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Fluorine in PDB 7bil: Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Oligo Ggtttggtttggtt

Protein crystallography data

The structure of Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Oligo Ggtttggtttggtt, PDB code: 7bil 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) 44.02 / 2.21
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 88.052, 103.438, 251.566, 90, 90, 90
R / Rfree (%) 17.9 / 22

Other elements in 7bil:

The structure of Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Oligo Ggtttggtttggtt also contains other interesting chemical elements:

Aluminium (Al) 2 atoms
Potassium (K) 1 atom
Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Oligo Ggtttggtttggtt (pdb code 7bil). 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 Oligo Ggtttggtttggtt, PDB code: 7bil:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 7bil

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Fluorine binding site 1 out of 8 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Oligo Ggtttggtttggtt


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 Oligo Ggtttggtttggtt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:43.1
occ:1.00
 F1 A:ALF1003 0.0 43.1 1.0
AL A:ALF1003 1.8 36.6 1.0
F3 A:ALF1003 2.5 37.0 1.0
F4 A:ALF1003 2.5 38.3 1.0
O3B A:ADP1001 2.6 33.5 1.0
O A:HOH1108 2.8 38.5 1.0
NH2 A:ARG462 2.8 37.7 1.0
NH1 A:ARG256 2.9 39.7 1.0
N A:GLY94 2.9 35.9 1.0
CA A:ALA93 3.0 39.3 1.0
CB A:ALA93 3.1 35.4 1.0
C A:ALA93 3.4 42.1 1.0
NE2 A:GLN212 3.6 38.1 1.0
F2 A:ALF1003 3.6 44.0 1.0
CZ A:ARG462 3.7 43.9 1.0
NH1 A:ARG462 3.7 35.2 1.0
NH2 A:ARG256 3.8 40.0 1.0
CZ A:ARG256 3.8 43.6 1.0
OE1 A:GLN212 3.9 38.9 1.0
CA A:GLY94 4.0 35.7 1.0
PB A:ADP1001 4.1 39.6 1.0
CD A:GLN212 4.1 42.9 1.0
N A:ALA93 4.4 43.2 1.0
O A:ALA93 4.5 40.0 1.0
O1B A:ADP1001 4.6 34.7 1.0
NZ A:LYS97 4.6 35.5 1.0
OG1 A:THR461 4.8 42.6 1.0
O3A A:ADP1001 4.9 31.1 1.0
NE A:ARG462 4.9 39.0 1.0
O2B A:ADP1001 5.0 40.3 1.0
O A:PRO92 5.0 42.7 1.0
O A:HOH1136 5.0 37.5 1.0

Fluorine binding site 2 out of 8 in 7bil

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Fluorine binding site 2 out of 8 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Oligo Ggtttggtttggtt


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 Oligo Ggtttggtttggtt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:44.0
occ:1.00
 F2 A:ALF1003 0.0 44.0 1.0
AL A:ALF1003 1.8 36.6 1.0
MG A:MG1002 1.9 36.9 1.0
F3 A:ALF1003 2.5 37.0 1.0
F4 A:ALF1003 2.5 38.3 1.0
O A:HOH1153 2.6 40.4 1.0
O A:HOH1131 2.6 39.8 1.0
O3B A:ADP1001 2.7 33.5 1.0
O A:HOH1108 2.8 38.5 1.0
O2B A:ADP1001 2.9 40.3 1.0
OE1 A:GLU172 2.9 40.0 1.0
O A:HOH1136 3.0 37.5 1.0
O A:HOH1140 3.1 35.0 1.0
PB A:ADP1001 3.3 39.6 1.0
F1 A:ALF1003 3.6 43.1 1.0
CD A:GLU172 3.8 48.8 1.0
CA A:GLY436 3.9 38.3 1.0
OG1 A:THR98 4.0 36.6 1.0
O1B A:ADP1001 4.2 34.7 1.0
OE2 A:GLU172 4.4 47.0 1.0
NZ A:LYS97 4.4 35.5 1.0
CE A:LYS97 4.4 37.3 1.0
N A:GLY436 4.5 40.8 1.0
O3A A:ADP1001 4.5 31.1 1.0
O A:GLY436 4.6 37.5 1.0
C A:GLY436 4.7 41.5 1.0
CG A:GLU172 4.8 45.1 1.0
NH2 A:ARG256 4.9 40.0 1.0
OE1 A:GLN212 5.0 38.9 1.0
O2A A:ADP1001 5.0 34.6 1.0

Fluorine binding site 3 out of 8 in 7bil

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Fluorine binding site 3 out of 8 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Oligo Ggtttggtttggtt


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 Oligo Ggtttggtttggtt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:37.0
occ:1.00
 F3 A:ALF1003 0.0 37.0 1.0
AL A:ALF1003 1.8 36.6 1.0
F1 A:ALF1003 2.5 43.1 1.0
O3B A:ADP1001 2.5 33.5 1.0
F2 A:ALF1003 2.5 44.0 1.0
NZ A:LYS97 2.6 35.5 1.0
O A:HOH1136 2.8 37.5 1.0
O A:HOH1108 2.9 38.5 1.0
NE2 A:GLN212 3.0 38.1 1.0
CE A:LYS97 3.2 37.3 1.0
PB A:ADP1001 3.4 39.6 1.0
F4 A:ALF1003 3.6 38.3 1.0
O1B A:ADP1001 3.6 34.7 1.0
CA A:ALA93 3.6 39.3 1.0
N A:GLY94 3.8 35.9 1.0
CD A:GLN212 3.9 42.9 1.0
OE1 A:GLN212 3.9 38.9 1.0
O2B A:ADP1001 4.0 40.3 1.0
MG A:MG1002 4.1 36.9 1.0
O A:HOH1131 4.1 39.8 1.0
C A:ALA93 4.2 42.1 1.0
O A:PRO92 4.3 42.7 1.0
CB A:ALA93 4.4 35.4 1.0
OE1 A:GLU172 4.4 40.0 1.0
N A:ALA93 4.5 43.2 1.0
C A:PRO92 4.7 39.9 1.0
CD A:LYS97 4.7 40.8 1.0
CB A:ASP209 4.9 36.4 1.0
NH2 A:ARG462 4.9 37.7 1.0
O3A A:ADP1001 4.9 31.1 1.0
O A:GLY91 4.9 44.0 1.0
OE2 A:GLU172 4.9 47.0 1.0
CA A:GLY94 5.0 35.7 1.0

Fluorine binding site 4 out of 8 in 7bil

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Fluorine binding site 4 out of 8 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Oligo Ggtttggtttggtt


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 Oligo Ggtttggtttggtt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:38.3
occ:1.00
 F4 A:ALF1003 0.0 38.3 1.0
AL A:ALF1003 1.8 36.6 1.0
F1 A:ALF1003 2.5 43.1 1.0
F2 A:ALF1003 2.5 44.0 1.0
O3B A:ADP1001 2.6 33.5 1.0
NH2 A:ARG256 2.7 40.0 1.0
O A:HOH1108 2.8 38.5 1.0
NH1 A:ARG462 3.1 35.2 1.0
O A:HOH1140 3.2 35.0 1.0
CA A:GLY436 3.2 38.3 1.0
C A:GLY436 3.3 41.5 1.0
O A:GLY436 3.4 37.5 1.0
NH1 A:ARG256 3.5 39.7 1.0
CZ A:ARG256 3.6 43.6 1.0
F3 A:ALF1003 3.6 37.0 1.0
MG A:MG1002 3.6 36.9 1.0
N A:GLY436 3.7 40.8 1.0
PB A:ADP1001 3.7 39.6 1.0
NH2 A:ARG462 3.8 37.7 1.0
CZ A:ARG462 3.9 43.9 1.0
O2B A:ADP1001 4.0 40.3 1.0
O A:HOH1153 4.1 40.4 1.0
N A:LEU437 4.2 42.7 1.0
O2A A:ADP1001 4.3 34.6 1.0
OE1 A:GLU172 4.4 40.0 1.0
O3A A:ADP1001 4.4 31.1 1.0
O A:LEU437 4.4 37.3 1.0
N A:GLY94 4.6 35.9 1.0
C A:LEU437 4.8 41.6 1.0
NE A:ARG256 4.8 46.2 1.0
O1B A:ADP1001 5.0 34.7 1.0

