Fluorine in PDB 5fhe: Crystal Structure of Bacteroides PIF1 Bound to Ssdna

The structure of Crystal Structure of Bacteroides PIF1 Bound to Ssdna, PDB code: 5fhe was solved by X.Zhou, W.Ren, S.R.Bharath, H.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.79 / 2.90
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	87.442, 87.442, 149.822, 90.00, 90.00, 120.00
R / Rfree (%)	22.3 / 27.7

The structure of Crystal Structure of Bacteroides PIF1 Bound to Ssdna also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Aluminium	(Al)	1 atom

The binding sites of Fluorine atom in the Crystal Structure of Bacteroides PIF1 Bound to Ssdna (pdb code 5fhe). 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 Bacteroides PIF1 Bound to Ssdna, PDB code: 5fhe:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of Bacteroides PIF1 Bound to Ssdna


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 Bacteroides PIF1 Bound to Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:F503 b:66.2 occ:1.00 F1 A:ALF503 0.0 66.2 1.0 AL A:ALF503 1.8 66.2 1.0 F3 A:ALF503 2.5 66.2 1.0 F4 A:ALF503 2.5 66.4 1.0 NH2 A:ARG188 2.6 85.6 1.0 NH1 A:ARG390 2.8 72.1 1.0 O A:GLY365 3.0 67.0 1.0 O3B A:ADP501 3.0 71.2 1.0 C A:GLY365 3.1 67.6 1.0 NH1 A:ARG188 3.2 87.1 1.0 CA A:GLY365 3.3 72.1 1.0 CZ A:ARG188 3.3 86.4 1.0 NH2 A:ARG390 3.4 73.9 1.0 CZ A:ARG390 3.5 73.1 1.0 O2B A:ADP501 3.5 71.8 1.0 F2 A:ALF503 3.6 67.7 1.0 PB A:ADP501 3.7 70.8 1.0 O A:LEU366 3.7 65.5 1.0 N A:GLY365 3.8 73.5 1.0 O2A A:ADP501 3.8 75.7 1.0 N A:LEU366 3.9 64.7 1.0 O3A A:ADP501 3.9 74.0 1.0 C A:LEU366 4.4 65.7 1.0 N A:GLY31 4.5 84.0 1.0 MG A:MG502 4.5 58.6 1.0 PA A:ADP501 4.6 72.5 1.0 OE2 A:GLU106 4.6 78.9 1.0 NE A:ARG188 4.6 84.0 1.0 NE A:ARG390 4.7 73.2 1.0 CA A:LEU366 4.7 64.7 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Bacteroides PIF1 Bound to Ssdna


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 Bacteroides PIF1 Bound to Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:F503 b:67.7 occ:1.00 F2 A:ALF503 0.0 67.7 1.0 AL A:ALF503 1.8 66.2 1.0 F4 A:ALF503 2.5 66.4 1.0 F3 A:ALF503 2.6 66.2 1.0 O3B A:ADP501 2.8 71.2 1.0 OE2 A:GLU106 3.0 78.9 1.0 NZ A:LYS34 3.1 75.9 1.0 CE A:LYS34 3.3 76.8 1.0 MG A:MG502 3.4 58.6 1.0 F1 A:ALF503 3.6 66.2 1.0 O2B A:ADP501 3.6 71.8 1.0 OE1 A:GLU106 3.6 80.8 1.0 PB A:ADP501 3.7 70.8 1.0 CD A:GLU106 3.7 78.9 1.0 OE1 A:GLN145 3.7 72.5 1.0 NE2 A:GLN145 3.8 76.8 1.0 CD A:GLN145 4.1 75.7 1.0 O1B A:ADP501 4.4 71.9 1.0 CA A:GLY365 4.5 72.1 1.0 NH2 A:ARG390 4.6 73.9 1.0 N A:GLY365 4.7 73.5 1.0 CA A:ALA30 4.8 86.9 1.0 CD A:LYS34 4.8 78.4 1.0 OG1 A:THR35 4.8 0.1 1.0 N A:GLY31 5.0 84.0 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Bacteroides PIF1 Bound to Ssdna


