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Fluorine in PDB 3kql: Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism

Enzymatic activity of Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism

All present enzymatic activity of Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism:
3.4.21.98; 3.6.1.15;

Protein crystallography data

The structure of Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism, PDB code: 3kql was solved by M.Gu, C.M.Rice, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.50
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 43.535, 75.315, 144.229, 90.00, 90.16, 90.00
R / Rfree (%) 18.4 / 21.1

Other elements in 3kql:

The structure of Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Aluminium (Al) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism (pdb code 3kql). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism, PDB code: 3kql:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 3kql

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Fluorine binding site 1 out of 8 in the Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:25.4
occ:1.00
 F1 A:ALF1 0.0 25.4 1.0
AL A:ALF1 1.6 26.5 1.0
MG A:MG3 2.1 18.7 1.0
F4 A:ALF1 2.3 26.1 1.0
F3 A:ALF1 2.3 23.0 1.0
O2B A:ADP2 2.5 11.9 1.0
O A:HOH626 2.6 22.5 1.0
O3B A:ADP2 2.8 16.5 1.0
OE1 A:GLU291 3.1 21.1 1.0
O A:HOH627 3.1 15.5 1.0
O A:HOH4 3.2 12.8 1.0
PB A:ADP2 3.2 18.4 1.0
F2 A:ALF1 3.3 24.5 1.0
O A:HOH628 3.5 21.5 1.0
NZ A:LYS210 3.5 17.9 1.0
O A:HOH5 3.6 20.6 1.0
O1B A:ADP2 4.1 15.6 1.0
O A:HOH57 4.1 33.1 1.0
CD A:GLU291 4.1 22.9 1.0
OG A:SER211 4.2 17.8 1.0
CA A:GLY417 4.3 21.3 1.0
N A:GLY417 4.3 22.1 1.0
O3A A:ADP2 4.4 18.5 1.0
OE2 A:GLU291 4.6 23.8 1.0
CE A:LYS210 4.7 18.4 1.0
NH2 A:ARG467 4.9 19.5 1.0
O2A A:ADP2 5.0 22.7 1.0

Fluorine binding site 2 out of 8 in 3kql

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Fluorine binding site 2 out of 8 in the Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:24.5
occ:1.00
 F2 A:ALF1 0.0 24.5 1.0
AL A:ALF1 1.6 26.5 1.0
F4 A:ALF1 2.3 26.1 1.0
F3 A:ALF1 2.3 23.0 1.0
O2B A:ADP2 2.6 11.9 1.0
O A:HOH626 2.8 22.5 1.0
NH2 A:ARG464 2.8 16.9 1.0
NH1 A:ARG467 2.8 17.1 1.0
CB A:THR206 3.1 20.0 1.0
N A:GLY207 3.2 22.3 1.0
CA A:THR206 3.3 21.1 1.0
F1 A:ALF1 3.3 25.4 1.0
NH1 A:ARG464 3.3 18.3 1.0
CZ A:ARG464 3.5 17.6 1.0
CG2 A:THR206 3.5 16.4 1.0
NH2 A:ARG467 3.6 19.5 1.0
CZ A:ARG467 3.6 18.2 1.0
C A:THR206 3.7 22.3 1.0
PB A:ADP2 4.1 18.4 1.0
CA A:GLY207 4.3 22.4 1.0
OE1 A:GLN460 4.3 14.4 1.0
OG1 A:THR206 4.4 16.5 1.0
O A:GLY463 4.4 16.0 1.0
NZ A:LYS210 4.5 17.9 1.0
N A:THR206 4.6 21.3 1.0
O3A A:ADP2 4.7 18.5 1.0
NE A:ARG464 4.8 17.8 1.0
N A:GLY417 4.8 22.1 1.0
O1B A:ADP2 4.8 15.6 1.0
O A:THR206 4.8 21.8 1.0
O3B A:ADP2 4.8 16.5 1.0
O A:HOH5 4.8 20.6 1.0
MG A:MG3 4.9 18.7 1.0
NE A:ARG467 4.9 18.9 1.0
O A:HOH628 4.9 21.5 1.0

Fluorine binding site 3 out of 8 in 3kql

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Fluorine binding site 3 out of 8 in the Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:23.0
occ:1.00
 F3 A:ALF1 0.0 23.0 1.0
AL A:ALF1 1.6 26.5 1.0
F2 A:ALF1 2.3 24.5 1.0
F1 A:ALF1 2.3 25.4 1.0
O2B A:ADP2 2.6 11.9 1.0
O A:HOH626 2.7 22.5 1.0
O A:HOH628 2.8 21.5 1.0
CA A:GLY417 3.0 21.3 1.0
NH1 A:ARG464 3.1 18.3 1.0
NH2 A:ARG467 3.1 19.5 1.0
N A:GLY417 3.2 22.1 1.0
F4 A:ALF1 3.3 26.1 1.0
MG A:MG3 3.3 18.7 1.0
NH1 A:ARG467 3.7 17.1 1.0
C A:GLY417 3.7 20.9 1.0
PB A:ADP2 3.7 18.4 1.0
CZ A:ARG467 3.8 18.2 1.0
NH2 A:ARG464 3.8 16.9 1.0
CZ A:ARG464 3.9 17.6 1.0
O3B A:ADP2 3.9 16.5 1.0
OE1 A:GLU291 4.0 21.1 1.0
O A:HOH627 4.1 15.5 1.0
O A:GLY417 4.2 19.4 1.0
O3A A:ADP2 4.3 18.5 1.0
O2A A:ADP2 4.3 22.7 1.0
N A:PHE418 4.4 20.3 1.0
C A:THR416 4.4 21.0 1.0
O A:HOH6 4.7 12.4 1.0
N A:GLY207 4.8 22.3 1.0
NE A:ARG467 5.0 18.9 1.0
PA A:ADP2 5.0 23.3 1.0
O1B A:ADP2 5.0 15.6 1.0

Fluorine binding site 4 out of 8 in 3kql

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Fluorine binding site 4 out of 8 in the Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:26.1
occ:1.00
 F4 A:ALF1 0.0 26.1 1.0
AL A:ALF1 1.6 26.5 1.0
F2 A:ALF1 2.3 24.5 1.0
F1 A:ALF1 2.3 25.4 1.0
NZ A:LYS210 2.5 17.9 1.0
O2B A:ADP2 2.5 11.9 1.0
O A:HOH626 2.7 22.5 1.0
O A:HOH5 3.0 20.6 1.0
F3 A:ALF1 3.3 23.0 1.0
CA A:THR206 3.3 21.1 1.0
PB A:ADP2 3.6 18.4 1.0
CG2 A:THR206 3.8 16.4 1.0
CB A:THR206 3.8 20.0 1.0
CE A:LYS210 3.8 18.4 1.0
CB A:ALA323 3.9 20.7 1.0
O1B A:ADP2 3.9 15.6 1.0
N A:GLY207 4.0 22.3 1.0
O3B A:ADP2 4.1 16.5 1.0
N A:THR206 4.2 21.3 1.0
C A:THR206 4.2 22.3 1.0
MG A:MG3 4.2 18.7 1.0
OE1 A:GLN460 4.3 14.4 1.0
OE1 A:GLU291 4.4 21.1 1.0
NH2 A:ARG464 4.4 16.9 1.0
O A:PRO205 4.4 22.3 1.0
C A:PRO205 4.6 21.2 1.0
O A:HOH4 4.8 12.8 1.0
N A:ALA323 4.8 21.6 1.0
NE2 A:GLN460 4.8 17.2 1.0
CD A:LYS210 4.8 16.0 1.0
O3A A:ADP2 4.9 18.5 1.0
CA A:ALA323 4.9 21.4 1.0
CD A:GLN460 5.0 16.4 1.0

Fluorine binding site 5 out of 8 in 3kql

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Fluorine binding site 5 out of 8 in the Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1

b:28.7
occ:1.00
 F1 B:ALF1 0.0 28.7 1.0
AL B:ALF1 1.6 31.1 1.0
NZ B:LYS210 2.3 19.2 1.0
F4 B:ALF1 2.3 29.5 1.0
F3 B:ALF1 2.3 28.8 1.0
O2B B:ADP2 2.5 11.4 1.0
O B:HOH7 2.8 27.3 1.0
O B:HOH12 3.0 17.2 1.0
F2 B:ALF1 3.3 27.4 1.0
CA B:THR206 3.4 22.8 1.0
PB B:ADP2 3.6 17.1 1.0
CE B:LYS210 3.6 22.3 1.0
CB B:ALA323 3.9 25.7 1.0
N B:GLY207 3.9 23.5 1.0
CG2 B:THR206 3.9 21.1 1.0
CB B:THR206 4.0 22.4 1.0
O1B B:ADP2 4.0 14.7 1.0
O3B B:ADP2 4.0 14.5 1.0
MG B:MG3 4.1 22.0 1.0
C B:THR206 4.2 23.9 1.0
OE1 B:GLN460 4.3 17.1 1.0
N B:THR206 4.3 24.0 1.0
O B:PRO205 4.4 26.2 1.0
OE1 B:GLU291 4.4 16.3 1.0
NH2 B:ARG464 4.6 16.9 1.0
C B:PRO205 4.7 25.5 1.0
CD B:LYS210 4.7 20.7 1.0
N B:ALA323 4.7 24.4 1.0
O B:HOH9 4.8 16.1 1.0
O3A B:ADP2 4.9 18.4 1.0
OE2 B:GLU291 4.9 20.3 1.0
CA B:ALA323 4.9 24.8 1.0
NE2 B:GLN460 4.9 16.8 1.0

Fluorine binding site 6 out of 8 in 3kql

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Fluorine binding site 6 out of 8 in the Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1

b:27.4
occ:1.00
 F2 B:ALF1 0.0 27.4 1.0
AL B:ALF1 1.6 31.1 1.0
F4 B:ALF1 2.3 29.5 1.0
F3 B:ALF1 2.3 28.8 1.0
O2B B:ADP2 2.6 11.4 1.0
O B:HOH7 2.6 27.3 1.0
O B:HOH8 2.6 11.2 1.0
NH2 B:ARG467 3.0 18.9 1.0
CA B:GLY417 3.0 21.3 1.0
NH1 B:ARG464 3.1 16.1 1.0
N B:GLY417 3.2 22.1 1.0
F1 B:ALF1 3.3 28.7 1.0
MG B:MG3 3.3 22.0 1.0
NH1 B:ARG467 3.5 18.4 1.0
CZ B:ARG467 3.6 19.4 1.0
PB B:ADP2 3.7 17.1 1.0
C B:GLY417 3.7 21.4 1.0
O3B B:ADP2 3.9 14.5 1.0
NH2 B:ARG464 4.0 16.9 1.0
CZ B:ARG464 4.0 15.3 1.0
O B:GLY417 4.1 22.8 1.0
O3A B:ADP2 4.2 18.4 1.0
OE1 B:GLU291 4.2 16.3 1.0
O2A B:ADP2 4.3 21.6 1.0
O B:HOH10 4.3 16.8 1.0
N B:PHE418 4.5 19.8 1.0
O B:HOH11 4.5 19.5 1.0
C B:THR416 4.5 21.6 1.0
N B:GLY207 4.5 23.5 1.0
NE B:ARG467 4.8 19.4 1.0
PA B:ADP2 4.9 22.0 1.0
NZ B:LYS210 4.9 19.2 1.0
O1B B:ADP2 5.0 14.7 1.0

Fluorine binding site 7 out of 8 in 3kql

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Fluorine binding site 7 out of 8 in the Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1

b:28.8
occ:1.00
 F3 B:ALF1 0.0 28.8 1.0
AL B:ALF1 1.6 31.1 1.0
F2 B:ALF1 2.3 27.4 1.0
F1 B:ALF1 2.3 28.7 1.0
O2B B:ADP2 2.6 11.4 1.0
NH1 B:ARG467 2.8 18.4 1.0
O B:HOH7 3.0 27.3 1.0
N B:GLY207 3.0 23.5 1.0
NH2 B:ARG464 3.1 16.9 1.0
CB B:THR206 3.1 22.4 1.0
CA B:THR206 3.2 22.8 1.0
F4 B:ALF1 3.3 29.5 1.0
NH1 B:ARG464 3.4 16.1 1.0
C B:THR206 3.5 23.9 1.0
CG2 B:THR206 3.6 21.1 1.0
NH2 B:ARG467 3.6 18.9 1.0
CZ B:ARG467 3.6 19.4 1.0
CZ B:ARG464 3.7 15.3 1.0
PB B:ADP2 4.0 17.1 1.0
CA B:GLY207 4.1 22.5 1.0
NZ B:LYS210 4.3 19.2 1.0
OG1 B:THR206 4.4 19.0 1.0
OE1 B:GLN460 4.4 17.1 1.0
O B:GLY463 4.5 17.0 1.0
N B:THR206 4.6 24.0 1.0
O3A B:ADP2 4.6 18.4 1.0
O B:THR206 4.7 23.8 1.0
O B:HOH8 4.8 11.2 1.0
O1B B:ADP2 4.8 14.7 1.0
O3B B:ADP2 4.8 14.5 1.0
N B:GLY417 4.8 22.1 1.0
MG B:MG3 4.9 22.0 1.0
NE B:ARG467 4.9 19.4 1.0
O B:HOH12 4.9 17.2 1.0
NE B:ARG464 5.0 16.5 1.0

Fluorine binding site 8 out of 8 in 3kql

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Fluorine binding site 8 out of 8 in the Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1

b:29.5
occ:1.00
 F4 B:ALF1 0.0 29.5 1.0
AL B:ALF1 1.6 31.1 1.0
MG B:MG3 2.0 22.0 1.0
F1 B:ALF1 2.3 28.7 1.0
F2 B:ALF1 2.3 27.4 1.0
O B:HOH7 2.4 27.3 1.0
O2B B:ADP2 2.5 11.4 1.0
O3B B:ADP2 2.9 14.5 1.0
OE1 B:GLU291 3.0 16.3 1.0
O B:HOH10 3.1 16.8 1.0
O B:HOH8 3.2 11.2 1.0
F3 B:ALF1 3.3 28.8 1.0
PB B:ADP2 3.3 17.1 1.0
NZ B:LYS210 3.3 19.2 1.0
O B:HOH9 3.4 16.1 1.0
O B:HOH12 3.6 17.2 1.0
CD B:GLU291 4.1 19.9 1.0
CA B:GLY417 4.1 21.3 1.0
N B:GLY417 4.2 22.1 1.0
O1B B:ADP2 4.2 14.7 1.0
OG B:SER211 4.3 19.2 1.0
O B:HOH183 4.3 39.1 1.0
O3A B:ADP2 4.4 18.4 1.0
OE2 B:GLU291 4.5 20.3 1.0
CE B:LYS210 4.7 22.3 1.0
NH2 B:ARG467 4.9 18.9 1.0

Reference:

M.Gu, C.M.Rice. Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism. Proc.Natl.Acad.Sci.Usa V. 107 521 2010.
ISSN: ISSN 0027-8424
PubMed: 20080715
DOI: 10.1073/PNAS.0913380107
Page generated: Wed Jul 31 19:56:36 2024

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