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Fluorine in PDB 6l3g: Structural Basis For Dna Unwinding at Forked Dsdna By Two Coordinating PIF1 Helicases

Protein crystallography data

The structure of Structural Basis For Dna Unwinding at Forked Dsdna By Two Coordinating PIF1 Helicases, PDB code: 6l3g was solved by N.Su, S.R.Bharath, H.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.57 / 3.30
Space group P 31 1 2
Cell size a, b, c (Å), α, β, γ (°) 131.265, 131.265, 117.183, 90.00, 90.00, 120.00
R / Rfree (%) 24.4 / 30.3

Other elements in 6l3g:

The structure of Structural Basis For Dna Unwinding at Forked Dsdna By Two Coordinating PIF1 Helicases 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 Structural Basis For Dna Unwinding at Forked Dsdna By Two Coordinating PIF1 Helicases (pdb code 6l3g). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Structural Basis For Dna Unwinding at Forked Dsdna By Two Coordinating PIF1 Helicases, PDB code: 6l3g:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 6l3g

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Fluorine binding site 1 out of 8 in the Structural Basis For Dna Unwinding at Forked Dsdna By Two Coordinating PIF1 Helicases


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structural Basis For Dna Unwinding at Forked Dsdna By Two Coordinating PIF1 Helicases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:70.6
occ:1.00
 F1 A:ALF503 0.0 70.6 1.0
AL A:ALF503 1.8 58.8 1.0
F4 A:ALF503 2.5 54.0 1.0
F3 A:ALF503 2.5 77.2 1.0
NH2 A:ARG188 2.8 75.3 1.0
MG A:MG502 3.0 44.3 1.0
O A:GLY365 3.1 73.8 1.0
CA A:GLY365 3.1 57.2 1.0
O3A A:ADP501 3.1 72.0 1.0
O3B A:ADP501 3.2 68.8 1.0
C A:GLY365 3.3 62.8 1.0
O1B A:ADP501 3.5 52.8 1.0
PB A:ADP501 3.5 60.6 1.0
NH1 A:ARG390 3.6 66.8 1.0
F2 A:ALF503 3.6 55.3 1.0
O2A A:ADP501 3.6 79.1 1.0
N A:GLY365 3.8 56.6 1.0
CZ A:ARG188 4.0 71.1 1.0
PA A:ADP501 4.1 63.4 1.0
OE2 A:GLU106 4.1 59.6 1.0
NH1 A:ARG188 4.2 63.8 1.0
N A:LEU366 4.2 54.1 1.0
CZ A:ARG390 4.5 70.5 1.0
NH2 A:ARG390 4.6 66.9 1.0
O A:LEU366 4.7 65.6 1.0
O A:HOH602 4.8 61.1 1.0
OG1 A:THR35 4.9 76.1 1.0
O2B A:ADP501 5.0 64.6 1.0

Fluorine binding site 2 out of 8 in 6l3g

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Fluorine binding site 2 out of 8 in the Structural Basis For Dna Unwinding at Forked Dsdna By Two Coordinating PIF1 Helicases


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structural Basis For Dna Unwinding at Forked Dsdna By Two Coordinating PIF1 Helicases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:55.3
occ:1.00
 F2 A:ALF503 0.0 55.3 1.0
AL A:ALF503 1.8 58.8 1.0
F3 A:ALF503 2.5 77.2 1.0
NE2 A:GLN145 2.5 60.5 1.0
F4 A:ALF503 2.5 54.0 1.0
O3B A:ADP501 2.9 68.8 1.0
NZ A:LYS34 3.3 61.5 1.0
CD A:GLN145 3.3 67.0 1.0
OE1 A:GLN145 3.3 72.9 1.0
F1 A:ALF503 3.6 70.6 1.0
CE A:LYS34 3.8 76.8 1.0
O1B A:ADP501 4.0 52.8 1.0
PB A:ADP501 4.0 60.6 1.0
OE2 A:GLU106 4.1 59.6 1.0
CA A:ALA30 4.1 55.6 1.0
NH2 A:ARG390 4.4 66.9 1.0
MG A:MG502 4.4 44.3 1.0
N A:GLY31 4.5 72.7 1.0
OE1 A:GLU106 4.5 68.9 1.0
O A:HOH602 4.6 61.1 1.0
CB A:ALA30 4.7 74.1 1.0
CD A:GLU106 4.7 64.2 1.0
CB A:ASP142 4.7 72.4 1.0
CG A:GLN145 4.8 72.1 1.0
N A:ALA30 4.8 58.6 1.0
O A:LYS29 4.8 80.2 1.0
C A:ALA30 4.9 65.5 1.0
O3A A:ADP501 5.0 72.0 1.0
NH1 A:ARG390 5.0 66.8 1.0

