Fluorine in PDB 6t66: Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4

All present enzymatic activity of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4:
3.6.4.12;

The structure of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4, PDB code: 6t66 was solved by P.Legrand, S.Quevillon-Cheruel, I.Li De La Sierra-Gallay, H.Walbott, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.63 / 3.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	118.978, 123.292, 263.493, 90, 90, 90
R / Rfree (%)	25.5 / 27.6

The structure of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 also contains other interesting chemical elements:

Aluminium	(Al)	6 atoms
Magnesium	(Mg)	6 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 (pdb code 6t66). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 24 binding sites of Fluorine where determined in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4, PDB code: 6t66:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 24 in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 within 5.0Å range: probe atom residue distance (Å) B Occ A:F503 b:175.6 occ:1.00 F1 A:ALF503 0.0 175.6 1.0 AL A:ALF503 1.8 175.6 1.0 F4 A:ALF503 2.5 176.0 1.0 F3 A:ALF503 2.5 175.5 1.0 O3B A:GDP501 2.7 151.9 1.0 CE B:LYS437 3.1 171.5 1.0 NZ B:LYS437 3.3 177.6 1.0 O B:GLU406 3.5 152.0 1.0 F2 A:ALF503 3.6 175.2 1.0 CB A:PRO230 3.6 147.2 1.0 N A:SER231 3.7 144.5 1.0 NH1 B:ARG439 3.7 183.1 1.0 CA A:PRO230 3.9 145.4 1.0 PB A:GDP501 4.1 152.1 1.0 O B:GLN407 4.2 149.3 1.0 C A:PRO230 4.2 148.4 1.0 CA B:GLN407 4.3 147.6 1.0 OE1 A:GLU259 4.4 176.5 1.0 C B:GLU406 4.4 152.5 1.0 NE B:ARG439 4.5 180.4 1.0 O3A A:GDP501 4.5 153.0 1.0 CZ B:ARG439 4.5 194.6 1.0 CD B:LYS437 4.5 166.4 1.0 NE2 A:GLN381 4.6 185.1 1.0 CA A:SER231 4.6 144.1 1.0 C B:GLN407 4.6 149.9 1.0 O B:ALA409 4.7 143.8 1.0 N B:GLN407 4.8 148.2 1.0 NZ A:LYS234 4.8 170.7 1.0 O2B A:GDP501 4.8 151.4 1.0 CB A:SER231 5.0 147.5 1.0

Fluorine binding site 2 out of 24 in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 within 5.0Å range: probe atom residue distance (Å) B Occ A:F503 b:175.2 occ:1.00 F2 A:ALF503 0.0 175.2 1.0 AL A:ALF503 1.8 175.6 1.0 MG A:MG502 2.3 63.7 1.0 F4 A:ALF503 2.5 176.0 1.0 F3 A:ALF503 2.5 175.5 1.0 O2B A:GDP501 2.7 151.4 1.0 OE1 A:GLU259 2.7 176.5 1.0 O3B A:GDP501 2.7 151.9 1.0 PB A:GDP501 3.2 152.1 1.0 CD A:GLU259 3.5 184.8 1.0 CE1 A:TYR341 3.5 159.2 1.0 F1 A:ALF503 3.6 175.6 1.0 OE2 A:GLU259 3.6 177.3 1.0 CE A:LYS234 3.8 164.3 1.0 CD1 A:TYR341 4.0 158.3 1.0 OG1 A:THR235 4.1 151.9 1.0 NZ A:LYS234 4.1 170.7 1.0 O3A A:GDP501 4.2 153.0 1.0 O1B A:GDP501 4.4 152.4 1.0 CZ A:TYR341 4.6 165.2 1.0 NH1 B:ARG439 4.7 183.1 1.0 OH A:TYR341 4.8 166.0 1.0 CE A:MET260 4.8 165.0 1.0 CG A:GLU259 4.9 168.8 1.0 CB A:LYS234 4.9 145.2 1.0 CD A:LYS234 5.0 159.3 1.0

