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Fluorine in PDB 5e4f: The Spring Alpha-Helix Coordinates Multiple Modes of Hcv NS3 Helicase Action

Enzymatic activity of The Spring Alpha-Helix Coordinates Multiple Modes of Hcv NS3 Helicase Action

All present enzymatic activity of The Spring Alpha-Helix Coordinates Multiple Modes of Hcv NS3 Helicase Action:
3.4.21.98; 3.6.1.15; 3.6.4.13;

Protein crystallography data

The structure of The Spring Alpha-Helix Coordinates Multiple Modes of Hcv NS3 Helicase Action, PDB code: 5e4f 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 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 95.451, 46.104, 109.041, 90.00, 104.05, 90.00
R / Rfree (%) 21.4 / 25.2

Other elements in 5e4f:

The structure of The Spring Alpha-Helix Coordinates Multiple Modes of Hcv NS3 Helicase Action 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 The Spring Alpha-Helix Coordinates Multiple Modes of Hcv NS3 Helicase Action (pdb code 5e4f). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the The Spring Alpha-Helix Coordinates Multiple Modes of Hcv NS3 Helicase Action, PDB code: 5e4f:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 5e4f

Go back to Fluorine Binding Sites List in 5e4f
Fluorine binding site 1 out of 8 in the The Spring Alpha-Helix Coordinates Multiple Modes of Hcv NS3 Helicase Action


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The Spring Alpha-Helix Coordinates Multiple Modes of Hcv NS3 Helicase Action within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:10.6
occ:1.00
 F1 A:ALF701 0.0 10.6 1.0
AL A:ALF701 1.6 15.6 1.0
MG A:MG703 2.1 12.0 1.0
F3 A:ALF701 2.3 14.2 1.0
F4 A:ALF701 2.3 12.2 1.0
O A:HOH854 2.3 4.3 1.0
O2B A:ADP702 2.5 6.6 1.0
O A:HOH839 2.7 8.3 1.0
O1B A:ADP702 2.9 7.8 1.0
OE1 A:GLU291 3.1 13.0 1.0
O A:HOH908 3.1 5.2 1.0
O A:HOH837 3.2 9.0 1.0
F2 A:ALF701 3.3 15.2 1.0
PB A:ADP702 3.3 9.2 1.0
OE2 A:GLU291 3.5 16.1 1.0
CD A:GLU291 3.6 16.1 1.0
O A:HOH897 3.7 1.0 1.0
CA A:GLY417 4.1 11.6 1.0
CE A:LYS210 4.1 5.7 1.0
NZ A:LYS210 4.1 3.5 1.0
O3B A:ADP702 4.2 7.2 1.0
OG A:SER211 4.4 10.7 1.0
O3A A:ADP702 4.4 12.3 1.0
NH2 A:ARG467 4.8 7.3 1.0
O2A A:ADP702 4.9 14.4 1.0
CG A:GLU291 4.9 12.3 1.0
N A:GLY417 5.0 12.2 1.0
O A:GLY417 5.0 9.6 1.0
C A:GLY417 5.0 11.5 1.0

Fluorine binding site 2 out of 8 in 5e4f

Go back to Fluorine Binding Sites List in 5e4f
Fluorine binding site 2 out of 8 in the The Spring Alpha-Helix Coordinates Multiple Modes of Hcv NS3 Helicase Action


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The Spring Alpha-Helix Coordinates Multiple Modes of Hcv NS3 Helicase Action within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:15.2
occ:1.00
 F2 A:ALF701 0.0 15.2 1.0
AL A:ALF701 1.6 15.6 1.0
F4 A:ALF701 2.3 12.2 1.0
F3 A:ALF701 2.3 14.2 1.0
O2B A:ADP702 2.6 6.6 1.0
O A:HOH854 2.7 4.3 1.0
NH2 A:ARG464 2.9 8.9 1.0
NH1 A:ARG467 3.0 7.6 1.0
N A:GLY207 3.1 8.7 1.0
CA A:THR206 3.1 8.2 1.0
CB A:THR206 3.1 8.3 1.0
F1 A:ALF701 3.3 10.6 1.0
CG2 A:THR206 3.5 6.8 1.0
C A:THR206 3.6 10.7 1.0
CZ A:ARG464 3.7 9.3 1.0
NH1 A:ARG464 3.7 6.3 1.0
NH2 A:ARG467 3.8 7.3 1.0
CZ A:ARG467 3.9 7.8 1.0
PB A:ADP702 4.1 9.2 1.0
CA A:GLY207 4.2 10.5 1.0
O A:GLY463 4.4 10.0 1.0
OE1 A:GLN460 4.4 9.7 1.0
N A:THR206 4.5 9.9 1.0
OG1 A:THR206 4.5 7.7 1.0
NZ A:LYS210 4.7 3.5 1.0
O A:THR206 4.7 11.2 1.0
O3A A:ADP702 4.8 12.3 1.0
O3B A:ADP702 4.8 7.2 1.0
O A:HOH897 4.8 1.0 1.0
O1B A:ADP702 4.9 7.8 1.0
NE A:ARG464 5.0 10.2 1.0