Fluorine binding site 5 out of 8 in 7bil

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Fluorine binding site 5 out of 8 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Oligo Ggtttggtttggtt


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 Oligo Ggtttggtttggtt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:56.4
occ:1.00
 F1 B:ALF1003 0.0 56.4 1.0
AL B:ALF1003 1.8 57.7 1.0
F3 B:ALF1003 2.5 53.7 1.0
F4 B:ALF1003 2.6 57.8 1.0
O1B B:ADP1001 2.8 62.2 1.0
O B:HOH1102 2.8 53.7 1.0
NH2 B:ARG462 2.8 50.1 1.0
CB B:ALA93 3.1 54.0 1.0
CA B:ALA93 3.1 55.0 1.0
N B:GLY94 3.2 57.1 1.0
NH1 B:ARG256 3.2 52.4 1.0
NH1 B:ARG462 3.5 55.6 1.0
NE2 B:GLN212 3.5 56.2 1.0
F2 B:ALF1003 3.6 52.9 1.0
C B:ALA93 3.6 56.2 1.0
CZ B:ARG462 3.6 53.2 1.0
OE1 B:GLN212 3.7 56.5 1.0
NH2 B:ARG256 3.9 56.8 1.0
CD B:GLN212 3.9 60.2 1.0
CZ B:ARG256 4.0 62.6 1.0
PB B:ADP1001 4.2 58.0 1.0
CA B:GLY94 4.3 62.3 1.0
N B:ALA93 4.4 60.7 1.0
NZ B:LYS97 4.6 55.0 1.0
O2B B:ADP1001 4.7 57.6 1.0
O B:ALA93 4.7 57.1 1.0
OG1 B:THR461 4.8 54.3 1.0
NE B:ARG462 4.9 49.3 1.0
O3A B:ADP1001 5.0 64.6 1.0

Fluorine binding site 6 out of 8 in 7bil

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Fluorine binding site 6 out of 8 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Oligo Ggtttggtttggtt


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 Oligo Ggtttggtttggtt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:52.9
occ:1.00
 F2 B:ALF1003 0.0 52.9 1.0
AL B:ALF1003 1.8 57.7 1.0
MG B:MG1002 1.8 62.3 1.0
F3 B:ALF1003 2.4 53.7 1.0
F4 B:ALF1003 2.6 57.8 1.0
O B:HOH1111 2.7 59.6 1.0
O1B B:ADP1001 2.8 62.2 1.0
O3B B:ADP1001 2.9 62.7 1.0
O B:HOH1115 2.9 60.9 1.0
O B:HOH1102 3.0 53.7 1.0
OE1 B:GLU172 3.1 58.1 1.0
O B:HOH1107 3.1 58.3 1.0
PB B:ADP1001 3.2 58.0 1.0
F1 B:ALF1003 3.6 56.4 1.0
OG1 B:THR98 3.9 65.6 1.0
CA B:GLY436 4.0 54.1 1.0
CD B:GLU172 4.0 64.0 1.0
O2B B:ADP1001 4.1 57.6 1.0
NZ B:LYS97 4.4 55.0 1.0
CE B:LYS97 4.4 56.4 1.0
O3A B:ADP1001 4.5 64.6 1.0
OE2 B:GLU172 4.5 64.3 1.0
O B:GLY436 4.5 59.0 1.0
N B:GLY436 4.6 54.4 1.0
C B:GLY436 4.7 54.7 1.0
NH2 B:ARG256 4.9 56.8 1.0
O1A B:ADP1001 4.9 61.3 1.0
CG B:GLU172 4.9 58.9 1.0
CB B:THR98 5.0 65.5 1.0
OE1 B:GLN212 5.0 56.5 1.0

Fluorine binding site 7 out of 8 in 7bil

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Fluorine binding site 7 out of 8 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Oligo Ggtttggtttggtt


