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Fluorine in PDB 3o8d: Visualizing Atp-Dependent Rna Translocation By the NS3 Helicase From Hcv

Enzymatic activity of Visualizing Atp-Dependent Rna Translocation By the NS3 Helicase From Hcv

All present enzymatic activity of Visualizing Atp-Dependent Rna Translocation By the NS3 Helicase From Hcv:
3.4.21.98; 3.6.1.15; 3.6.4.13;

Protein crystallography data

The structure of Visualizing Atp-Dependent Rna Translocation By the NS3 Helicase From Hcv, PDB code: 3o8d was solved by T.C.Appleby, J.R.Somoza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.02 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.749, 110.416, 144.374, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 23.3

Other elements in 3o8d:

The structure of Visualizing Atp-Dependent Rna Translocation By the NS3 Helicase From Hcv also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Visualizing Atp-Dependent Rna Translocation By the NS3 Helicase From Hcv (pdb code 3o8d). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Visualizing Atp-Dependent Rna Translocation By the NS3 Helicase From Hcv, PDB code: 3o8d:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3o8d

Go back to Fluorine Binding Sites List in 3o8d
Fluorine binding site 1 out of 6 in the Visualizing Atp-Dependent Rna Translocation By the NS3 Helicase From Hcv


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Visualizing Atp-Dependent Rna Translocation By the NS3 Helicase From Hcv within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F885

b:18.4
occ:1.00
 F1 A:BEF885 0.0 18.4 1.0
BE A:BEF885 1.5 17.6 1.0
MG A:MG850 2.1 18.4 1.0
F3 A:BEF885 2.5 15.5 1.0
F2 A:BEF885 2.5 18.9 1.0
O3B A:ADP875 2.7 16.8 1.0
O A:HOH1 2.7 16.3 1.0
OE2 A:GLU291 3.0 15.6 1.0
O A:HOH633 3.0 16.4 1.0
O1B A:ADP875 3.1 15.7 1.0
O A:HOH2 3.1 15.8 1.0
OE1 A:GLU291 3.1 17.2 1.0
O A:HOH638 3.3 16.2 1.0
PB A:ADP875 3.4 16.7 1.0
CD A:GLU291 3.4 18.6 1.0
CA A:GLY417 4.1 18.3 1.0
NH2 A:ARG467 4.2 17.8 1.0
OG A:SER211 4.3 15.9 1.0
N A:GLY417 4.3 18.5 1.0
NZ A:LYS210 4.5 13.8 1.0
O2B A:ADP875 4.5 15.5 1.0
CE A:LYS210 4.5 17.3 1.0
NH2 A:ARG464 4.5 14.8 1.0
O3A A:ADP875 4.6 16.9 1.0
NH1 A:ARG464 4.7 16.6 1.0
O A:GLY417 4.7 20.4 1.0
C A:GLY417 4.8 18.4 1.0
OE1 A:GLN460 4.9 15.7 1.0
O2A A:ADP875 4.9 20.6 1.0
NH1 A:ARG467 4.9 20.0 1.0
CG A:GLU291 4.9 17.5 1.0
CZ A:ARG467 5.0 20.2 1.0

Fluorine binding site 2 out of 6 in 3o8d

Go back to Fluorine Binding Sites List in 3o8d
Fluorine binding site 2 out of 6 in the Visualizing Atp-Dependent Rna Translocation By the NS3 Helicase From Hcv


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Visualizing Atp-Dependent Rna Translocation By the NS3 Helicase From Hcv within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F885

b:18.9
occ:1.00
 F2 A:BEF885 0.0 18.9 1.0
BE A:BEF885 1.5 17.6 1.0
F1 A:BEF885 2.5 18.4 1.0
F3 A:BEF885 2.5 15.5 1.0
O3B A:ADP875 2.6 16.8 1.0
NH2 A:ARG464 2.7 14.8 1.0
NH1 A:ARG467 2.8 20.0 1.0
NH2 A:ARG467 3.3 17.8 1.0
O A:HOH1 3.3 16.3 1.0
NH1 A:ARG464 3.3 16.6 1.0
CZ A:ARG467 3.4 20.2 1.0
CZ A:ARG464 3.4 19.1 1.0
CB A:THR206 3.5 18.2 1.0
CG2 A:THR206 3.6 16.7 1.0
CA A:THR206 3.6 16.5 1.0
N A:GLY207 3.8 18.0 1.0
PB A:ADP875 4.1 16.7 1.0
C A:THR206 4.2 17.4 1.0
OE1 A:GLN460 4.3 15.7 1.0
O A:HOH638 4.3 16.2 1.0
O A:HOH633 4.4 16.4 1.0
MG A:MG850 4.4 18.4 1.0
O1B A:ADP875 4.6 15.7 1.0
O A:GLY463 4.7 17.3 1.0
NE A:ARG467 4.7 18.3 1.0
NE A:ARG464 4.7 18.3 1.0
N A:GLY417 4.8 18.5 1.0
O3A A:ADP875 4.8 16.9 1.0
OG1 A:THR206 4.8 18.4 1.0
CA A:GLY207 4.8 17.4 1.0
N A:THR206 4.9 19.4 1.0
CA A:GLY417 4.9 18.3 1.0

