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Fluorine in PDB 5fhd: Structure of Bacteroides Sp PIF1 Complexed with Tailed Dsdna Resulting in Ssdna Bound Complex

Protein crystallography data

The structure of Structure of Bacteroides Sp PIF1 Complexed with Tailed Dsdna Resulting in Ssdna Bound Complex, PDB code: 5fhd 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) 29.54 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.471, 149.640, 185.140, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 21.2

Other elements in 5fhd:

The structure of Structure of Bacteroides Sp PIF1 Complexed with Tailed Dsdna Resulting in Ssdna Bound Complex 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 Structure of Bacteroides Sp PIF1 Complexed with Tailed Dsdna Resulting in Ssdna Bound Complex (pdb code 5fhd). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Structure of Bacteroides Sp PIF1 Complexed with Tailed Dsdna Resulting in Ssdna Bound Complex, PDB code: 5fhd:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 5fhd

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Fluorine binding site 1 out of 8 in the Structure of Bacteroides Sp PIF1 Complexed with Tailed Dsdna Resulting in Ssdna Bound Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Bacteroides Sp PIF1 Complexed with Tailed Dsdna Resulting in Ssdna Bound Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:19.4
occ:1.00
 F1 A:ALF503 0.0 19.4 1.0
AL A:ALF503 1.8 20.3 1.0
F4 A:ALF503 2.5 19.5 1.0
F3 A:ALF503 2.5 18.2 1.0
O1B A:ADP501 2.6 18.2 1.0
NH2 A:ARG188 2.7 19.8 1.0
O A:HOH626 2.7 17.6 1.0
NH1 A:ARG390 2.9 15.8 1.0
CA A:GLY365 3.1 20.1 1.0
O A:HOH655 3.2 16.9 1.0
C A:GLY365 3.3 21.7 1.0
O A:GLY365 3.3 20.6 1.0
NH1 A:ARG188 3.4 18.7 1.0
CZ A:ARG188 3.5 20.9 1.0
N A:GLY365 3.6 19.3 1.0
F2 A:ALF503 3.6 17.2 1.0
MG A:MG502 3.7 20.0 1.0
CZ A:ARG390 3.8 18.1 1.0
PB A:ADP501 3.8 19.1 1.0
NH2 A:ARG390 3.9 19.8 1.0
O3B A:ADP501 4.0 15.3 1.0
N A:LEU366 4.1 18.5 1.0
OE2 A:GLU106 4.2 20.3 1.0
O1A A:ADP501 4.2 21.1 1.0
O A:LEU366 4.3 20.2 1.0
O A:HOH660 4.4 17.8 1.0
O3A A:ADP501 4.4 19.1 1.0
O A:HOH659 4.6 26.0 1.0
N A:GLY31 4.7 18.7 1.0
NE A:ARG188 4.7 24.2 1.0
C A:LEU366 4.8 26.1 1.0
C A:GLN364 4.9 18.9 1.0
CA A:LEU366 5.0 18.6 1.0

Fluorine binding site 2 out of 8 in 5fhd

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Fluorine binding site 2 out of 8 in the Structure of Bacteroides Sp PIF1 Complexed with Tailed Dsdna Resulting in Ssdna Bound Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Bacteroides Sp PIF1 Complexed with Tailed Dsdna Resulting in Ssdna Bound Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:17.2
occ:1.00
 F2 A:ALF503 0.0 17.2 1.0
AL A:ALF503 1.8 20.3 1.0
F4 A:ALF503 2.5 19.5 1.0
F3 A:ALF503 2.6 18.2 1.0
NZ A:LYS34 2.6 17.5 1.0
O1B A:ADP501 2.7 18.2 1.0
O A:HOH626 2.8 17.6 1.0
O A:HOH616 2.9 20.9 1.0
NE2 A:GLN145 2.9 17.2 1.0
CE A:LYS34 3.4 16.0 1.0
PB A:ADP501 3.6 19.1 1.0
F1 A:ALF503 3.6 19.4 1.0
OE1 A:GLN145 3.7 18.4 1.0
CA A:ALA30 3.7 18.0 1.0
O2B A:ADP501 3.7 17.4 1.0
CD A:GLN145 3.7 19.0 1.0
O3B A:ADP501 4.0 15.3 1.0
N A:GLY31 4.0 18.7 1.0
O A:HOH656 4.2 19.7 1.0
O A:LYS29 4.2 19.7 1.0
MG A:MG502 4.2 20.0 1.0
OE2 A:GLU106 4.4 20.3 1.0
N A:ALA30 4.4 16.4 1.0
C A:ALA30 4.4 16.6 1.0
CB A:ALA30 4.5 17.0 1.0
C A:LYS29 4.6 19.4 1.0
CB A:ASP142 4.7 18.6 1.0
OE1 A:GLU106 4.8 23.7 1.0
NH2 A:ARG390 4.9 19.8 1.0
CD A:LYS34 4.9 16.9 1.0
O A:GLY28 5.0 19.3 1.0
CD A:GLU106 5.0 25.5 1.0
O3A A:ADP501 5.0 19.1 1.0

Fluorine binding site 3 out of 8 in 5fhd

Go back to Fluorine Binding Sites List in 5fhd
Fluorine binding site 3 out of 8 in the Structure of Bacteroides Sp PIF1 Complexed with Tailed Dsdna Resulting in Ssdna Bound Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Bacteroides Sp PIF1 Complexed with Tailed Dsdna Resulting in Ssdna Bound Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:18.2
occ:1.00
 F3 A:ALF503 0.0 18.2 1.0
AL A:ALF503 1.8 20.3 1.0
MG A:MG502 1.9 20.0 1.0
F1 A:ALF503 2.5 19.4 1.0
F2 A:ALF503 2.6 17.2 1.0
O A:HOH626 2.7 17.6 1.0
O1B A:ADP501 2.7 18.2 1.0
O3B A:ADP501 2.7 15.3 1.0
O A:HOH660 2.8 17.8 1.0
O A:HOH656 2.8 19.7 1.0
OE2 A:GLU106 2.9 20.3 1.0
O A:HOH655 3.0 16.9 1.0
O A:HOH616 3.1 20.9 1.0
PB A:ADP501 3.2 19.1 1.0
F4 A:ALF503 3.6 19.5 1.0
CA A:GLY365 3.8 20.1 1.0
CD A:GLU106 3.8 25.5 1.0
OG1 A:THR35 4.0 19.4 1.0
O2B A:ADP501 4.2 17.4 1.0
NZ A:LYS34 4.2 17.5 1.0
OE1 A:GLU106 4.3 23.7 1.0
N A:GLY365 4.4 19.3 1.0
O A:GLY365 4.5 20.6 1.0
O3A A:ADP501 4.5 19.1 1.0
CE A:LYS34 4.6 16.0 1.0
C A:GLY365 4.6 21.7 1.0
NH2 A:ARG188 4.8 19.8 1.0
O1A A:ADP501 4.8 21.1 1.0
OE1 A:GLN145 4.9 18.4 1.0
CG A:GLU106 4.9 19.6 1.0

Fluorine binding site 4 out of 8 in 5fhd

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Fluorine binding site 4 out of 8 in the Structure of Bacteroides Sp PIF1 Complexed with Tailed Dsdna Resulting in Ssdna Bound Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Bacteroides Sp PIF1 Complexed with Tailed Dsdna Resulting in Ssdna Bound Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:19.5
occ:1.00
 F4 A:ALF503 0.0 19.5 1.0
AL A:ALF503 1.8 20.3 1.0
F1 A:ALF503 2.5 19.4 1.0
F2 A:ALF503 2.5 17.2 1.0
O1B A:ADP501 2.7 18.2 1.0
NH2 A:ARG390 2.8 19.8 1.0
O A:HOH626 2.8 17.6 1.0
NH1 A:ARG188 2.8 18.7 1.0
CA A:ALA30 3.1 18.0 1.0
N A:GLY31 3.1 18.7 1.0
CB A:ALA30 3.2 17.0 1.0
NH1 A:ARG390 3.5 15.8 1.0
CZ A:ARG390 3.5 18.1 1.0
F3 A:ALF503 3.6 18.2 1.0
C A:ALA30 3.6 16.6 1.0
NE2 A:GLN145 3.6 17.2 1.0
NH2 A:ARG188 3.7 19.8 1.0
CZ A:ARG188 3.7 20.9 1.0
OE1 A:GLN145 3.9 18.4 1.0
CD A:GLN145 4.1 19.0 1.0
PB A:ADP501 4.1 19.1 1.0
CA A:GLY31 4.2 17.0 1.0
N A:ALA30 4.4 16.4 1.0
NZ A:LYS34 4.7 17.5 1.0
O2B A:ADP501 4.7 17.4 1.0
O A:ALA30 4.8 19.9 1.0
NE A:ARG390 4.8 18.7 1.0
OG A:SER389 4.8 19.7 1.0
O3A A:ADP501 4.9 19.1 1.0
O3B A:ADP501 4.9 15.3 1.0
NE A:ARG188 5.0 24.2 1.0
O A:LYS29 5.0 19.7 1.0

