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

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

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

Fluorine	(F)	8 atoms
Magnesium	(Mg)	2 atoms
Aluminium	(Al)	2 atoms

The binding sites of Potassium atom in the Structure of PIF1-G4 Complex (pdb code 8xak). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Structure of PIF1-G4 Complex, PDB code: 8xak:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in the Structure of PIF1-G4 Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure of PIF1-G4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:K2001 b:35.8 occ:1.00 O6 D:DG34 2.7 57.1 1.0 O6 D:DG33 2.8 58.7 1.0 O6 D:DG28 2.8 27.2 1.0 O6 D:DG27 2.8 40.0 1.0 O6 D:DG25 2.9 48.1 1.0 O6 D:DG30 3.0 56.0 1.0 O6 D:DG31 3.0 41.8 1.0 N1 D:DG25 3.4 44.1 1.0 C6 D:DG25 3.5 46.3 1.0 C6 D:DG34 3.6 57.1 1.0 K D:K2002 3.7 50.7 1.0 C6 D:DG31 3.7 39.8 1.0 O6 D:DG24 3.7 51.2 1.0 C6 D:DG33 3.7 54.5 1.0 C6 D:DG30 3.7 50.6 1.0 C6 D:DG28 3.8 31.1 1.0 N1 D:DG31 3.8 40.3 1.0 C6 D:DG27 3.8 41.9 1.0 N1 D:DG30 3.8 47.6 1.0 N1 D:DG34 3.9 54.1 1.0 N1 D:DG27 4.1 45.3 1.0 N1 D:DG28 4.1 32.9 1.0 N1 D:DG33 4.1 53.7 1.0 C6 D:DG24 4.4 53.5 1.0 C2 D:DG25 4.6 40.4 1.0 N1 D:DG24 4.6 55.7 1.0 C5 D:DG33 4.8 53.0 1.0 C5 D:DG25 4.8 44.9 1.0 C5 D:DG31 4.9 38.5 1.0 C5 D:DG34 4.9 55.0 1.0 C2 D:DG31 5.0 42.1 1.0 C5 D:DG30 5.0 45.0 1.0 C5 D:DG28 5.0 33.5 1.0 N2 D:DG25 5.0 40.0 1.0

Potassium binding site 2 out of 6 in the Structure of PIF1-G4 Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of PIF1-G4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:K2002 b:50.7 occ:1.00 O6 D:DG16 2.7 56.3 1.0 O6 D:DG13 2.7 39.2 1.0 O6 D:DG24 2.8 51.2 1.0 O6 D:DG22 2.8 55.8 1.0 O6 D:DG33 2.9 58.7 1.0 O6 D:DG27 2.9 40.0 1.0 O6 D:DG30 2.9 56.0 1.0 O6 D:DG10 3.1 43.6 1.0 C6 D:DG27 3.6 41.9 1.0 C6 D:DG13 3.6 38.1 1.0 C6 D:DG22 3.6 57.5 1.0 C6 D:DG24 3.7 53.5 1.0 K D:K2003 3.7 49.2 1.0 K D:K2001 3.7 35.8 1.0 C6 D:DG33 3.7 54.5 1.0 N1 D:DG27 3.8 45.3 1.0 C6 D:DG16 3.8 60.6 1.0 C6 D:DG30 3.8 50.6 1.0 N1 D:DG24 3.8 55.7 1.0 N1 D:DG13 3.8 38.0 1.0 N1 D:DG10 3.8 38.0 1.0 C6 D:DG10 3.8 39.2 1.0 N1 D:DG33 4.0 53.7 1.0 N1 D:DG22 4.0 56.1 1.0 N1 D:DG30 4.1 47.6 1.0 N1 D:DG16 4.3 60.7 1.0 C5 D:DG27 4.7 39.2 1.0 C5 D:DG22 4.8 63.6 1.0 C5 D:DG13 4.8 37.3 1.0 C2 D:DG27 4.9 46.2 1.0 C5 D:DG16 5.0 61.2 1.0 C5 D:DG33 5.0 53.0 1.0 C5 D:DG30 5.0 45.0 1.0 C5 D:DG24 5.0 52.9 1.0