Fluorine binding site 3 out of 6 in 3o8d

Go back to Fluorine Binding Sites List in 3o8d
Fluorine binding site 3 out of 6 in the Visualizing Atp-Dependent Rna Translocation By the NS3 Helicase From Hcv


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Visualizing Atp-Dependent Rna Translocation By the NS3 Helicase From Hcv within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F885

b:15.5
occ:1.00
 F3 A:BEF885 0.0 15.5 1.0
BE A:BEF885 1.5 17.6 1.0
F1 A:BEF885 2.5 18.4 1.0
F2 A:BEF885 2.5 18.9 1.0
O A:HOH638 2.7 16.2 1.0
O3B A:ADP875 2.7 16.8 1.0
NZ A:LYS210 2.7 13.8 1.0
CA A:THR206 3.2 16.5 1.0
CE A:LYS210 3.3 17.3 1.0
CB A:ALA323 3.5 15.8 1.0
PB A:ADP875 3.6 16.7 1.0
CG2 A:THR206 3.7 16.7 1.0
CB A:THR206 3.8 18.2 1.0
N A:THR206 3.9 19.4 1.0
O A:HOH1 3.9 16.3 1.0
O2B A:ADP875 3.9 15.5 1.0
N A:GLY207 4.0 18.0 1.0
O1B A:ADP875 4.1 15.7 1.0
MG A:MG850 4.1 18.4 1.0
O A:HOH2 4.1 15.8 1.0
O A:PRO205 4.1 19.3 1.0
C A:THR206 4.1 17.4 1.0
C A:PRO205 4.3 17.0 1.0
OE1 A:GLU291 4.4 17.2 1.0
N A:ALA323 4.4 15.3 1.0
CA A:ALA323 4.5 17.7 1.0
O A:ALA204 4.6 20.2 1.0
OE1 A:GLN460 4.7 15.7 1.0
NH2 A:ARG464 4.7 14.8 1.0
NE2 A:GLN460 4.8 12.3 1.0
CD A:LYS210 4.8 16.6 1.0
NH1 A:ARG467 4.9 20.0 1.0
O3A A:ADP875 5.0 16.9 1.0

Fluorine binding site 4 out of 6 in 3o8d

Go back to Fluorine Binding Sites List in 3o8d
Fluorine binding site 4 out of 6 in the Visualizing Atp-Dependent Rna Translocation By the NS3 Helicase From Hcv


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Visualizing Atp-Dependent Rna Translocation By the NS3 Helicase From Hcv within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F885

b:18.0
occ:1.00
 F1 B:BEF885 0.0 18.0 1.0
BE B:BEF885 1.5 20.0 1.0
MG B:MG850 2.1 20.4 1.0
F2 B:BEF885 2.5 19.3 1.0
F3 B:BEF885 2.5 24.4 1.0
O B:HOH632 2.6 17.1 1.0
O3B B:ADP875 2.7 20.0 1.0
OE2 B:GLU291 3.0 22.1 1.0
OE1 B:GLU291 3.1 24.2 1.0
O B:HOH644 3.1 21.4 1.0
O1B B:ADP875 3.2 16.8 1.0
O B:HOH637 3.2 16.7 1.0
PB B:ADP875 3.3 20.0 1.0
O B:HOH662 3.4 19.7 1.0
CD B:GLU291 3.4 28.1 1.0
CA B:GLY417 4.1 20.2 1.0
NH2 B:ARG467 4.1 21.0 1.0
OG B:SER211 4.2 19.3 1.0
N B:GLY417 4.3 18.6 1.0
NZ B:LYS210 4.4 18.3 1.0
O2B B:ADP875 4.4 19.8 1.0
NH2 B:ARG464 4.4 16.7 1.0
CE B:LYS210 4.5 19.5 1.0
O3A B:ADP875 4.6 21.0 1.0
O B:GLY417 4.7 21.0 1.0
O2A B:ADP875 4.8 19.8 1.0
C B:GLY417 4.8 19.8 1.0
NH1 B:ARG467 4.8 18.4 1.0
CZ B:ARG467 4.9 18.1 1.0
CG B:GLU291 5.0 17.3 1.0
OE1 B:GLN460 5.0 17.6 1.0

