Fluorine in PDB 6s3h: Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Adp-ALF4 and (Dt)7DS11BP

The structure of Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Adp-ALF4 and (Dt)7DS11BP, PDB code: 6s3h was solved by Y.X.Dai, W.F.Chen, F.Y.Teng, N.N.Liu, X.M.Hou, S.X.Dou, S.Rety, X.G.Xi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.51 / 2.06
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.682, 200.13, 53.955, 90, 93.44, 90
R / Rfree (%)	20.1 / 22.7

The structure of Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Adp-ALF4 and (Dt)7DS11BP also contains other interesting chemical elements:

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

The binding sites of Fluorine atom in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Adp-ALF4 and (Dt)7DS11BP (pdb code 6s3h). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Adp-ALF4 and (Dt)7DS11BP, PDB code: 6s3h:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Adp-ALF4 and (Dt)7DS11BP


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 Helicase PIF1 From Thermus Oshimai in Complex with Adp-ALF4 and (Dt)7DS11BP within 5.0Å range: probe atom residue distance (Å) B Occ A:F1002 b:20.5 occ:1.00 F1 A:ALF1002 0.0 20.5 1.0 AL A:ALF1002 1.8 21.6 1.0 F3 A:ALF1002 2.5 25.1 1.0 F4 A:ALF1002 2.6 22.5 1.0 O3B A:ADP1001 2.6 18.3 1.0 O A:HOH1101 2.7 20.2 1.0 NH2 A:ARG462 2.8 18.9 1.0 NH1 A:ARG256 2.9 17.4 1.0 N A:GLY94 3.0 20.6 1.0 CA A:ALA93 3.1 20.2 1.0 CB A:ALA93 3.1 19.7 1.0 NH1 A:ARG462 3.5 18.3 1.0 C A:ALA93 3.5 23.3 1.0 F2 A:ALF1002 3.6 28.8 1.0 CZ A:ARG462 3.6 20.5 1.0 NE2 A:GLN212 3.6 18.7 1.0 NH2 A:ARG256 3.6 18.2 1.0 CZ A:ARG256 3.7 25.0 1.0 OE1 A:GLN212 3.8 17.9 1.0 CD A:GLN212 4.0 27.5 1.0 CA A:GLY94 4.1 20.9 1.0 PB A:ADP1001 4.1 21.4 1.0 N A:ALA93 4.5 20.7 1.0 O1B A:ADP1001 4.7 18.9 1.0 O A:ALA93 4.7 21.6 1.0 NZ A:LYS97 4.8 18.4 1.0 OG1 A:THR461 4.8 22.0 1.0 NE A:ARG462 4.8 19.1 1.0 O2B A:ADP1001 4.9 18.9 1.0 O3A A:ADP1001 4.9 22.1 1.0 O A:THR461 5.0 24.6 1.0 NE A:ARG256 5.0 25.3 1.0

Fluorine binding site 2 out of 8 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Adp-ALF4 and (Dt)7DS11BP


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 Helicase PIF1 From Thermus Oshimai in Complex with Adp-ALF4 and (Dt)7DS11BP within 5.0Å range: probe atom residue distance (Å) B Occ A:F1002 b:28.8 occ:1.00 F2 A:ALF1002 0.0 28.8 1.0 AL A:ALF1002 1.8 21.6 1.0 MG A:MG1003 1.9 93.4 1.0 O A:HOH1101 2.5 20.2 1.0 F4 A:ALF1002 2.5 22.5 1.0 F3 A:ALF1002 2.6 25.1 1.0 O3B A:ADP1001 2.7 18.3 1.0 O A:HOH1170 2.8 20.9 1.0 O A:HOH1243 2.8 23.5 1.0 OE1 A:GLU172 2.9 19.5 1.0 O2B A:ADP1001 2.9 18.9 1.0 O A:HOH1140 3.1 21.3 1.0 O A:HOH1197 3.1 20.3 1.0 PB A:ADP1001 3.3 21.4 1.0 F1 A:ALF1002 3.6 20.5 1.0 CA A:GLY436 3.7 20.1 1.0 CD A:GLU172 3.8 24.0 1.0 O1B A:ADP1001 4.2 18.9 1.0 OE2 A:GLU172 4.3 24.1 1.0 OG1 A:THR98 4.3 25.1 1.0 N A:GLY436 4.4 20.9 1.0 O A:GLY436 4.5 22.1 1.0 C A:GLY436 4.5 22.9 1.0 CE A:LYS97 4.6 20.4 1.0 O3A A:ADP1001 4.6 22.1 1.0 NZ A:LYS97 4.6 18.4 1.0 NH2 A:ARG256 4.8 18.2 1.0 CG A:GLU172 4.8 23.7 1.0 OE1 A:GLN212 4.8 17.9 1.0 O2A A:ADP1001 5.0 23.8 1.0 NH1 A:ARG462 5.0 18.3 1.0 NE2 A:GLN212 5.0 18.7 1.0

