Fluorine in PDB 8fm4: Hiv-1 GP120 Complex with Cjf-IV-047

Protein crystallography data

The structure of Hiv-1 GP120 Complex with Cjf-IV-047, PDB code: 8fm4 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) 48.65 / 2.18
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.91, 121.26, 194.6, 90, 90, 90
R / Rfree (%) 23.7 / 26.1

Other elements in 8fm4:

The structure of Hiv-1 GP120 Complex with Cjf-IV-047 also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Fluorine atom in the Hiv-1 GP120 Complex with Cjf-IV-047 (pdb code 8fm4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 16 binding sites of Fluorine where determined in the Hiv-1 GP120 Complex with Cjf-IV-047, PDB code: 8fm4:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 16 in 8fm4

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Fluorine binding site 1 out of 16 in the Hiv-1 GP120 Complex with Cjf-IV-047


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-IV-047 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F507

b:31.4
occ:1.00
 F25 B:Y2K507 0.0 31.4 1.0
C24 B:Y2K507 1.3 26.0 1.0
C22 B:Y2K507 2.3 28.0 1.0
C26 B:Y2K507 2.3 29.0 1.0
CL23 B:Y2K507 2.8 25.3 1.0
OG B:SER375 3.2 25.4 1.0
O B:SER375 3.3 29.3 1.0
CA B:SER256 3.5 28.6 1.0
C19 B:Y2K507 3.6 28.6 1.0
C21 B:Y2K507 3.6 29.0 1.0
CG1 B:VAL255 3.6 27.4 1.0
N B:SER256 3.7 28.1 1.0
C B:SER375 3.8 29.7 1.0
C B:SER256 3.8 28.5 1.0
N B:THR257 4.0 24.4 1.0
CE B:MET475 4.0 24.7 1.0
C B:VAL255 4.0 27.6 1.0
C20 B:Y2K507 4.0 25.6 1.0
O B:VAL255 4.1 31.4 1.0
CG2 B:THR257 4.1 24.8 1.0
CB B:SER375 4.1 25.2 1.0
N B:PHE376 4.2 30.5 1.0
CA B:PHE376 4.3 30.6 1.0
O B:SER256 4.4 25.8 1.0
CA B:SER375 4.6 27.4 1.0
O27 B:Y2K507 4.7 31.0 1.0
CB B:SER256 4.8 28.7 1.0
N18 B:Y2K507 4.8 29.2 1.0
CB B:VAL255 4.8 27.4 1.0
CB B:THR257 5.0 25.2 1.0
CA B:VAL255 5.0 27.3 1.0

Fluorine binding site 2 out of 16 in 8fm4

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Fluorine binding site 2 out of 16 in the Hiv-1 GP120 Complex with Cjf-IV-047


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-IV-047 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F507

b:66.8
occ:1.00
 F37 B:Y2K507 0.0 66.8 1.0
C36 B:Y2K507 1.3 51.2 1.0
F38 B:Y2K507 2.2 53.3 1.0
F39 B:Y2K507 2.3 59.8 1.0
C35 B:Y2K507 2.3 43.9 1.0
O34 B:Y2K507 2.7 41.4 1.0
C02 B:Y2K507 3.1 36.8 1.0
O01 B:Y2K507 3.2 39.4 1.0
O B:HOH642 3.4 36.2 1.0
N03 B:Y2K507 4.2 34.4 1.0
C29 B:Y2K507 4.2 34.7 1.0
C13 B:Y2K507 4.7 33.6 1.0
O B:HOH622 4.9 45.0 1.0

Fluorine binding site 3 out of 16 in 8fm4

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Fluorine binding site 3 out of 16 in the Hiv-1 GP120 Complex with Cjf-IV-047


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-IV-047 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F507

b:53.3
occ:1.00
 F38 B:Y2K507 0.0 53.3 1.0
C36 B:Y2K507 1.4 51.2 1.0
F37 B:Y2K507 2.2 66.8 1.0
F39 B:Y2K507 2.2 59.8 1.0
C35 B:Y2K507 2.5 43.9 1.0
O34 B:Y2K507 2.7 41.4 1.0
CA B:GLU429 3.3 35.9 1.0
N B:GLU429 3.6 37.4 1.0
O B:GLN428 3.6 31.4 1.0
C B:GLN428 3.7 32.3 1.0
O B:HOH622 3.7 45.0 1.0
O B:TRP427 3.8 31.6 1.0
C02 B:Y2K507 3.9 36.8 1.0
C B:GLU429 3.9 36.1 1.0
C29 B:Y2K507 4.1 34.7 1.0
N B:VAL430 4.2 34.5 1.0
O01 B:Y2K507 4.4 39.4 1.0
O B:GLU429 4.5 37.7 1.0
N30 B:Y2K507 4.5 33.7 1.0
CB B:GLU429 4.6 31.7 1.0
C B:TRP427 4.7 30.2 1.0
C13 B:Y2K507 4.7 33.6 1.0
N03 B:Y2K507 4.7 34.4 1.0
CA B:GLN428 4.8 30.2 1.0
CG2 B:VAL430 5.0 33.8 1.0

