Fluorine in PDB 4dvx: Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Mae-II-188

The structure of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Mae-II-188, PDB code: 4dvx 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)	28.46 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.610, 68.295, 93.956, 90.00, 91.47, 90.00
R / Rfree (%)	20 / 26.3

The structure of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Mae-II-188 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 Mae-II-188 (pdb code 4dvx). 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 Core in Complex with Mae-II-188, PDB code: 4dvx:
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 Core in Complex with Mae-II-188


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 Mae-II-188 within 5.0Å range: probe atom residue distance (Å) B Occ A:F512 b:64.4 occ:1.00 F A:0M5512 0.0 64.4 1.0 C01 A:0M5512 1.3 53.4 1.0 C06 A:0M5512 2.4 48.7 1.0 C02 A:0M5512 2.4 53.0 1.0 H03 A:0M5512 2.5 58.4 1.0 O A:SER375 2.8 56.3 1.0 OG A:SER375 2.9 71.9 1.0 CA A:SER256 3.0 52.7 1.0 CL A:0M5512 3.1 74.7 1.0 C A:SER256 3.2 57.4 1.0 CG2 A:THR257 3.4 43.4 1.0 N A:THR257 3.4 53.2 1.0 C A:SER375 3.4 58.5 1.0 N A:SER256 3.5 55.0 1.0 C03 A:0M5512 3.7 56.0 1.0 C05 A:0M5512 3.7 60.6 1.0 CB A:SER375 3.8 46.6 1.0 O A:SER256 3.9 57.3 1.0 C A:VAL255 4.0 50.4 1.0 CG1 A:VAL255 4.0 42.5 1.0 O A:VAL255 4.0 67.3 1.0 N A:PHE376 4.1 56.1 1.0 C04 A:0M5512 4.1 55.9 1.0 CA A:SER375 4.2 53.7 1.0 CB A:THR257 4.2 50.4 1.0 OG1 A:THR257 4.3 48.6 1.0 CA A:PHE376 4.3 48.7 1.0 CB A:SER256 4.3 54.6 1.0 CA A:THR257 4.4 46.3 1.0 H01 A:0M5512 4.5 67.2 1.0 O01 A:0M5512 4.8 57.0 1.0 CD1 A:ILE475 4.8 35.5 1.0 N A:SER375 4.9 61.2 1.0 N01 A:0M5512 4.9 61.8 1.0 CB A:VAL255 5.0 42.5 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Mae-II-188


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 Mae-II-188 within 5.0Å range: probe atom residue distance (Å) B Occ B:F512 b:64.4 occ:1.00 F B:0M5512 0.0 64.4 1.0 C01 B:0M5512 1.3 53.4 1.0 C06 B:0M5512 2.4 48.7 1.0 C02 B:0M5512 2.4 53.0 1.0 H03 B:0M5512 2.5 58.4 1.0 OG B:SER375 2.8 80.5 1.0 O B:SER375 3.1 56.8 1.0 CA B:SER256 3.1 54.0 1.0 CL B:0M5512 3.1 74.7 1.0 C B:SER256 3.2 59.2 1.0 CG2 B:THR257 3.4 49.7 1.0 N B:THR257 3.5 64.7 1.0 C B:SER375 3.5 61.8 1.0 CB B:SER375 3.6 69.5 1.0 N B:SER256 3.6 54.8 1.0 C03 B:0M5512 3.7 56.0 1.0 C05 B:0M5512 3.7 60.6 1.0 O B:SER256 3.7 62.1 1.0 O B:VAL255 4.0 59.0 1.0 C B:VAL255 4.0 58.1 1.0 N B:PHE376 4.1 59.0 1.0 CA B:SER375 4.1 63.1 1.0 C04 B:0M5512 4.2 55.9 1.0 OG1 B:THR257 4.2 57.3 1.0 CB B:THR257 4.2 59.4 1.0 CG1 B:VAL255 4.2 45.9 1.0 CA B:PHE376 4.3 53.0 1.0 CB B:SER256 4.4 49.4 1.0 CA B:THR257 4.4 64.1 1.0 H01 B:0M5512 4.5 67.2 1.0 O01 B:0M5512 4.8 57.0 1.0 CD1 B:ILE475 4.8 63.4 1.0 N B:SER375 4.9 52.1 1.0 N01 B:0M5512 4.9 61.8 1.0

Y.D.Kwon, J.M.Lalonde, Y.Yang, M.A.Elban, A.Sugawara, J.R.Courter, D.M.Jones, A.B.Smith, A.K.Debnath, P.D.Kwong. Crystal Structures of Hiv-1 GP120 Envelope Glycoprotein in Complex with Nbd Analogues That Target the CD4-Binding Site. Plos One V. 9 85940 2014.
ISSN: ESSN 1932-6203
PubMed: 24489681
DOI: 10.1371/JOURNAL.PONE.0085940