Fluorine binding site 3 out of 8 in 6l3g

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Fluorine binding site 3 out of 8 in the Structural Basis For Dna Unwinding at Forked Dsdna By Two Coordinating PIF1 Helicases


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structural Basis For Dna Unwinding at Forked Dsdna By Two Coordinating PIF1 Helicases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:77.2
occ:1.00
 F3 A:ALF503 0.0 77.2 1.0
AL A:ALF503 1.8 58.8 1.0
MG A:MG502 2.0 44.3 1.0
F2 A:ALF503 2.5 55.3 1.0
O1B A:ADP501 2.5 52.8 1.0
F1 A:ALF503 2.5 70.6 1.0
O A:HOH602 2.6 61.1 1.0
OE2 A:GLU106 3.0 59.6 1.0
O3B A:ADP501 3.2 68.8 1.0
PB A:ADP501 3.4 60.6 1.0
F4 A:ALF503 3.6 54.0 1.0
CD A:GLU106 3.8 64.2 1.0
OG1 A:THR35 3.9 76.1 1.0
NZ A:LYS34 4.0 61.5 1.0
CE A:LYS34 4.0 76.8 1.0
O3A A:ADP501 4.0 72.0 1.0
CA A:GLY365 4.2 57.2 1.0
OE1 A:GLU106 4.2 68.9 1.0
N A:GLY365 4.7 56.6 1.0
O2B A:ADP501 4.7 64.6 1.0
O2A A:ADP501 4.7 79.1 1.0
PA A:ADP501 4.9 63.4 1.0
O A:GLY365 4.9 73.8 1.0
NE2 A:GLN145 4.9 60.5 1.0
CG A:GLU106 4.9 57.9 1.0
CB A:LYS34 5.0 62.8 1.0
OD1 A:ASP105 5.0 70.7 1.0
CB A:THR35 5.0 69.4 1.0

Fluorine binding site 4 out of 8 in 6l3g

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Fluorine binding site 4 out of 8 in the Structural Basis For Dna Unwinding at Forked Dsdna By Two Coordinating PIF1 Helicases


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structural Basis For Dna Unwinding at Forked Dsdna By Two Coordinating PIF1 Helicases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:54.0
occ:1.00
 F4 A:ALF503 0.0 54.0 1.0
AL A:ALF503 1.8 58.8 1.0
F1 A:ALF503 2.5 70.6 1.0
NH2 A:ARG390 2.5 66.9 1.0
F2 A:ALF503 2.5 55.3 1.0
O3B A:ADP501 2.9 68.8 1.0
NH1 A:ARG390 2.9 66.8 1.0
NH1 A:ARG188 3.0 63.8 1.0
CZ A:ARG390 3.1 70.5 1.0
NH2 A:ARG188 3.2 75.3 1.0
CZ A:ARG188 3.5 71.1 1.0
F3 A:ALF503 3.6 77.2 1.0
N A:GLY31 3.8 72.7 1.0
CA A:ALA30 4.0 55.6 1.0
CB A:ALA30 4.0 74.1 1.0
NE2 A:GLN145 4.0 60.5 1.0
PB A:ADP501 4.1 60.6 1.0
OE1 A:GLN145 4.2 72.9 1.0
O3A A:ADP501 4.3 72.0 1.0
C A:ALA30 4.4 65.5 1.0
NE A:ARG390 4.4 75.3 1.0
N A:GLY365 4.5 56.6 1.0
CD A:GLN145 4.5 67.0 1.0
CA A:GLY365 4.6 57.2 1.0
O1B A:ADP501 4.6 52.8 1.0
CA A:GLY31 4.8 64.9 1.0
NE A:ARG188 4.8 69.5 1.0
OE2 A:GLU106 5.0 59.6 1.0
C A:GLY365 5.0 62.8 1.0
MG A:MG502 5.0 44.3 1.0

