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Fluorine in PDB 8fm7: Hiv-1 GP120 Complex with Cjf-III-192

Protein crystallography data

The structure of Hiv-1 GP120 Complex with Cjf-III-192, PDB code: 8fm7 was solved by Z.Gong, W.A.Hendrickson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.78 / 2.34
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.36, 121.1, 195.11, 90, 90, 90
R / Rfree (%) 23.7 / 27.1

Other elements in 8fm7:

The structure of Hiv-1 GP120 Complex with Cjf-III-192 also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Hiv-1 GP120 Complex with Cjf-III-192 (pdb code 8fm7). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Hiv-1 GP120 Complex with Cjf-III-192, PDB code: 8fm7:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 8fm7

Go back to Fluorine Binding Sites List in 8fm7
Fluorine binding site 1 out of 4 in the Hiv-1 GP120 Complex with Cjf-III-192


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Hiv-1 GP120 Complex with Cjf-III-192 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F507

b:29.6
occ:1.00
F26 A:Y2O507 0.0 29.6 1.0
C25 A:Y2O507 1.3 25.4 1.0
C24 A:Y2O507 2.3 23.0 1.0
C27 A:Y2O507 2.3 23.3 1.0
CL28 A:Y2O507 2.9 43.8 1.0
O A:SER375 3.2 23.8 1.0
OG A:SER375 3.3 23.6 1.0
CA A:SER256 3.5 20.8 1.0
C23 A:Y2O507 3.5 22.7 1.0
C29 A:Y2O507 3.6 24.9 1.0
CG1 A:VAL255 3.6 23.6 1.0
C A:SER375 3.7 22.8 1.0
N A:SER256 3.8 22.8 1.0
C A:SER256 3.8 19.7 1.0
CE A:MET475 3.9 20.2 1.0
CG2 A:THR257 4.0 19.0 1.0
C A:VAL255 4.0 22.2 1.0
CB A:SER375 4.0 23.1 1.0
N A:THR257 4.0 19.5 1.0
C30 A:Y2O507 4.0 24.1 1.0
O A:VAL255 4.1 27.2 1.0
N A:PHE376 4.1 25.7 1.0
CA A:PHE376 4.2 26.2 1.0
O A:SER256 4.4 24.0 1.0
CA A:SER375 4.5 19.6 1.0
O31 A:Y2O507 4.6 21.2 1.0
CB A:SER256 4.8 19.8 1.0
N22 A:Y2O507 4.8 25.1 1.0
CB A:VAL255 4.9 21.1 1.0
CB A:THR257 4.9 19.4 1.0
OG1 A:THR257 5.0 24.8 1.0

Fluorine binding site 2 out of 4 in 8fm7

Go back to Fluorine Binding Sites List in 8fm7
Fluorine binding site 2 out of 4 in the Hiv-1 GP120 Complex with Cjf-III-192


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Hiv-1 GP120 Complex with Cjf-III-192 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F507

b:28.9
occ:1.00
F26 B:Y2O507 0.0 28.9 1.0
C25 B:Y2O507 1.3 25.1 1.0
C24 B:Y2O507 2.3 24.8 1.0
C27 B:Y2O507 2.3 22.1 1.0
CL28 B:Y2O507 2.9 42.5 1.0
O B:SER375 3.2 25.9 1.0
OG B:SER375 3.3 20.6 1.0
CA B:SER256 3.5 24.3 1.0
C23 B:Y2O507 3.5 22.9 1.0
C29 B:Y2O507 3.6 22.2 1.0
CG1 B:VAL255 3.6 23.0 1.0
C B:SER375 3.7 26.2 1.0
N B:SER256 3.8 24.9 1.0
C B:SER256 3.8 23.1 1.0
CE B:MET475 3.9 20.7 1.0
CG2 B:THR257 4.0 21.3 1.0
C B:VAL255 4.0 24.9 1.0
N B:THR257 4.0 21.6 1.0
CB B:SER375 4.0 25.7 1.0
C30 B:Y2O507 4.0 20.3 1.0
O B:VAL255 4.1 24.1 1.0
N B:PHE376 4.1 24.7 1.0
CA B:PHE376 4.2 26.1 1.0
O B:SER256 4.4 20.9 1.0
CA B:SER375 4.5 26.8 1.0
O31 B:Y2O507 4.6 23.5 1.0
CB B:SER256 4.8 25.0 1.0
N22 B:Y2O507 4.8 25.8 1.0
CB B:VAL255 4.9 24.4 1.0
CB B:THR257 4.9 21.1 1.0
OG1 B:THR257 5.0 24.3 1.0