Fluorine binding site 5 out of 8 in 5fhd

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Fluorine binding site 5 out of 8 in the Structure of Bacteroides Sp PIF1 Complexed with Tailed Dsdna Resulting in Ssdna Bound Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Bacteroides Sp PIF1 Complexed with Tailed Dsdna Resulting in Ssdna Bound Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F503

b:17.9
occ:1.00
 F1 B:ALF503 0.0 17.9 1.0
AL B:ALF503 1.8 21.0 1.0
MG B:MG502 2.0 21.8 1.0
F3 B:ALF503 2.5 21.1 1.0
F4 B:ALF503 2.5 21.2 1.0
O B:HOH619 2.6 20.6 1.0
O3B B:ADP501 2.7 19.7 1.0
O1B B:ADP501 2.8 20.3 1.0
O B:HOH674 2.8 19.3 1.0
O B:HOH659 2.9 19.3 1.0
OE2 B:GLU106 2.9 23.3 1.0
O B:HOH641 3.0 21.2 1.0
O B:HOH617 3.2 17.9 1.0
PB B:ADP501 3.2 20.0 1.0
F2 B:ALF503 3.6 18.7 1.0
CD B:GLU106 3.8 26.4 1.0
CA B:GLY365 3.8 20.3 1.0
OG1 B:THR35 4.1 21.3 1.0
O2B B:ADP501 4.2 16.1 1.0
NZ B:LYS34 4.2 14.9 1.0
OE1 B:GLU106 4.3 24.0 1.0
N B:GLY365 4.4 20.8 1.0
CE B:LYS34 4.4 17.4 1.0
O3A B:ADP501 4.5 19.5 1.0
O B:GLY365 4.6 20.4 1.0
C B:GLY365 4.6 24.1 1.0
NH2 B:ARG188 4.8 18.1 1.0
O1A B:ADP501 4.8 21.4 1.0
OE1 B:GLN145 4.8 19.1 1.0
CG B:GLU106 4.9 20.2 1.0

Fluorine binding site 6 out of 8 in 5fhd

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Fluorine binding site 6 out of 8 in the Structure of Bacteroides Sp PIF1 Complexed with Tailed Dsdna Resulting in Ssdna Bound Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Bacteroides Sp PIF1 Complexed with Tailed Dsdna Resulting in Ssdna Bound Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F503

b:18.7
occ:1.00
 F2 B:ALF503 0.0 18.7 1.0
AL B:ALF503 1.8 21.0 1.0
F4 B:ALF503 2.5 21.2 1.0
F3 B:ALF503 2.6 21.1 1.0
NH2 B:ARG390 2.7 16.0 1.0
O3B B:ADP501 2.8 19.7 1.0
O B:HOH619 2.9 20.6 1.0
NH1 B:ARG188 2.9 19.3 1.0
CA B:ALA30 3.1 21.0 1.0
CB B:ALA30 3.1 18.5 1.0
N B:GLY31 3.2 19.6 1.0
NH1 B:ARG390 3.5 18.0 1.0
CZ B:ARG390 3.5 21.9 1.0
F1 B:ALF503 3.6 17.9 1.0
NE2 B:GLN145 3.6 16.0 1.0
C B:ALA30 3.6 18.4 1.0
NH2 B:ARG188 3.6 18.1 1.0
CZ B:ARG188 3.7 23.3 1.0
OE1 B:GLN145 3.9 19.1 1.0
CD B:GLN145 4.1 19.5 1.0
PB B:ADP501 4.3 20.0 1.0
CA B:GLY31 4.3 17.5 1.0
N B:ALA30 4.4 15.3 1.0
NZ B:LYS34 4.7 14.9 1.0
O B:ALA30 4.7 19.2 1.0
NE B:ARG390 4.8 17.0 1.0
O2B B:ADP501 4.8 16.1 1.0
OG B:SER389 4.9 16.1 1.0
O3A B:ADP501 4.9 19.5 1.0
NE B:ARG188 5.0 20.8 1.0

