Chlorine in PDB 8fm5: Hiv-1 GP120 Complex with Dy-III-065

The structure of Hiv-1 GP120 Complex with Dy-III-065, PDB code: 8fm5 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)	48.81 / 1.88
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.52, 121.66, 195.23, 90, 90, 90
R / Rfree (%)	26.7 / 28.8

The structure of Hiv-1 GP120 Complex with Dy-III-065 also contains other interesting chemical elements:

Fluorine

(F)

16 atoms

The binding sites of Chlorine atom in the Hiv-1 GP120 Complex with Dy-III-065 (pdb code 8fm5). 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 Dy-III-065, PDB code: 8fm5:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Hiv-1 GP120 Complex with Dy-III-065


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 Dy-III-065 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl507 b:23.9 occ:1.00 CL27 D:Y2E507 0.0 23.9 1.0 C26 D:Y2E507 1.8 13.4 1.0 C24 D:Y2E507 2.7 20.4 1.0 C28 D:Y2E507 2.7 22.9 1.0 F25 D:Y2E507 2.9 33.5 1.0 C D:PHE376 3.5 20.1 1.0 CA D:PHE376 3.5 19.0 1.0 CD2 D:PHE382 3.7 25.6 1.0 N D:ASN377 3.7 15.4 1.0 N D:PHE376 3.9 20.6 1.0 CG1 D:VAL255 3.9 18.2 1.0 O D:PHE376 3.9 22.1 1.0 CE2 D:PHE382 3.9 24.3 1.0 C23 D:Y2E507 4.0 22.9 1.0 C29 D:Y2E507 4.0 16.6 1.0 O D:VAL255 4.1 28.5 1.0 CH2 D:TRP112 4.3 23.9 1.0 CB D:ASN377 4.3 18.0 1.0 C D:SER375 4.4 23.6 1.0 CA D:ASN377 4.4 20.3 1.0 C22 D:Y2E507 4.5 20.6 1.0 O D:SER375 4.5 24.1 1.0 OG D:SER375 4.7 25.8 1.0 C D:VAL255 4.7 21.8 1.0 CB D:VAL255 4.7 17.9 1.0 O D:HOH607 4.8 33.3 1.0 CG D:PHE382 4.9 24.9 1.0 CZ3 D:TRP112 4.9 25.2 1.0 CB D:PHE376 4.9 19.4 1.0

Chlorine binding site 2 out of 4 in the Hiv-1 GP120 Complex with Dy-III-065


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 Dy-III-065 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl507 b:23.9 occ:1.00 CL27 A:Y2E507 0.0 23.9 1.0 C26 A:Y2E507 1.8 13.4 1.0 C24 A:Y2E507 2.7 20.4 1.0 C28 A:Y2E507 2.7 22.9 1.0 F25 A:Y2E507 2.9 33.5 1.0 C A:PHE376 3.5 20.1 1.0 CA A:PHE376 3.5 19.0 1.0 CD2 A:PHE382 3.7 25.6 1.0 N A:ASN377 3.7 15.4 1.0 N A:PHE376 3.9 20.6 1.0 CG1 A:VAL255 3.9 18.2 1.0 O A:PHE376 3.9 22.1 1.0 CE2 A:PHE382 3.9 24.3 1.0 C23 A:Y2E507 4.0 22.9 1.0 C29 A:Y2E507 4.0 16.6 1.0 O A:VAL255 4.1 28.5 1.0 CH2 A:TRP112 4.3 23.9 1.0 CB A:ASN377 4.3 18.0 1.0 C A:SER375 4.4 23.6 1.0 CA A:ASN377 4.4 20.3 1.0 C22 A:Y2E507 4.5 20.6 1.0 O A:SER375 4.5 24.1 1.0 OG A:SER375 4.7 25.8 1.0 C A:VAL255 4.7 21.8 1.0 CB A:VAL255 4.7 17.9 1.0 CG A:PHE382 4.9 24.9 1.0 CZ3 A:TRP112 4.9 25.2 1.0 CB A:PHE376 4.9 19.4 1.0

Chlorine binding site 3 out of 4 in the Hiv-1 GP120 Complex with Dy-III-065


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 Dy-III-065 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl507 b:23.9 occ:1.00 CL27 C:Y2E507 0.0 23.9 1.0 C26 C:Y2E507 1.8 13.4 1.0 C24 C:Y2E507 2.7 20.4 1.0 C28 C:Y2E507 2.7 22.9 1.0 F25 C:Y2E507 2.9 33.5 1.0 C C:PHE376 3.5 20.1 1.0 CA C:PHE376 3.5 19.0 1.0 CD2 C:PHE382 3.7 25.6 1.0 N C:ASN377 3.7 15.4 1.0 N C:PHE376 3.9 20.6 1.0 CG1 C:VAL255 3.9 18.2 1.0 O C:PHE376 3.9 22.1 1.0 CE2 C:PHE382 3.9 24.3 1.0 C23 C:Y2E507 4.0 22.9 1.0 C29 C:Y2E507 4.0 16.6 1.0 O C:VAL255 4.1 28.5 1.0 CH2 C:TRP112 4.3 23.9 1.0 CB C:ASN377 4.3 18.0 1.0 C C:SER375 4.4 23.6 1.0 CA C:ASN377 4.4 20.3 1.0 C22 C:Y2E507 4.5 20.6 1.0 O C:SER375 4.5 24.1 1.0 OG C:SER375 4.7 25.8 1.0 C C:VAL255 4.7 21.8 1.0 CB C:VAL255 4.7 17.9 1.0 CG C:PHE382 4.9 24.9 1.0 CZ3 C:TRP112 4.9 25.2 1.0 CB C:PHE376 4.9 19.4 1.0

Chlorine binding site 4 out of 4 in the Hiv-1 GP120 Complex with Dy-III-065


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 Dy-III-065 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl507 b:23.9 occ:1.00 CL27 B:Y2E507 0.0 23.9 1.0 C26 B:Y2E507 1.8 13.4 1.0 C24 B:Y2E507 2.7 20.4 1.0 C28 B:Y2E507 2.7 22.9 1.0 F25 B:Y2E507 2.9 33.5 1.0 C B:PHE376 3.5 20.1 1.0 CA B:PHE376 3.5 19.0 1.0 CD2 B:PHE382 3.7 25.6 1.0 N B:ASN377 3.7 15.4 1.0 N B:PHE376 3.9 20.6 1.0 CG1 B:VAL255 3.9 18.2 1.0 O B:PHE376 3.9 22.1 1.0 CE2 B:PHE382 3.9 24.3 1.0 C23 B:Y2E507 4.0 22.9 1.0 C29 B:Y2E507 4.0 16.6 1.0 O B:VAL255 4.1 28.5 1.0 CH2 B:TRP112 4.3 23.9 1.0 CB B:ASN377 4.3 18.0 1.0 C B:SER375 4.4 23.6 1.0 CA B:ASN377 4.4 20.3 1.0 C22 B:Y2E507 4.5 20.6 1.0 O B:SER375 4.5 24.1 1.0 OG B:SER375 4.7 25.8 1.0 C B:VAL255 4.7 21.8 1.0 CB B:VAL255 4.7 17.9 1.0 CG B:PHE382 4.9 24.9 1.0 CZ3 B:TRP112 4.9 25.2 1.0 CB B:PHE376 4.9 19.4 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