Fluorine in PDB 8fa0: Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-14208, An Hiv-1 GP120 Antagonist

The structure of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-14208, An Hiv-1 GP120 Antagonist, PDB code: 8fa0 was solved by Y.D.Kwon, P.D.Kwong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.35 / 2.09
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.213, 66.97, 90.351, 90, 90, 90
R / Rfree (%)	24.3 / 29.8

The structure of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-14208, An Hiv-1 GP120 Antagonist 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 Core in Complex with Nbd-14208, An Hiv-1 GP120 Antagonist (pdb code 8fa0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-14208, An Hiv-1 GP120 Antagonist, PDB code: 8fa0:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-14208, An Hiv-1 GP120 Antagonist


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 Nbd-14208, An Hiv-1 GP120 Antagonist within 5.0Å range: probe atom residue distance (Å) B Occ A:F509 b:71.4 occ:1.00 F15 A:XKR509 0.0 71.4 1.0 C14 A:XKR509 1.3 72.8 1.0 C16 A:XKR509 2.3 74.4 1.0 C13 A:XKR509 2.4 70.8 1.0 H131 A:XKR509 2.5 85.0 1.0 CL17 A:XKR509 2.9 82.4 1.0 CG2 A:ILE424 3.2 60.1 1.0 CD2 A:PHE382 3.2 46.5 1.0 CE2 A:PHE382 3.2 47.8 1.0 C18 A:XKR509 3.6 71.0 1.0 C12 A:XKR509 3.7 68.4 1.0 C20 A:XKR509 4.1 70.1 1.0 OH A:TYR384 4.1 55.2 1.0 O A:ASN425 4.3 50.8 1.0 CG A:PHE382 4.5 46.7 1.0 CZ A:PHE382 4.5 49.4 1.0 CB A:ILE424 4.6 59.8 1.0 F19 A:XKR509 4.6 69.8 1.0 H111 A:XKR509 4.7 80.9 1.0 CD1 A:TRP427 4.8 46.1 1.0 CE1 A:TYR384 4.8 51.5 1.0 CZ A:TYR384 4.8 53.5 1.0 C10 A:XKR509 4.9 67.4 1.0 CG A:GLU370 4.9 65.5 1.0 CG1 A:ILE424 5.0 58.2 1.0 H201 A:XKR509 5.0 84.2 1.0 CD1 A:ILE424 5.0 56.6 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-14208, An Hiv-1 GP120 Antagonist


