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

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

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

The binding sites of Potassium 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 Potassium atom.
In total 3 binding sites of Potassium where determined in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Parallel G-Quadruplex, PDB code: 7oar:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 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 Potassium with other atoms in the K 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 C:K101 b:147.3 occ:1.00 O6 C:DG11 2.6 149.3 1.0 O6 C:DG19 2.6 149.7 1.0 O6 C:DG8 2.7 126.2 1.0 O6 C:DG7 2.8 128.7 1.0 O6 C:DG20 2.8 165.9 1.0 O6 C:DG12 2.9 131.0 1.0 O6 C:DG16 3.0 166.1 1.0 O6 C:DG15 3.2 148.6 1.0 C6 C:DG11 3.5 131.5 1.0 C6 C:DG19 3.5 152.2 1.0 K C:K102 3.5 176.9 1.0 C6 C:DG8 3.6 126.7 1.0 C6 C:DG7 3.6 119.2 1.0 N1 C:DG19 3.7 155.5 1.0 N1 C:DG7 3.8 120.2 1.0 C6 C:DG20 3.8 156.3 1.0 N1 C:DG8 3.9 128.4 1.0 C6 C:DG12 3.9 132.8 1.0 N1 C:DG11 4.0 136.4 1.0 C6 C:DG16 4.0 167.3 1.0 C6 C:DG15 4.0 149.7 1.0 N1 C:DG15 4.2 144.5 1.0 N1 C:DG20 4.2 135.7 1.0 N1 C:DG12 4.3 133.8 1.0 N1 C:DG16 4.5 166.1 1.0 C5 C:DG11 4.6 127.7 1.0 C5 C:DG19 4.8 159.8 1.0 C5 C:DG7 4.9 120.0 1.0 C5 C:DG8 4.9 126.1 1.0 NE A:ARG392 5.0 156.1 1.0

Potassium binding site 2 out of 3 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 Potassium with other atoms in the K 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 C:K102 b:176.9 occ:1.00 O6 C:DG17 2.7 182.4 1.0 O6 C:DG9 2.8 133.0 1.0 O6 C:DG16 2.8 166.1 1.0 O6 C:DG12 3.0 131.0 1.0 O6 C:DG21 3.0 130.0 1.0 O6 C:DG20 3.1 165.9 1.0 O6 C:DG8 3.1 126.2 1.0 O6 C:DG13 3.1 177.3 1.0 N1 C:DG9 3.4 136.2 1.0 C6 C:DG9 3.5 134.5 1.0 C6 C:DG17 3.5 168.6 1.0 K C:K101 3.5 147.3 1.0 C6 C:DG16 3.7 167.3 1.0 N1 C:DG17 3.7 153.9 1.0 C6 C:DG8 3.8 126.7 1.0 C6 C:DG13 3.8 164.7 1.0 N1 C:DG13 3.9 157.4 1.0 C6 C:DG12 3.9 132.8 1.0 C6 C:DG20 3.9 156.3 1.0 C6 C:DG21 4.0 124.5 1.0 N1 C:DG8 4.0 128.4 1.0 N1 C:DG16 4.2 166.1 1.0 N1 C:DG20 4.3 135.7 1.0 N1 C:DG21 4.3 121.0 1.0 N1 C:DG12 4.3 133.8 1.0 K C:K103 4.4 148.5 1.0 C2 C:DG9 4.7 138.1 1.0 C5 C:DG17 4.8 167.0 1.0 C5 C:DG16 4.8 174.9 1.0 C5 C:DG9 4.9 135.0 1.0 C5 C:DG8 5.0 126.1 1.0

Potassium binding site 3 out of 3 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 Potassium with other atoms in the K 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 C:K103 b:148.5 occ:1.00 O6 C:DG17 3.2 182.4 1.0 O6 C:DG13 3.6 177.3 1.0 O4 C:DT22 3.7 146.7 1.0 C6 C:DG17 3.8 168.6 1.0 C6 C:DG13 4.1 164.7 1.0 N1 C:DG13 4.1 157.4 1.0 N1 C:DG17 4.2 153.9 1.0 O6 C:DG21 4.2 130.0 1.0 K C:K102 4.4 176.9 1.0 O6 C:DG9 4.5 133.0 1.0 NH2 B:ARG448 4.6 107.1 1.0 N1 C:DG9 4.6 136.2 1.0 C4 C:DT22 4.6 131.9 1.0 N3 C:DT22 4.8 119.5 1.0 C6 C:DG9 4.8 134.5 1.0 C5 C:DG17 4.8 167.0 1.0 O B:ARG448 5.0 98.1 1.0

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