Fluorine in PDB 4dvt: Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with As-II-37

The structure of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with As-II-37, PDB code: 4dvt 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)	28.19 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.809, 68.402, 93.988, 90.00, 91.94, 90.00
R / Rfree (%)	19.6 / 24.8

The structure of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with As-II-37 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 As-II-37 (pdb code 4dvt). 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 As-II-37, PDB code: 4dvt:
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 As-II-37


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 As-II-37 within 5.0Å range: probe atom residue distance (Å) B Occ A:F512 b:80.6 occ:1.00 F14 A:0LZ512 0.0 80.6 1.0 C11 A:0LZ512 1.3 68.7 1.0 C10 A:0LZ512 2.3 71.3 1.0 C12 A:0LZ512 2.4 72.0 1.0 H5 A:0LZ512 2.6 86.4 1.0 CL1 A:0LZ512 2.9 87.8 1.0 OG A:SER375 2.9 63.0 1.0 CA A:SER256 3.0 49.0 1.0 C A:SER256 3.1 54.7 1.0 CG2 A:THR257 3.2 48.5 1.0 O A:SER375 3.2 56.0 1.0 N A:SER256 3.4 53.3 1.0 N A:THR257 3.4 54.2 1.0 O A:SER256 3.6 50.0 1.0 C09 A:0LZ512 3.6 81.7 1.0 C05 A:0LZ512 3.7 78.5 1.0 CG1 A:VAL255 3.8 41.2 1.0 C A:SER375 3.8 53.8 1.0 C A:VAL255 4.0 55.8 1.0 CB A:SER375 4.0 59.1 1.0 C08 A:0LZ512 4.1 82.0 1.0 CB A:THR257 4.1 50.9 1.0 O A:VAL255 4.2 61.0 1.0 OG1 A:THR257 4.3 46.2 1.0 CA A:THR257 4.3 40.0 1.0 CB A:SER256 4.4 45.7 1.0 CD1 A:ILE475 4.4 35.5 1.0 H4 A:0LZ512 4.5 98.1 1.0 CA A:SER375 4.5 59.4 1.0 N A:PHE376 4.5 54.7 1.0 CA A:PHE376 4.7 50.3 1.0 O06 A:0LZ512 4.8 64.3 1.0 N04 A:0LZ512 4.9 78.1 1.0 CB A:VAL255 4.9 37.7 1.0 CA A:VAL255 5.0 42.1 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 As-II-37


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 As-II-37 within 5.0Å range: probe atom residue distance (Å) B Occ B:F512 b:98.3 occ:1.00 F14 B:0LZ512 0.0 98.3 1.0 C11 B:0LZ512 1.3 93.7 1.0 C10 B:0LZ512 2.3 89.7 1.0 C12 B:0LZ512 2.4 0.8 1.0 H5 B:0LZ512 2.6 0.3 1.0 CL1 B:0LZ512 2.9 0.5 1.0 OG B:SER375 3.0 67.6 1.0 CA B:SER256 3.3 59.2 1.0 C B:SER256 3.3 62.7 1.0 CG2 B:THR257 3.4 48.3 1.0 C09 B:0LZ512 3.6 93.2 1.0 O B:SER375 3.6 63.3 1.0 C05 B:0LZ512 3.7 0.3 1.0 N B:SER256 3.7 58.8 1.0 N B:THR257 3.7 58.3 1.0 O B:SER256 3.7 65.2 1.0 CG1 B:VAL255 3.8 44.0 1.0 CB B:SER375 3.9 67.6 1.0 C B:SER375 4.0 65.9 1.0 C B:VAL255 4.0 60.3 1.0 C08 B:0LZ512 4.1 0.6 1.0 O B:VAL255 4.1 76.0 1.0 CB B:THR257 4.3 58.2 1.0 CD1 B:ILE475 4.4 79.3 1.0 OG1 B:THR257 4.5 56.9 1.0 H4 B:0LZ512 4.5 0.9 1.0 CA B:THR257 4.5 59.9 1.0 N B:PHE376 4.6 63.1 1.0 CA B:SER375 4.6 65.0 1.0 CB B:SER256 4.7 55.7 1.0 O06 B:0LZ512 4.8 0.4 1.0 CA B:PHE376 4.8 56.6 1.0 N04 B:0LZ512 4.9 0.4 1.0 CB B:VAL255 4.9 52.3 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