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Fluorine in PDB 3kqn: 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: 3kqn 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 / 2.05
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 116.764, 116.764, 71.100, 90.00, 90.00, 120.00
R / Rfree (%) 19 / 22.3

Other elements in 3kqn:

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) 1 atom

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 3kqn). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 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: 3kqn:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 3kqn

Go back to Fluorine Binding Sites List in 3kqn
Fluorine binding site 1 out of 3 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:11.6
occ:1.00
 F1 A:BEF1 0.0 11.6 1.0
BE A:BEF1 1.6 10.2 1.0
F2 A:BEF1 2.7 12.4 1.0
F3 A:BEF1 2.7 7.9 1.0
NZ A:LYS210 2.7 10.8 1.0
O A:HOH627 2.7 9.5 1.0
O2B A:ADP2 2.8 10.7 1.0
CA A:THR206 3.2 13.0 1.0
CE A:LYS210 3.2 10.2 1.0
CB A:ALA323 3.3 16.3 1.0
CG2 A:THR206 3.4 12.6 1.0
CB A:THR206 3.7 14.5 1.0
PB A:ADP2 3.8 14.0 1.0
N A:THR206 3.9 14.8 1.0
O A:HOH626 3.9 6.5 1.0
O A:PRO205 4.0 16.4 1.0
N A:GLY207 4.1 13.1 1.0
O1B A:ADP2 4.1 13.4 1.0
O3B A:ADP2 4.1 13.8 1.0
C A:THR206 4.2 14.6 1.0
C A:PRO205 4.2 17.0 1.0
N A:ALA323 4.3 16.5 1.0
MN A:MN3 4.3 11.4 1.0
O A:HOH4 4.3 11.8 1.0
CA A:ALA323 4.4 17.9 1.0
OE1 A:GLN460 4.5 12.7 1.0
O A:ALA204 4.5 18.8 1.0
NE2 A:GLN460 4.5 10.3 1.0
OE2 A:GLU291 4.6 11.1 1.0
NH2 A:ARG464 4.6 9.7 1.0
CD A:LYS210 4.7 11.6 1.0
CD A:GLN460 5.0 14.5 1.0

Fluorine binding site 2 out of 3 in 3kqn

Go back to Fluorine Binding Sites List in 3kqn
Fluorine binding site 2 out of 3 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:12.4
occ:1.00
 F2 A:BEF1 0.0 12.4 1.0
BE A:BEF1 1.6 10.2 1.0
NH2 A:ARG464 2.5 9.7 1.0
F3 A:BEF1 2.6 7.9 1.0
F1 A:BEF1 2.7 11.6 1.0
O2B A:ADP2 2.8 10.7 1.0
NH1 A:ARG467 2.8 8.3 1.0
NH1 A:ARG464 3.2 7.2 1.0
CZ A:ARG464 3.3 9.7 1.0
O A:HOH626 3.3 6.5 1.0
NH2 A:ARG467 3.4 8.3 1.0
CB A:THR206 3.5 14.5 1.0
CZ A:ARG467 3.5 10.6 1.0
CG2 A:THR206 3.6 12.6 1.0
CA A:THR206 3.7 13.0 1.0
N A:GLY207 3.8 13.1 1.0
OE1 A:GLN460 4.1 12.7 1.0
PB A:ADP2 4.2 14.0 1.0
C A:THR206 4.2 14.6 1.0
O A:HOH627 4.4 9.5 1.0
MN A:MN3 4.5 11.4 1.0
O A:GLY463 4.5 8.9 1.0
NE A:ARG464 4.6 8.4 1.0
O A:HOH628 4.6 9.0 1.0
O3B A:ADP2 4.6 13.8 1.0
NE A:ARG467 4.7 11.4 1.0
N A:GLY417 4.7 17.5 1.0
OG1 A:THR206 4.8 14.0 1.0
O3A A:ADP2 4.8 11.7 1.0
CA A:GLY207 4.8 16.0 1.0

Fluorine binding site 3 out of 3 in 3kqn

Go back to Fluorine Binding Sites List in 3kqn
Fluorine binding site 3 out of 3 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:7.9
occ:1.00
 F3 A:BEF1 0.0 7.9 1.0
BE A:BEF1 1.6 10.2 1.0
MN A:MN3 2.0 11.4 1.0
F2 A:BEF1 2.6 12.4 1.0
O2B A:ADP2 2.6 10.7 1.0
F1 A:BEF1 2.7 11.6 1.0
O A:HOH626 2.9 6.5 1.0
O3B A:ADP2 2.9 13.8 1.0
O A:HOH628 3.0 9.0 1.0
OE1 A:GLU291 3.0 11.5 1.0
O A:HOH4 3.1 11.8 1.0
OE2 A:GLU291 3.2 11.1 1.0
PB A:ADP2 3.3 14.0 1.0
O A:HOH627 3.5 9.5 1.0
CD A:GLU291 3.5 12.5 1.0
CA A:GLY417 4.2 15.8 1.0
NH2 A:ARG467 4.2 8.3 1.0
OG A:SER211 4.2 14.3 1.0
CE A:LYS210 4.3 10.2 1.0
NZ A:LYS210 4.3 10.8 1.0
N A:GLY417 4.3 17.5 1.0
O3A A:ADP2 4.4 11.7 1.0
O1B A:ADP2 4.4 13.4 1.0
NH2 A:ARG464 4.6 9.7 1.0
O2A A:ADP2 4.7 16.2 1.0
NH1 A:ARG464 4.8 7.2 1.0
O A:GLY417 4.8 14.7 1.0
OE1 A:GLN460 4.9 12.7 1.0
NH1 A:ARG467 4.9 8.3 1.0
C A:GLY417 4.9 14.4 1.0
CG A:GLU291 5.0 11.1 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: Mon Jul 14 17:31:27 2025

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