Fluorine in PDB 4i54: Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 H375S Core in Complex with Dmj-II-121

The structure of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 H375S Core in Complex with Dmj-II-121, PDB code: 4i54 was solved by M.Le-Khac, W.A.Hendrickson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.63 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.324, 68.775, 94.443, 90.00, 90.89, 90.00
R / Rfree (%)	19.6 / 26.1

The structure of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 H375S Core in Complex with Dmj-II-121 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 H375S Core in Complex with Dmj-II-121 (pdb code 4i54). 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 Clade A/E 93TH057 Hiv-1 GP120 H375S Core in Complex with Dmj-II-121, PDB code: 4i54:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 H375S Core in Complex with Dmj-II-121


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 H375S Core in Complex with Dmj-II-121 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:28.1 occ:1.00 F23 A:1C1501 0.0 28.1 1.0 C22 A:1C1501 1.3 28.6 1.0 C24 A:1C1501 2.4 29.0 1.0 C21 A:1C1501 2.4 29.0 1.0 CL1 A:1C1501 2.9 34.9 1.0 CA A:SER256 3.2 39.0 1.0 O A:SER375 3.2 28.6 1.0 OG A:SER375 3.4 53.8 1.0 C A:SER256 3.4 34.8 1.0 N A:THR257 3.6 33.5 1.0 N A:SER256 3.6 37.4 1.0 C20 A:1C1501 3.6 41.0 1.0 C26 A:1C1501 3.7 29.6 1.0 C A:SER375 3.8 32.4 1.0 CG2 A:THR257 3.8 35.7 1.0 CG1 A:VAL255 3.8 27.8 1.0 O A:VAL255 3.9 47.2 1.0 C A:VAL255 3.9 35.9 1.0 O A:SER256 4.1 29.5 1.0 C27 A:1C1501 4.1 36.0 1.0 N A:PHE376 4.2 33.1 1.0 CA A:PHE376 4.3 28.3 1.0 CB A:SER375 4.3 29.5 1.0 CB A:SER256 4.6 42.0 1.0 CA A:SER375 4.6 33.3 1.0 CB A:THR257 4.7 28.0 1.0 CA A:THR257 4.7 31.1 1.0 CD1 A:ILE475 4.7 28.5 1.0 CB A:VAL255 4.8 31.3 1.0 O18 A:1C1501 4.8 29.3 1.0 N19 A:1C1501 4.8 30.1 1.0 OG1 A:THR257 4.8 38.7 1.0 CA A:VAL255 4.9 27.1 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 H375S Core in Complex with Dmj-II-121


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 Clade A/E 93TH057 Hiv-1 GP120 H375S Core in Complex with Dmj-II-121 within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:48.2 occ:1.00 F23 B:1C1501 0.0 48.2 1.0 C22 B:1C1501 1.3 49.0 1.0 C21 B:1C1501 2.4 50.2 1.0 C24 B:1C1501 2.4 51.7 1.0 CL1 B:1C1501 3.1 55.6 1.0 CA B:SER256 3.3 46.4 1.0 OG B:SER375 3.3 65.5 1.0 O B:SER375 3.4 49.4 1.0 C B:SER256 3.5 50.1 1.0 CG1 B:VAL255 3.6 46.3 1.0 C20 B:1C1501 3.6 62.8 1.0 O B:VAL255 3.6 49.1 1.0 N B:SER256 3.7 45.7 1.0 C26 B:1C1501 3.7 49.6 1.0 N B:THR257 3.8 48.5 1.0 C B:VAL255 3.8 44.9 1.0 CG2 B:THR257 3.8 51.1 1.0 C B:SER375 3.8 53.6 1.0 O B:SER256 4.0 56.7 1.0 C27 B:1C1501 4.1 66.3 1.0 CB B:SER375 4.2 64.5 1.0 N B:PHE376 4.2 47.2 1.0 CA B:PHE376 4.4 45.8 1.0 CB B:SER256 4.6 45.6 1.0 CD1 B:ILE475 4.6 49.2 1.0 CB B:VAL255 4.6 44.9 1.0 CA B:SER375 4.6 60.2 1.0 CB B:THR257 4.7 56.7 1.0 O18 B:1C1501 4.7 55.3 1.0 OG1 B:THR257 4.8 51.1 1.0 CA B:THR257 4.8 58.3 1.0 N19 B:1C1501 4.8 60.4 1.0 CA B:VAL255 4.8 44.4 1.0

J.M.Lalonde, M.Le-Khac, D.M.Jones, J.R.Courter, J.Park, A.Schon, A.M.Princiotto, X.Wu, J.R.Mascola, E.Freire, J.Sodroski, N.Madani, W.A.Hendrickson, A.B.Smith. Structure-Based Design and Synthesis of An Hiv-1 Entry Inhibitor Exploiting X-Ray and Thermodynamic Characterization. Acs Med Chem Lett V. 4 338 2013.
PubMed: 23667716
DOI: 10.1021/ML300407Y