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 Oligo Ggtttggtttggtt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:53.7
occ:1.00
 F3 B:ALF1003 0.0 53.7 1.0
AL B:ALF1003 1.8 57.7 1.0
F2 B:ALF1003 2.4 52.9 1.0
F1 B:ALF1003 2.5 56.4 1.0
O1B B:ADP1001 2.7 62.2 1.0
O B:HOH1102 2.8 53.7 1.0
NH2 B:ARG256 2.9 56.8 1.0
NH1 B:ARG462 3.0 55.6 1.0
CA B:GLY436 3.1 54.1 1.0
C B:GLY436 3.3 54.7 1.0
O B:GLY436 3.3 59.0 1.0
O B:HOH1107 3.3 58.3 1.0
N B:GLY436 3.6 54.4 1.0
F4 B:ALF1003 3.6 57.8 1.0
MG B:MG1002 3.6 62.3 1.0
NH1 B:ARG256 3.8 52.4 1.0
CZ B:ARG256 3.8 62.6 1.0
PB B:ADP1001 3.9 58.0 1.0
CZ B:ARG462 3.9 53.2 1.0
NH2 B:ARG462 4.0 50.1 1.0
N B:LEU437 4.1 50.9 1.0
OE1 B:GLU172 4.2 58.1 1.0
O3B B:ADP1001 4.2 62.7 1.0
O B:HOH1115 4.2 60.9 1.0
O1A B:ADP1001 4.4 61.3 1.0
O B:LEU437 4.5 56.6 1.0
O3A B:ADP1001 4.5 64.6 1.0
N B:GLY94 4.8 57.1 1.0
OE1 B:GLN212 4.8 56.5 1.0
C B:GLN435 4.9 55.1 1.0
C B:LEU437 4.9 56.7 1.0

Fluorine binding site 8 out of 8 in 7bil

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Fluorine binding site 8 out of 8 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Oligo Ggtttggtttggtt


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 Oligo Ggtttggtttggtt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:57.8
occ:1.00
 F4 B:ALF1003 0.0 57.8 1.0
AL B:ALF1003 1.8 57.7 1.0
F1 B:ALF1003 2.6 56.4 1.0
NZ B:LYS97 2.6 55.0 1.0
F2 B:ALF1003 2.6 52.9 1.0
O1B B:ADP1001 2.9 62.2 1.0
NE2 B:GLN212 2.9 56.2 1.0
O B:HOH1102 3.0 53.7 1.0
CE B:LYS97 3.2 56.4 1.0
PB B:ADP1001 3.5 58.0 1.0
F3 B:ALF1003 3.6 53.7 1.0
O2B B:ADP1001 3.6 57.6 1.0
CA B:ALA93 3.8 55.0 1.0
CD B:GLN212 3.8 60.2 1.0
OE1 B:GLN212 3.8 56.5 1.0
O B:HOH1111 4.0 59.6 1.0
O3B B:ADP1001 4.0 62.7 1.0
N B:GLY94 4.0 57.1 1.0
MG B:MG1002 4.2 62.3 1.0
O B:PRO92 4.3 62.0 1.0
OE1 B:GLU172 4.4 58.1 1.0
CB B:ALA93 4.4 54.0 1.0
C B:ALA93 4.4 56.2 1.0
N B:ALA93 4.5 60.7 1.0
CD B:LYS97 4.7 62.4 1.0
C B:PRO92 4.7 63.8 1.0
O B:GLY91 4.8 63.2 1.0
CB B:ASP209 4.8 60.4 1.0
OE2 B:GLU172 4.9 64.3 1.0
O3A B:ADP1001 5.0 64.6 1.0

Reference:

Y.X.Dai, W.F.Chen, N.N.Liu, F.Y.Teng, H.L.Guo, X.M.Hou, S.X.Dou, S.Rety, X.G.Xi. Structural and Functional Studies of SF1B PIF1 From Thermus Oshimai Reveal Dimerization-Induced Helicase Inhibition. Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962
PubMed: 33784404
DOI: 10.1093/NAR/GKAB188
Page generated: Fri Aug 2 05:58:42 2024

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