Fluorine in PDB 6s3i: Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-MGF4

The structure of Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-MGF4, PDB code: 6s3i 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)	59.57 / 2.46
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.195, 61.195, 260.358, 90, 90, 90
R / Rfree (%)	24.4 / 30.2

The structure of Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-MGF4 also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-MGF4 (pdb code 6s3i). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-MGF4, PDB code: 6s3i:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-MGF4


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 Ssdna (Dt)18 and Adp-MGF4 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1003 b:61.3 occ:1.00 F1 A:MF41003 0.0 61.3 1.0 MG A:MF41003 1.8 72.6 1.0 MG A:MG1002 1.9 62.8 1.0 HA2 A:GLY436 2.5 60.8 1.0 O3B A:ADP1001 2.7 45.0 1.0 O A:HOH1105 2.7 45.7 1.0 O1B A:ADP1001 2.9 56.0 1.0 F2 A:MF41003 2.9 45.0 1.0 O A:HOH1111 3.0 45.3 1.0 F3 A:MF41003 3.0 44.6 1.0 F4 A:MF41003 3.0 54.3 1.0 O A:HOH1106 3.1 48.8 1.0 OE2 A:GLU172 3.2 44.6 1.0 PB A:ADP1001 3.2 44.9 1.0 CA A:GLY436 3.5 50.4 1.0 OG1 A:THR98 3.5 45.0 1.0 O A:GLY436 3.8 52.0 1.0 HA3 A:GLY436 3.8 60.8 1.0 HH22 A:ARG256 4.0 85.0 1.0 C A:GLY436 4.0 44.9 1.0 HH12 A:ARG462 4.1 66.1 1.0 O2B A:ADP1001 4.1 50.2 1.0 HZ1 A:LYS97 4.2 55.8 1.0 O1A A:ADP1001 4.2 44.8 1.0 CD A:GLU172 4.3 44.6 1.0 H A:GLY436 4.3 54.2 1.0 N A:GLY436 4.3 44.9 1.0 H A:THR98 4.4 54.1 1.0 HB A:THR98 4.4 54.4 1.0 HH22 A:ARG462 4.5 72.7 1.0 HH12 A:ARG256 4.5 55.2 1.0 HZ2 A:LYS97 4.5 55.8 1.0 HE22 A:GLN212 4.6 62.0 1.0 CB A:THR98 4.6 45.1 1.0 O3A A:ADP1001 4.6 49.7 1.0 HE2 A:LYS97 4.7 53.7 1.0 H A:GLY94 4.7 54.2 1.0 HB2 A:LYS97 4.7 54.2 1.0 NZ A:LYS97 4.7 46.3 1.0 NH2 A:ARG256 4.8 70.6 1.0 NH1 A:ARG462 4.9 54.8 1.0 OE1 A:GLU172 4.9 44.5 1.0 HG2 A:GLU172 4.9 54.2 1.0 PA A:ADP1001 5.0 44.3 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-MGF4


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 Ssdna (Dt)18 and Adp-MGF4 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1003 b:45.0 occ:1.00 F2 A:MF41003 0.0 45.0 1.0 MG A:MF41003 1.8 72.6 1.0 HA2 A:GLY436 2.7 60.8 1.0 OE1 A:GLN212 2.7 54.0 1.0 H A:GLY436 2.7 54.2 1.0 HG3 A:GLN435 2.8 54.2 1.0 OE2 A:GLU172 2.8 44.6 1.0 F3 A:MF41003 2.8 44.6 1.0 F4 A:MF41003 2.8 54.3 1.0 F1 A:MF41003 2.9 61.3 1.0 HE22 A:GLN212 2.9 62.0 1.0 HH22 A:ARG462 3.0 72.7 1.0 N A:GLY436 3.1 44.9 1.0 CA A:GLY436 3.3 50.4 1.0 HH12 A:ARG462 3.4 66.1 1.0 CD A:GLN212 3.5 54.6 1.0 NE2 A:GLN212 3.5 51.4 1.0 HG2 A:GLN435 3.5 54.2 1.0 NH2 A:ARG462 3.5 60.4 1.0 CG A:GLN435 3.5 44.9 1.0 CD A:GLU172 3.7 44.6 1.0 NH1 A:ARG462 3.9 54.8 1.0 HA3 A:GLY436 3.9 60.8 1.0 OE1 A:GLU172 3.9 44.5 1.0 C A:GLN435 4.0 45.0 1.0 CZ A:ARG462 4.0 66.4 1.0 HH21 A:ARG462 4.0 72.7 1.0 HE21 A:GLN435 4.1 57.8 1.0 O A:HOH1105 4.1 45.7 1.0 HA A:GLN435 4.1 68.5 1.0 HE21 A:GLN212 4.3 62.0 1.0 CD A:GLN435 4.4 52.4 1.0 C A:GLY436 4.4 44.9 1.0 CA A:GLN435 4.5 56.8 1.0 HH11 A:ARG462 4.5 66.1 1.0 O1B A:ADP1001 4.5 56.0 1.0 NE2 A:GLN435 4.5 47.9 1.0 HH12 A:ARG256 4.5 55.2 1.0 MG A:MG1002 4.6 62.8 1.0 HB1 A:ALA93 4.6 54.8 1.0 CB A:GLN435 4.6 53.3 1.0 HZ2 A:LYS97 4.6 55.8 1.0 HB2 A:ALA93 4.8 54.8 1.0 HA A:ALA93 4.8 54.5 1.0 O A:GLN435 4.8 48.0 1.0 HG22 A:VAL458 4.9 62.6 1.0 CG A:GLN212 4.9 47.4 1.0 O A:GLY436 5.0 52.0 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-MGF4