Fluorine binding site 3 out of 8 in 5e4f

Go back to Fluorine Binding Sites List in 5e4f
Fluorine binding site 3 out of 8 in the The Spring Alpha-Helix Coordinates Multiple Modes of Hcv NS3 Helicase Action


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of The Spring Alpha-Helix Coordinates Multiple Modes of Hcv NS3 Helicase Action within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:14.2
occ:1.00
 F3 A:ALF701 0.0 14.2 1.0
AL A:ALF701 1.6 15.6 1.0
F1 A:ALF701 2.3 10.6 1.0
F2 A:ALF701 2.3 15.2 1.0
O A:HOH854 2.5 4.3 1.0
O2B A:ADP702 2.5 6.6 1.0
NH2 A:ARG467 2.9 7.3 1.0
NH1 A:ARG464 3.0 6.3 1.0
O A:HOH837 3.1 9.0 1.0
F4 A:ALF701 3.3 12.2 1.0
CA A:GLY417 3.3 11.6 1.0
NH1 A:ARG467 3.5 7.6 1.0
CZ A:ARG467 3.5 7.8 1.0
MG A:MG703 3.6 12.0 1.0
NH2 A:ARG464 3.6 8.9 1.0
PB A:ADP702 3.7 9.2 1.0
C A:GLY417 3.7 11.5 1.0
O A:GLY417 3.8 9.6 1.0
CZ A:ARG464 3.8 9.3 1.0
O1B A:ADP702 3.9 7.8 1.0
OE1 A:GLU291 4.1 13.0 1.0
O3A A:ADP702 4.2 12.3 1.0
O A:HOH908 4.2 5.2 1.0
O2A A:ADP702 4.3 14.4 1.0
N A:GLY417 4.3 12.2 1.0
N A:GLY207 4.5 8.7 1.0
N A:PHE418 4.6 10.4 1.0
O A:HOH858 4.6 7.8 1.0
NE A:ARG467 4.7 8.8 1.0
PA A:ADP702 4.9 14.2 1.0
O3B A:ADP702 4.9 7.2 1.0
O A:HOH839 5.0 8.3 1.0

Fluorine binding site 4 out of 8 in 5e4f

Go back to Fluorine Binding Sites List in 5e4f
Fluorine binding site 4 out of 8 in the The Spring Alpha-Helix Coordinates Multiple Modes of Hcv NS3 Helicase Action


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of The Spring Alpha-Helix Coordinates Multiple Modes of Hcv NS3 Helicase Action within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:12.2
occ:1.00
 F4 A:ALF701 0.0 12.2 1.0
AL A:ALF701 1.6 15.6 1.0
F2 A:ALF701 2.3 15.2 1.0
F1 A:ALF701 2.3 10.6 1.0
O A:HOH854 2.6 4.3 1.0
O2B A:ADP702 2.6 6.6 1.0
O A:HOH897 2.9 1.0 1.0
NZ A:LYS210 2.9 3.5 1.0
F3 A:ALF701 3.3 14.2 1.0
CE A:LYS210 3.4 5.7 1.0
CA A:THR206 3.6 8.2 1.0
PB A:ADP702 3.7 9.2 1.0
CB A:ALA323 3.8 11.5 1.0
O A:HOH839 4.0 8.3 1.0
O3B A:ADP702 4.0 7.2 1.0
CG2 A:THR206 4.0 6.8 1.0
N A:GLY207 4.1 8.7 1.0
O1B A:ADP702 4.1 7.8 1.0
CB A:THR206 4.2 8.3 1.0
MG A:MG703 4.2 12.0 1.0
OE1 A:GLN460 4.3 9.7 1.0
N A:THR206 4.3 9.9 1.0
C A:THR206 4.4 10.7 1.0
OE2 A:GLU291 4.4 16.1 1.0
OE1 A:GLU291 4.5 13.0 1.0
O A:PRO205 4.5 9.7 1.0
NH2 A:ARG464 4.6 8.9 1.0
N A:ALA323 4.6 10.9 1.0
NE2 A:GLN460 4.7 8.0 1.0
C A:PRO205 4.7 11.4 1.0
CA A:ALA323 4.8 10.6 1.0
CD A:GLU291 4.9 16.1 1.0
CD A:GLN460 4.9 12.8 1.0
CD A:LYS210 4.9 5.2 1.0
O A:ALA204 4.9 13.2 1.0