Fluorine binding site 3 out of 24 in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 within 5.0Å range: probe atom residue distance (Å) B Occ A:F503 b:175.5 occ:1.00 F3 A:ALF503 0.0 175.5 1.0 AL A:ALF503 1.8 175.6 1.0 F1 A:ALF503 2.5 175.6 1.0 F2 A:ALF503 2.5 175.2 1.0 O3B A:GDP501 2.7 151.9 1.0 NE B:ARG439 2.8 180.4 1.0 OE1 A:GLU259 2.8 176.5 1.0 NH1 B:ARG439 3.1 183.1 1.0 CZ B:ARG439 3.2 194.6 1.0 PB A:GDP501 3.3 152.1 1.0 O3A A:GDP501 3.4 153.0 1.0 O2B A:GDP501 3.5 151.4 1.0 MG A:MG502 3.6 63.7 1.0 F4 A:ALF503 3.6 176.0 1.0 NZ B:LYS437 3.7 177.6 1.0 CD B:ARG439 3.8 173.2 1.0 CD A:GLU259 4.0 184.8 1.0 O2A A:GDP501 4.0 154.4 1.0 CG B:ARG439 4.2 165.1 1.0 NH2 B:ARG439 4.3 180.5 1.0 PA A:GDP501 4.3 154.2 1.0 CE B:LYS437 4.4 171.5 1.0 CE A:MET260 4.5 165.0 1.0 OE2 A:GLU259 4.6 177.3 1.0 O1B A:GDP501 4.8 152.4 1.0 N A:SER231 4.9 144.5 1.0 O B:GLN407 4.9 149.3 1.0

Fluorine binding site 4 out of 24 in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 within 5.0Å range: probe atom residue distance (Å) B Occ A:F503 b:176.0 occ:1.00 F4 A:ALF503 0.0 176.0 1.0 AL A:ALF503 1.8 175.6 1.0 F1 A:ALF503 2.5 175.6 1.0 F2 A:ALF503 2.5 175.2 1.0 O3B A:GDP501 2.7 151.9 1.0 NZ A:LYS234 2.9 170.7 1.0 NE2 A:GLN381 3.0 185.1 1.0 CE A:LYS234 3.3 164.3 1.0 OH A:TYR341 3.4 166.0 1.0 CE1 A:TYR341 3.6 159.2 1.0 F3 A:ALF503 3.6 175.5 1.0 CZ A:TYR341 3.9 165.2 1.0 CA A:PRO230 3.9 145.4 1.0 PB A:GDP501 4.0 152.1 1.0 CB A:PRO230 4.0 147.2 1.0 CD A:GLN381 4.2 193.5 1.0 OE1 A:GLU259 4.3 176.5 1.0 OE2 A:GLU259 4.3 177.3 1.0 O2B A:GDP501 4.3 151.4 1.0 CA B:GLN407 4.3 147.6 1.0 O B:GLN407 4.5 149.3 1.0 CG A:GLN381 4.5 175.1 1.0 N A:SER231 4.7 144.5 1.0 CD A:GLU259 4.7 184.8 1.0 CB B:GLN407 4.7 149.1 1.0 CD1 A:TYR341 4.7 158.3 1.0 O1B A:GDP501 4.8 152.4 1.0 N A:PRO230 4.8 145.8 1.0 CD A:LYS234 4.8 159.3 1.0 MG A:MG502 4.8 63.7 1.0 C A:PRO230 4.9 148.4 1.0 C B:GLN407 4.9 149.9 1.0 O B:GLU406 5.0 152.0 1.0

Fluorine binding site 5 out of 24 in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 within 5.0Å range: probe atom residue distance (Å) B Occ B:F503 b:160.2 occ:1.00 F1 B:ALF503 0.0 160.2 1.0 AL B:ALF503 1.8 160.6 1.0 F4 B:ALF503 2.5 161.0 1.0 F3 B:ALF503 2.5 160.5 1.0 O3B B:GDP501 2.7 146.2 1.0 CE C:LYS437 3.1 188.0 1.0 O C:GLU406 3.2 161.3 1.0 NZ C:LYS437 3.5 196.7 1.0 F2 B:ALF503 3.6 160.8 1.0 CB B:PRO230 3.6 132.3 1.0 N B:SER231 3.7 129.8 1.0 NH1 C:ARG439 3.9 190.4 1.0 CA B:PRO230 3.9 130.6 1.0 PB B:GDP501 4.1 146.1 1.0 CA C:GLN407 4.1 156.9 1.0 O C:GLN407 4.1 158.8 1.0 C C:GLU406 4.1 162.0 1.0 C B:PRO230 4.2 133.4 1.0 OE1 B:GLU259 4.4 160.7 1.0 C C:GLN407 4.5 159.3 1.0 O3A B:GDP501 4.5 145.3 1.0 CD C:LYS437 4.5 178.3 1.0 N C:GLN407 4.5 157.5 1.0 NE2 B:GLN381 4.6 177.7 1.0 CA B:SER231 4.6 129.6 1.0 O C:ALA409 4.7 151.8 1.0 NE C:ARG439 4.7 187.6 1.0 CZ C:ARG439 4.7 202.7 1.0 NZ B:LYS234 4.8 160.1 1.0 O2B B:GDP501 4.8 145.8 1.0 CB B:SER231 5.0 133.3 1.0

