Fluorine in PDB 4dkq: Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Dmj-I-228

The structure of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Dmj-I-228, PDB code: 4dkq was solved by Y.D.Kwon, J.M.Lalonde, D.M.Jones, A.W.Sun, J.R.Courter, T.Soeta, T.Kobayashi, A.M.Princiotto, X.Wu, J.Mascola, A.Schon, E.Freire, J.Sodroski, N.Madani, A.B.Smith Iii, P.D.Kwong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.35 / 1.89
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.741, 67.523, 89.255, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 23.3

The structure of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Dmj-I-228 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Dmj-I-228 (pdb code 4dkq). 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 Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Dmj-I-228, PDB code: 4dkq:

Fluorine binding site 1 out of 1 in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Dmj-I-228


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 Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Dmj-I-228 within 5.0Å range: probe atom residue distance (Å) B Occ A:F613 b:21.4 occ:1.00 F24 A:0LK613 0.0 21.4 1.0 C21 A:0LK613 1.3 22.0 1.0 C20 A:0LK613 2.3 23.8 1.0 C22 A:0LK613 2.4 19.6 1.0 CL A:0LK613 2.9 25.9 1.0 O A:SER375 3.3 19.2 1.0 CA A:SER256 3.3 18.5 1.0 OG A:SER375 3.4 32.1 1.0 CG1 A:VAL255 3.5 19.5 1.0 C A:SER256 3.6 18.6 1.0 C19 A:0LK613 3.6 22.1 1.0 N A:SER256 3.6 15.4 1.0 C15 A:0LK613 3.7 21.6 1.0 O A:VAL255 3.8 18.2 1.0 C A:VAL255 3.8 16.5 1.0 N A:THR257 3.8 15.8 1.0 C A:SER375 3.8 19.2 1.0 CG2 A:THR257 3.9 20.3 1.0 C18 A:0LK613 4.1 18.5 1.0 O A:SER256 4.1 18.5 1.0 CB A:SER375 4.2 27.5 1.0 N A:PHE376 4.3 19.2 1.0 CA A:PHE376 4.4 19.9 1.0 CB A:VAL255 4.5 21.8 1.0 CA A:SER375 4.6 19.4 1.0 CD1 A:ILE475 4.6 20.9 1.0 O16 A:0LK613 4.7 21.7 1.0 CB A:SER256 4.7 22.1 1.0 CA A:VAL255 4.8 16.5 1.0 CB A:THR257 4.8 21.4 1.0 N14 A:0LK613 4.8 20.2 1.0 CA A:THR257 4.9 19.2 1.0

J.M.Lalonde, Y.D.Kwon, D.M.Jones, A.W.Sun, J.R.Courter, T.Soeta, T.Kobayashi, A.M.Princiotto, X.Wu, A.Schon, E.Freire, P.D.Kwong, J.R.Mascola, J.Sodroski, N.Madani, A.B.Smith. Structure-Based Design, Synthesis, and Characterization of Dual Hotspot Small-Molecule Hiv-1 Entry Inhibitors. J.Med.Chem. V. 55 4382 2012.
ISSN: ISSN 0022-2623
PubMed: 22497421
DOI: 10.1021/JM300265J