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 Core in Complex with Nbd-14208, An Hiv-1 GP120 Antagonist within 5.0Å range: probe atom residue distance (Å) B Occ A:F509 b:69.8 occ:1.00 F19 A:XKR509 0.0 69.8 1.0 C18 A:XKR509 1.3 71.0 1.0 C16 A:XKR509 2.3 74.4 1.0 C20 A:XKR509 2.3 70.1 1.0 H201 A:XKR509 2.5 84.2 1.0 CL17 A:XKR509 2.9 82.4 1.0 CA A:SER256 3.2 41.6 1.0 C A:SER256 3.4 44.6 1.0 N A:SER256 3.5 43.7 1.0 CG2 A:THR257 3.5 43.0 1.0 C14 A:XKR509 3.5 72.8 1.0 O A:SER375 3.6 44.8 1.0 N A:THR257 3.6 41.6 1.0 C12 A:XKR509 3.6 68.4 1.0 CG1 A:VAL255 3.7 47.9 1.0 C A:VAL255 3.8 46.3 1.0 O A:SER256 3.9 44.6 1.0 OG A:SER375 3.9 69.9 1.0 O A:VAL255 3.9 48.4 1.0 C13 A:XKR509 4.0 70.8 1.0 C A:SER375 4.1 46.9 1.0 CD1 A:ILE475 4.2 54.3 1.0 CB A:SER375 4.4 60.7 1.0 CB A:THR257 4.5 44.8 1.0 N A:PHE376 4.5 44.5 1.0 CA A:THR257 4.6 42.8 1.0 F15 A:XKR509 4.6 71.4 1.0 CB A:SER256 4.6 42.2 1.0 CA A:PHE376 4.6 44.5 1.0 CB A:VAL255 4.7 47.5 1.0 OG1 A:THR257 4.8 42.6 1.0 CA A:VAL255 4.8 45.1 1.0 CA A:SER375 4.8 51.0 1.0 C10 A:XKR509 4.9 67.4 1.0 H131 A:XKR509 5.0 85.0 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-14208, An Hiv-1 GP120 Antagonist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-14208, An Hiv-1 GP120 Antagonist within 5.0Å range: probe atom residue distance (Å) B Occ A:F510 b:57.9 occ:1.00 F15 A:XKR510 0.0 57.9 1.0 C14 A:XKR510 1.3 57.3 1.0 C16 A:XKR510 2.3 57.1 1.0 C13 A:XKR510 2.3 57.6 1.0 H131 A:XKR510 2.5 69.1 1.0 CL17 A:XKR510 3.0 56.0 1.0 N A:MET434 3.1 55.8 1.0 CB A:MET434 3.3 64.7 1.0 C A:ALA433 3.3 53.6 1.0 CA A:ALA433 3.5 57.0 1.0 C18 A:XKR510 3.6 57.2 1.0 C12 A:XKR510 3.6 58.6 1.0 CA A:MET434 3.7 58.1 1.0 O A:VAL120 3.9 59.4 1.0 CB A:VAL120 3.9 63.4 1.0 CG A:MET434 4.0 69.8 1.0 O A:ALA433 4.1 49.6 1.0 C20 A:XKR510 4.1 58.1 1.0 O A:GLN432 4.1 56.5 1.0 CG1 A:VAL120 4.2 65.4 1.0 N A:ALA433 4.2 55.0 1.0 C A:VAL120 4.4 61.8 1.0 C A:GLN432 4.5 55.1 1.0 F19 A:XKR510 4.6 58.7 1.0 CB A:ALA433 4.7 56.8 1.0 H111 A:XKR510 4.7 77.4 1.0 CG2 A:VAL120 4.7 62.7 1.0 CA A:VAL120 4.7 62.8 1.0 SD A:MET434 4.8 78.2 1.0 C10 A:XKR510 4.9 61.7 1.0 H201 A:XKR510 5.0 69.7 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-14208, An Hiv-1 GP120 Antagonist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-14208, An Hiv-1 GP120 Antagonist within 5.0Å range: probe atom residue distance (Å) B Occ A:F510 b:58.7 occ:1.00 F19 A:XKR510 0.0 58.7 1.0 C18 A:XKR510 1.3 57.2 1.0 C16 A:XKR510 2.3 57.1 1.0 C20 A:XKR510 2.4 58.1 1.0 H201 A:XKR510 2.5 69.7 1.0 O3S A:EPE511 2.7 110.6 1.0 CL17 A:XKR510 2.9 56.0 1.0 O2S A:EPE511 3.1 109.1 1.0 S A:EPE511 3.3 108.7 1.0 C9 A:EPE511 3.4 92.8 1.0 C14 A:XKR510 3.6 57.3 1.0 C12 A:XKR510 3.7 58.6 1.0 C10 A:EPE511 3.7 100.6 1.0 C13 A:XKR510 4.1 57.6 1.0 O A:HOH601 4.1 76.6 1.0 CG1 A:VAL120 4.1 65.4 1.0 CG1 A:VAL200 4.2 78.2 1.0 F15 A:XKR510 4.6 57.9 1.0 O1S A:EPE511 4.6 110.9 1.0 N1 A:EPE511 4.8 85.4 1.0 C10 A:XKR510 4.9 61.7 1.0 H131 A:XKR510 5.0 69.1 1.0

F.Curreli, Y.D.Kwon, I.Nicolau, G.Burgos, A.Altieri, A.V.Kurkin, R.Verardi, P.D.Kwong, A.K.Debnath. Antiviral Activity and Crystal Structures of Hiv-1 GP120 Antagonists. Int J Mol Sci V. 23 2022.
ISSN: ESSN 1422-0067
PubMed: 36555641
DOI: 10.3390/IJMS232415999