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

Go back to Fluorine Binding Sites List in 8fm4
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

Go back to Fluorine Binding Sites List in 8fm4
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

Go back to Fluorine Binding Sites List in 8fm4
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

Go back to Fluorine Binding Sites List in 8fm4
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

Go back to Fluorine Binding Sites List in 8fm4
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

Go back to Fluorine Binding Sites List in 8fm4
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

Go back to Fluorine Binding Sites List in 8fm4
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy