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Fluorine in PDB 3kqu: 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: 3kqu 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 / 2.40
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 116.534, 116.467, 71.114, 90.00, 90.00, 119.97
R / Rfree (%) 19.7 / 21.5

Other elements in 3kqu:

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

Manganese (Mn) 6 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

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 3kqu). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 18 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: 3kqu:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 18 in 3kqu

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Fluorine binding site 1 out of 18 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:27.7
occ:1.00
 F1 A:BEF1 0.0 27.7 1.0
BE A:BEF1 1.6 25.9 1.0
NZ A:LYS210 2.5 23.0 1.0
F2 A:BEF1 2.6 28.4 1.0
F3 A:BEF1 2.6 24.0 1.0
O2B A:ADP2 2.8 29.0 1.0
O A:HOH627 2.8 20.0 1.0
CA A:THR206 3.2 27.5 1.0
CE A:LYS210 3.3 24.1 1.0
CB A:ALA323 3.4 28.3 1.0
CG2 A:THR206 3.5 22.4 1.0
PB A:ADP2 3.7 26.3 1.0
CB A:THR206 3.7 25.2 1.0
O1B A:ADP2 3.8 28.3 1.0
N A:THR206 4.0 30.7 1.0
O A:HOH626 4.0 16.0 1.0
O A:PRO205 4.0 32.9 1.0
N A:GLY207 4.0 30.3 1.0
O A:HOH4 4.1 20.0 1.0
O3B A:ADP2 4.1 23.4 1.0
C A:THR206 4.2 27.9 1.0
C A:PRO205 4.2 33.2 1.0
MN A:MN3 4.3 25.9 1.0
N A:ALA323 4.3 29.9 1.0
CA A:ALA323 4.5 30.5 1.0
O A:ALA204 4.5 33.4 1.0
OE2 A:GLU291 4.6 38.9 1.0
OE1 A:GLN460 4.7 27.2 1.0
CD A:LYS210 4.8 26.2 1.0
NE2 A:GLN460 4.9 26.6 1.0
NH2 A:ARG464 5.0 22.1 1.0

Fluorine binding site 2 out of 18 in 3kqu

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Fluorine binding site 2 out of 18 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:28.4
occ:1.00
 F2 A:BEF1 0.0 28.4 1.0
BE A:BEF1 1.6 25.9 1.0
F1 A:BEF1 2.6 27.7 1.0
O2B A:ADP2 2.6 29.0 1.0
F3 A:BEF1 2.7 24.0 1.0
NH1 A:ARG467 2.8 21.4 1.0
NH2 A:ARG464 2.9 22.1 1.0
CB A:THR206 3.3 25.2 1.0
NH2 A:ARG467 3.3 18.9 1.0
O A:HOH626 3.4 16.0 1.0
CG2 A:THR206 3.4 22.4 1.0
CZ A:ARG467 3.5 19.6 1.0
NH1 A:ARG464 3.5 25.4 1.0
CA A:THR206 3.6 27.5 1.0
CZ A:ARG464 3.6 25.3 1.0
N A:GLY207 3.7 30.3 1.0
C A:THR206 4.1 27.9 1.0
PB A:ADP2 4.1 26.3 1.0
OE1 A:GLN460 4.3 27.2 1.0
O A:HOH628 4.4 19.2 1.0
O A:GLY463 4.5 29.5 1.0
O A:HOH627 4.5 20.0 1.0
OG1 A:THR206 4.6 22.4 1.0
MN A:MN3 4.6 25.9 1.0
O3B A:ADP2 4.7 23.4 1.0
N A:GLY417 4.7 33.9 1.0
NE A:ARG467 4.8 19.6 1.0
CA A:GLY207 4.8 32.5 1.0
O3A A:ADP2 4.8 25.9 1.0
NZ A:LYS210 4.9 23.0 1.0
N A:THR206 4.9 30.7 1.0
NE A:ARG464 4.9 23.6 1.0
O1B A:ADP2 4.9 28.3 1.0
CA A:GLY417 4.9 32.4 1.0

Fluorine binding site 3 out of 18 in 3kqu

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Fluorine binding site 3 out of 18 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:24.0
occ:1.00
 F3 A:BEF1 0.0 24.0 1.0
BE A:BEF1 1.6 25.9 1.0
MN A:MN3 2.1 25.9 1.0
O2B A:ADP2 2.6 29.0 1.0
F1 A:BEF1 2.6 27.7 1.0
F2 A:BEF1 2.7 28.4 1.0
O A:HOH626 2.7 16.0 1.0
O A:HOH628 2.9 19.2 1.0
O A:HOH4 2.9 20.0 1.0
O3B A:ADP2 3.0 23.4 1.0
OE1 A:GLU291 3.1 36.8 1.0
OE2 A:GLU291 3.3 38.9 1.0
PB A:ADP2 3.4 26.3 1.0
CD A:GLU291 3.6 37.3 1.0
O A:HOH627 3.7 20.0 1.0
CA A:GLY417 4.0 32.4 1.0
N A:GLY417 4.1 33.9 1.0
NZ A:LYS210 4.2 23.0 1.0
NH2 A:ARG467 4.2 18.9 1.0
OG A:SER211 4.3 27.3 1.0
O1B A:ADP2 4.4 28.3 1.0
O3A A:ADP2 4.5 25.9 1.0
CE A:LYS210 4.5 24.1 1.0
NH2 A:ARG464 4.8 22.1 1.0
O A:GLY417 4.8 33.1 1.0
C A:GLY417 4.8 31.7 1.0
O2A A:ADP2 4.9 31.6 1.0
NH1 A:ARG464 4.9 25.4 1.0
OE1 A:GLN460 5.0 27.2 1.0

Fluorine binding site 4 out of 18 in 3kqu

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Fluorine binding site 4 out of 18 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
B:F1

b:25.2
occ:1.00
 F1 B:BEF1 0.0 25.2 1.0
BE B:BEF1 1.6 24.6 1.0
NZ B:LYS210 2.5 20.9 1.0
F2 B:BEF1 2.6 28.8 1.0
F3 B:BEF1 2.6 22.4 1.0
O2B B:ADP2 2.8 27.8 1.0
O B:HOH7 2.8 19.4 1.0
CE B:LYS210 3.3 24.1 1.0
CA B:THR206 3.3 28.0 1.0
CB B:ALA323 3.4 28.7 1.0
CG2 B:THR206 3.6 25.3 1.0
PB B:ADP2 3.7 26.1 1.0
CB B:THR206 3.8 26.5 1.0
O1B B:ADP2 3.8 26.9 1.0
O B:HOH9 3.9 17.4 1.0
O B:HOH6 4.0 12.5 1.0
N B:THR206 4.0 28.9 1.0
O B:PRO205 4.0 31.3 1.0
O3B B:ADP2 4.0 26.7 1.0
N B:GLY207 4.1 30.8 1.0
C B:THR206 4.3 29.2 1.0
MN B:MN3 4.3 23.1 1.0
C B:PRO205 4.3 31.7 1.0
N B:ALA323 4.3 30.2 1.0
CA B:ALA323 4.5 30.8 1.0
OE2 B:GLU291 4.5 36.3 1.0
O B:ALA204 4.5 34.3 1.0
OE1 B:GLN460 4.7 22.8 1.0
CD B:LYS210 4.7 26.1 1.0
NE2 B:GLN460 4.9 20.4 1.0
NH2 B:ARG464 5.0 17.6 1.0

Fluorine binding site 5 out of 18 in 3kqu

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Fluorine binding site 5 out of 18 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:28.8
occ:1.00
 F2 B:BEF1 0.0 28.8 1.0
BE B:BEF1 1.6 24.6 1.0
F1 B:BEF1 2.6 25.2 1.0
F3 B:BEF1 2.6 22.4 1.0
O2B B:ADP2 2.7 27.8 1.0
NH2 B:ARG464 2.8 17.6 1.0
NH1 B:ARG467 2.9 19.4 1.0
CB B:THR206 3.3 26.5 1.0
NH2 B:ARG467 3.3 19.5 1.0
O B:HOH6 3.4 12.5 1.0
CG2 B:THR206 3.5 25.3 1.0
NH1 B:ARG464 3.5 23.3 1.0
CZ B:ARG467 3.5 20.7 1.0
CZ B:ARG464 3.6 22.0 1.0
CA B:THR206 3.7 28.0 1.0
N B:GLY207 3.8 30.8 1.0
PB B:ADP2 4.1 26.1 1.0
C B:THR206 4.2 29.2 1.0
OE1 B:GLN460 4.2 22.8 1.0
O B:HOH8 4.4 24.1 1.0
O B:GLY463 4.5 25.9 1.0
O B:HOH7 4.6 19.4 1.0
N B:GLY417 4.6 33.1 1.0
OG1 B:THR206 4.6 23.8 1.0
MN B:MN3 4.7 23.1 1.0
O3B B:ADP2 4.7 26.7 1.0
NE B:ARG467 4.8 20.8 1.0
CA B:GLY207 4.9 32.1 1.0
O3A B:ADP2 4.9 28.7 1.0
CA B:GLY417 4.9 32.1 1.0
NE B:ARG464 4.9 20.1 1.0
NZ B:LYS210 4.9 20.9 1.0
N B:THR206 5.0 28.9 1.0
O1B B:ADP2 5.0 26.9 1.0

Fluorine binding site 6 out of 18 in 3kqu

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Fluorine binding site 6 out of 18 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:22.4
occ:1.00
 F3 B:BEF1 0.0 22.4 1.0
BE B:BEF1 1.6 24.6 1.0
MN B:MN3 2.2 23.1 1.0
O2B B:ADP2 2.6 27.8 1.0
F1 B:BEF1 2.6 25.2 1.0
F2 B:BEF1 2.6 28.8 1.0
O B:HOH6 2.7 12.5 1.0
O B:HOH8 2.9 24.1 1.0
O B:HOH9 2.9 17.4 1.0
OE1 B:GLU291 3.1 36.5 1.0
O3B B:ADP2 3.1 26.7 1.0
OE2 B:GLU291 3.2 36.3 1.0
PB B:ADP2 3.4 26.1 1.0
CD B:GLU291 3.5 36.9 1.0
O B:HOH7 3.8 19.4 1.0
CA B:GLY417 3.9 32.1 1.0
N B:GLY417 4.1 33.1 1.0
NH2 B:ARG467 4.2 19.5 1.0
NZ B:LYS210 4.3 20.9 1.0
OG B:SER211 4.3 28.6 1.0
O1B B:ADP2 4.4 26.9 1.0
O3A B:ADP2 4.5 28.7 1.0
CE B:LYS210 4.6 24.1 1.0
O B:GLY417 4.8 30.9 1.0
C B:GLY417 4.8 30.5 1.0
NH2 B:ARG464 4.8 17.6 1.0
NH1 B:ARG464 4.9 23.3 1.0
O2A B:ADP2 4.9 30.7 1.0
OE1 B:GLN460 4.9 22.8 1.0

Fluorine binding site 7 out of 18 in 3kqu

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Fluorine binding site 7 out of 18 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
C:F1

b:27.5
occ:1.00
 F1 C:BEF1 0.0 27.5 1.0
BE C:BEF1 1.6 26.1 1.0
NZ C:LYS210 2.5 21.2 1.0
F3 C:BEF1 2.6 25.3 1.0
F2 C:BEF1 2.6 31.3 1.0
O2B C:ADP2 2.7 29.0 1.0
O C:HOH12 2.8 24.8 1.0
CA C:THR206 3.2 28.4 1.0
CE C:LYS210 3.3 23.3 1.0
CB C:ALA323 3.4 29.0 1.0
CG2 C:THR206 3.5 24.4 1.0
PB C:ADP2 3.7 28.1 1.0
CB C:THR206 3.7 26.9 1.0
O1B C:ADP2 3.9 25.0 1.0
N C:THR206 4.0 30.5 1.0
O C:HOH14 4.0 25.0 1.0
O C:PRO205 4.0 33.2 1.0
O C:HOH11 4.0 17.9 1.0
N C:GLY207 4.0 30.5 1.0
O3B C:ADP2 4.0 22.8 1.0
C C:THR206 4.2 28.5 1.0
C C:PRO205 4.3 32.4 1.0
N C:ALA323 4.3 31.8 1.0
MN C:MN3 4.3 25.0 1.0
CA C:ALA323 4.5 31.7 1.0
O C:ALA204 4.5 33.8 1.0
OE2 C:GLU291 4.6 37.6 1.0
OE1 C:GLN460 4.6 28.5 1.0
CD C:LYS210 4.8 27.1 1.0
NE2 C:GLN460 4.9 23.9 1.0
NH2 C:ARG464 5.0 25.7 1.0

Fluorine binding site 8 out of 18 in 3kqu

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Fluorine binding site 8 out of 18 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
C:F1

b:31.3
occ:1.00
 F2 C:BEF1 0.0 31.3 1.0
BE C:BEF1 1.6 26.1 1.0
F1 C:BEF1 2.6 27.5 1.0
F3 C:BEF1 2.6 25.3 1.0
O2B C:ADP2 2.7 29.0 1.0
NH2 C:ARG464 2.8 25.7 1.0
NH1 C:ARG467 2.8 21.4 1.0
CB C:THR206 3.3 26.9 1.0
CG2 C:THR206 3.4 24.4 1.0
O C:HOH11 3.4 17.9 1.0
NH2 C:ARG467 3.4 21.3 1.0
NH1 C:ARG464 3.5 28.3 1.0
CZ C:ARG467 3.5 22.4 1.0
CZ C:ARG464 3.6 27.6 1.0
CA C:THR206 3.6 28.4 1.0
N C:GLY207 3.7 30.5 1.0
C C:THR206 4.1 28.5 1.0
PB C:ADP2 4.1 28.1 1.0
OE1 C:GLN460 4.2 28.5 1.0
O C:GLY463 4.5 29.5 1.0
O C:HOH12 4.5 24.8 1.0
OG1 C:THR206 4.6 25.4 1.0
O C:HOH13 4.6 25.8 1.0
MN C:MN3 4.7 25.0 1.0
O3B C:ADP2 4.7 22.8 1.0
N C:GLY417 4.7 31.9 1.0
NE C:ARG467 4.8 23.2 1.0
CA C:GLY207 4.8 33.4 1.0
O3A C:ADP2 4.9 27.5 1.0
NE C:ARG464 4.9 25.7 1.0
N C:THR206 4.9 30.5 1.0
NZ C:LYS210 4.9 21.2 1.0
CA C:GLY417 4.9 31.2 1.0
O1B C:ADP2 5.0 25.0 1.0

Fluorine binding site 9 out of 18 in 3kqu

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Fluorine binding site 9 out of 18 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 9 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
C:F1

b:25.3
occ:1.00
 F3 C:BEF1 0.0 25.3 1.0
BE C:BEF1 1.6 26.1 1.0
MN C:MN3 2.2 25.0 1.0
O2B C:ADP2 2.6 29.0 1.0
F1 C:BEF1 2.6 27.5 1.0
O C:HOH11 2.6 17.9 1.0
F2 C:BEF1 2.6 31.3 1.0
O C:HOH14 2.9 25.0 1.0
O C:HOH13 3.0 25.8 1.0
O3B C:ADP2 3.0 22.8 1.0
OE1 C:GLU291 3.1 35.0 1.0
OE2 C:GLU291 3.3 37.6 1.0
PB C:ADP2 3.4 28.1 1.0
CD C:GLU291 3.6 36.0 1.0
O C:HOH12 3.6 24.8 1.0
CA C:GLY417 4.0 31.2 1.0
N C:GLY417 4.1 31.9 1.0
NH2 C:ARG467 4.2 21.3 1.0
NZ C:LYS210 4.3 21.2 1.0
O1B C:ADP2 4.4 25.0 1.0
OG C:SER211 4.4 29.9 1.0
O3A C:ADP2 4.5 27.5 1.0
CE C:LYS210 4.5 23.3 1.0
NH2 C:ARG464 4.7 25.7 1.0
O C:GLY417 4.8 31.8 1.0
C C:GLY417 4.8 30.7 1.0
OE1 C:GLN460 4.9 28.5 1.0
NH1 C:ARG464 4.9 28.3 1.0
O2A C:ADP2 4.9 30.1 1.0
NH1 C:ARG467 5.0 21.4 1.0

Fluorine binding site 10 out of 18 in 3kqu

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Fluorine binding site 10 out of 18 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 10 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
D:F1

b:26.1
occ:1.00
 F1 D:BEF1 0.0 26.1 1.0
BE D:BEF1 1.6 24.4 1.0
NZ D:LYS210 2.5 20.0 1.0
F2 D:BEF1 2.6 28.4 1.0
F3 D:BEF1 2.6 23.3 1.0
O2B D:ADP2 2.8 30.0 1.0
O D:HOH17 2.8 18.3 1.0
CA D:THR206 3.3 27.5 1.0
CE D:LYS210 3.3 22.1 1.0
CB D:ALA323 3.4 28.8 1.0
CG2 D:THR206 3.5 22.4 1.0
PB D:ADP2 3.7 25.1 1.0
CB D:THR206 3.8 25.2 1.0
O1B D:ADP2 3.9 28.1 1.0
O D:HOH16 4.0 18.2 1.0
N D:THR206 4.0 30.0 1.0
O D:PRO205 4.0 32.8 1.0
N D:GLY207 4.0 29.6 1.0
O3B D:ADP2 4.1 23.9 1.0
O D:HOH19 4.1 18.7 1.0
C D:THR206 4.2 28.0 1.0
C D:PRO205 4.3 32.8 1.0
MN D:MN3 4.3 24.8 1.0
N D:ALA323 4.3 30.2 1.0
CA D:ALA323 4.5 30.4 1.0
O D:ALA204 4.5 35.1 1.0
OE2 D:GLU291 4.5 38.2 1.0
OE1 D:GLN460 4.6 25.9 1.0
CD D:LYS210 4.8 25.3 1.0
NE2 D:GLN460 4.9 23.8 1.0
NH2 D:ARG464 5.0 23.4 1.0

Reference:

M.Gu, C.M.Rice. Inaugural Article: 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 20:12:41 2024

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