Potassium binding site 3 out of 6 in the Structure of PIF1-G4 Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure of PIF1-G4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:K2003 b:49.2 occ:1.00 O6 D:DG22 2.8 55.8 1.0 O6 D:DG15 2.8 49.3 1.0 O6 D:DG13 2.8 39.2 1.0 O6 D:DG12 2.8 33.9 1.0 O6 D:DG16 3.0 56.3 1.0 O6 D:DG9 3.0 54.9 1.0 O6 D:DG19 3.1 77.0 1.0 C6 D:DG13 3.4 38.1 1.0 C6 D:DG15 3.5 49.6 1.0 C6 D:DG12 3.5 34.2 1.0 N1 D:DG13 3.6 38.0 1.0 N1 D:DG15 3.6 45.1 1.0 K D:K2002 3.7 50.7 1.0 N1 D:DG12 3.7 34.6 1.0 C6 D:DG16 3.7 60.6 1.0 C6 D:DG22 3.7 57.5 1.0 C6 D:DG19 3.8 71.5 1.0 N1 D:DG19 3.9 66.6 1.0 C6 D:DG9 3.9 50.8 1.0 O6 D:DG10 4.0 43.6 1.0 N1 D:DG16 4.1 60.7 1.0 N1 D:DG10 4.1 38.0 1.0 N1 D:DG22 4.2 56.1 1.0 N1 D:DG9 4.2 51.5 1.0 C6 D:DG10 4.4 39.2 1.0 C5 D:DG13 4.6 37.3 1.0 C5 D:DG12 4.7 36.0 1.0 C5 D:DG15 4.7 52.4 1.0 C2 D:DG13 4.7 39.9 1.0 C5 D:DG16 4.8 61.2 1.0 C2 D:DG15 4.8 46.5 1.0 C2 D:DG12 4.9 37.7 1.0 C5 D:DG22 4.9 63.6 1.0

Potassium binding site 4 out of 6 in the Structure of PIF1-G4 Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Structure of PIF1-G4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:K101 b:42.1 occ:1.00 O6 B:DG25 2.7 34.9 1.0 O6 B:DG33 2.7 51.1 1.0 O6 B:DG31 2.8 38.0 1.0 O6 B:DG27 2.8 31.1 1.0 O6 B:DG34 2.9 49.9 1.0 O6 B:DG28 2.9 29.1 1.0 O6 B:DG30 2.9 48.7 1.0 O6 B:DG24 3.3 58.3 1.0 C6 B:DG25 3.4 34.2 1.0 N1 B:DG25 3.5 33.3 1.0 K B:K102 3.5 37.7 1.0 C6 B:DG27 3.6 32.9 1.0 C6 B:DG31 3.6 37.4 1.0 C6 B:DG34 3.6 51.9 1.0 N1 B:DG27 3.7 34.5 1.0 C6 B:DG33 3.7 53.6 1.0 C6 B:DG30 3.8 42.4 1.0 N1 B:DG34 3.8 51.6 1.0 C6 B:DG28 3.9 30.1 1.0 N1 B:DG31 3.9 38.7 1.0 C6 B:DG24 4.1 48.9 1.0 N1 B:DG30 4.2 43.1 1.0 N1 B:DG33 4.3 56.3 1.0 N1 B:DG24 4.3 45.5 1.0 N1 B:DG28 4.4 31.2 1.0 C5 B:DG25 4.6 33.3 1.0 C2 B:DG25 4.7 31.3 1.0 C5 B:DG31 4.8 34.6 1.0 C5 B:DG33 4.8 50.8 1.0 C5 B:DG34 4.9 50.7 1.0 C5 B:DG27 4.9 32.4 1.0 C2 B:DG27 4.9 34.3 1.0 C5 B:DG30 4.9 37.9 1.0

Potassium binding site 5 out of 6 in the Structure of PIF1-G4 Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Structure of PIF1-G4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:K102 b:37.7 occ:1.00 O6 B:DG13 2.6 36.9 1.0 O6 B:DG30 2.7 48.7 1.0 O6 B:DG24 2.7 58.3 1.0 O6 B:DG22 2.7 46.8 1.0 O6 B:DG27 2.8 31.1 1.0 O6 B:DG16 3.1 42.0 1.0 O6 B:DG33 3.1 51.1 1.0 N1 B:DG27 3.2 34.5 1.0 O6 B:DG10 3.3 36.1 1.0 C6 B:DG27 3.3 32.9 1.0 C6 B:DG22 3.4 48.8 1.0 K B:K101 3.5 42.1 1.0 C6 B:DG24 3.5 48.9 1.0 N1 B:DG22 3.6 45.9 1.0 K B:K103 3.6 48.8 1.0 C6 B:DG13 3.6 37.5 1.0 N1 B:DG24 3.7 45.5 1.0 C6 B:DG30 3.8 42.4 1.0 C6 B:DG10 4.1 37.4 1.0 C6 B:DG33 4.1 53.6 1.0 N1 B:DG13 4.1 40.4 1.0 N1 B:DG10 4.2 41.0 1.0 C6 B:DG16 4.3 42.1 1.0 C2 B:DG27 4.3 34.3 1.0 N1 B:DG30 4.4 43.1 1.0 C5 B:DG27 4.5 32.4 1.0 N1 B:DG33 4.5 56.3 1.0 C5 B:DG22 4.6 50.6 1.0 N1 B:DG16 4.7 42.4 1.0 N2 B:DG27 4.7 34.8 1.0 C2 B:DG22 4.8 42.2 1.0 C5 B:DG13 4.8 36.6 1.0 C5 B:DG30 4.8 37.9 1.0 C5 B:DG24 4.9 43.8 1.0 C2 B:DG24 5.0 38.1 1.0

Potassium binding site 6 out of 6 in the Structure of PIF1-G4 Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Structure of PIF1-G4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:K103 b:48.8 occ:1.00 O6 B:DG15 2.7 50.4 1.0 O6 B:DG9 2.7 45.4 1.0 O6 B:DG22 2.7 46.8 1.0 O6 B:DG13 2.7 36.9 1.0 O6 B:DG12 2.9 42.1 1.0 O6 B:DG19 3.2 68.3 1.0 O6 B:DG16 3.3 42.0 1.0 C6 B:DG15 3.3 47.6 1.0 C6 B:DG13 3.3 37.5 1.0 N1 B:DG15 3.4 47.0 1.0 N1 B:DG13 3.5 40.4 1.0 C6 B:DG22 3.6 48.8 1.0 K B:K102 3.6 37.7 1.0 C6 B:DG9 3.7 44.8 1.0 C6 B:DG12 3.7 41.1 1.0 N1 B:DG12 3.9 41.6 1.0 C6 B:DG16 3.9 42.1 1.0 N1 B:DG22 3.9 45.9 1.0 C6 B:DG19 4.0 68.1 1.0 N1 B:DG9 4.0 42.8 1.0 O6 B:DG10 4.1 36.1 1.0 N1 B:DG19 4.4 70.9 1.0 N1 B:DG16 4.5 42.4 1.0 C5 B:DG15 4.5 46.0 1.0 C5 B:DG13 4.5 36.6 1.0 C2 B:DG15 4.6 46.1 1.0 C2 B:DG13 4.7 42.0 1.0 C5 B:DG16 4.8 43.0 1.0 C5 B:DG22 4.8 50.6 1.0 C6 B:DG10 4.9 37.4 1.0 N1 B:DG10 4.9 41.0 1.0 C5 B:DG12 4.9 41.0 1.0 C5 B:DG9 4.9 45.1 1.0 C5 B:DG19 5.0 63.1 1.0

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