 4.8 21.8 1.0 OG B:SER375 4.8 18.9 1.0 C B:VAL255 4.8 20.3 1.0 CB B:PHE376 4.9 16.7 1.0 CZ3 B:TRP112 4.9 19.1 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl507 b:34.8 occ:1.00 CL23 A:Y1X507 0.0 34.8 1.0 C22 A:Y1X507 1.8 19.2 1.0 C24 A:Y1X507 2.7 20.1 1.0 C21 A:Y1X507 2.8 22.3 1.0 F25 A:Y1X507 2.8 32.9 1.0 CA A:PHE376 3.5 21.8 1.0 C A:PHE376 3.5 19.0 1.0 CD1 A:PHE382 3.6 25.5 1.0 N A:ASN377 3.8 14.1 1.0 CG1 A:VAL255 3.9 11.3 1.0 CE1 A:PHE382 3.9 24.8 1.0 N A:PHE376 3.9 13.5 1.0 O A:PHE376 4.0 20.6 1.0 C26 A:Y1X507 4.0 19.3 1.0 C20 A:Y1X507 4.0 23.1 1.0 O A:VAL255 4.3 24.9 1.0 CB A:ASN377 4.3 21.1 1.0 CH2 A:TRP112 4.3 15.6 1.0 C A:SER375 4.4 10.7 1.0 CA A:ASN377 4.5 11.5 1.0 C19 A:Y1X507 4.5 22.8 1.0 O A:SER375 4.6 15.4 1.0 CB A:VAL255 4.7 9.0 1.0 CG A:PHE382 4.8 16.3 1.0 OG A:SER375 4.8 19.0 1.0 C A:VAL255 4.8 13.6 1.0 CB A:PHE376 4.9 19.1 1.0 CZ3 A:TRP112 4.9 26.1 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl507 b:34.8 occ:1.00 CL23 C:Y1X507 0.0 34.8 1.0 C22 C:Y1X507 1.8 8.2 1.0 C24 C:Y1X507 2.7 15.6 1.0 C21 C:Y1X507 2.8 15.6 1.0 F25 C:Y1X507 2.8 26.6 1.0 CA C:PHE376 3.5 15.7 1.0 C C:PHE376 3.5 14.5 1.0 CD1 C:PHE382 3.6 21.4 1.0 N C:ASN377 3.8 15.9 1.0 CG1 C:VAL255 3.9 18.6 1.0 CE1 C:PHE382 3.9 24.4 1.0 N C:PHE376 3.9 20.4 1.0 O C:PHE376 4.0 17.8 1.0 C26 C:Y1X507 4.0 13.6 1.0 C20 C:Y1X507 4.0 17.7 1.0 O C:VAL255 4.3 29.9 1.0 CB C:ASN377 4.3 14.5 1.0 CH2 C:TRP112 4.3 12.8 1.0 C C:SER375 4.4 22.0 1.0 CA C:ASN377 4.5 16.6 1.0 C19 C:Y1X507 4.5 14.2 1.0 O C:SER375 4.6 17.0 1.0 CB C:VAL255 4.7 16.5 1.0 CG C:PHE382 4.8 21.7 1.0 OG C:SER375 4.8 19.6 1.0 C C:VAL255 4.8 24.5 1.0 CB C:PHE376 4.9 15.8 1.0 CZ3 C:TRP112 4.9 14.6 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