Atomistry » Fluorine » PDB 5esf-5fct » 5f4p
Atomistry »
  Fluorine »
    PDB 5esf-5fct »
      5f4p »

Fluorine in PDB 5f4p: Hiv-1 GP120 Complex with Bnm-III-170

Protein crystallography data

The structure of Hiv-1 GP120 Complex with Bnm-III-170, PDB code: 5f4p was solved by S.Liang, W.A.Hendrickson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.24 / 2.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 67.378, 127.517, 192.945, 90.00, 90.00, 90.00
R / Rfree (%) 27.4 / 31.1

Other elements in 5f4p:

The structure of Hiv-1 GP120 Complex with Bnm-III-170 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Hiv-1 GP120 Complex with Bnm-III-170 (pdb code 5f4p). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Hiv-1 GP120 Complex with Bnm-III-170, PDB code: 5f4p:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5f4p

Go back to Fluorine Binding Sites List in 5f4p
Fluorine binding site 1 out of 2 in the Hiv-1 GP120 Complex with Bnm-III-170


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 Bnm-III-170 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F507

b:76.2
occ:1.00
F23 D:5VG507 0.0 76.2 1.0
C22 D:5VG507 1.4 74.5 1.0
C21 D:5VG507 2.4 72.9 1.0
C24 D:5VG507 2.4 72.4 1.0
OG D:SER375 2.5 69.9 1.0
O D:SER375 2.6 59.3 1.0
CL25 D:5VG507 3.0 87.8 1.0
C D:SER375 3.0 59.4 1.0
CB D:SER375 3.2 63.9 1.0
N D:PHE376 3.6 58.5 1.0
C20 D:5VG507 3.7 69.0 1.0
C26 D:5VG507 3.7 76.2 1.0
CA D:SER375 3.7 66.8 1.0
CA D:SER256 3.7 65.8 1.0
CG2 D:THR257 3.8 66.6 1.0
N D:THR257 3.8 64.2 1.0
C D:SER256 3.9 65.5 1.0
CA D:PHE376 4.0 60.0 1.0
O D:VAL255 4.2 65.1 1.0
CE D:MET475 4.2 68.8 1.0
C27 D:5VG507 4.2 70.3 1.0
N D:SER256 4.2 67.1 1.0
OG1 D:THR257 4.3 59.2 1.0
C D:VAL255 4.4 64.3 1.0
N D:SER375 4.5 59.8 1.0
CB D:THR257 4.5 65.5 1.0
CG1 D:VAL255 4.5 67.7 1.0
O D:SER256 4.7 68.3 1.0
CA D:THR257 4.7 63.6 1.0
C D:PHE376 4.9 58.4 1.0
N19 D:5VG507 4.9 71.4 1.0
O18 D:5VG507 4.9 74.0 1.0
O D:GLU370 4.9 65.1 1.0
CB D:SER256 4.9 63.3 1.0

Fluorine binding site 2 out of 2 in 5f4p

Go back to Fluorine Binding Sites List in 5f4p
Fluorine binding site 2 out of 2 in the Hiv-1 GP120 Complex with Bnm-III-170


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 Bnm-III-170 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:75.2
occ:1.00
F23 A:5VG501 0.0 75.2 1.0
C22 A:5VG501 1.4 64.8 1.0
C21 A:5VG501 2.4 69.3 1.0
C24 A:5VG501 2.4 71.8 1.0
O A:SER375 2.5 38.7 1.0
OG A:SER375 2.7 56.3 1.0
C A:SER375 3.0 42.6 1.0
CL25 A:5VG501 3.0 92.8 1.0
CB A:SER375 3.3 53.3 1.0
N A:PHE376 3.6 43.8 1.0
C20 A:5VG501 3.7 75.6 1.0
C26 A:5VG501 3.7 66.9 1.0
CA A:SER256 3.7 51.3 1.0
CA A:SER375 3.7 46.0 1.0
CG2 A:THR257 3.8 57.9 1.0
N A:THR257 3.9 55.6 1.0
CA A:PHE376 3.9 50.6 1.0
C A:SER256 3.9 56.0 1.0
O A:VAL255 4.1 52.1 1.0
CE A:MET475 4.2 43.8 1.0
C27 A:5VG501 4.2 67.7 1.0
N A:SER256 4.3 45.8 1.0
OG1 A:THR257 4.3 58.2 1.0
C A:VAL255 4.4 47.6 1.0
N A:SER375 4.5 46.4 1.0
CB A:THR257 4.5 55.6 1.0
CG1 A:VAL255 4.6 46.0 1.0
O A:SER256 4.7 59.8 1.0
C A:PHE376 4.8 48.4 1.0
CA A:THR257 4.8 53.7 1.0
CB A:SER256 4.9 52.3 1.0
O18 A:5VG501 4.9 71.8 1.0
N19 A:5VG501 4.9 81.6 1.0
O A:GLU370 4.9 49.8 1.0

Reference:

B.Melillo, S.Liang, J.Park, A.Schon, J.R.Courter, J.M.Lalonde, D.J.Wendler, A.M.Princiotto, M.S.Seaman, E.Freire, J.Sodroski, N.Madani, W.A.Hendrickson, A.B.Smith. Small-Molecule CD4-Mimics: Structure-Based Optimization of Hiv-1 Entry Inhibition. Acs Med.Chem.Lett. V. 7 330 2016.
ISSN: ISSN 1948-5875
PubMed: 26985324
DOI: 10.1021/ACSMEDCHEMLETT.5B00471
Page generated: Thu Aug 1 09:17:20 2024

Last articles

Cl in 2REE
Cl in 2RDC
Cl in 2RD7
Cl in 2RCD
Cl in 2RCF
Cl in 2RC8
Cl in 2RBS
Cl in 2RB4
Cl in 2RBC
Cl in 2RAG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy