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Fluorine in PDB 7oar: Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Parallel G-Quadruplex

Protein crystallography data

The structure of Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Parallel G-Quadruplex, PDB code: 7oar was solved by Y.X.Dai, N.N.Liu, H.L.Guo, W.F.Chen, S.Rety, X.G.Xi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.39 / 2.58
Space group P 62 2 2
Cell size a, b, c (Å), α, β, γ (°) 151.782, 151.782, 219.534, 90, 90, 120
R / Rfree (%) 19.4 / 24.3

Other elements in 7oar:

The structure of Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Parallel G-Quadruplex also contains other interesting chemical elements:

Aluminium (Al) 2 atoms
Potassium (K) 3 atoms
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 Parallel G-Quadruplex (pdb code 7oar). 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 Parallel G-Quadruplex, PDB code: 7oar:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 7oar

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Fluorine binding site 1 out of 8 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Parallel G-Quadruplex


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 Parallel G-Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:89.0
occ:1.00
 F1 A:ALF1003 0.0 89.0 1.0
AL A:ALF1003 1.8 86.1 1.0
O A:HOH1102 2.5 90.0 1.0
F4 A:ALF1003 2.5 83.6 1.0
F3 A:ALF1003 2.5 81.7 1.0
NH2 A:ARG462 2.6 81.0 1.0
O3B A:ADP1001 3.0 61.8 1.0
CB A:ALA93 3.2 69.7 1.0
NH1 A:ARG256 3.2 95.2 1.0
N A:GLY94 3.3 81.6 1.0
CA A:ALA93 3.3 79.4 1.0
NE2 A:GLN212 3.4 81.9 1.0
NH1 A:ARG462 3.4 90.1 1.0
CZ A:ARG462 3.4 81.8 1.0
F2 A:ALF1003 3.6 102.7 1.0
C A:ALA93 3.7 80.7 1.0
OE1 A:GLN212 3.7 87.0 1.0
NH2 A:ARG256 3.8 84.5 1.0
CD A:GLN212 3.9 90.0 1.0
CZ A:ARG256 4.0 88.8 1.0
CA A:GLY94 4.3 86.9 1.0
PB A:ADP1001 4.4 96.2 1.0
N A:ALA93 4.6 85.5 1.0
NE A:ARG462 4.6 80.0 1.0
O1B A:ADP1001 4.9 79.7 1.0
NZ A:LYS97 4.9 81.8 1.0
O A:ALA93 4.9 89.1 1.0
OG1 A:THR461 4.9 85.3 1.0

Fluorine binding site 2 out of 8 in 7oar

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Fluorine binding site 2 out of 8 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Parallel G-Quadruplex


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 Parallel G-Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:102.7
occ:1.00
 F2 A:ALF1003 0.0 102.7 1.0
AL A:ALF1003 1.8 86.1 1.0
MG A:MG1002 1.9 81.8 1.0
F4 A:ALF1003 2.5 83.6 1.0
F3 A:ALF1003 2.5 81.7 1.0
O3B A:ADP1001 2.6 61.8 1.0
O A:HOH1114 2.6 72.1 1.0
O A:HOH1107 2.9 84.6 1.0
O2B A:ADP1001 2.9 87.6 1.0
O A:HOH1102 3.0 90.0 1.0
PB A:ADP1001 3.2 96.2 1.0
O A:HOH1105 3.2 79.5 1.0
O A:HOH1101 3.3 84.1 1.0
OE2 A:GLU172 3.5 103.7 1.0
F1 A:ALF1003 3.6 89.0 1.0
CD A:GLU172 3.6 102.6 1.0
OE1 A:GLU172 3.7 114.1 1.0
OG1 A:THR98 3.8 110.0 1.0
O1B A:ADP1001 4.1 79.7 1.0
CA A:GLY436 4.2 99.3 1.0
CG A:GLU172 4.4 102.8 1.0
CE A:LYS97 4.5 67.6 1.0
NZ A:LYS97 4.5 81.8 1.0
O A:GLY436 4.6 104.8 1.0
O3A A:ADP1001 4.6 98.5 1.0
O2A A:ADP1001 4.7 80.7 1.0
NH2 A:ARG256 4.8 84.5 1.0
N A:GLY436 4.8 102.4 1.0
C A:GLY436 4.8 103.2 1.0
CB A:THR98 5.0 90.9 1.0

Fluorine binding site 3 out of 8 in 7oar

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Fluorine binding site 3 out of 8 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Parallel G-Quadruplex


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 Parallel G-Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:81.7
occ:1.00
 F3 A:ALF1003 0.0 81.7 1.0
AL A:ALF1003 1.8 86.1 1.0
F1 A:ALF1003 2.5 89.0 1.0
F2 A:ALF1003 2.5 102.7 1.0
NZ A:LYS97 2.7 81.8 1.0
O3B A:ADP1001 2.8 61.8 1.0
O A:HOH1101 3.0 84.1 1.0
O A:HOH1102 3.1 90.0 1.0
NE2 A:GLN212 3.2 81.9 1.0
CE A:LYS97 3.2 67.6 1.0
PB A:ADP1001 3.4 96.2 1.0
O1B A:ADP1001 3.5 79.7 1.0
F4 A:ALF1003 3.6 83.6 1.0
CA A:ALA93 3.7 79.4 1.0
N A:GLY94 3.8 81.6 1.0
O2B A:ADP1001 4.0 87.6 1.0
CD A:GLN212 4.1 90.0 1.0
OE2 A:GLU172 4.1 103.7 1.0
OE1 A:GLN212 4.1 87.0 1.0
O A:PRO92 4.2 89.3 1.0
MG A:MG1002 4.2 81.8 1.0
C A:ALA93 4.3 80.7 1.0
O A:HOH1107 4.3 84.6 1.0
CB A:ALA93 4.4 69.7 1.0
N A:ALA93 4.5 85.5 1.0
C A:PRO92 4.7 91.4 1.0
CD A:LYS97 4.7 89.5 1.0
CD A:GLU172 4.8 102.6 1.0
NH2 A:ARG462 4.9 81.0 1.0
CB A:ASP209 4.9 76.1 1.0
OE1 A:GLU172 4.9 114.1 1.0
O3A A:ADP1001 4.9 98.5 1.0
O A:GLY91 4.9 79.7 1.0
CA A:GLY94 5.0 86.9 1.0

Fluorine binding site 4 out of 8 in 7oar

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Fluorine binding site 4 out of 8 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Parallel G-Quadruplex


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 Parallel G-Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:83.6
occ:1.00
 F4 A:ALF1003 0.0 83.6 1.0
AL A:ALF1003 1.8 86.1 1.0
F2 A:ALF1003 2.5 102.7 1.0
F1 A:ALF1003 2.5 89.0 1.0
O3B A:ADP1001 2.5 61.8 1.0
O A:HOH1102 2.6 90.0 1.0
NH2 A:ARG256 2.9 84.5 1.0
NH1 A:ARG462 2.9 90.1 1.0
O A:GLY436 3.1 104.8 1.0
CA A:GLY436 3.2 99.3 1.0
O A:HOH1105 3.3 79.5 1.0
C A:GLY436 3.3 103.2 1.0
F3 A:ALF1003 3.6 81.7 1.0
MG A:MG1002 3.6 81.8 1.0
N A:GLY436 3.7 102.4 1.0
CZ A:ARG256 3.7 88.8 1.0
NH1 A:ARG256 3.7 95.2 1.0
CZ A:ARG462 3.9 81.8 1.0
PB A:ADP1001 3.9 96.2 1.0
NH2 A:ARG462 3.9 81.0 1.0
O A:HOH1114 4.0 72.1 1.0
O2A A:ADP1001 4.0 80.7 1.0
O2B A:ADP1001 4.2 87.6 1.0
N A:LEU437 4.2 82.1 1.0
O A:LEU437 4.4 104.6 1.0
OE1 A:GLU172 4.6 114.1 1.0
O3A A:ADP1001 4.7 98.5 1.0
N A:GLY94 4.8 81.6 1.0
C A:LEU437 4.9 101.0 1.0
NE A:ARG256 5.0 88.7 1.0

Fluorine binding site 5 out of 8 in 7oar

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Fluorine binding site 5 out of 8 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Parallel G-Quadruplex


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 Parallel G-Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:66.4
occ:1.00
 F1 B:ALF1003 0.0 66.4 1.0
AL B:ALF1003 1.8 75.5 1.0
F4 B:ALF1003 2.5 70.8 1.0
F3 B:ALF1003 2.5 68.8 1.0
NH2 B:ARG462 2.7 66.3 1.0
O3B B:ADP1001 2.8 59.7 1.0
O B:HOH1107 2.8 66.5 1.0
NH1 B:ARG256 3.0 67.8 1.0
N B:GLY94 3.0 68.6 1.0
CB B:ALA93 3.1 67.1 1.0
CA B:ALA93 3.2 65.2 1.0
NH1 B:ARG462 3.5 67.0 1.0
CZ B:ARG462 3.5 57.2 1.0
F2 B:ALF1003 3.5 69.7 1.0
C B:ALA93 3.5 63.1 1.0
NE2 B:GLN212 3.6 62.0 1.0
OE1 B:GLN212 3.6 78.5 1.0
NH2 B:ARG256 3.6 66.5 1.0
CZ B:ARG256 3.7 72.8 1.0
CD B:GLN212 4.0 69.6 1.0
CA B:GLY94 4.1 63.6 1.0
PB B:ADP1001 4.2 81.8 1.0
N B:ALA93 4.5 72.1 1.0
O B:ALA93 4.7 76.9 1.0
NE B:ARG462 4.8 63.5 1.0
O2B B:ADP1001 4.8 66.0 1.0
OG1 B:THR461 4.8 77.2 1.0
O B:HOH1109 4.8 74.7 1.0
NZ B:LYS97 4.8 65.2 1.0
O1B B:ADP1001 4.9 72.2 1.0
O3A B:ADP1001 4.9 77.0 1.0

Fluorine binding site 6 out of 8 in 7oar

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Fluorine binding site 6 out of 8 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Parallel G-Quadruplex


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 Parallel G-Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:69.7
occ:1.00
 F2 B:ALF1003 0.0 69.7 1.0
AL B:ALF1003 1.8 75.5 1.0
MG B:MG1002 2.1 77.4 1.0
F4 B:ALF1003 2.5 70.8 1.0
O B:HOH1116 2.5 73.8 1.0
F3 B:ALF1003 2.5 68.8 1.0
O B:HOH1107 2.6 66.5 1.0
O B:HOH1110 2.8 63.0 1.0
O1B B:ADP1001 2.8 72.2 1.0
O3B B:ADP1001 2.8 59.7 1.0
OE2 B:GLU172 2.9 71.1 1.0
O B:HOH1109 3.1 74.7 1.0
PB B:ADP1001 3.3 81.8 1.0
F1 B:ALF1003 3.5 66.4 1.0
CA B:GLY436 3.6 61.9 1.0
CD B:GLU172 3.8 74.7 1.0
OG1 B:THR98 4.0 73.4 1.0
O2B B:ADP1001 4.2 66.0 1.0
O B:GLY436 4.3 72.7 1.0
N B:GLY436 4.3 68.2 1.0
OE1 B:GLU172 4.4 70.8 1.0
C B:GLY436 4.4 76.9 1.0
O3A B:ADP1001 4.6 77.0 1.0
NH2 B:ARG256 4.6 66.5 1.0
CE B:LYS97 4.7 72.2 1.0
O1A B:ADP1001 4.7 64.9 1.0
NH1 B:ARG462 4.8 67.0 1.0
CG B:GLU172 4.8 79.7 1.0
NZ B:LYS97 4.9 65.2 1.0
OE1 B:GLN212 4.9 78.5 1.0

Fluorine binding site 7 out of 8 in 7oar

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Fluorine binding site 7 out of 8 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Parallel G-Quadruplex


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 Parallel G-Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:68.8
occ:1.00
 F3 B:ALF1003 0.0 68.8 1.0
AL B:ALF1003 1.8 75.5 1.0
F1 B:ALF1003 2.5 66.4 1.0
F2 B:ALF1003 2.5 69.7 1.0
O3B B:ADP1001 2.6 59.7 1.0
O B:HOH1109 2.6 74.7 1.0
O B:HOH1107 2.8 66.5 1.0
NZ B:LYS97 2.9 65.2 1.0
NE2 B:GLN212 3.0 62.0 1.0
CE B:LYS97 3.2 72.2 1.0
PB B:ADP1001 3.5 81.8 1.0
F4 B:ALF1003 3.5 70.8 1.0
O2B B:ADP1001 3.6 66.0 1.0
OE1 B:GLN212 3.8 78.5 1.0
CD B:GLN212 3.8 69.6 1.0
CA B:ALA93 3.9 65.2 1.0
O1B B:ADP1001 3.9 72.2 1.0
MG B:MG1002 4.0 77.4 1.0
N B:GLY94 4.0 68.6 1.0
OE2 B:GLU172 4.3 71.1 1.0
C B:ALA93 4.5 63.1 1.0
O B:PRO92 4.5 59.9 1.0
CB B:ALA93 4.5 67.1 1.0
CD B:LYS97 4.7 62.0 1.0
N B:ALA93 4.7 72.1 1.0
OE1 B:GLU172 4.8 70.8 1.0
NH2 B:ARG462 4.8 66.3 1.0
O3A B:ADP1001 4.8 77.0 1.0
O B:HOH1116 4.9 73.8 1.0
C B:PRO92 4.9 71.9 1.0
CD B:GLU172 4.9 74.7 1.0

Fluorine binding site 8 out of 8 in 7oar

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Fluorine binding site 8 out of 8 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Parallel G-Quadruplex


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 Parallel G-Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:70.8
occ:1.00
 F4 B:ALF1003 0.0 70.8 1.0
AL B:ALF1003 1.8 75.5 1.0
F1 B:ALF1003 2.5 66.4 1.0
F2 B:ALF1003 2.5 69.7 1.0
O B:HOH1107 2.6 66.5 1.0
NH1 B:ARG462 2.7 67.0 1.0
NH2 B:ARG256 2.7 66.5 1.0
O3B B:ADP1001 2.9 59.7 1.0
CA B:GLY436 3.0 61.9 1.0
C B:GLY436 3.2 76.9 1.0
O B:GLY436 3.3 72.7 1.0
O B:HOH1110 3.4 63.0 1.0
N B:GLY436 3.5 68.2 1.0
NH1 B:ARG256 3.5 67.8 1.0
CZ B:ARG256 3.5 72.8 1.0
F3 B:ALF1003 3.5 68.8 1.0
CZ B:ARG462 3.6 57.2 1.0
NH2 B:ARG462 3.7 66.3 1.0
N B:LEU437 4.0 76.9 1.0
PB B:ADP1001 4.0 81.8 1.0
O1B B:ADP1001 4.1 72.2 1.0
O B:HOH1116 4.1 73.8 1.0
OE2 B:GLU172 4.2 71.1 1.0
O B:LEU437 4.3 75.0 1.0
O1A B:ADP1001 4.3 64.9 1.0
MG B:MG1002 4.4 77.4 1.0
O B:HOH1104 4.6 68.8 1.0
O3A B:ADP1001 4.6 77.0 1.0
C B:LEU437 4.7 81.5 1.0
N B:GLY94 4.7 68.6 1.0
OE1 B:GLN212 4.7 78.5 1.0
NE B:ARG256 4.7 66.7 1.0
C B:GLN435 4.8 76.6 1.0
NE B:ARG462 4.8 63.5 1.0
CA B:LEU437 4.9 79.1 1.0

Reference:

Y.X.Dai, H.L.Guo, N.N.Liu, W.F.Chen, X.Ai, H.H.Li, B.Sun, X.M.Hou, S.Rety, X.G.Xi. Structural Mechanism Underpinning Thermus Oshimai PIF1-Mediated G-Quadruplex Unfolding. Embo Rep. V. 23 53874 2022.
ISSN: ESSN 1469-3178
PubMed: 35736675
DOI: 10.15252/EMBR.202153874
Page generated: Fri Aug 2 10:42:32 2024

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