Magnesium 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
Potassium	(K)	3 atoms
Fluorine	(F)	8 atoms

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

Magnesium binding site 1 out of 2 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 Magnesium with other atoms in the Mg 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:Mg1002 b:81.8 occ:1.00 F2 A:ALF1003 1.9 102.7 1.0 OG1 A:THR98 2.0 110.0 1.0 O A:HOH1114 2.0 72.1 1.0 O A:HOH1105 2.1 79.5 1.0 O A:HOH1107 2.2 84.6 1.0 O2B A:ADP1001 2.2 87.6 1.0 CB A:THR98 3.2 90.9 1.0 PB A:ADP1001 3.3 96.2 1.0 O3B A:ADP1001 3.5 61.8 1.0 AL A:ALF1003 3.5 86.1 1.0 F4 A:ALF1003 3.6 83.6 1.0 OD2 A:ASP171 3.8 103.7 1.0 N A:THR98 3.8 81.7 1.0 CA A:THR98 4.0 93.0 1.0 O A:HOH1108 4.1 83.8 1.0 O2A A:ADP1001 4.1 80.7 1.0 CG2 A:THR98 4.2 98.5 1.0 F3 A:ALF1003 4.2 81.7 1.0 OD1 A:ASP171 4.3 76.8 1.0 CD A:GLU172 4.4 102.6 1.0 O A:HOH1101 4.4 84.1 1.0 O3A A:ADP1001 4.4 98.5 1.0 O A:GLY436 4.4 104.8 1.0 CG A:ASP171 4.4 100.5 1.0 O1B A:ADP1001 4.4 79.7 1.0 OE2 A:GLU172 4.5 103.7 1.0 CG A:GLU172 4.5 102.8 1.0 CA A:GLY436 4.5 99.3 1.0 PA A:ADP1001 4.6 99.6 1.0 OE1 A:GLU172 4.7 114.1 1.0 O A:HOH1102 4.7 90.0 1.0 CB A:LYS97 4.8 79.1 1.0 C A:LYS97 4.9 103.3 1.0 O1A A:ADP1001 4.9 92.8 1.0 C A:GLY436 5.0 103.2 1.0

Magnesium binding site 2 out of 2 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 Magnesium with other atoms in the Mg 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 B:Mg1002 b:77.4 occ:1.00 O B:HOH1116 1.9 73.8 1.0 F2 B:ALF1003 2.1 69.7 1.0 OG1 B:THR98 2.1 73.4 1.0 O1B B:ADP1001 2.4 72.2 1.0 O B:HOH1110 2.7 63.0 1.0 CB B:THR98 3.4 65.1 1.0 OD1 B:ASP171 3.5 80.7 1.0 OD2 B:ASP171 3.5 74.7 1.0 PB B:ADP1001 3.6 81.8 1.0 O B:HOH1109 3.7 74.7 1.0 OE2 B:GLU172 3.7 71.1 1.0 AL B:ALF1003 3.8 75.5 1.0 N B:THR98 3.8 69.2 1.0 CG B:ASP171 3.9 77.4 1.0 F3 B:ALF1003 4.0 68.8 1.0 O3B B:ADP1001 4.0 59.7 1.0 O B:HOH1106 4.0 72.2 1.0 CA B:THR98 4.1 71.2 1.0 CD B:GLU172 4.2 74.7 1.0 O2B B:ADP1001 4.3 66.0 1.0 F4 B:ALF1003 4.4 70.8 1.0 CB B:LYS97 4.4 59.3 1.0 O B:HOH1107 4.5 66.5 1.0 CG2 B:THR98 4.5 70.7 1.0 CE B:LYS97 4.6 72.2 1.0 CG B:GLU172 4.7 79.7 1.0 C B:LYS97 4.7 81.3 1.0 CA B:GLY436 4.8 61.9 1.0 OE1 B:GLU172 4.8 70.8 1.0 O3A B:ADP1001 4.9 77.0 1.0 O1A B:ADP1001 4.9 64.9 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