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 Bacteroides PIF1 Bound to Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:F503 b:66.2 occ:1.00 F3 A:ALF503 0.0 66.2 1.0 AL A:ALF503 1.8 66.2 1.0 MG A:MG502 2.0 58.6 1.0 O2B A:ADP501 2.1 71.8 1.0 F1 A:ALF503 2.5 66.2 1.0 F2 A:ALF503 2.6 67.7 1.0 OG1 A:THR35 2.9 0.1 1.0 OE2 A:GLU106 3.0 78.9 1.0 CA A:GLY365 3.1 72.1 1.0 PB A:ADP501 3.1 70.8 1.0 O3B A:ADP501 3.1 71.2 1.0 O A:GLY365 3.3 67.0 1.0 F4 A:ALF503 3.6 66.4 1.0 C A:GLY365 3.6 67.6 1.0 O2A A:ADP501 4.0 75.7 1.0 N A:GLY365 4.0 73.5 1.0 O3A A:ADP501 4.1 74.0 1.0 CD A:GLU106 4.1 78.9 1.0 CB A:THR35 4.1 0.5 1.0 O1B A:ADP501 4.3 71.9 1.0 NH1 A:ARG390 4.6 72.1 1.0 PA A:ADP501 4.6 72.5 1.0 NZ A:LYS34 4.6 75.9 1.0 CE A:LYS34 4.7 76.8 1.0 NH2 A:ARG188 4.7 85.6 1.0 OE1 A:GLU106 4.8 80.8 1.0 N A:LEU366 4.9 64.7 1.0 OD2 A:ASP105 4.9 91.8 1.0 OD1 A:ASN61 4.9 67.1 1.0 CG2 A:THR35 5.0 0.7 1.0 N A:THR35 5.0 88.6 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Bacteroides PIF1 Bound to Ssdna


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 Bacteroides PIF1 Bound to Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:F503 b:66.4 occ:1.00 F4 A:ALF503 0.0 66.4 1.0 AL A:ALF503 1.8 66.2 1.0 NH2 A:ARG390 2.4 73.9 1.0 F2 A:ALF503 2.5 67.7 1.0 F1 A:ALF503 2.5 66.2 1.0 O3B A:ADP501 2.8 71.2 1.0 NH2 A:ARG188 3.1 85.6 1.0 CZ A:ARG390 3.3 73.1 1.0 CA A:ALA30 3.4 86.9 1.0 NH1 A:ARG390 3.4 72.1 1.0 NE2 A:GLN145 3.4 76.8 1.0 CB A:ALA30 3.4 89.3 1.0 OE1 A:GLN145 3.5 72.5 1.0 F3 A:ALF503 3.6 66.2 1.0 N A:GLY31 3.7 84.0 1.0 CD A:GLN145 3.9 75.7 1.0 C A:ALA30 4.0 86.6 1.0 PB A:ADP501 4.2 70.8 1.0 NZ A:LYS34 4.2 75.9 1.0 CZ A:ARG188 4.4 86.4 1.0 N A:GLY365 4.5 73.5 1.0 NE A:ARG390 4.5 73.2 1.0 O2B A:ADP501 4.6 71.8 1.0 N A:ALA30 4.6 84.6 1.0 OE2 A:GLU106 4.6 78.9 1.0 CA A:GLY365 4.6 72.1 1.0 CA A:GLY31 4.9 88.0 1.0 O3A A:ADP501 4.9 74.0 1.0 NH1 A:ARG188 4.9 87.1 1.0

X.Zhou, W.Ren, S.R.Bharath, X.Tang, Y.He, C.Chen, Z.Liu, D.Li, H.Song. Structural and Functional Insights Into the Unwinding Mechanism of Bacteroides Sp PIF1 Cell Rep V. 14 2030 2016.
ISSN: ESSN 2211-1247
PubMed: 26904952
DOI: 10.1016/J.CELREP.2016.02.008