Fluorine in PDB 4e91: Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Inhibitor BD3

The structure of Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Inhibitor BD3, PDB code: 4e91 was solved by C.T.Lemke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.61 / 1.70
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	65.783, 65.783, 143.323, 90.00, 90.00, 120.00
R / Rfree (%)	22 / 24.3

The structure of Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Inhibitor BD3 also contains other interesting chemical elements:

Iodine	(I)	4 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Fluorine atom in the Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Inhibitor BD3 (pdb code 4e91). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Inhibitor BD3, PDB code: 4e91:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Inhibitor BD3


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 the N-Terminal Domain of Hiv-1 Capsid in Complex with Inhibitor BD3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:13.4 occ:1.00 F21 A:0OF202 0.0 13.4 1.0 C20 A:0OF202 1.4 14.5 1.0 F23 A:0OF202 2.2 17.4 1.0 F22 A:0OF202 2.2 15.6 1.0 C11 A:0OF202 2.4 12.3 1.0 C10 A:0OF202 2.8 13.2 1.0 CG1 A:VAL36 3.4 13.6 1.0 CD1 A:LEU138 3.7 13.3 1.0 C12 A:0OF202 3.7 13.2 1.0 CZ2 A:TRP23 3.7 14.8 1.0 CB A:PHE40 3.9 11.5 1.0 C5 A:0OF202 4.2 11.1 1.0 CD1 A:PHE40 4.2 15.5 1.0 CD2 A:LEU138 4.3 14.1 1.0 CG A:PHE40 4.3 12.7 1.0 CH2 A:TRP23 4.4 15.5 1.0 CG2 A:VAL27 4.6 13.9 1.0 CE2 A:TRP23 4.6 14.8 1.0 CG A:LEU138 4.6 12.1 1.0 O A:VAL36 4.8 12.5 1.0 NE1 A:TRP23 4.8 15.1 1.0 C13 A:0OF202 4.8 13.5 1.0 CB A:VAL36 4.9 12.8 1.0 C14 A:0OF202 4.9 12.1 1.0 C19 A:0OF202 4.9 13.8 1.0 N6 A:0OF202 5.0 11.7 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Inhibitor BD3


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 the N-Terminal Domain of Hiv-1 Capsid in Complex with Inhibitor BD3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:15.6 occ:1.00 F22 A:0OF202 0.0 15.6 1.0 C20 A:0OF202 1.4 14.5 1.0 F23 A:0OF202 2.2 17.4 1.0 F21 A:0OF202 2.2 13.4 1.0 C11 A:0OF202 2.3 12.3 1.0 C12 A:0OF202 2.8 13.2 1.0 C10 A:0OF202 3.5 13.2 1.0 CD1 A:PHE40 3.6 15.5 1.0 CD2 A:LEU56 3.7 14.4 1.0 CD1 A:LEU138 3.8 13.3 1.0 CE A:MET55 3.9 18.7 1.0 CE1 A:PHE40 4.0 15.4 1.0 CD2 A:LEU138 4.0 14.1 1.0 C13 A:0OF202 4.2 13.5 1.0 SD A:MET55 4.2 18.6 1.0 CG A:PHE40 4.2 12.7 1.0 CG2 A:ILE134 4.4 13.2 1.0 CG A:LEU138 4.4 12.1 1.0 CB A:PHE40 4.5 11.5 1.0 C5 A:0OF202 4.7 11.1 1.0 CZ A:PHE40 4.9 15.1 1.0 CZ2 A:TRP23 4.9 14.8 1.0 C4 A:0OF202 4.9 12.7 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Inhibitor BD3


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 the N-Terminal Domain of Hiv-1 Capsid in Complex with Inhibitor BD3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:17.4 occ:1.00 F23 A:0OF202 0.0 17.4 1.0 C20 A:0OF202 1.4 14.5 1.0 F22 A:0OF202 2.2 15.6 1.0 F21 A:0OF202 2.2 13.4 1.0 C11 A:0OF202 2.4 12.3 1.0 C12 A:0OF202 3.0 13.2 1.0 NE1 A:TRP23 3.2 15.1 1.0 C10 A:0OF202 3.4 13.2 1.0 CZ2 A:TRP23 3.4 14.8 1.0 SD A:MET55 3.4 18.6 1.0 CE2 A:TRP23 3.6 14.8 1.0 CG2 A:VAL27 4.0 13.9 1.0 CE A:MET55 4.0 18.7 1.0 CG2 A:VAL59 4.0 14.4 1.0 C13 A:0OF202 4.3 13.5 1.0 CD1 A:PHE40 4.4 15.5 1.0 CD1 A:TRP23 4.4 14.5 1.0 CG1 A:VAL59 4.4 15.5 1.0 CB A:VAL59 4.6 14.2 1.0 C5 A:0OF202 4.6 11.1 1.0 CH2 A:TRP23 4.6 15.5 1.0 CD2 A:LEU56 4.8 14.4 1.0 CG1 A:VAL27 4.8 13.4 1.0 CD2 A:TRP23 4.9 15.7 1.0 CB A:PHE40 4.9 11.5 1.0 C4 A:0OF202 4.9 12.7 1.0 CG A:MET55 5.0 16.3 1.0 CG1 A:VAL36 5.0 13.6 1.0

C.T.Lemke, S.Titolo, U.Von Schwedler, N.Goudreau, J.F.Mercier, E.Wardrop, A.M.Faucher, R.Coulombe, S.S.Banik, L.Fader, A.Gagnon, S.H.Kawai, J.Rancourt, M.Tremblay, C.Yoakim, B.Simoneau, J.Archambault, W.I.Sundquist, S.W.Mason. Distinct Effects of Two Hiv-1 Capsid Assembly Inhibitor Families That Bind the Same Site Within the N-Terminal Domain of the Viral Ca Protein. J.Virol. V. 86 6643 2012.
ISSN: ISSN 0022-538X
PubMed: 22496222
DOI: 10.1128/JVI.00493-12