Fluorine binding site 3 out of 8 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Adp-ALF4 and (Dt)7DS11BP


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 Helicase PIF1 From Thermus Oshimai in Complex with Adp-ALF4 and (Dt)7DS11BP within 5.0Å range: probe atom residue distance (Å) B Occ A:F1002 b:25.1 occ:1.00 F3 A:ALF1002 0.0 25.1 1.0 AL A:ALF1002 1.8 21.6 1.0 F1 A:ALF1002 2.5 20.5 1.0 F2 A:ALF1002 2.6 28.8 1.0 O3B A:ADP1001 2.7 18.3 1.0 O A:HOH1101 2.7 20.2 1.0 NZ A:LYS97 2.8 18.4 1.0 O A:HOH1140 2.8 21.3 1.0 NE2 A:GLN212 2.9 18.7 1.0 CE A:LYS97 3.3 20.4 1.0 PB A:ADP1001 3.5 21.4 1.0 F4 A:ALF1002 3.6 22.5 1.0 O1B A:ADP1001 3.6 18.9 1.0 CA A:ALA93 3.7 20.2 1.0 CD A:GLN212 3.7 27.5 1.0 OE1 A:GLN212 3.7 17.9 1.0 N A:GLY94 3.9 20.6 1.0 O2B A:ADP1001 4.0 18.9 1.0 O A:HOH1243 4.1 23.5 1.0 MG A:MG1003 4.2 93.4 1.0 O A:PRO92 4.3 23.4 1.0 OE1 A:GLU172 4.4 19.5 1.0 C A:ALA93 4.4 23.3 1.0 CB A:ALA93 4.4 19.7 1.0 N A:ALA93 4.5 20.7 1.0 C A:PRO92 4.7 24.9 1.0 OE2 A:GLU172 4.8 24.1 1.0 CD A:LYS97 4.8 22.1 1.0 NH2 A:ARG462 4.8 18.9 1.0 CB A:ASP209 4.9 22.9 1.0 CD A:GLU172 4.9 24.0 1.0 O3A A:ADP1001 5.0 22.1 1.0

Fluorine binding site 4 out of 8 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Adp-ALF4 and (Dt)7DS11BP


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 Helicase PIF1 From Thermus Oshimai in Complex with Adp-ALF4 and (Dt)7DS11BP within 5.0Å range: probe atom residue distance (Å) B Occ A:F1002 b:22.5 occ:1.00 F4 A:ALF1002 0.0 22.5 1.0 AL A:ALF1002 1.8 21.6 1.0 F2 A:ALF1002 2.5 28.8 1.0 F1 A:ALF1002 2.6 20.5 1.0 NH2 A:ARG256 2.6 18.2 1.0 O3B A:ADP1001 2.7 18.3 1.0 O A:HOH1101 2.7 20.2 1.0 NH1 A:ARG462 2.8 18.3 1.0 CA A:GLY436 3.1 20.1 1.0 O A:HOH1197 3.2 20.3 1.0 C A:GLY436 3.2 22.9 1.0 O A:GLY436 3.3 22.1 1.0 CZ A:ARG256 3.5 25.0 1.0 NH1 A:ARG256 3.5 17.4 1.0 F3 A:ALF1002 3.6 25.1 1.0 N A:GLY436 3.7 20.9 1.0 MG A:MG1003 3.7 93.4 1.0 CZ A:ARG462 3.8 20.5 1.0 PB A:ADP1001 3.9 21.4 1.0 NH2 A:ARG462 3.9 18.9 1.0 N A:LEU437 4.0 18.9 1.0 O2B A:ADP1001 4.1 18.9 1.0 O A:LEU437 4.3 22.3 1.0 O A:HOH1170 4.3 20.9 1.0 OE1 A:GLU172 4.3 19.5 1.0 O A:HOH1125 4.3 24.6 1.0 O2A A:ADP1001 4.4 23.8 1.0 O3A A:ADP1001 4.5 22.1 1.0 C A:LEU437 4.7 22.7 1.0 NE A:ARG256 4.7 25.3 1.0 N A:GLY94 4.7 20.6 1.0 CA A:LEU437 4.9 18.6 1.0 OE1 A:GLN212 5.0 17.9 1.0 C A:GLN435 5.0 23.1 1.0