Fluorine binding site 5 out of 8 in 6l3g

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Fluorine binding site 5 out of 8 in the Structural Basis For Dna Unwinding at Forked Dsdna By Two Coordinating PIF1 Helicases


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structural Basis For Dna Unwinding at Forked Dsdna By Two Coordinating PIF1 Helicases within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F503

b:67.2
occ:1.00
 F1 B:ALF503 0.0 67.2 1.0
AL B:ALF503 1.8 54.4 1.0
NH1 B:ARG390 2.5 70.4 1.0
F4 B:ALF503 2.5 52.8 1.0
NH2 B:ARG188 2.5 76.2 1.0
F3 B:ALF503 2.5 67.3 1.0
CA B:GLY365 3.2 77.8 1.0
CZ B:ARG188 3.3 69.1 1.0
C B:GLY365 3.3 76.4 1.0
NH1 B:ARG188 3.4 61.4 1.0
O2B B:ADP501 3.4 58.1 1.0
O3A B:ADP501 3.4 80.9 1.0
CZ B:ARG390 3.4 62.8 1.0
O B:GLY365 3.5 82.5 1.0
N B:GLY365 3.5 77.5 1.0
F2 B:ALF503 3.6 64.8 1.0
NH2 B:ARG390 3.6 60.2 1.0
PB B:ADP501 4.0 65.0 1.0
N B:LEU366 4.0 65.8 1.0
O B:LEU366 4.1 80.7 1.0
MG B:MG502 4.2 55.7 1.0
O3B B:ADP501 4.4 65.7 1.0
O2A B:ADP501 4.5 86.3 1.0
NE B:ARG188 4.6 71.3 1.0
PA B:ADP501 4.6 82.4 1.0
NE B:ARG390 4.7 57.9 1.0
C B:LEU366 4.7 78.7 1.0
OE2 B:GLU106 4.7 72.5 1.0
N B:GLY31 4.8 75.3 1.0
C B:GLN364 4.8 74.5 1.0
CA B:LEU366 4.9 72.5 1.0

Fluorine binding site 6 out of 8 in 6l3g

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Fluorine binding site 6 out of 8 in the Structural Basis For Dna Unwinding at Forked Dsdna By Two Coordinating PIF1 Helicases


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structural Basis For Dna Unwinding at Forked Dsdna By Two Coordinating PIF1 Helicases within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F503

b:64.8
occ:1.00
 F2 B:ALF503 0.0 64.8 1.0
AL B:ALF503 1.8 54.4 1.0
F3 B:ALF503 2.5 67.3 1.0
F4 B:ALF503 2.5 52.8 1.0
O2B B:ADP501 2.7 58.1 1.0
NE2 B:GLN145 2.9 53.0 1.0
NZ B:LYS34 3.2 60.5 1.0
CE B:LYS34 3.6 65.8 1.0
F1 B:ALF503 3.6 67.2 1.0
OE1 B:GLN145 3.6 67.6 1.0
CD B:GLN145 3.6 60.6 1.0
MG B:MG502 3.7 55.7 1.0
PB B:ADP501 3.9 65.0 1.0
O3B B:ADP501 3.9 65.7 1.0
CA B:ALA30 4.1 64.1 1.0
OE2 B:GLU106 4.1 72.5 1.0
O B:HOH602 4.3 50.9 1.0
N B:GLY31 4.4 75.3 1.0
NH2 B:ARG390 4.6 60.2 1.0
O3A B:ADP501 4.7 80.9 1.0
OE1 B:GLU106 4.7 73.5 1.0
O B:LYS29 4.7 67.8 1.0
CB B:ALA30 4.7 59.0 1.0
CD B:GLU106 4.8 74.5 1.0
C B:ALA30 4.8 70.8 1.0
N B:ALA30 4.8 65.6 1.0
CB B:ASP142 4.9 46.2 1.0

