Fluorine in PDB 8gd5: Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Dl-I-102

The structure of Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Dl-I-102, PDB code: 8gd5 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)	32.54 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.395, 66.792, 92.123, 90, 90, 90
R / Rfree (%)	21.9 / 27.4

The structure of Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Dl-I-102 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Dl-I-102 (pdb code 8gd5). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Dl-I-102, PDB code: 8gd5:

Fluorine binding site 1 out of 1 in the Crystal Structure of Hiv-1 Lm/Ht Clade A/E CRF01 GP120 Core in Complex with Dl-I-102


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 Dl-I-102 within 5.0Å range: probe atom residue distance (Å) B Occ A:F512 b:123.0 occ:1.00 F18 A:Z2O512 0.0 123.0 1.0 C17 A:Z2O512 1.4 116.6 1.0 C16 A:Z2O512 2.4 106.2 1.0 C19 A:Z2O512 2.4 120.8 1.0 CL1 A:Z2O512 3.0 163.1 1.0 CG2 A:THR257 3.5 82.2 1.0 C A:SER256 3.6 83.0 1.0 CA A:SER256 3.6 86.3 1.0 C15 A:Z2O512 3.6 108.0 1.0 C21 A:Z2O512 3.7 127.6 1.0 O A:SER375 3.8 85.2 1.0 N A:THR257 3.8 78.9 1.0 CE A:MET475 3.8 70.9 1.0 N A:SER256 3.9 81.0 1.0 CB A:SER375 3.9 76.4 1.0 CG1 A:VAL255 4.0 75.4 1.0 O A:SER256 4.0 80.9 1.0 C A:SER375 4.1 83.6 1.0 C22 A:Z2O512 4.1 111.4 1.0 CB A:THR257 4.4 80.2 1.0 OG1 A:THR257 4.5 78.2 1.0 C A:VAL255 4.5 83.8 1.0 N A:PHE376 4.6 75.9 1.0 CA A:THR257 4.6 78.9 1.0 CA A:SER375 4.6 76.1 1.0 OG A:SER375 4.8 76.2 1.0 O13 A:Z2O512 4.8 110.4 1.0 O A:VAL255 4.8 84.8 1.0 CA A:PHE376 4.8 76.5 1.0 N14 A:Z2O512 4.8 109.2 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