Fluorine binding site 5 out of 8 in 5e4f

Go back to Fluorine Binding Sites List in 5e4f
Fluorine binding site 5 out of 8 in the The Spring Alpha-Helix Coordinates Multiple Modes of Hcv NS3 Helicase Action


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of The Spring Alpha-Helix Coordinates Multiple Modes of Hcv NS3 Helicase Action within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F701

b:22.6
occ:1.00
 F1 B:ALF701 0.0 22.6 1.0
AL B:ALF701 1.6 21.8 1.0
F3 B:ALF701 2.3 22.9 1.0
F4 B:ALF701 2.3 22.9 1.0
O1B B:ADP702 2.7 25.3 1.0
NH2 B:ARG467 2.8 19.9 1.0
O B:HOH835 2.9 17.6 1.0
CA B:GLY417 3.0 24.9 1.0
O B:HOH859 3.0 21.0 1.0
NH1 B:ARG464 3.1 17.3 1.0
F2 B:ALF701 3.3 22.8 1.0
CZ B:ARG467 3.5 20.4 1.0
NH1 B:ARG467 3.5 15.8 1.0
C B:GLY417 3.5 25.7 1.0
MG B:MG703 3.6 36.3 1.0
NH2 B:ARG464 3.6 13.4 1.0
O B:GLY417 3.7 26.4 1.0
CZ B:ARG464 3.8 15.2 1.0
PB B:ADP702 3.8 31.9 1.0
O1A B:ADP702 4.0 34.7 1.0
O3B B:ADP702 4.0 27.7 1.0
N B:GLY417 4.1 25.7 1.0
OE1 B:GLU291 4.1 23.0 1.0
O3A B:ADP702 4.3 31.2 1.0
N B:PHE418 4.3 25.7 1.0
O B:HOH823 4.3 19.3 1.0
N B:GLY207 4.6 24.6 1.0
NE B:ARG467 4.6 18.2 1.0
O B:HOH832 4.6 14.8 1.0
PA B:ADP702 4.8 32.0 1.0
O B:PHE418 4.9 26.0 1.0

Fluorine binding site 6 out of 8 in 5e4f

Go back to Fluorine Binding Sites List in 5e4f
Fluorine binding site 6 out of 8 in the The Spring Alpha-Helix Coordinates Multiple Modes of Hcv NS3 Helicase Action


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of The Spring Alpha-Helix Coordinates Multiple Modes of Hcv NS3 Helicase Action within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F701

b:22.8
occ:1.00
 F2 B:ALF701 0.0 22.8 1.0
AL B:ALF701 1.6 21.8 1.0
F3 B:ALF701 2.3 22.9 1.0
F4 B:ALF701 2.3 22.9 1.0
O1B B:ADP702 2.5 25.3 1.0
O B:HOH835 2.6 17.6 1.0
O B:HOH868 2.9 20.7 1.0
NZ B:LYS210 3.0 33.5 1.0
F1 B:ALF701 3.3 22.6 1.0
CE B:LYS210 3.5 34.8 1.0
PB B:ADP702 3.5 31.9 1.0
CA B:THR206 3.6 24.1 1.0
CB B:ALA323 3.8 27.8 1.0
O3B B:ADP702 3.9 27.7 1.0
O2B B:ADP702 3.9 29.4 1.0
O B:HOH845 4.0 42.3 1.0
N B:GLY207 4.0 24.6 1.0
CB B:THR206 4.1 23.9 1.0
MG B:MG703 4.1 36.3 1.0
CG2 B:THR206 4.2 23.1 1.0
C B:THR206 4.3 25.3 1.0
OE1 B:GLN460 4.4 17.7 1.0
N B:THR206 4.4 24.3 1.0
OE1 B:GLU291 4.5 23.0 1.0
O B:PRO205 4.5 25.6 1.0
NH2 B:ARG464 4.5 13.4 1.0
OE2 B:GLU291 4.6 26.9 1.0
N B:ALA323 4.7 26.9 1.0
NE2 B:GLN460 4.8 14.9 1.0
C B:PRO205 4.8 26.8 1.0
O3A B:ADP702 4.8 31.2 1.0
CA B:ALA323 4.9 27.8 1.0
O B:ALA204 5.0 33.2 1.0

