Chlorine in PDB 8fly: Hiv-1 GP120 Complex with Bnm-III-170

The structure of Hiv-1 GP120 Complex with Bnm-III-170, PDB code: 8fly 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)	48.73 / 2.04
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.79, 120.78, 194.9, 90, 90, 90
R / Rfree (%)	24.7 / 27.6

The structure of Hiv-1 GP120 Complex with Bnm-III-170 also contains other interesting chemical elements:

Fluorine

(F)

4 atoms

The binding sites of Chlorine atom in the Hiv-1 GP120 Complex with Bnm-III-170 (pdb code 8fly). 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 Bnm-III-170, PDB code: 8fly:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Hiv-1 GP120 Complex with Bnm-III-170


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 Bnm-III-170 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl507 b:44.8 occ:1.00 CL25 A:5VG507 0.0 44.8 1.0 C24 A:5VG507 1.8 25.1 1.0 C22 A:5VG507 2.7 28.3 1.0 C26 A:5VG507 2.8 26.6 1.0 F23 A:5VG507 2.8 31.4 1.0 C A:PHE376 3.6 27.3 1.0 CA A:PHE376 3.6 23.3 1.0 CD1 A:PHE382 3.7 27.2 1.0 N A:ASN377 3.7 24.5 1.0 CG1 A:VAL255 3.8 21.5 1.0 N A:PHE376 3.9 24.5 1.0 CE1 A:PHE382 4.0 25.3 1.0 C21 A:5VG507 4.0 27.5 1.0 O A:PHE376 4.0 26.4 1.0 C27 A:5VG507 4.0 24.1 1.0 O A:VAL255 4.1 28.1 1.0 CH2 A:TRP112 4.2 24.3 1.0 C A:SER375 4.3 23.6 1.0 CB A:ASN377 4.4 25.6 1.0 O A:SER375 4.5 24.4 1.0 CA A:ASN377 4.5 24.9 1.0 C20 A:5VG507 4.5 23.2 1.0 OG A:SER375 4.7 27.2 1.0 CB A:VAL255 4.7 23.6 1.0 C A:VAL255 4.7 24.4 1.0 CZ3 A:TRP112 4.9 25.9 1.0 CB A:SER375 4.9 23.9 1.0 CG A:PHE382 4.9 25.5 1.0

Chlorine binding site 2 out of 4 in the Hiv-1 GP120 Complex with Bnm-III-170


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 Bnm-III-170 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl507 b:25.5 occ:1.00 CL25 B:5VG507 0.0 25.5 1.0 C24 B:5VG507 1.8 23.8 1.0 C22 B:5VG507 2.7 23.8 1.0 C26 B:5VG507 2.8 26.1 1.0 F23 B:5VG507 2.8 27.1 1.0 C B:PHE376 3.6 24.9 1.0 CA B:PHE376 3.6 28.7 1.0 CD1 B:PHE382 3.7 23.9 1.0 N B:ASN377 3.7 24.4 1.0 CG1 B:VAL255 3.8 26.2 1.0 N B:PHE376 3.9 27.4 1.0 CE1 B:PHE382 4.0 30.2 1.0 C21 B:5VG507 4.0 28.0 1.0 O B:PHE376 4.0 27.2 1.0 C27 B:5VG507 4.0 22.3 1.0 O B:VAL255 4.1 29.4 1.0 CH2 B:TRP112 4.2 30.2 1.0 C B:SER375 4.3 27.6 1.0 CB B:ASN377 4.4 28.0 1.0 O B:SER375 4.5 26.8 1.0 CA B:ASN377 4.5 27.8 1.0 C20 B:5VG507 4.5 23.2 1.0 OG B:SER375 4.7 23.2 1.0 CB B:VAL255 4.7 25.9 1.0 C B:VAL255 4.7 25.6 1.0 CZ3 B:TRP112 4.9 26.7 1.0 CB B:SER375 4.9 25.3 1.0 CG B:PHE382 4.9 28.3 1.0

Chlorine binding site 3 out of 4 in the Hiv-1 GP120 Complex with Bnm-III-170


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 Bnm-III-170 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl507 b:25.2 occ:1.00 CL25 C:5VG507 0.0 25.2 1.0 C24 C:5VG507 1.8 19.3 1.0 C22 C:5VG507 2.7 23.4 1.0 C26 C:5VG507 2.8 23.1 1.0 F23 C:5VG507 2.8 26.3 1.0 C C:PHE376 3.6 24.5 1.0 CA C:PHE376 3.6 23.6 1.0 CD1 C:PHE382 3.7 21.3 1.0 N C:ASN377 3.7 24.5 1.0 CG1 C:VAL255 3.8 24.2 1.0 N C:PHE376 3.9 25.0 1.0 CE1 C:PHE382 4.0 20.2 1.0 C21 C:5VG507 4.0 22.0 1.0 O C:PHE376 4.0 23.0 1.0 C27 C:5VG507 4.0 23.3 1.0 O C:VAL255 4.1 27.9 1.0 CH2 C:TRP112 4.2 19.0 1.0 C C:SER375 4.3 22.4 1.0 CB C:ASN377 4.4 24.0 1.0 O C:SER375 4.5 24.6 1.0 CA C:ASN377 4.5 26.9 1.0 C20 C:5VG507 4.5 21.1 1.0 OG C:SER375 4.7 23.7 1.0 CB C:VAL255 4.7 19.4 1.0 C C:VAL255 4.7 25.7 1.0 CZ3 C:TRP112 4.9 19.0 1.0 CB C:SER375 4.9 22.3 1.0 CG C:PHE382 4.9 24.8 1.0

Chlorine binding site 4 out of 4 in the Hiv-1 GP120 Complex with Bnm-III-170


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 Bnm-III-170 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl507 b:30.8 occ:1.00 CL25 D:5VG507 0.0 30.8 1.0 C24 D:5VG507 1.8 26.7 1.0 C22 D:5VG507 2.7 27.0 1.0 C26 D:5VG507 2.8 25.2 1.0 F23 D:5VG507 2.8 31.0 1.0 C D:PHE376 3.6 29.7 1.0 CA D:PHE376 3.6 28.6 1.0 CD1 D:PHE382 3.7 27.0 1.0 N D:ASN377 3.7 32.6 1.0 CG1 D:VAL255 3.8 24.5 1.0 N D:PHE376 3.9 26.9 1.0 CE1 D:PHE382 4.0 27.0 1.0 C21 D:5VG507 4.0 31.9 1.0 O D:PHE376 4.0 30.1 1.0 C27 D:5VG507 4.0 28.3 1.0 O D:VAL255 4.1 32.1 1.0 CH2 D:TRP112 4.2 26.2 1.0 C D:SER375 4.3 26.6 1.0 CB D:ASN377 4.4 30.6 1.0 O D:SER375 4.5 26.0 1.0 CA D:ASN377 4.5 32.9 1.0 C20 D:5VG507 4.5 29.4 1.0 OG D:SER375 4.7 27.9 1.0 CB D:VAL255 4.7 24.6 1.0 C D:VAL255 4.7 29.9 1.0 O D:HOH611 4.8 32.2 1.0 CZ3 D:TRP112 4.9 28.5 1.0 CB D:SER375 4.9 27.4 1.0 CG D:PHE382 4.9 31.6 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