Fluorine binding site 4 out of 16 in 8fm4

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Fluorine binding site 4 out of 16 in the Hiv-1 GP120 Complex with Cjf-IV-047


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-IV-047 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F507

b:59.8
occ:1.00
 F39 B:Y2K507 0.0 59.8 1.0
C36 B:Y2K507 1.4 51.2 1.0
F38 B:Y2K507 2.2 53.3 1.0
F37 B:Y2K507 2.3 66.8 1.0
C35 B:Y2K507 2.4 43.9 1.0
O B:HOH622 2.8 45.0 1.0
O34 B:Y2K507 3.6 41.4 1.0
NH1 B:ARG476 4.2 49.4 1.0
O B:GLN428 4.3 31.4 1.0
O01 B:Y2K507 4.3 39.4 1.0
C02 B:Y2K507 4.4 36.8 1.0
O B:TRP427 4.9 31.6 1.0
C B:GLN428 4.9 32.3 1.0
NE2 B:HIS105 4.9 30.2 1.0

Fluorine binding site 5 out of 16 in 8fm4

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Fluorine binding site 5 out of 16 in the Hiv-1 GP120 Complex with Cjf-IV-047


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Hiv-1 GP120 Complex with Cjf-IV-047 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F507

b:33.5
occ:1.00
 F25 D:Y2K507 0.0 33.5 1.0
C24 D:Y2K507 1.3 29.5 1.0
C22 D:Y2K507 2.3 27.1 1.0
C26 D:Y2K507 2.3 32.0 1.0
CL23 D:Y2K507 2.8 25.1 1.0
OG D:SER375 3.2 33.4 1.0
O D:SER375 3.3 30.5 1.0
CA D:SER256 3.5 28.3 1.0
C19 D:Y2K507 3.6 31.9 1.0
C21 D:Y2K507 3.6 27.8 1.0
CG1 D:VAL255 3.6 26.4 1.0
N D:SER256 3.7 25.8 1.0
C D:SER375 3.8 32.6 1.0
C D:SER256 3.8 31.7 1.0
N D:THR257 4.0 28.9 1.0
CE D:MET475 4.0 30.1 1.0
C D:VAL255 4.0 31.4 1.0
C20 D:Y2K507 4.0 32.3 1.0
O D:VAL255 4.1 29.1 1.0
CG2 D:THR257 4.1 31.9 1.0
CB D:SER375 4.1 29.9 1.0
N D:PHE376 4.2 29.7 1.0
CA D:PHE376 4.3 31.1 1.0
O D:SER256 4.4 29.1 1.0
CA D:SER375 4.6 33.4 1.0
O27 D:Y2K507 4.7 33.1 1.0
CB D:SER256 4.8 28.0 1.0
CB D:VAL255 4.8 27.5 1.0
N18 D:Y2K507 4.8 28.1 1.0
CB D:THR257 5.0 30.5 1.0
CA D:VAL255 5.0 27.4 1.0

Fluorine binding site 6 out of 16 in 8fm4

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Fluorine binding site 6 out of 16 in the Hiv-1 GP120 Complex with Cjf-IV-047


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Hiv-1 GP120 Complex with Cjf-IV-047 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F507

b:75.3
occ:1.00
 F37 D:Y2K507 0.0 75.3 1.0
C36 D:Y2K507 1.3 58.4 1.0
F38 D:Y2K507 2.2 54.5 1.0
F39 D:Y2K507 2.3 72.8 1.0
C35 D:Y2K507 2.3 47.1 1.0
O34 D:Y2K507 2.7 45.3 1.0
C02 D:Y2K507 3.1 39.7 1.0
O01 D:Y2K507 3.2 36.9 1.0
N03 D:Y2K507 4.2 35.1 1.0
C29 D:Y2K507 4.2 33.5 1.0
C13 D:Y2K507 4.7 34.8 1.0
O D:HOH633 4.9 44.5 1.0

Fluorine binding site 7 out of 16 in 8fm4

Go back to Fluorine Binding Sites List in 8fm4
Fluorine binding site 7 out of 16 in the Hiv-1 GP120 Complex with Cjf-IV-047