Fluorine binding site 7 out of 8 in 5fhd

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Fluorine binding site 7 out of 8 in the Structure of Bacteroides Sp PIF1 Complexed with Tailed Dsdna Resulting in Ssdna Bound Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structure of Bacteroides Sp PIF1 Complexed with Tailed Dsdna Resulting in Ssdna Bound Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F503

b:21.1
occ:1.00
 F3 B:ALF503 0.0 21.1 1.0
AL B:ALF503 1.8 21.0 1.0
F1 B:ALF503 2.5 17.9 1.0
F2 B:ALF503 2.6 18.7 1.0
NZ B:LYS34 2.6 14.9 1.0
O3B B:ADP501 2.7 19.7 1.0
O B:HOH619 2.8 20.6 1.0
O B:HOH641 2.9 21.2 1.0
NE2 B:GLN145 2.9 16.0 1.0
CE B:LYS34 3.3 17.4 1.0
PB B:ADP501 3.6 20.0 1.0
F4 B:ALF503 3.6 21.2 1.0
CA B:ALA30 3.6 21.0 1.0
O2B B:ADP501 3.7 16.1 1.0
OE1 B:GLN145 3.7 19.1 1.0
CD B:GLN145 3.7 19.5 1.0
N B:GLY31 4.0 19.6 1.0
O1B B:ADP501 4.1 20.3 1.0
O B:HOH674 4.1 19.3 1.0
O B:LYS29 4.1 18.4 1.0
MG B:MG502 4.2 21.8 1.0
N B:ALA30 4.3 15.3 1.0
C B:ALA30 4.4 18.4 1.0
OE2 B:GLU106 4.4 23.3 1.0
CB B:ALA30 4.4 18.5 1.0
C B:LYS29 4.5 18.8 1.0
CB B:ASP142 4.7 20.5 1.0
CD B:LYS34 4.8 16.2 1.0
NH2 B:ARG390 4.9 16.0 1.0
OE1 B:GLU106 4.9 24.0 1.0
O B:GLY28 5.0 20.2 1.0
O3A B:ADP501 5.0 19.5 1.0

Fluorine binding site 8 out of 8 in 5fhd

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Fluorine binding site 8 out of 8 in the Structure of Bacteroides Sp PIF1 Complexed with Tailed Dsdna Resulting in Ssdna Bound Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structure of Bacteroides Sp PIF1 Complexed with Tailed Dsdna Resulting in Ssdna Bound Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F503

b:21.2
occ:1.00
 F4 B:ALF503 0.0 21.2 1.0
AL B:ALF503 1.8 21.0 1.0
F2 B:ALF503 2.5 18.7 1.0
F1 B:ALF503 2.5 17.9 1.0
NH2 B:ARG188 2.7 18.1 1.0
O3B B:ADP501 2.7 19.7 1.0
O B:HOH619 2.7 20.6 1.0
NH1 B:ARG390 2.9 18.0 1.0
CA B:GLY365 3.2 20.3 1.0
O B:HOH617 3.2 17.9 1.0
C B:GLY365 3.3 24.1 1.0
O B:GLY365 3.3 20.4 1.0
N B:GLY365 3.5 20.8 1.0
CZ B:ARG188 3.5 23.3 1.0
NH1 B:ARG188 3.6 19.3 1.0
F3 B:ALF503 3.6 21.1 1.0
MG B:MG502 3.7 21.8 1.0
CZ B:ARG390 3.8 21.9 1.0
NH2 B:ARG390 3.9 16.0 1.0
PB B:ADP501 3.9 20.0 1.0
O1B B:ADP501 4.0 20.3 1.0
N B:LEU366 4.1 21.7 1.0
OE2 B:GLU106 4.2 23.3 1.0
O1A B:ADP501 4.2 21.4 1.0
O B:LEU366 4.3 21.8 1.0
O B:HOH659 4.3 19.3 1.0
O3A B:ADP501 4.4 19.5 1.0
N B:GLY31 4.7 19.6 1.0
NE B:ARG188 4.8 20.8 1.0
C B:LEU366 4.8 22.8 1.0
C B:GLN364 4.8 19.3 1.0
CA B:LEU366 4.9 21.9 1.0
PA B:ADP501 5.0 19.2 1.0
OE1 B:GLN145 5.0 19.1 1.0

Reference:

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
Page generated: Thu Aug 1 09:23:12 2024

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