Fluorine in PDB 8fm5: Hiv-1 GP120 Complex with Dy-III-065

Protein crystallography data

The structure of Hiv-1 GP120 Complex with Dy-III-065, PDB code: 8fm5 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) 48.81 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.52, 121.66, 195.23, 90, 90, 90
R / Rfree (%) 26.7 / 28.8

Other elements in 8fm5:

The structure of Hiv-1 GP120 Complex with Dy-III-065 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 Dy-III-065 (pdb code 8fm5). 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 Dy-III-065, PDB code: 8fm5:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 16 in 8fm5

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Fluorine binding site 1 out of 16 in the Hiv-1 GP120 Complex with Dy-III-065


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 Dy-III-065 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F507

b:47.7
occ:1.00
 F07 D:Y2E507 0.0 47.7 1.0
C06 D:Y2E507 1.4 25.6 1.0
F09 D:Y2E507 2.2 40.9 1.0
F08 D:Y2E507 2.2 83.6 1.0
C05 D:Y2E507 2.3 36.7 1.0
C04 D:Y2E507 3.7 30.6 1.0
O03 D:Y2E507 3.9 34.7 1.0
CG2 D:VAL430 4.7 25.0 1.0
C02 D:Y2E507 4.7 28.4 1.0
O D:HOH617 4.8 39.5 1.0
O01 D:Y2E507 5.0 30.8 1.0

Fluorine binding site 2 out of 16 in 8fm5

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Fluorine binding site 2 out of 16 in the Hiv-1 GP120 Complex with Dy-III-065


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 Dy-III-065 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F507

b:83.6
occ:1.00
 F08 D:Y2E507 0.0 83.6 1.0
C06 D:Y2E507 1.4 25.6 1.0
F07 D:Y2E507 2.2 47.7 1.0
F09 D:Y2E507 2.2 40.9 1.0
O03 D:Y2E507 2.3 34.7 1.0
C05 D:Y2E507 2.4 36.7 1.0
C04 D:Y2E507 2.8 30.6 1.0
C02 D:Y2E507 3.1 28.4 1.0
C12 D:Y2E507 3.2 21.4 1.0
O01 D:Y2E507 3.7 30.8 1.0
N10 D:Y2E507 3.8 23.8 1.0
C11 D:Y2E507 3.9 28.9 1.0
N13 D:Y2E507 3.9 21.5 1.0
CG2 D:VAL430 4.0 25.0 1.0
N D:VAL430 4.3 32.0 1.0
C D:GLU429 4.4 28.3 1.0
CA D:GLU429 4.5 27.1 1.0
O D:TRP427 4.9 23.9 1.0
O D:GLU429 4.9 24.4 1.0
CA D:VAL430 5.0 30.0 1.0
N D:GLU429 5.0 28.9 1.0
C32 D:Y2E507 5.0 29.2 1.0

Fluorine binding site 3 out of 16 in 8fm5

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Fluorine binding site 3 out of 16 in the Hiv-1 GP120 Complex with Dy-III-065


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 Dy-III-065 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F507

b:40.9
occ:1.00
 F09 D:Y2E507 0.0 40.9 1.0
C06 D:Y2E507 1.4 25.6 1.0
F07 D:Y2E507 2.2 47.7 1.0
F08 D:Y2E507 2.2 83.6 1.0
C05 D:Y2E507 2.4 36.7 1.0
O D:GLN428 3.1 30.0 1.0
C04 D:Y2E507 3.1 30.6 1.0
CA D:GLU429 3.2 27.1 1.0
O03 D:Y2E507 3.4 34.7 1.0
O D:HOH617 3.5 39.5 1.0
C D:GLN428 3.6 23.1 1.0
N D:GLU429 3.7 28.9 1.0
C D:GLU429 3.9 28.3 1.0
N D:VAL430 4.1 32.0 1.0
CB D:GLU429 4.4 25.9 1.0
O D:TRP427 4.4 23.9 1.0
C02 D:Y2E507 4.6 28.4 1.0
O D:GLU429 4.7 24.4 1.0
CA D:GLN428 4.9 29.4 1.0
C12 D:Y2E507 4.9 21.4 1.0
CG2 D:VAL430 5.0 25.0 1.0

Fluorine binding site 4 out of 16 in 8fm5

Go back to Fluorine Binding Sites List in 8fm5
Fluorine binding site 4 out of 16 in the Hiv-1 GP120 Complex with Dy-III-065