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 Ssdna (Dt)18 and Adp-MGF4 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1003 b:44.6 occ:1.00 F3 A:MF41003 0.0 44.6 1.0 MG A:MF41003 1.8 72.6 1.0 HE22 A:GLN212 1.9 62.0 1.0 HZ2 A:LYS97 2.1 55.8 1.0 HZ1 A:LYS97 2.3 55.8 1.0 NZ A:LYS97 2.6 46.3 1.0 HA A:ALA93 2.7 54.5 1.0 NE2 A:GLN212 2.8 51.4 1.0 F2 A:MF41003 2.8 45.0 1.0 F4 A:MF41003 2.9 54.3 1.0 F1 A:MF41003 3.0 61.3 1.0 HZ3 A:LYS97 3.1 55.8 1.0 HE21 A:GLN212 3.2 62.0 1.0 O1B A:ADP1001 3.2 56.0 1.0 H A:GLY94 3.4 54.2 1.0 O2B A:ADP1001 3.6 50.2 1.0 HE2 A:LYS97 3.7 53.7 1.0 CA A:ALA93 3.7 45.2 1.0 CE A:LYS97 3.7 44.5 1.0 PB A:ADP1001 3.8 44.9 1.0 CD A:GLN212 3.8 54.6 1.0 HH22 A:ARG462 3.9 72.7 1.0 OE1 A:GLN212 3.9 54.0 1.0 HB1 A:ALA93 3.9 54.8 1.0 HB2 A:ALA93 4.0 54.8 1.0 CB A:ALA93 4.1 45.4 1.0 N A:GLY94 4.1 44.9 1.0 HE3 A:LYS97 4.2 53.7 1.0 O3B A:ADP1001 4.3 45.0 1.0 OE2 A:GLU172 4.3 44.6 1.0 O A:PRO92 4.4 55.8 1.0 HB2 A:ASP209 4.4 63.8 1.0 C A:ALA93 4.5 45.0 1.0 N A:ALA93 4.5 45.3 1.0 HH12 A:ARG256 4.6 55.2 1.0 O A:HOH1106 4.6 48.8 1.0 HA2 A:GLY436 4.6 60.8 1.0 HB2 A:LYS97 4.6 54.2 1.0 HB3 A:ASP209 4.6 63.8 1.0 NH2 A:ARG462 4.6 60.4 1.0 HD3 A:LYS97 4.7 71.4 1.0 MG A:MG1002 4.7 62.8 1.0 C A:PRO92 4.7 46.2 1.0 CD A:LYS97 4.9 59.3 1.0 OE1 A:GLU172 4.9 44.5 1.0 HH21 A:ARG462 5.0 72.7 1.0 HH12 A:ARG462 5.0 66.1 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-MGF4


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 Ssdna (Dt)18 and Adp-MGF4 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1003 b:54.3 occ:1.00 F4 A:MF41003 0.0 54.3 1.0 MG A:MF41003 1.8 72.6 1.0 HH22 A:ARG462 1.8 72.7 1.0 HH12 A:ARG256 1.8 55.2 1.0 HH12 A:ARG462 2.4 66.1 1.0 O1B A:ADP1001 2.5 56.0 1.0 NH2 A:ARG462 2.6 60.4 1.0 NH1 A:ARG256 2.7 45.7 1.0 F2 A:MF41003 2.8 45.0 1.0 F3 A:MF41003 2.9 44.6 1.0 HH22 A:ARG256 2.9 85.0 1.0 H A:GLY94 3.0 54.2 1.0 F1 A:MF41003 3.0 61.3 1.0 NH1 A:ARG462 3.1 54.8 1.0 HB1 A:ALA93 3.1 54.8 1.0 HH11 A:ARG256 3.2 55.2 1.0 CZ A:ARG462 3.3 66.4 1.0 HH21 A:ARG462 3.3 72.7 1.0 NH2 A:ARG256 3.5 70.6 1.0 CZ A:ARG256 3.5 57.6 1.0 HA2 A:GLY436 3.6 60.8 1.0 HA A:ALA93 3.6 54.5 1.0 N A:GLY94 3.7 44.9 1.0 HE22 A:GLN212 3.8 62.0 1.0 HH11 A:ARG462 3.8 66.1 1.0 H A:GLY436 3.9 54.2 1.0 CB A:ALA93 3.9 45.4 1.0 PB A:ADP1001 3.9 44.9 1.0 HA2 A:GLY94 4.1 54.3 1.0 CA A:ALA93 4.1 45.2 1.0 HB2 A:ALA93 4.1 54.8 1.0 CA A:GLY436 4.3 50.4 1.0 C A:ALA93 4.3 45.0 1.0 HH21 A:ARG256 4.3 85.0 1.0 CA A:GLY94 4.4 45.0 1.0 N A:GLY436 4.5 44.9 1.0 OE1 A:GLN212 4.5 54.0 1.0 NE2 A:GLN212 4.5 51.4 1.0 C A:GLY436 4.5 44.9 1.0 O3B A:ADP1001 4.5 45.0 1.0 NE A:ARG462 4.6 60.8 1.0 O1A A:ADP1001 4.6 44.8 1.0 O A:GLY436 4.6 52.0 1.0 HZ1 A:LYS97 4.6 55.8 1.0 O2B A:ADP1001 4.7 50.2 1.0 HB3 A:ALA93 4.7 54.8 1.0 MG A:MG1002 4.8 62.8 1.0 NE A:ARG256 4.8 58.9 1.0 HA3 A:GLY94 4.8 54.3 1.0 HZ2 A:LYS97 4.9 55.8 1.0 CD A:GLN212 4.9 54.6 1.0 O A:HOH1111 4.9 45.3 1.0 HE A:ARG462 4.9 73.2 1.0 O3A A:ADP1001 5.0 49.7 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.