Fluorine binding site 6 out of 24 in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 within 5.0Å range: probe atom residue distance (Å) B Occ B:F503 b:160.8 occ:1.00 F2 B:ALF503 0.0 160.8 1.0 AL B:ALF503 1.8 160.6 1.0 MG B:MG502 2.3 52.1 1.0 F4 B:ALF503 2.5 161.0 1.0 F3 B:ALF503 2.5 160.5 1.0 O2B B:GDP501 2.7 145.8 1.0 OE1 B:GLU259 2.7 160.7 1.0 O3B B:GDP501 2.8 146.2 1.0 PB B:GDP501 3.2 146.1 1.0 CD B:GLU259 3.5 171.8 1.0 CE1 B:TYR341 3.5 144.8 1.0 F1 B:ALF503 3.6 160.2 1.0 OE2 B:GLU259 3.6 165.3 1.0 CE B:LYS234 3.8 151.9 1.0 CD1 B:TYR341 4.0 143.6 1.0 OG1 B:THR235 4.1 131.2 1.0 NZ B:LYS234 4.2 160.1 1.0 O3A B:GDP501 4.2 145.3 1.0 O1B B:GDP501 4.4 146.7 1.0 CZ B:TYR341 4.6 151.4 1.0 NH1 C:ARG439 4.6 190.4 1.0 OH B:TYR341 4.8 152.3 1.0 CE B:MET260 4.8 155.6 1.0 O C:GLN407 4.8 158.8 1.0 CG B:GLU259 4.9 156.5 1.0 CB B:LYS234 4.9 129.6 1.0 CD B:LYS234 5.0 145.4 1.0

Fluorine binding site 7 out of 24 in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 within 5.0Å range: probe atom residue distance (Å) B Occ B:F503 b:160.5 occ:1.00 F3 B:ALF503 0.0 160.5 1.0 AL B:ALF503 1.8 160.6 1.0 F1 B:ALF503 2.5 160.2 1.0 F2 B:ALF503 2.5 160.8 1.0 O3B B:GDP501 2.7 146.2 1.0 OE1 B:GLU259 2.8 160.7 1.0 NE C:ARG439 3.0 187.6 1.0 NH1 C:ARG439 3.0 190.4 1.0 CZ C:ARG439 3.3 202.7 1.0 PB B:GDP501 3.3 146.1 1.0 O3A B:GDP501 3.4 145.3 1.0 O2B B:GDP501 3.5 145.8 1.0 MG B:MG502 3.6 52.1 1.0 F4 B:ALF503 3.6 161.0 1.0 NZ C:LYS437 3.6 196.7 1.0 CD B:GLU259 4.0 171.8 1.0 O2A B:GDP501 4.0 145.2 1.0 CD C:ARG439 4.0 177.3 1.0 CE C:LYS437 4.2 188.0 1.0 PA B:GDP501 4.3 145.0 1.0 NH2 C:ARG439 4.4 189.5 1.0 CG C:ARG439 4.4 167.2 1.0 CE B:MET260 4.5 155.6 1.0 OE2 B:GLU259 4.6 165.3 1.0 O C:GLN407 4.7 158.8 1.0 O1B B:GDP501 4.8 146.7 1.0 N B:SER231 4.9 129.8 1.0

Fluorine binding site 8 out of 24 in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 within 5.0Å range: probe atom residue distance (Å) B Occ B:F503 b:161.0 occ:1.00 F4 B:ALF503 0.0 161.0 1.0 AL B:ALF503 1.8 160.6 1.0 F1 B:ALF503 2.5 160.2 1.0 F2 B:ALF503 2.5 160.8 1.0 O3B B:GDP501 2.7 146.2 1.0 NZ B:LYS234 2.9 160.1 1.0 NE2 B:GLN381 3.0 177.7 1.0 CE B:LYS234 3.3 151.9 1.0 OH B:TYR341 3.4 152.3 1.0 CE1 B:TYR341 3.6 144.8 1.0 F3 B:ALF503 3.6 160.5 1.0 CZ B:TYR341 3.9 151.4 1.0 CA B:PRO230 3.9 130.6 1.0 CA C:GLN407 4.0 156.9 1.0 PB B:GDP501 4.0 146.1 1.0 CB B:PRO230 4.0 132.3 1.0 CD B:GLN381 4.2 185.3 1.0 OE1 B:GLU259 4.3 160.7 1.0 OE2 B:GLU259 4.3 165.3 1.0 O2B B:GDP501 4.3 145.8 1.0 O C:GLN407 4.3 158.8 1.0 CB C:GLN407 4.4 158.3 1.0 CG B:GLN381 4.5 163.9 1.0 N B:SER231 4.7 129.8 1.0 C C:GLN407 4.7 159.3 1.0 CD B:GLU259 4.7 171.8 1.0 O1B B:GDP501 4.8 146.7 1.0 CD1 B:TYR341 4.8 143.6 1.0 O C:GLU406 4.8 161.3 1.0 N B:PRO230 4.8 131.2 1.0 CD B:LYS234 4.8 145.4 1.0 MG B:MG502 4.8 52.1 1.0 N C:GLN407 4.9 157.5 1.0 C B:PRO230 4.9 133.4 1.0