Fluorine binding site 3 out of 4 in 8fm7

Go back to Fluorine Binding Sites List in 8fm7
Fluorine binding site 3 out of 4 in the Hiv-1 GP120 Complex with Cjf-III-192


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Hiv-1 GP120 Complex with Cjf-III-192 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F507

b:25.6
occ:1.00
F26 C:Y2O507 0.0 25.6 1.0
C25 C:Y2O507 1.3 18.0 1.0
C24 C:Y2O507 2.3 17.1 1.0
C27 C:Y2O507 2.3 19.7 1.0
CL28 C:Y2O507 2.9 32.8 1.0
O C:SER375 3.2 21.0 1.0
OG C:SER375 3.3 24.0 1.0
CA C:SER256 3.5 20.8 1.0
C23 C:Y2O507 3.5 18.3 1.0
C29 C:Y2O507 3.6 19.2 1.0
CG1 C:VAL255 3.6 18.6 1.0
C C:SER375 3.7 20.7 1.0
N C:SER256 3.8 21.2 1.0
C C:SER256 3.8 18.9 1.0
CE C:MET475 3.9 18.7 1.0
CG2 C:THR257 4.0 14.5 1.0
C C:VAL255 4.0 22.6 1.0
CB C:SER375 4.0 18.2 1.0
N C:THR257 4.0 19.3 1.0
C30 C:Y2O507 4.0 20.5 1.0
O C:VAL255 4.1 21.7 1.0
N C:PHE376 4.1 21.0 1.0
CA C:PHE376 4.2 22.4 1.0
O C:SER256 4.4 19.0 1.0
CA C:SER375 4.5 19.7 1.0
O31 C:Y2O507 4.6 16.9 1.0
CB C:SER256 4.8 20.3 1.0
N22 C:Y2O507 4.8 17.8 1.0
CB C:VAL255 4.9 16.9 1.0
CB C:THR257 4.9 17.1 1.0
OG1 C:THR257 5.0 17.9 1.0

Fluorine binding site 4 out of 4 in 8fm7

Go back to Fluorine Binding Sites List in 8fm7
Fluorine binding site 4 out of 4 in the Hiv-1 GP120 Complex with Cjf-III-192


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Hiv-1 GP120 Complex with Cjf-III-192 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F507

b:25.9
occ:1.00
F26 D:Y2O507 0.0 25.9 1.0
C25 D:Y2O507 1.3 22.5 1.0
C24 D:Y2O507 2.3 24.1 1.0
C27 D:Y2O507 2.3 20.9 1.0
CL28 D:Y2O507 2.9 41.4 1.0
O D:SER375 3.2 24.1 1.0
OG D:SER375 3.3 28.9 1.0
CA D:SER256 3.5 21.9 1.0
C23 D:Y2O507 3.5 22.8 1.0
C29 D:Y2O507 3.6 20.0 1.0
CG1 D:VAL255 3.6 21.7 1.0
C D:SER375 3.7 25.8 1.0
N D:SER256 3.8 21.3 1.0
C D:SER256 3.8 25.3 1.0
CE D:MET475 3.9 21.6 1.0
CG2 D:THR257 4.0 25.2 1.0
C D:VAL255 4.0 24.4 1.0
N D:THR257 4.0 23.8 1.0
CB D:SER375 4.0 22.4 1.0
C30 D:Y2O507 4.0 23.8 1.0
O D:VAL255 4.1 26.6 1.0
N D:PHE376 4.1 26.4 1.0
CA D:PHE376 4.2 25.2 1.0
O D:SER256 4.4 22.7 1.0
CA D:SER375 4.5 26.4 1.0
O31 D:Y2O507 4.6 24.8 1.0
CB D:SER256 4.8 22.7 1.0
N22 D:Y2O507 4.8 20.6 1.0
CB D:VAL255 4.9 20.0 1.0
CB D:THR257 4.9 24.3 1.0
OG1 D:THR257 5.0 20.1 1.0

Reference:

C.J.Fritschi, S.Anang, Z.Gong, M.Mohammadi, J.Richard, C.Bourassa, K.T.Severino, H.Richter, D.Yang, H.C.Chen, T.J.Chiu, M.S.Seaman, N.Madani, C.Abrams, A.Finzi, W.A.Hendrickson, J.G.Sodroski, A.B.Smith Iii. Indoline CD4-Mimetic Compounds Mediate Potent and Broad Hiv-1 Inhibition and Sensitization to Antibody-Dependent Cellular Cytotoxicity. Proc.Natl.Acad.Sci.Usa V. 120 73120 2023.
ISSN: ESSN 1091-6490
PubMed: 36961924
DOI: 10.1073/PNAS.2222073120
Page generated: Wed Jul 16 04:38:11 2025

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