Chlorine in PDB 8gd0: Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Tfh-I-070-A6

The structure of Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Tfh-I-070-A6, PDB code: 8gd0 was solved by W.D.Tolbert, D.N.Nguyen, M.Pazgier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.88 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.577, 66.275, 91.388, 90, 90, 90
R / Rfree (%)	21.8 / 27.4

The structure of Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Tfh-I-070-A6 also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Chlorine atom in the Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Tfh-I-070-A6 (pdb code 8gd0). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Tfh-I-070-A6, PDB code: 8gd0:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Tfh-I-070-A6


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Tfh-I-070-A6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl513 b:41.4 occ:1.00 CL1 A:Z3F513 0.0 41.4 1.0 C17 A:Z3F513 1.8 38.6 1.0 C15 A:Z3F513 2.7 37.9 1.0 C19 A:Z3F513 2.8 36.2 1.0 F16 A:Z3F513 2.9 39.5 1.0 CD2 A:PHE382 3.6 35.8 1.0 C A:PHE376 3.7 40.8 1.0 CE2 A:PHE382 3.8 38.0 1.0 CG1 A:VAL255 3.8 31.6 1.0 CA A:PHE376 3.8 41.6 1.0 N A:ASN377 3.9 33.5 1.0 CG2 A:THR375 4.0 38.4 1.0 O A:PHE376 4.1 45.6 1.0 C14 A:Z3F513 4.1 35.3 1.0 C20 A:Z3F513 4.1 38.1 1.0 N A:PHE376 4.1 37.5 1.0 O A:THR375 4.2 42.4 1.0 CH2 A:TRP112 4.2 32.0 1.0 O A:VAL255 4.3 34.9 1.0 C A:THR375 4.3 40.1 1.0 CB A:ASN377 4.4 41.5 1.0 CB A:VAL255 4.5 35.8 1.0 C13 A:Z3F513 4.6 37.8 1.0 CA A:ASN377 4.6 37.4 1.0 C A:VAL255 4.7 38.5 1.0 CZ3 A:TRP112 4.9 33.8 1.0 CG A:PHE382 4.9 40.4 1.0 CB A:THR375 5.0 37.5 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Tfh-I-070-A6


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Tfh-I-070-A6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl515 b:79.5 occ:1.00 CG2 A:VAL75 4.0 46.4 1.0 CE1 A:PHE53 4.1 46.2 1.0 CZ A:PHE53 4.3 44.5 1.0 O A:PRO76 4.3 48.3 1.0 CB A:ASP78 4.9 70.2 1.0 N A:ASP78 4.9 66.5 1.0 CA A:ASP78 5.0 67.5 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Tfh-I-070-A6


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Tfh-I-070-A6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl516 b:86.5 occ:1.00 CE2 A:PHE53 4.7 39.9 1.0 CD2 A:PHE53 4.7 46.0 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Tfh-I-070-A6


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Tfh-I-070-A6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl517 b:58.0 occ:1.00 N A:LEU369 2.4 44.3 1.0 N A:ASP368 2.5 52.0 1.0 N A:THR372 2.6 44.4 1.0 N A:ILE371 2.7 40.2 1.0 C A:GLY367 3.1 56.6 1.0 CA A:LEU369 3.1 44.5 1.0 CA A:ILE371 3.2 40.1 1.0 CB A:ILE371 3.2 49.0 1.0 C A:LEU369 3.2 40.4 1.0 C A:ASP368 3.2 49.1 1.0 CG2 A:THR372 3.3 41.1 1.0 CA A:GLY367 3.3 54.7 1.0 C A:ILE371 3.3 44.5 1.0 CA A:ASP368 3.3 52.2 1.0 OG1 A:THR372 3.3 43.3 1.0 N A:GLU370 3.4 43.6 1.0 CB A:THR372 3.6 44.0 1.0 CA A:THR372 3.6 41.9 1.0 O A:LEU369 3.8 39.6 1.0 CG1 A:ILE371 3.8 49.4 1.0 C A:GLU370 3.8 40.5 1.0 CB A:ASP368 4.1 50.8 1.0 O A:GLY367 4.1 62.6 1.0 CA A:GLU370 4.2 42.2 1.0 N A:GLY367 4.4 65.8 1.0 O A:ASP368 4.4 48.0 1.0 O A:ILE371 4.5 42.5 1.0 CG2 A:ILE371 4.5 48.4 1.0 CB A:LEU369 4.6 44.2 1.0 C A:THR372 4.7 38.2 1.0 N A:MET373 4.8 42.2 1.0 O A:GLU370 4.9 39.0 1.0 CD1 A:ILE371 4.9 38.0 1.0

S.Ding, W.D.Tolbert, H.Zhu, D.Lee, L.Marchitto, T.Higgins, X.Zhao, D.Nguyen, R.Sherburn, J.Richard, G.Gendron-Lepage, H.Medjahed, M.Mohammadi, C.Abrams, M.Pazgier, A.B.Smith Iii, A.Finzi. Piperidine CD4-Mimetic Compounds Expose Vulnerable Env Epitopes Sensitizing Hiv-1-Infected Cells to Adcc. Viruses V. 15 2023.
ISSN: ESSN 1999-4915
PubMed: 37243271
DOI: 10.3390/V15051185