Fluorine binding site 9 out of 24 in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 within 5.0Å range: probe atom residue distance (Å) B Occ C:F503 b:161.8 occ:1.00 F1 C:ALF503 0.0 161.8 1.0 AL C:ALF503 1.8 161.9 1.0 F4 C:ALF503 2.5 161.8 1.0 F3 C:ALF503 2.5 162.0 1.0 O1B C:GDP501 2.7 142.9 1.0 CE D:LYS437 3.1 196.2 1.0 O D:GLU406 3.2 176.9 1.0 NZ D:LYS437 3.4 204.2 1.0 F2 C:ALF503 3.6 161.8 1.0 CB C:PRO230 3.6 139.2 1.0 N C:SER231 3.7 135.9 1.0 NH1 D:ARG439 3.7 200.1 1.0 CA C:PRO230 3.9 137.3 1.0 O D:GLN407 4.0 175.7 1.0 CA D:GLN407 4.1 173.3 1.0 PB C:GDP501 4.1 142.3 1.0 C D:GLU406 4.1 177.6 1.0 C C:PRO230 4.2 140.0 1.0 OE1 C:GLU259 4.4 177.6 1.0 C D:GLN407 4.4 176.1 1.0 O3A C:GDP501 4.5 142.3 1.0 CD D:LYS437 4.5 188.8 1.0 N D:GLN407 4.5 173.7 1.0 NE2 C:GLN381 4.6 181.2 1.0 NE D:ARG439 4.6 198.4 1.0 CA C:SER231 4.6 135.6 1.0 CZ D:ARG439 4.6 212.2 1.0 O D:ALA409 4.6 173.2 1.0 NZ C:LYS234 4.8 162.3 1.0 O3B C:GDP501 4.8 142.2 1.0 CB C:SER231 5.0 138.8 1.0

Fluorine binding site 10 out of 24 in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 within 5.0Å range: probe atom residue distance (Å) B Occ C:F503 b:161.8 occ:1.00 F2 C:ALF503 0.0 161.8 1.0 AL C:ALF503 1.8 161.9 1.0 MG C:MG502 2.3 34.8 1.0 F3 C:ALF503 2.5 162.0 1.0 F4 C:ALF503 2.5 161.8 1.0 O3B C:GDP501 2.7 142.2 1.0 OE1 C:GLU259 2.7 177.6 1.0 O1B C:GDP501 2.8 142.9 1.0 PB C:GDP501 3.2 142.3 1.0 CD C:GLU259 3.5 186.5 1.0 CE1 C:TYR341 3.5 156.3 1.0 F1 C:ALF503 3.6 161.8 1.0 OE2 C:GLU259 3.6 178.6 1.0 CE C:LYS234 3.8 155.6 1.0 CD1 C:TYR341 4.0 155.6 1.0 OG1 C:THR235 4.1 139.6 1.0 NZ C:LYS234 4.2 162.3 1.0 O3A C:GDP501 4.2 142.3 1.0 O2B C:GDP501 4.4 142.2 1.0 NH1 D:ARG439 4.5 200.1 1.0 CZ C:TYR341 4.6 162.5 1.0 OH C:TYR341 4.8 163.3 1.0 O D:GLN407 4.8 175.7 1.0 CE C:MET260 4.8 172.0 1.0 CG C:GLU259 4.9 172.5 1.0 CZ D:ARG439 4.9 212.2 1.0 CB C:LYS234 4.9 135.5 1.0 CD C:LYS234 5.0 148.8 1.0

S.Marsin, Y.Adam, C.Cargemel, J.Andreani, S.Baconnais, P.Legrand, I.Li De La Sierra-Gallay, A.Humbert, M.Aumont-Nicaise, C.Velours, F.Ochsenbein, D.Durand, E.Le Cam, H.Walbott, C.Possoz, S.Quevillon-Cheruel, J.-L.Ferat. Study of the Dnab:Dcia Interplay Reveals Insights Into the Primary Mode of Loading of the Bacterial Replicative Helicase To Be Published.