Fluorine binding site 5 out of 8 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Adp-ALF4 and (Dt)7DS11BP


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 Helicase PIF1 From Thermus Oshimai in Complex with Adp-ALF4 and (Dt)7DS11BP within 5.0Å range: probe atom residue distance (Å) B Occ B:F603 b:41.0 occ:1.00 F1 B:ALF603 0.0 41.0 1.0 AL B:ALF603 1.8 41.1 1.0 F4 B:ALF603 2.5 38.2 1.0 F3 B:ALF603 2.5 41.1 1.0 O3B B:ADP602 2.7 37.2 1.0 NH2 B:ARG462 2.8 34.3 1.0 O B:HOH703 2.9 33.9 1.0 NH1 B:ARG256 2.9 35.1 1.0 N B:GLY94 3.0 37.9 1.0 CA B:ALA93 3.1 35.8 1.0 CB B:ALA93 3.1 36.9 1.0 NH1 B:ARG462 3.5 32.0 1.0 C B:ALA93 3.5 38.5 1.0 F2 B:ALF603 3.6 46.0 1.0 CZ B:ARG462 3.6 39.6 1.0 NH2 B:ARG256 3.6 32.6 1.0 OE1 B:GLN212 3.7 45.0 1.0 CZ B:ARG256 3.7 39.8 1.0 NE2 B:GLN212 3.7 36.5 1.0 CD B:GLN212 4.1 45.2 1.0 CA B:GLY94 4.1 37.9 1.0 PB B:ADP602 4.1 37.6 1.0 N B:ALA93 4.5 35.9 1.0 O2B B:ADP602 4.7 36.6 1.0 O B:ALA93 4.7 33.3 1.0 NZ B:LYS97 4.8 39.8 1.0 OG1 B:THR461 4.8 41.1 1.0 NE B:ARG462 4.8 37.5 1.0 O1B B:ADP602 4.9 38.5 1.0 O3A B:ADP602 4.9 36.8 1.0 O B:THR461 5.0 38.6 1.0

Fluorine binding site 6 out of 8 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Adp-ALF4 and (Dt)7DS11BP


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 Helicase PIF1 From Thermus Oshimai in Complex with Adp-ALF4 and (Dt)7DS11BP within 5.0Å range: probe atom residue distance (Å) B Occ B:F603 b:46.0 occ:1.00 F2 B:ALF603 0.0 46.0 1.0 AL B:ALF603 1.8 41.1 1.0 MG B:MG601 1.9 121.1 1.0 F3 B:ALF603 2.5 41.1 1.0 F4 B:ALF603 2.5 38.2 1.0 O B:HOH703 2.6 33.9 1.0 O3B B:ADP602 2.7 37.2 1.0 O B:HOH759 2.8 37.5 1.0 O B:HOH771 2.8 36.5 1.0 O1B B:ADP602 2.9 38.5 1.0 OE1 B:GLU172 2.9 45.8 1.0 O B:HOH764 3.0 37.5 1.0 O B:HOH763 3.1 32.3 1.0 PB B:ADP602 3.3 37.6 1.0 F1 B:ALF603 3.6 41.0 1.0 CA B:GLY436 3.8 38.1 1.0 CD B:GLU172 3.8 54.8 1.0 O2B B:ADP602 4.2 36.6 1.0 OG1 B:THR98 4.3 41.8 1.0 OE2 B:GLU172 4.3 42.4 1.0 CE B:LYS97 4.4 41.1 1.0 N B:GLY436 4.5 40.2 1.0 NZ B:LYS97 4.5 39.8 1.0 O B:GLY436 4.5 37.5 1.0 O3A B:ADP602 4.6 36.8 1.0 C B:GLY436 4.6 39.7 1.0 NH2 B:ARG256 4.8 32.6 1.0 CG B:GLU172 4.8 52.5 1.0 OE1 B:GLN212 4.9 45.0 1.0 NE2 B:GLN212 5.0 36.5 1.0 O1A B:ADP602 5.0 38.8 1.0

