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Fluorine in PDB 8xak: Structure of PIF1-G4 Complex

Protein crystallography data

The structure of Structure of PIF1-G4 Complex, PDB code: 8xak was solved by Z.Hong, H.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.00 / 3.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 56.163, 125.141, 258.233, 90, 91.47, 90
R / Rfree (%) 28.2 / 32.4

Other elements in 8xak:

The structure of Structure of PIF1-G4 Complex also contains other interesting chemical elements:

Potassium (K) 6 atoms
Magnesium (Mg) 2 atoms
Aluminium (Al) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of PIF1-G4 Complex (pdb code 8xak). 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 PIF1-G4 Complex, PDB code: 8xak:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 8xak

Go back to Fluorine Binding Sites List in 8xak
Fluorine binding site 1 out of 8 in the Structure of PIF1-G4 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 PIF1-G4 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1002

b:21.8
occ:1.00
 F1 A:ALF1002 0.0 21.8 1.0
AL A:ALF1002 1.8 22.2 1.0
NH2 A:ARG734 2.3 21.0 1.0
F4 A:ALF1002 2.5 24.0 1.0
F3 A:ALF1002 2.5 23.8 1.0
NH1 A:ARG417 2.7 37.0 1.0
CB A:ALA260 3.1 21.6 1.0
CA A:ALA260 3.2 21.3 1.0
NE2 A:GLN381 3.3 28.4 1.0
O2B A:ADP1001 3.4 29.7 1.0
CZ A:ARG734 3.6 19.2 1.0
F2 A:ALF1002 3.6 20.1 1.0
N A:GLY261 3.7 24.0 1.0
CZ A:ARG417 3.8 34.4 1.0
OE1 A:GLN381 3.8 24.1 1.0
CD A:GLN381 4.0 27.8 1.0
C A:ALA260 4.0 20.8 1.0
NH1 A:ARG734 4.2 27.1 1.0
NH2 A:ARG417 4.3 40.0 1.0
N A:ALA260 4.3 22.3 1.0
NE A:ARG734 4.5 19.4 1.0
PB A:ADP1001 4.7 30.4 1.0
OG A:SER733 4.7 22.6 1.0
N A:GLY709 4.8 20.7 1.0
NE A:ARG417 4.9 25.9 1.0
O1B A:ADP1001 4.9 31.8 1.0
CA A:GLY261 4.9 24.9 1.0

Fluorine binding site 2 out of 8 in 8xak

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Fluorine binding site 2 out of 8 in the Structure of PIF1-G4 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 PIF1-G4 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1002

b:20.1
occ:1.00
 F2 A:ALF1002 0.0 20.1 1.0
AL A:ALF1002 1.8 22.2 1.0
OE2 A:GLU342 2.4 13.8 1.0
F3 A:ALF1002 2.5 23.8 1.0
F4 A:ALF1002 2.5 24.0 1.0
MG A:MG1003 2.7 19.4 1.0
CD A:GLU342 3.3 23.1 1.0
O2B A:ADP1001 3.4 29.7 1.0
O3B A:ADP1001 3.6 30.1 1.0
F1 A:ALF1002 3.6 21.8 1.0
CA A:GLY709 3.7 21.1 1.0
PB A:ADP1001 3.8 30.4 1.0
OE1 A:GLU342 3.8 22.4 1.0
N A:GLY709 4.0 20.7 1.0
O1B A:ADP1001 4.2 31.8 1.0
NZ A:LYS264 4.3 38.2 1.0
CE A:LYS264 4.4 36.3 1.0
CG A:GLU342 4.5 23.3 1.0
NH2 A:ARG734 4.6 21.0 1.0
OG A:SER265 4.6 26.9 1.0
NH1 A:ARG417 4.7 37.0 1.0
C A:GLY709 4.8 21.6 1.0
OD2 A:ASP341 4.8 25.2 1.0
NH2 A:ARG417 4.8 40.0 1.0
NE2 A:GLN381 4.8 28.4 1.0
OE1 A:GLN381 4.9 24.1 1.0
C A:GLN708 4.9 17.4 1.0
O A:GLY709 5.0 23.2 1.0

Fluorine binding site 3 out of 8 in 8xak

Go back to Fluorine Binding Sites List in 8xak
Fluorine binding site 3 out of 8 in the Structure of PIF1-G4 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 PIF1-G4 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1002

b:23.8
occ:1.00
 F3 A:ALF1002 0.0 23.8 1.0
AL A:ALF1002 1.8 22.2 1.0
NE2 A:GLN381 2.4 28.4 1.0
F2 A:ALF1002 2.5 20.1 1.0
F1 A:ALF1002 2.5 21.8 1.0
CD A:GLN381 3.2 27.8 1.0
OE1 A:GLN381 3.3 24.1 1.0
NZ A:LYS264 3.4 38.2 1.0
F4 A:ALF1002 3.6 24.0 1.0
OE2 A:GLU342 3.9 13.8 1.0
CE A:LYS264 3.9 36.3 1.0
O2B A:ADP1001 4.1 29.7 1.0
OE1 A:GLU342 4.2 22.4 1.0
CA A:ALA260 4.2 21.3 1.0
CB A:ASP378 4.3 26.7 1.0
NH2 A:ARG734 4.3 21.0 1.0
CD A:GLU342 4.5 23.1 1.0
O1B A:ADP1001 4.5 31.8 1.0
CG A:GLN381 4.6 14.0 1.0
PB A:ADP1001 4.7 30.4 1.0
N A:ALA260 4.7 22.3 1.0
NH1 A:ARG417 4.8 37.0 1.0
CB A:ALA260 4.8 21.6 1.0
N A:ASP378 4.9 24.5 1.0
MG A:MG1003 4.9 19.4 1.0
O A:SER259 5.0 29.8 1.0
O A:GLY258 5.0 31.8 1.0
N A:GLY261 5.0 24.0 1.0

Fluorine binding site 4 out of 8 in 8xak

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Fluorine binding site 4 out of 8 in the Structure of PIF1-G4 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 PIF1-G4 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1002

b:24.0
occ:1.00
 F4 A:ALF1002 0.0 24.0 1.0
AL A:ALF1002 1.8 22.2 1.0
NH2 A:ARG417 2.5 40.0 1.0
O2B A:ADP1001 2.5 29.7 1.0
NH1 A:ARG417 2.5 37.0 1.0
F1 A:ALF1002 2.5 21.8 1.0
F2 A:ALF1002 2.5 20.1 1.0
NH2 A:ARG734 2.8 21.0 1.0
CZ A:ARG417 2.8 34.4 1.0
CA A:GLY709 3.0 21.1 1.0
N A:GLY709 3.3 20.7 1.0
C A:GLY709 3.4 21.6 1.0
F3 A:ALF1002 3.6 23.8 1.0
O A:GLY709 3.7 23.2 1.0
PB A:ADP1001 3.7 30.4 1.0
CZ A:ARG734 3.9 19.2 1.0
O3B A:ADP1001 4.0 30.1 1.0
OE2 A:GLU342 4.0 13.8 1.0
MG A:MG1003 4.1 19.4 1.0
NE A:ARG417 4.2 25.9 1.0
NE A:ARG734 4.2 19.4 1.0
N A:GLN710 4.2 21.8 1.0
O A:GLN710 4.4 22.6 1.0
O2A A:ADP1001 4.5 29.9 1.0
C A:GLN708 4.6 17.4 1.0
O1B A:ADP1001 4.6 31.8 1.0
N A:GLY261 4.7 24.0 1.0
O3A A:ADP1001 4.8 32.5 1.0
NH1 A:ARG734 5.0 27.1 1.0

Fluorine binding site 5 out of 8 in 8xak

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Fluorine binding site 5 out of 8 in the Structure of PIF1-G4 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 PIF1-G4 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1002

b:28.6
occ:1.00
 F1 C:ALF1002 0.0 28.6 1.0
AL C:ALF1002 1.8 29.0 1.0
NH2 C:ARG734 2.4 33.4 1.0
F4 C:ALF1002 2.5 30.7 1.0
F3 C:ALF1002 2.5 30.6 1.0
NH1 C:ARG417 3.1 36.3 1.0
CZ C:ARG734 3.1 37.0 1.0
NE2 C:GLN381 3.3 23.2 1.0
CB C:ALA260 3.3 30.3 1.0
O2B C:ADP1001 3.3 33.0 1.0
CA C:ALA260 3.4 30.4 1.0
F2 C:ALF1002 3.6 26.8 1.0
NH1 C:ARG734 3.7 39.3 1.0
OE1 C:GLN381 3.8 31.7 1.0
N C:GLY261 3.8 30.3 1.0
NE C:ARG734 3.9 37.4 1.0
CD C:GLN381 3.9 23.0 1.0
CZ C:ARG417 4.0 35.7 1.0
NH2 C:ARG417 4.1 41.6 1.0
C C:ALA260 4.1 32.2 1.0
O C:SER259 4.4 34.9 1.0
OG C:SER733 4.5 20.7 1.0
PB C:ADP1001 4.6 33.8 1.0
N C:ALA260 4.7 30.4 1.0
O3B C:ADP1001 4.8 35.2 1.0
OE2 C:GLU342 4.9 47.7 1.0
CA C:GLY261 5.0 34.1 1.0

Fluorine binding site 6 out of 8 in 8xak

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Fluorine binding site 6 out of 8 in the Structure of PIF1-G4 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 PIF1-G4 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1002

b:26.8
occ:1.00
 F2 C:ALF1002 0.0 26.8 1.0
AL C:ALF1002 1.8 29.0 1.0
OE2 C:GLU342 2.1 47.7 1.0
F3 C:ALF1002 2.5 30.6 1.0
F4 C:ALF1002 2.5 30.7 1.0
MG C:MG1003 2.9 30.9 1.0
O2B C:ADP1001 3.1 33.0 1.0
CA C:GLY709 3.2 22.9 1.0
CD C:GLU342 3.3 43.7 1.0
O1B C:ADP1001 3.5 33.5 1.0
N C:GLY709 3.5 24.9 1.0
F1 C:ALF1002 3.6 28.6 1.0
PB C:ADP1001 3.7 33.8 1.0
OE1 C:GLU342 4.0 40.5 1.0
C C:GLY709 4.3 22.4 1.0
CG C:GLU342 4.3 37.5 1.0
O3B C:ADP1001 4.3 35.2 1.0
C C:GLN708 4.5 25.3 1.0
OG C:SER265 4.6 25.0 1.0
OE1 C:GLN381 4.6 31.7 1.0
O C:GLY709 4.6 23.0 1.0
NH2 C:ARG417 4.6 41.6 1.0
CG C:GLN708 4.8 26.2 1.0
NE2 C:GLN381 4.8 23.2 1.0
NH1 C:ARG734 4.9 39.3 1.0
O C:GLN708 5.0 24.3 1.0

Fluorine binding site 7 out of 8 in 8xak

Go back to Fluorine Binding Sites List in 8xak
Fluorine binding site 7 out of 8 in the Structure of PIF1-G4 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 PIF1-G4 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1002

b:30.6
occ:1.00
 F3 C:ALF1002 0.0 30.6 1.0
AL C:ALF1002 1.8 29.0 1.0
NE2 C:GLN381 2.5 23.2 1.0
F2 C:ALF1002 2.5 26.8 1.0
F1 C:ALF1002 2.5 28.6 1.0
OE1 C:GLN381 3.2 31.7 1.0
CD C:GLN381 3.2 23.0 1.0
OE2 C:GLU342 3.3 47.7 1.0
F4 C:ALF1002 3.6 30.7 1.0
O2B C:ADP1001 3.7 33.0 1.0
OE1 C:GLU342 4.0 40.5 1.0
O C:SER259 4.0 34.9 1.0
NZ C:LYS264 4.0 26.9 1.0
O3B C:ADP1001 4.1 35.2 1.0
CD C:GLU342 4.1 43.7 1.0
PB C:ADP1001 4.2 33.8 1.0
NH2 C:ARG734 4.4 33.4 1.0
CE C:LYS264 4.4 26.8 1.0
CA C:ALA260 4.6 30.4 1.0
CG C:GLN381 4.6 31.7 1.0
O1B C:ADP1001 4.7 33.5 1.0
CB C:ASP378 4.7 28.9 1.0
NH1 C:ARG734 4.9 39.3 1.0
CZ C:ARG734 4.9 37.0 1.0
CB C:ALA260 5.0 30.3 1.0

Fluorine binding site 8 out of 8 in 8xak

Go back to Fluorine Binding Sites List in 8xak
Fluorine binding site 8 out of 8 in the Structure of PIF1-G4 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 PIF1-G4 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1002

b:30.7
occ:1.00
 F4 C:ALF1002 0.0 30.7 1.0
AL C:ALF1002 1.8 29.0 1.0
F1 C:ALF1002 2.5 28.6 1.0
F2 C:ALF1002 2.5 26.8 1.0
NH2 C:ARG417 2.6 41.6 1.0
O2B C:ADP1001 2.7 33.0 1.0
NH1 C:ARG417 3.1 36.3 1.0
CA C:GLY709 3.2 22.9 1.0
CZ C:ARG417 3.2 35.7 1.0
N C:GLY709 3.3 24.9 1.0
C C:GLY709 3.5 22.4 1.0
CZ C:ARG734 3.6 37.0 1.0
F3 C:ALF1002 3.6 30.6 1.0
NH1 C:ARG734 3.8 39.3 1.0
NH2 C:ARG734 3.8 33.4 1.0
O C:GLY709 3.8 23.0 1.0
NE C:ARG734 3.8 37.4 1.0
O C:GLN710 4.1 25.5 1.0
PB C:ADP1001 4.1 33.8 1.0
N C:GLN710 4.2 19.4 1.0
OE2 C:GLU342 4.2 47.7 1.0
MG C:MG1003 4.4 30.9 1.0
CD C:ARG734 4.4 33.6 1.0
O1A C:ADP1001 4.5 33.2 1.0
NE C:ARG417 4.5 30.4 1.0
O1B C:ADP1001 4.5 33.5 1.0
C C:GLN708 4.6 25.3 1.0
C C:GLN710 4.8 21.2 1.0
N C:GLY261 5.0 30.3 1.0
O3B C:ADP1001 5.0 35.2 1.0

Reference:

Z.Hong, A.K.Byrd, J.Gao, P.Das, V.Q.Tan, E.G.Malone, B.Osei, J.C.Marecki, R.U.Protacio, W.P.Wahls, K.D.Raney, H.Song. Eukaryotic PIF1 Helicase Unwinds G-Quadruplex and Dsdna Using A Conserved Wedge. Nat Commun V. 15 6104 2024.
ISSN: ESSN 2041-1723
PubMed: 39030241
DOI: 10.1038/S41467-024-50575-8
Page generated: Wed Jul 16 10:11:57 2025

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