Fluorine binding site 5 out of 6 in 3o8d

Go back to Fluorine Binding Sites List in 3o8d
Fluorine binding site 5 out of 6 in the Visualizing Atp-Dependent Rna Translocation By the NS3 Helicase From Hcv


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Visualizing Atp-Dependent Rna Translocation By the NS3 Helicase From Hcv within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F885

b:19.3
occ:1.00
 F2 B:BEF885 0.0 19.3 1.0
BE B:BEF885 1.5 20.0 1.0
F1 B:BEF885 2.5 18.0 1.0
O3B B:ADP875 2.5 20.0 1.0
F3 B:BEF885 2.5 24.4 1.0
NH1 B:ARG467 2.7 18.4 1.0
NH2 B:ARG464 3.1 16.7 1.0
NH2 B:ARG467 3.2 21.0 1.0
NH1 B:ARG464 3.3 20.0 1.0
O B:HOH632 3.3 17.1 1.0
CZ B:ARG467 3.4 18.1 1.0
CB B:THR206 3.6 19.6 1.0
CZ B:ARG464 3.6 19.1 1.0
CG2 B:THR206 3.6 21.8 1.0
CA B:THR206 3.7 20.0 1.0
N B:GLY207 3.8 20.2 1.0
PB B:ADP875 4.0 20.0 1.0
C B:THR206 4.2 22.4 1.0
OE1 B:GLN460 4.3 17.6 1.0
MG B:MG850 4.3 20.4 1.0
O B:HOH662 4.4 19.7 1.0
O B:HOH644 4.4 21.4 1.0
O1B B:ADP875 4.6 16.8 1.0
NE B:ARG467 4.7 20.8 1.0
O B:GLY463 4.7 20.8 1.0
O3A B:ADP875 4.8 21.0 1.0
N B:GLY417 4.8 18.6 1.0
CA B:GLY207 4.9 22.7 1.0
O2B B:ADP875 4.9 19.8 1.0
OG1 B:THR206 4.9 23.4 1.0
NZ B:LYS210 4.9 18.3 1.0
NE B:ARG464 5.0 23.0 1.0
CA B:GLY417 5.0 20.2 1.0

Fluorine binding site 6 out of 6 in 3o8d

Go back to Fluorine Binding Sites List in 3o8d
Fluorine binding site 6 out of 6 in the Visualizing Atp-Dependent Rna Translocation By the NS3 Helicase From Hcv


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Visualizing Atp-Dependent Rna Translocation By the NS3 Helicase From Hcv within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F885

b:24.4
occ:1.00
 F3 B:BEF885 0.0 24.4 1.0
BE B:BEF885 1.5 20.0 1.0
F1 B:BEF885 2.5 18.0 1.0
F2 B:BEF885 2.5 19.3 1.0
NZ B:LYS210 2.6 18.3 1.0
O3B B:ADP875 2.7 20.0 1.0
O B:HOH662 2.7 19.7 1.0
CE B:LYS210 3.3 19.5 1.0
CA B:THR206 3.3 20.0 1.0
PB B:ADP875 3.5 20.0 1.0
CB B:ALA323 3.6 19.2 1.0
O2B B:ADP875 3.7 19.8 1.0
CG2 B:THR206 3.8 21.8 1.0
O B:HOH632 3.9 17.1 1.0
CB B:THR206 4.0 19.6 1.0
N B:GLY207 4.0 20.2 1.0
N B:THR206 4.1 18.4 1.0
MG B:MG850 4.1 20.4 1.0
O B:PRO205 4.1 20.2 1.0
O1B B:ADP875 4.1 16.8 1.0
O B:HOH637 4.2 16.7 1.0
C B:THR206 4.2 22.4 1.0
C B:PRO205 4.4 19.6 1.0
OE1 B:GLU291 4.4 24.2 1.0
N B:ALA323 4.4 15.1 1.0
O B:ALA204 4.5 23.9 1.0
CA B:ALA323 4.6 20.0 1.0
OE1 B:GLN460 4.7 17.6 1.0
CD B:LYS210 4.8 18.6 1.0
O3A B:ADP875 4.9 21.0 1.0
NH1 B:ARG467 4.9 18.4 1.0
NE2 B:GLN460 4.9 16.9 1.0

Reference:

T.C.Appleby, R.Anderson, O.Fedorova, A.M.Pyle, R.Wang, X.Liu, K.M.Brendza, J.R.Somoza. Visualizing Atp-Dependent Rna Translocation By the NS3 Helicase From Hcv. J.Mol.Biol. V. 405 1139 2011.
ISSN: ISSN 0022-2836
PubMed: 21145896
DOI: 10.1016/J.JMB.2010.11.034
Page generated: Wed Jul 31 21:11:07 2024

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