Fluorine binding site 7 out of 8 in 6l3g

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Fluorine binding site 7 out of 8 in the Structural Basis For Dna Unwinding at Forked Dsdna By Two Coordinating PIF1 Helicases


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structural Basis For Dna Unwinding at Forked Dsdna By Two Coordinating PIF1 Helicases within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F503

b:67.3
occ:1.00
 F3 B:ALF503 0.0 67.3 1.0
AL B:ALF503 1.8 54.4 1.0
MG B:MG502 1.9 55.7 1.0
F2 B:ALF503 2.5 64.8 1.0
F1 B:ALF503 2.5 67.2 1.0
O3B B:ADP501 3.0 65.7 1.0
O2B B:ADP501 3.1 58.1 1.0
OE2 B:GLU106 3.3 72.5 1.0
O B:HOH602 3.3 50.9 1.0
PB B:ADP501 3.4 65.0 1.0
CA B:GLY365 3.5 77.8 1.0
O3A B:ADP501 3.5 80.9 1.0
F4 B:ALF503 3.6 52.8 1.0
OG1 B:THR35 3.8 56.5 1.0
N B:GLY365 4.1 77.5 1.0
O B:GLY365 4.2 82.5 1.0
C B:GLY365 4.3 76.4 1.0
CD B:GLU106 4.3 74.5 1.0
NH2 B:ARG188 4.4 76.2 1.0
O2A B:ADP501 4.6 86.3 1.0
NH1 B:ARG390 4.6 70.4 1.0
PA B:ADP501 4.7 82.4 1.0
CB B:THR35 4.8 71.9 1.0
NZ B:LYS34 4.8 60.5 1.0
OE1 B:GLU106 4.8 73.5 1.0
O1B B:ADP501 4.9 73.8 1.0
CE B:LYS34 5.0 65.8 1.0

Fluorine binding site 8 out of 8 in 6l3g

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Fluorine binding site 8 out of 8 in the Structural Basis For Dna Unwinding at Forked Dsdna By Two Coordinating PIF1 Helicases


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structural Basis For Dna Unwinding at Forked Dsdna By Two Coordinating PIF1 Helicases within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F503

b:52.8
occ:1.00
 F4 B:ALF503 0.0 52.8 1.0
AL B:ALF503 1.8 54.4 1.0
NH2 B:ARG390 2.4 60.2 1.0
F1 B:ALF503 2.5 67.2 1.0
F2 B:ALF503 2.5 64.8 1.0
O2B B:ADP501 3.0 58.1 1.0
NH1 B:ARG188 3.1 61.4 1.0
NH1 B:ARG390 3.2 70.4 1.0
CZ B:ARG390 3.2 62.8 1.0
CB B:ALA30 3.2 59.0 1.0
CA B:ALA30 3.3 64.1 1.0
N B:GLY31 3.5 75.3 1.0
NE2 B:GLN145 3.6 53.0 1.0
F3 B:ALF503 3.6 67.3 1.0
NH2 B:ARG188 3.8 76.2 1.0
C B:ALA30 3.8 70.8 1.0
CZ B:ARG188 3.9 69.1 1.0
OE1 B:GLN145 4.0 67.6 1.0
CD B:GLN145 4.1 60.6 1.0
PB B:ADP501 4.4 65.0 1.0
NE B:ARG390 4.5 57.9 1.0
O3A B:ADP501 4.5 80.9 1.0
N B:ALA30 4.5 65.6 1.0
CA B:GLY31 4.6 73.1 1.0
OG B:SER389 4.7 63.8 1.0
NZ B:LYS34 4.9 60.5 1.0
N B:GLY365 5.0 77.5 1.0
O B:ALA30 5.0 77.6 1.0

Reference:

N.Su, A.K.Byrd, S.R.Bharath, O.Yang, Y.Jia, X.Tang, T.Ha, K.D.Raney, H.Song. Structural Basis For Dna Unwinding at Forked Dsdna By Two Coordinating PIF1 Helicases. Nat Commun V. 10 5375 2019.
ISSN: ESSN 2041-1723
PubMed: 31772234
DOI: 10.1038/S41467-019-13414-9
Page generated: Thu Aug 1 21:56:50 2024

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