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 Dy-III-065 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F507

b:33.5
occ:1.00
 F25 D:Y2E507 0.0 33.5 1.0
C24 D:Y2E507 1.4 20.4 1.0
C26 D:Y2E507 2.3 13.4 1.0
C23 D:Y2E507 2.4 22.9 1.0
CL27 D:Y2E507 2.9 23.9 1.0
OG D:SER375 3.1 25.8 1.0
O D:SER375 3.2 24.1 1.0
CA D:SER256 3.3 15.7 1.0
N D:SER256 3.6 19.3 1.0
CG1 D:VAL255 3.6 18.2 1.0
C22 D:Y2E507 3.6 20.6 1.0
C28 D:Y2E507 3.6 22.9 1.0
C D:SER256 3.6 15.9 1.0
C D:SER375 3.7 23.6 1.0
CE D:MET475 3.7 22.0 1.0
N D:THR257 3.9 19.1 1.0
C D:VAL255 3.9 21.8 1.0
O D:VAL255 3.9 28.5 1.0
CG2 D:THR257 4.0 16.1 1.0
C29 D:Y2E507 4.1 16.6 1.0
N D:PHE376 4.1 20.6 1.0
CB D:SER375 4.2 18.5 1.0
CA D:PHE376 4.2 19.0 1.0
O D:SER256 4.3 21.7 1.0
CA D:SER375 4.5 20.7 1.0
CB D:SER256 4.6 18.8 1.0
O30 D:Y2E507 4.7 20.8 1.0
CB D:VAL255 4.7 17.9 1.0
CA D:VAL255 4.8 20.2 1.0
N21 D:Y2E507 4.8 16.0 1.0
SD D:MET475 4.9 23.3 1.0
CA D:THR257 5.0 19.1 1.0
CB D:THR257 5.0 11.5 1.0

Fluorine binding site 5 out of 16 in 8fm5

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Fluorine binding site 5 out of 16 in the Hiv-1 GP120 Complex with Dy-III-065


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 Dy-III-065 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F507

b:47.7
occ:1.00
 F07 A:Y2E507 0.0 47.7 1.0
C06 A:Y2E507 1.4 25.6 1.0
F09 A:Y2E507 2.2 40.9 1.0
F08 A:Y2E507 2.2 83.6 1.0
C05 A:Y2E507 2.3 36.7 1.0
C04 A:Y2E507 3.7 30.6 1.0
O A:HOH643 3.8 56.8 1.0
O03 A:Y2E507 3.9 34.7 1.0
CG2 A:VAL430 4.7 25.0 1.0
C02 A:Y2E507 4.7 28.4 1.0
O A:HOH618 4.8 39.5 1.0
O01 A:Y2E507 5.0 30.8 1.0

Fluorine binding site 6 out of 16 in 8fm5

Go back to Fluorine Binding Sites List in 8fm5
Fluorine binding site 6 out of 16 in the Hiv-1 GP120 Complex with Dy-III-065


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 Dy-III-065 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F507

b:83.6
occ:1.00
 F08 A:Y2E507 0.0 83.6 1.0
C06 A:Y2E507 1.4 25.6 1.0
F07 A:Y2E507 2.2 47.7 1.0
F09 A:Y2E507 2.2 40.9 1.0
O03 A:Y2E507 2.3 34.7 1.0
C05 A:Y2E507 2.4 36.7 1.0
C04 A:Y2E507 2.8 30.6 1.0
C02 A:Y2E507 3.1 28.4 1.0
C12 A:Y2E507 3.2 21.4 1.0
O A:HOH643 3.3 56.8 1.0
O01 A:Y2E507 3.7 30.8 1.0
N10 A:Y2E507 3.8 23.8 1.0
C11 A:Y2E507 3.9 28.9 1.0
N13 A:Y2E507 3.9 21.5 1.0
CG2 A:VAL430 4.0 25.0 1.0
N A:VAL430 4.3 32.0 1.0
C A:GLU429 4.4 28.3 1.0
CA A:GLU429 4.5 27.1 1.0
O A:TRP427 4.9 23.9 1.0
O A:GLU429 4.9 24.4 1.0
CA A:VAL430 5.0 30.0 1.0
N A:GLU429 5.0 28.9 1.0
C32 A:Y2E507 5.0 29.2 1.0

Fluorine binding site 7 out of 16 in 8fm5

Go back to Fluorine Binding Sites List in 8fm5
Fluorine binding site 7 out of 16 in the Hiv-1 GP120 Complex with Dy-III-065


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 Dy-III-065 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F507

b:40.9
occ:1.00
 F09 A:Y2E507 0.0 40.9 1.0
C06 A:Y2E507 1.4 25.6 1.0
F07 A:Y2E507 2.2 47.7 1.0
F08 A:Y2E507 2.2 83.6 1.0
C05 A:Y2E507 2.4 36.7 1.0
O A:GLN428 3.1 30.0 1.0
C04 A:Y2E507 3.1 30.6 1.0
CA A:GLU429 3.2 27.1 1.0
O03 A:Y2E507 3.4 34.7 1.0
O A:HOH618 3.5 39.5 1.0
C A:GLN428 3.6 23.1 1.0
N A:GLU429 3.7 28.9 1.0
C A:GLU429 3.9 28.3 1.0
N A:VAL430 4.1 32.0 1.0
CB A:GLU429 4.4 25.9 1.0
O A:TRP427 4.4 23.9 1.0
C02 A:Y2E507 4.6 28.4 1.0
O A:GLU429 4.7 24.4 1.0
CA A:GLN428 4.9 29.4 1.0
C12 A:Y2E507 4.9 21.4 1.0
CG2 A:VAL430 5.0 25.0 1.0

