Fluorine in PDB 6onf: Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with (S)-Mcg-III-188-A02.

The structure of Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with (S)-Mcg-III-188-A02., PDB code: 6onf was solved by W.D.Tolbert, R.Sherburn, M.Pazgier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.84
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.620, 66.790, 86.380, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 23.1

The structure of Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with (S)-Mcg-III-188-A02. also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with (S)-Mcg-III-188-A02. (pdb code 6onf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with (S)-Mcg-III-188-A02., PDB code: 6onf:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with (S)-Mcg-III-188-A02.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with (S)-Mcg-III-188-A02. within 5.0Å range: probe atom residue distance (Å) B Occ A:F511 b:24.4 occ:0.53 F14 A:MW4511 0.0 24.4 0.5 F14 A:MW4511 0.1 25.4 0.5 C13 A:MW4511 1.4 22.2 0.5 C13 A:MW4511 1.4 21.5 0.5 C12 A:MW4511 2.3 23.1 0.5 C12 A:MW4511 2.4 22.8 0.5 C15 A:MW4511 2.4 22.2 0.5 C15 A:MW4511 2.5 22.6 0.5 CL1 A:MW4511 3.1 28.1 0.5 O A:THR375 3.1 19.3 1.0 CL1 A:MW4511 3.2 28.4 0.5 CA A:SER256 3.3 17.5 1.0 C A:SER256 3.4 19.4 1.0 N A:SER256 3.6 19.9 1.0 N A:THR257 3.6 19.1 1.0 C A:THR375 3.6 20.2 1.0 CE A:MET475 3.6 22.2 1.0 C11 A:MW4511 3.7 24.8 0.5 CG1 A:VAL255 3.7 19.6 1.0 C11 A:MW4511 3.7 25.2 0.5 CG2 A:THR257 3.7 20.3 1.0 C17 A:MW4511 3.7 23.3 0.5 C17 A:MW4511 3.7 23.4 0.5 CG2 A:THR375 3.9 21.3 1.0 CB A:THR375 4.0 20.8 1.0 C A:VAL255 4.0 19.0 1.0 O A:SER256 4.0 19.2 1.0 N A:PHE376 4.2 20.4 1.0 C18 A:MW4511 4.2 23.2 0.5 C18 A:MW4511 4.2 23.1 0.5 O A:VAL255 4.2 20.9 1.0 CA A:THR375 4.3 17.3 1.0 CA A:PHE376 4.4 23.4 1.0 CB A:THR257 4.6 18.6 1.0 CB A:SER256 4.6 19.0 1.0 CA A:THR257 4.6 19.8 1.0 OG1 A:THR257 4.7 20.0 1.0 CB A:VAL255 4.8 20.8 1.0 O09 A:MW4511 4.8 29.2 0.5 N10 A:MW4511 4.9 25.6 0.5 O09 A:MW4511 4.9 29.3 0.5 SD A:MET475 4.9 20.8 1.0 N10 A:MW4511 4.9 25.6 0.5 CA A:VAL255 4.9 19.6 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with (S)-Mcg-III-188-A02.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with (S)-Mcg-III-188-A02. within 5.0Å range: probe atom residue distance (Å) B Occ A:F511 b:25.4 occ:0.47 F14 A:MW4511 0.0 25.4 0.5 F14 A:MW4511 0.1 24.4 0.5 C13 A:MW4511 1.4 22.2 0.5 C13 A:MW4511 1.4 21.5 0.5 C12 A:MW4511 2.4 23.1 0.5 C15 A:MW4511 2.4 22.2 0.5 C12 A:MW4511 2.4 22.8 0.5 C15 A:MW4511 2.4 22.6 0.5 CL1 A:MW4511 3.0 28.1 0.5 O A:THR375 3.1 19.3 1.0 CL1 A:MW4511 3.1 28.4 0.5 CA A:SER256 3.2 17.5 1.0 C A:SER256 3.4 19.4 1.0 N A:SER256 3.5 19.9 1.0 C A:THR375 3.6 20.2 1.0 N A:THR257 3.6 19.1 1.0 CG1 A:VAL255 3.6 19.6 1.0 CE A:MET475 3.7 22.2 1.0 C17 A:MW4511 3.7 23.3 0.5 C11 A:MW4511 3.7 24.8 0.5 C17 A:MW4511 3.7 23.4 0.5 C11 A:MW4511 3.8 25.2 0.5 CG2 A:THR257 3.8 20.3 1.0 CG2 A:THR375 3.9 21.3 1.0 C A:VAL255 3.9 19.0 1.0 CB A:THR375 4.0 20.8 1.0 O A:SER256 4.1 19.2 1.0 O A:VAL255 4.1 20.9 1.0 N A:PHE376 4.1 20.4 1.0 C18 A:MW4511 4.2 23.2 0.5 C18 A:MW4511 4.2 23.1 0.5 CA A:PHE376 4.3 23.4 1.0 CA A:THR375 4.4 17.3 1.0 CB A:SER256 4.6 19.0 1.0 CB A:THR257 4.6 18.6 1.0 CA A:THR257 4.7 19.8 1.0 CB A:VAL255 4.7 20.8 1.0 OG1 A:THR257 4.8 20.0 1.0 CA A:VAL255 4.9 19.6 1.0 SD A:MET475 4.9 20.8 1.0 O09 A:MW4511 4.9 29.2 0.5 N10 A:MW4511 4.9 25.6 0.5 O09 A:MW4511 5.0 29.3 0.5 N10 A:MW4511 5.0 25.6 0.5

S.Ding, M.C.Grenier, W.D.Tolbert, D.Vezina, R.Sherburn, J.Richard, J.Prevost, J.P.Chapleau, G.Gendron-Lepage, H.Medjahed, C.Abrams, J.Sodroski, M.Pazgier, A.B.Smith 3Rd, A.Finzi. A New Family of Small-Molecule CD4-Mimetic Compounds Contact the Highly Conserved Aspartic Acid 368 of Hiv-1 GP120 and Mediates Adcc. J.Virol. 2019.
ISSN: ESSN 1098-5514
PubMed: 31554684
DOI: 10.1128/JVI.01325-19