Fluorine in PDB 7lo6: Structure of CD4 Mimetic Bnm-III-170 in Complex with BG505 Sosip.664 Hiv-1 Env Trimer and 17B Fab

The structure of Structure of CD4 Mimetic Bnm-III-170 in Complex with BG505 Sosip.664 Hiv-1 Env Trimer and 17B Fab also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Fluorine atom in the Structure of CD4 Mimetic Bnm-III-170 in Complex with BG505 Sosip.664 Hiv-1 Env Trimer and 17B Fab (pdb code 7lo6). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Structure of CD4 Mimetic Bnm-III-170 in Complex with BG505 Sosip.664 Hiv-1 Env Trimer and 17B Fab, PDB code: 7lo6:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Structure of CD4 Mimetic Bnm-III-170 in Complex with BG505 Sosip.664 Hiv-1 Env Trimer and 17B Fab


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of CD4 Mimetic Bnm-III-170 in Complex with BG505 Sosip.664 Hiv-1 Env Trimer and 17B Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:F609 b:164.4 occ:1.00 F23 A:5VG609 0.0 164.4 1.0 C22 A:5VG609 1.4 164.4 1.0 C24 A:5VG609 2.4 164.4 1.0 C21 A:5VG609 2.4 164.4 1.0 CL25 A:5VG609 3.0 164.4 1.0 O A:SER375 3.5 179.3 1.0 C26 A:5VG609 3.6 164.4 1.0 C20 A:5VG609 3.6 164.4 1.0 O A:SER256 3.9 168.1 1.0 CG2 A:THR257 3.9 169.8 1.0 C A:SER256 4.0 168.1 1.0 OG A:SER375 4.0 179.3 1.0 C A:SER375 4.0 179.3 1.0 CG2 A:VAL255 4.1 156.1 1.0 C27 A:5VG609 4.1 164.4 1.0 CA A:SER256 4.2 168.1 1.0 N A:THR257 4.4 169.8 1.0 CA A:PHE376 4.5 179.1 1.0 N A:PHE376 4.5 179.1 1.0 CB A:SER375 4.5 179.3 1.0 N A:SER256 4.6 168.1 1.0 O18 A:5VG609 4.8 164.4 1.0 OG1 A:THR257 4.8 169.8 1.0 N19 A:5VG609 4.9 164.4 1.0 CB A:THR257 4.9 169.8 1.0 CA A:SER375 4.9 179.3 1.0

Fluorine binding site 2 out of 3 in the Structure of CD4 Mimetic Bnm-III-170 in Complex with BG505 Sosip.664 Hiv-1 Env Trimer and 17B Fab


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of CD4 Mimetic Bnm-III-170 in Complex with BG505 Sosip.664 Hiv-1 Env Trimer and 17B Fab within 5.0Å range: probe atom residue distance (Å) B Occ C:F609 b:84.5 occ:1.00 F23 C:5VG609 0.0 84.5 1.0 C22 C:5VG609 1.4 84.5 1.0 C24 C:5VG609 2.3 84.5 1.0 C21 C:5VG609 2.4 84.5 1.0 CL25 C:5VG609 2.9 84.5 1.0 C26 C:5VG609 3.6 84.5 1.0 CA C:SER256 3.6 71.6 1.0 C20 C:5VG609 3.6 84.5 1.0 N C:SER256 3.6 71.6 1.0 C C:SER256 3.9 71.6 1.0 C C:VAL255 4.0 66.3 1.0 O C:SER256 4.1 71.6 1.0 C27 C:5VG609 4.1 84.5 1.0 O C:SER375 4.1 84.0 1.0 O C:VAL255 4.2 66.3 1.0 OG C:SER375 4.2 84.0 1.0 CG2 C:VAL255 4.2 66.3 1.0 CB C:VAL255 4.3 66.3 1.0 CA C:PHE376 4.5 93.3 1.0 CG2 C:THR257 4.6 75.6 1.0 N C:THR257 4.6 75.6 1.0 SD C:MET475 4.6 80.9 1.0 C C:SER375 4.6 84.0 1.0 CA C:VAL255 4.8 66.3 1.0 O18 C:5VG609 4.8 84.5 1.0 N19 C:5VG609 4.9 84.5 1.0 N C:PHE376 4.9 93.3 1.0

Fluorine binding site 3 out of 3 in the Structure of CD4 Mimetic Bnm-III-170 in Complex with BG505 Sosip.664 Hiv-1 Env Trimer and 17B Fab


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of CD4 Mimetic Bnm-III-170 in Complex with BG505 Sosip.664 Hiv-1 Env Trimer and 17B Fab within 5.0Å range: probe atom residue distance (Å) B Occ E:F609 b:75.3 occ:1.00 F23 E:5VG609 0.0 75.3 1.0 C22 E:5VG609 1.3 75.3 1.0 OG E:SER375 2.3 97.5 1.0 C24 E:5VG609 2.3 75.3 1.0 C21 E:5VG609 2.4 75.3 1.0 CL25 E:5VG609 2.9 75.3 1.0 CB E:SER375 3.3 97.5 1.0 C26 E:5VG609 3.6 75.3 1.0 C20 E:5VG609 3.6 75.3 1.0 OG1 E:THR257 3.6 56.9 1.0 C E:SER375 3.8 97.5 1.0 O E:SER375 3.8 97.5 1.0 C27 E:5VG609 4.0 75.3 1.0 N E:PHE376 4.1 80.3 1.0 CA E:SER375 4.2 97.5 1.0 CA E:PHE376 4.3 80.3 1.0 CA E:SER256 4.5 59.8 1.0 C E:SER256 4.5 59.8 1.0 O E:SER256 4.6 59.8 1.0 O18 E:5VG609 4.8 75.3 1.0 CG2 E:VAL255 4.8 64.6 1.0 N19 E:5VG609 4.9 75.3 1.0 N E:SER375 4.9 97.5 1.0 CB E:THR257 4.9 56.9 1.0 N E:SER256 4.9 59.8 1.0 O E:VAL255 4.9 64.6 1.0 N E:THR257 4.9 56.9 1.0

C.A.Jette, C.O.Barnes, S.M.Kirk, B.Melillo, A.B.Smith Iii, P.J.Bjorkman. Cryo-Em Structures of Hiv-1 Trimer Bound to CD4-Mimetics Bnm-III-170 and M48U1 Adopt A CD4-Bound Open Conformation. Nat Commun V. 12 1950 2021.
ISSN: ESSN 2041-1723
PubMed: 33782388
DOI: 10.1038/S41467-021-21816-X