Fluorine binding site 7 out of 8 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Adp-ALF4 and (Dt)7DS11BP


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 Helicase PIF1 From Thermus Oshimai in Complex with Adp-ALF4 and (Dt)7DS11BP within 5.0Å range: probe atom residue distance (Å) B Occ B:F603 b:41.1 occ:1.00 F3 B:ALF603 0.0 41.1 1.0 AL B:ALF603 1.8 41.1 1.0 F1 B:ALF603 2.5 41.0 1.0 F2 B:ALF603 2.5 46.0 1.0 O3B B:ADP602 2.6 37.2 1.0 NH2 B:ARG256 2.7 32.6 1.0 O B:HOH703 2.7 33.9 1.0 NH1 B:ARG462 2.9 32.0 1.0 CA B:GLY436 3.1 38.1 1.0 O B:HOH763 3.3 32.3 1.0 C B:GLY436 3.3 39.7 1.0 O B:GLY436 3.3 37.5 1.0 CZ B:ARG256 3.5 39.8 1.0 NH1 B:ARG256 3.5 35.1 1.0 F4 B:ALF603 3.6 38.2 1.0 N B:GLY436 3.7 40.2 1.0 MG B:MG601 3.8 121.1 1.0 CZ B:ARG462 3.9 39.6 1.0 PB B:ADP602 3.9 37.6 1.0 NH2 B:ARG462 3.9 34.3 1.0 O1B B:ADP602 4.0 38.5 1.0 N B:LEU437 4.1 37.7 1.0 O B:HOH759 4.2 37.5 1.0 O B:HOH749 4.2 43.2 1.0 OE1 B:GLU172 4.3 45.8 1.0 O B:LEU437 4.3 39.9 1.0 O1A B:ADP602 4.3 38.8 1.0 O3A B:ADP602 4.5 36.8 1.0 N B:GLY94 4.7 37.9 1.0 C B:LEU437 4.7 42.2 1.0 NE B:ARG256 4.8 35.6 1.0 NE2 B:GLN212 4.9 36.5 1.0 CA B:LEU437 4.9 38.4 1.0

Fluorine binding site 8 out of 8 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Adp-ALF4 and (Dt)7DS11BP


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 Helicase PIF1 From Thermus Oshimai in Complex with Adp-ALF4 and (Dt)7DS11BP within 5.0Å range: probe atom residue distance (Å) B Occ B:F603 b:38.2 occ:1.00 F4 B:ALF603 0.0 38.2 1.0 AL B:ALF603 1.8 41.1 1.0 F1 B:ALF603 2.5 41.0 1.0 F2 B:ALF603 2.5 46.0 1.0 O3B B:ADP602 2.7 37.2 1.0 NZ B:LYS97 2.8 39.8 1.0 O B:HOH764 2.8 37.5 1.0 OE1 B:GLN212 2.9 45.0 1.0 O B:HOH703 2.9 33.9 1.0 CE B:LYS97 3.3 41.1 1.0 F3 B:ALF603 3.6 41.1 1.0 PB B:ADP602 3.6 37.6 1.0 O2B B:ADP602 3.7 36.6 1.0 CA B:ALA93 3.7 35.8 1.0 CD B:GLN212 3.7 45.2 1.0 NE2 B:GLN212 3.8 36.5 1.0 N B:GLY94 4.0 37.9 1.0 O1B B:ADP602 4.0 38.5 1.0 MG B:MG601 4.1 121.1 1.0 O B:HOH771 4.1 36.5 1.0 O B:PRO92 4.3 37.4 1.0 C B:ALA93 4.4 38.5 1.0 OE1 B:GLU172 4.4 45.8 1.0 CB B:ALA93 4.4 36.9 1.0 N B:ALA93 4.5 35.9 1.0 C B:PRO92 4.7 38.4 1.0 CD B:LYS97 4.8 44.6 1.0 OE2 B:GLU172 4.8 42.4 1.0 CB B:ASP209 4.8 44.5 1.0 NH2 B:ARG462 4.8 34.3 1.0 CD B:GLU172 5.0 54.8 1.0 O B:GLY91 5.0 40.9 1.0

Y.X.Dai, W.F.Chen, F.Y.Teng, N.N.Liu, X.M.Hou, S.X.Dou, S.Rety, X.G.Xi. Unraveling the Structural and Mechanistic Basis of SF1B Helicase Dimerization: Inhibitory Regulation of Thermus Oshimau PIF1 Activity To Be Published.