Fluorine binding site 7 out of 8 in 5e4f

Go back to Fluorine Binding Sites List in 5e4f
Fluorine binding site 7 out of 8 in the The Spring Alpha-Helix Coordinates Multiple Modes of Hcv NS3 Helicase Action


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of The Spring Alpha-Helix Coordinates Multiple Modes of Hcv NS3 Helicase Action within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F701

b:22.9
occ:1.00
 F3 B:ALF701 0.0 22.9 1.0
AL B:ALF701 1.6 21.8 1.0
MG B:MG703 2.1 36.3 1.0
F2 B:ALF701 2.3 22.8 1.0
F1 B:ALF701 2.3 22.6 1.0
O B:HOH835 2.6 17.6 1.0
O1B B:ADP702 2.7 25.3 1.0
O B:HOH845 2.9 42.3 1.0
O3B B:ADP702 3.0 27.7 1.0
OE1 B:GLU291 3.0 23.0 1.0
O B:HOH823 3.2 19.3 1.0
O B:HOH859 3.2 21.0 1.0
F4 B:ALF701 3.3 22.9 1.0
PB B:ADP702 3.4 31.9 1.0
CD B:GLU291 3.8 23.6 1.0
O B:HOH868 3.8 20.7 1.0
CA B:GLY417 3.9 24.9 1.0
OE2 B:GLU291 4.0 26.9 1.0
CE B:LYS210 4.4 34.8 1.0
NZ B:LYS210 4.4 33.5 1.0
O2B B:ADP702 4.4 29.4 1.0
OG B:SER211 4.5 33.1 1.0
O3A B:ADP702 4.5 31.2 1.0
O1A B:ADP702 4.6 34.7 1.0
NH2 B:ARG467 4.7 19.9 1.0
N B:GLY417 4.7 25.7 1.0
C B:GLY417 4.8 25.7 1.0
O B:GLY417 4.9 26.4 1.0

Fluorine binding site 8 out of 8 in 5e4f

Go back to Fluorine Binding Sites List in 5e4f
Fluorine binding site 8 out of 8 in the The Spring Alpha-Helix Coordinates Multiple Modes of Hcv NS3 Helicase Action


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of The Spring Alpha-Helix Coordinates Multiple Modes of Hcv NS3 Helicase Action within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F701

b:22.9
occ:1.00
 F4 B:ALF701 0.0 22.9 1.0
AL B:ALF701 1.6 21.8 1.0
F2 B:ALF701 2.3 22.8 1.0
F1 B:ALF701 2.3 22.6 1.0
O1B B:ADP702 2.6 25.3 1.0
NH2 B:ARG464 2.8 13.4 1.0
NH1 B:ARG467 2.9 15.8 1.0
O B:HOH835 2.9 17.6 1.0
CB B:THR206 3.1 23.9 1.0
N B:GLY207 3.1 24.6 1.0
CA B:THR206 3.2 24.1 1.0
F3 B:ALF701 3.3 22.9 1.0
C B:THR206 3.6 25.3 1.0
NH2 B:ARG467 3.6 19.9 1.0
CZ B:ARG467 3.7 20.4 1.0
CZ B:ARG464 3.7 15.2 1.0
CG2 B:THR206 3.7 23.1 1.0
NH1 B:ARG464 3.8 17.3 1.0
PB B:ADP702 4.1 31.9 1.0
CA B:GLY207 4.2 26.3 1.0
OG1 B:THR206 4.3 20.9 1.0
OE1 B:GLN460 4.4 17.7 1.0
O B:GLY463 4.5 20.6 1.0
N B:THR206 4.6 24.3 1.0
O3A B:ADP702 4.7 31.2 1.0
O B:THR206 4.7 25.9 1.0
O B:HOH868 4.8 20.7 1.0
O2B B:ADP702 4.8 29.4 1.0
O3B B:ADP702 4.8 27.7 1.0
CA B:GLY417 4.9 24.9 1.0
NZ B:LYS210 4.9 33.5 1.0
NE B:ARG464 4.9 16.8 1.0
NE B:ARG467 4.9 18.2 1.0

Reference:

M.Gu, C.M.Rice. The Spring Alpha-Helix Coordinates Multiple Modes of Hcv (Hepatitis C Virus) NS3 Helicase Action. J.Biol.Chem. V. 291 14499 2016.
ISSN: ESSN 1083-351X
PubMed: 27226535
DOI: 10.1074/JBC.M115.704379
Page generated: Thu Aug 1 08:59:03 2024

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