Fluorine binding site 8 out of 16 in 8fm5

Go back to Fluorine Binding Sites List in 8fm5
Fluorine binding site 8 out of 16 in the Hiv-1 GP120 Complex with Dy-III-065


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 Dy-III-065 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F507

b:33.5
occ:1.00
 F25 A:Y2E507 0.0 33.5 1.0
C24 A:Y2E507 1.4 20.4 1.0
C26 A:Y2E507 2.3 13.4 1.0
C23 A:Y2E507 2.4 22.9 1.0
CL27 A:Y2E507 2.9 23.9 1.0
OG A:SER375 3.1 25.8 1.0
O A:SER375 3.2 24.1 1.0
CA A:SER256 3.3 15.7 1.0
N A:SER256 3.6 19.3 1.0
CG1 A:VAL255 3.6 18.2 1.0
C22 A:Y2E507 3.6 20.6 1.0
C28 A:Y2E507 3.6 22.9 1.0
C A:SER256 3.6 15.9 1.0
C A:SER375 3.7 23.6 1.0
CE A:MET475 3.7 22.0 1.0
N A:THR257 3.9 19.1 1.0
C A:VAL255 3.9 21.8 1.0
O A:VAL255 3.9 28.5 1.0
CG2 A:THR257 4.0 16.1 1.0
C29 A:Y2E507 4.1 16.6 1.0
N A:PHE376 4.1 20.6 1.0
CB A:SER375 4.2 18.5 1.0
CA A:PHE376 4.2 19.0 1.0
O A:SER256 4.3 21.7 1.0
CA A:SER375 4.5 20.7 1.0
CB A:SER256 4.6 18.8 1.0
O30 A:Y2E507 4.7 20.8 1.0
CB A:VAL255 4.7 17.9 1.0
CA A:VAL255 4.8 20.2 1.0
N21 A:Y2E507 4.8 16.0 1.0
SD A:MET475 4.9 23.3 1.0
CA A:THR257 5.0 19.1 1.0
CB A:THR257 5.0 11.5 1.0

Fluorine binding site 9 out of 16 in 8fm5

Go back to Fluorine Binding Sites List in 8fm5
Fluorine binding site 9 out of 16 in the Hiv-1 GP120 Complex with Dy-III-065


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 Dy-III-065 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F507

b:47.7
occ:1.00
 F07 C:Y2E507 0.0 47.7 1.0
C06 C:Y2E507 1.4 25.6 1.0
F09 C:Y2E507 2.2 40.9 1.0
F08 C:Y2E507 2.2 83.6 1.0
C05 C:Y2E507 2.3 36.7 1.0
C04 C:Y2E507 3.7 30.6 1.0
O03 C:Y2E507 3.9 34.7 1.0
O C:HOH657 4.4 35.9 1.0
CG2 C:VAL430 4.7 25.0 1.0
C02 C:Y2E507 4.7 28.4 1.0
O C:HOH613 4.8 39.5 1.0
O C:HOH626 4.8 29.2 1.0
O01 C:Y2E507 5.0 30.8 1.0

Fluorine binding site 10 out of 16 in 8fm5

Go back to Fluorine Binding Sites List in 8fm5
Fluorine binding site 10 out of 16 in the Hiv-1 GP120 Complex with Dy-III-065


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 Dy-III-065 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F507

b:83.6
occ:1.00
 F08 C:Y2E507 0.0 83.6 1.0
C06 C:Y2E507 1.4 25.6 1.0
F07 C:Y2E507 2.2 47.7 1.0
F09 C:Y2E507 2.2 40.9 1.0
O03 C:Y2E507 2.3 34.7 1.0
C05 C:Y2E507 2.4 36.7 1.0
C04 C:Y2E507 2.8 30.6 1.0
C02 C:Y2E507 3.1 28.4 1.0
C12 C:Y2E507 3.2 21.4 1.0
O C:HOH657 3.6 35.9 1.0
O01 C:Y2E507 3.7 30.8 1.0
N10 C:Y2E507 3.8 23.8 1.0
C11 C:Y2E507 3.9 28.9 1.0
N13 C:Y2E507 3.9 21.5 1.0
CG2 C:VAL430 4.0 25.0 1.0
N C:VAL430 4.3 32.0 1.0
C C:GLU429 4.4 28.3 1.0
CA C:GLU429 4.5 27.1 1.0
O C:TRP427 4.9 23.9 1.0
O C:GLU429 4.9 24.4 1.0
CA C:VAL430 5.0 30.0 1.0
N C:GLU429 5.0 28.9 1.0
C32 C:Y2E507 5.0 29.2 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 19:14:13 2024

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