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Hiv-1 GP120 Complex with Cjf-IV-047 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F507

b:54.5
occ:1.00
 F38 D:Y2K507 0.0 54.5 1.0
C36 D:Y2K507 1.4 58.4 1.0
F37 D:Y2K507 2.2 75.3 1.0
F39 D:Y2K507 2.2 72.8 1.0
C35 D:Y2K507 2.5 47.1 1.0
O34 D:Y2K507 2.7 45.3 1.0
CA D:GLU429 3.3 39.8 1.0
N D:GLU429 3.6 40.9 1.0
O D:GLN428 3.6 39.1 1.0
C D:GLN428 3.7 36.4 1.0
O D:HOH633 3.7 44.5 1.0
O D:TRP427 3.8 29.7 1.0
C02 D:Y2K507 3.9 39.7 1.0
C D:GLU429 3.9 37.5 1.0
C29 D:Y2K507 4.1 33.5 1.0
N D:VAL430 4.2 40.1 1.0
O01 D:Y2K507 4.4 36.9 1.0
O D:GLU429 4.5 40.4 1.0
N30 D:Y2K507 4.5 36.9 1.0
CB D:GLU429 4.6 34.5 1.0
C D:TRP427 4.7 32.5 1.0
C13 D:Y2K507 4.7 34.8 1.0
N03 D:Y2K507 4.7 35.1 1.0
CA D:GLN428 4.8 34.6 1.0
CG2 D:VAL430 5.0 35.4 1.0

Fluorine binding site 8 out of 16 in 8fm4

Go back to Fluorine Binding Sites List in 8fm4
Fluorine binding site 8 out of 16 in the Hiv-1 GP120 Complex with Cjf-IV-047


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Hiv-1 GP120 Complex with Cjf-IV-047 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F507

b:72.8
occ:1.00
 F39 D:Y2K507 0.0 72.8 1.0
C36 D:Y2K507 1.4 58.4 1.0
F38 D:Y2K507 2.2 54.5 1.0
F37 D:Y2K507 2.3 75.3 1.0
C35 D:Y2K507 2.4 47.1 1.0
O D:HOH633 2.8 44.5 1.0
O34 D:Y2K507 3.6 45.3 1.0
NH1 D:ARG476 4.1 44.5 1.0
O D:GLN428 4.3 39.1 1.0
O01 D:Y2K507 4.3 36.9 1.0
C02 D:Y2K507 4.4 39.7 1.0
O D:TRP427 4.9 29.7 1.0
NE2 D:HIS105 4.9 33.0 1.0
C D:GLN428 4.9 36.4 1.0

Fluorine binding site 9 out of 16 in 8fm4

Go back to Fluorine Binding Sites List in 8fm4
Fluorine binding site 9 out of 16 in the Hiv-1 GP120 Complex with Cjf-IV-047


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Hiv-1 GP120 Complex with Cjf-IV-047 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F507

b:33.8
occ:1.00
 F25 A:Y2K507 0.0 33.8 1.0
C24 A:Y2K507 1.3 29.0 1.0
C22 A:Y2K507 2.3 29.6 1.0
C26 A:Y2K507 2.3 27.3 1.0
CL23 A:Y2K507 2.8 26.6 1.0
OG A:SER375 3.2 28.8 1.0
O A:SER375 3.3 27.6 1.0
CA A:SER256 3.5 26.5 1.0
C19 A:Y2K507 3.6 26.8 1.0
C21 A:Y2K507 3.6 29.4 1.0
CG1 A:VAL255 3.6 25.6 1.0
N A:SER256 3.7 27.9 1.0
C A:SER375 3.8 28.2 1.0
C A:SER256 3.8 24.3 1.0
N A:THR257 4.0 23.6 1.0
CE A:MET475 4.0 26.6 1.0
C A:VAL255 4.0 26.2 1.0
C20 A:Y2K507 4.0 26.5 1.0
O A:VAL255 4.1 30.1 1.0
CG2 A:THR257 4.1 24.9 1.0
CB A:SER375 4.1 26.8 1.0
N A:PHE376 4.2 27.6 1.0
CA A:PHE376 4.3 27.3 1.0
O A:SER256 4.5 28.2 1.0
CA A:SER375 4.6 27.2 1.0
O27 A:Y2K507 4.7 27.5 1.0
CB A:SER256 4.8 27.6 1.0
CB A:VAL255 4.8 27.5 1.0
N18 A:Y2K507 4.8 27.1 1.0
CB A:THR257 5.0 26.2 1.0
CA A:VAL255 5.0 26.2 1.0

Fluorine binding site 10 out of 16 in 8fm4

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Fluorine binding site 10 out of 16 in the Hiv-1 GP120 Complex with Cjf-IV-047


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Hiv-1 GP120 Complex with Cjf-IV-047 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F507

b:69.1
occ:1.00
 F37 A:Y2K507 0.0 69.1 1.0
C36 A:Y2K507 1.3 55.4 1.0
F38 A:Y2K507 2.2 55.8 1.0
F39 A:Y2K507 2.3 76.1 1.0
C35 A:Y2K507 2.3 41.9 1.0
O34 A:Y2K507 2.7 36.2 1.0
O A:HOH641 2.9 44.9 1.0
C02 A:Y2K507 3.1 38.8 1.0
O01 A:Y2K507 3.2 40.8 1.0
N03 A:Y2K507 4.2 33.2 1.0
C29 A:Y2K507 4.2 34.2 1.0
C13 A:Y2K507 4.7 32.0 1.0
O A:HOH629 4.9 45.0 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: Fri Aug 2 19:13:19 2024

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