Fluorine in PDB 6wph: Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)-Ftc

Enzymatic activity of Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)-Ftc

All present enzymatic activity of Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)-Ftc:
2.7.7.49; 2.7.7.7; 3.1.26.13;

Protein crystallography data

The structure of Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)-Ftc, PDB code: 6wph was solved by N.Bertoletti, K.S.Anderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.52 / 2.72
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 165.980, 168.054, 101.916, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 25.7

Other elements in 6wph:

The structure of Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)-Ftc also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)-Ftc (pdb code 6wph). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)-Ftc, PDB code: 6wph:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 6wph

Go back to Fluorine Binding Sites List in 6wph
Fluorine binding site 1 out of 2 in the Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)-Ftc


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)-Ftc within 5.0Å range:
probe atom residue distance (Å) B Occ
P:F901

b:85.0
occ:0.60
F5 P:43X901 0.0 85.0 0.6
C2' P:43X901 0.9 84.6 0.4
C1' P:43X901 1.2 86.3 0.4
C5 P:43X901 1.3 84.1 0.6
S3' P:43X901 1.4 84.5 0.4
O4' P:43X901 1.7 84.8 0.4
C4' P:43X901 1.8 84.4 0.4
N1 P:43X901 2.3 80.1 0.4
C6 P:43X901 2.3 85.0 0.6
C4 P:43X901 2.4 84.1 0.6
N4 P:43X901 2.8 83.1 0.6
C6 P:43X901 3.1 86.1 0.4
C5' P:43X901 3.1 83.3 0.4
C2 P:43X901 3.3 86.2 0.4
O2 P:43X901 3.5 82.4 0.4
O5' P:43X901 3.6 83.8 0.4
N1 P:43X901 3.6 86.0 0.6
N3 P:43X901 3.6 84.2 0.6
C2' P:DG822 4.1 55.7 1.0
C2 P:43X901 4.1 81.4 0.6
N3 P:DG822 4.1 47.0 1.0
OE1 A:GLN151 4.3 78.3 1.0
C5 P:43X901 4.3 79.4 0.4
O3A P:43X901 4.3 83.0 0.6
C2 P:DG822 4.4 47.1 1.0
C4 P:DG822 4.5 46.3 1.0
N3 P:43X901 4.5 81.9 0.4
N2 P:DG822 4.6 44.8 1.0
CZ A:TYR115 4.6 63.2 1.0
OH A:TYR115 4.7 70.8 1.0
O4' P:43X901 4.8 85.2 0.6
NE A:ARG72 4.8 68.1 1.0
C1' P:43X901 4.8 84.1 0.6
NH2 A:ARG72 4.8 61.7 1.0
CE1 A:TYR115 4.9 57.9 1.0
CE2 A:TYR115 4.9 64.0 1.0
N9 P:DG822 4.9 50.4 1.0
C4 P:43X901 5.0 83.1 0.4
C1' P:DG822 5.0 53.7 1.0

Fluorine binding site 2 out of 2 in 6wph

Go back to Fluorine Binding Sites List in 6wph
Fluorine binding site 2 out of 2 in the Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)-Ftc


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)-Ftc within 5.0Å range:
probe atom residue distance (Å) B Occ
P:F901

b:84.8
occ:0.40
F5 P:43X901 0.0 84.8 0.4
C1' P:43X901 0.6 84.1 0.6
C2' P:43X901 0.9 85.4 0.6
C5 P:43X901 1.3 79.4 0.4
O4' P:43X901 1.8 85.2 0.6
N1 P:43X901 1.9 86.0 0.6
S3' P:43X901 2.3 86.0 0.6
C6 P:43X901 2.3 86.1 0.4
C4 P:43X901 2.4 83.1 0.4
C4' P:43X901 2.4 84.5 0.6
O2 P:43X901 2.6 82.9 0.6
C2 P:43X901 2.6 81.4 0.6
N4 P:43X901 2.7 79.9 0.4
C6 P:43X901 3.0 85.0 0.6
N1 P:43X901 3.6 80.1 0.4
N3 P:43X901 3.6 81.9 0.4
NH2 A:ARG72 3.7 61.7 1.0
C5' P:43X901 3.8 82.4 0.6
N7 P:DG822 3.8 46.3 1.0
CZ A:ARG72 3.9 73.3 1.0
NH1 A:ARG72 3.9 76.1 1.0
N3 P:43X901 4.0 84.2 0.6
O P:HOH1003 4.0 51.4 1.0
O5' P:43X901 4.0 82.5 0.6
C2 P:43X901 4.1 86.2 0.4
C8 P:DG822 4.1 48.6 1.0
C5 P:43X901 4.2 84.1 0.6
C5 P:DG822 4.3 43.6 1.0
O2A P:43X901 4.4 81.7 0.4
C4 P:43X901 4.6 84.1 0.6
NE A:ARG72 4.7 68.1 1.0
O5' P:43X901 4.7 83.8 0.4
O4' P:43X901 4.7 84.8 0.4
N9 P:DG822 4.8 50.4 1.0
C1' P:43X901 4.8 86.3 0.4
C6 P:DG822 4.8 45.5 1.0
C4 P:DG822 4.9 46.3 1.0
O6 P:DG822 5.0 52.0 1.0

Reference:

N.Bertoletti, A.H.Chan, R.F.Schinazi, K.S.Anderson. Post-Catalytic Complexes with Emtricitabine or Stavudine and Hiv-1 Reverse Transcriptase Reveal New Mechanistic Insights For Nucleotide Incorporation and Drug Resistance. Molecules V. 25 2020.
ISSN: ESSN 1420-3049
PubMed: 33096918
DOI: 10.3390/MOLECULES25204868
Page generated: Sun Dec 13 13:34:33 2020

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