Magnesium 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:

Potassium	(K)	6 atoms
Fluorine	(F)	8 atoms
Aluminium	(Al)	2 atoms

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

Magnesium binding site 1 out of 2 in the Structure of PIF1-G4 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of PIF1-G4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1003 b:19.4 occ:1.00 OG A:SER265 2.0 26.9 1.0 O3B A:ADP1001 2.3 30.1 1.0 F2 A:ALF1002 2.7 20.1 1.0 CB A:SER265 3.2 31.5 1.0 OD2 A:ASP341 3.3 25.2 1.0 PB A:ADP1001 3.5 30.4 1.0 N A:SER265 3.9 36.0 1.0 OE2 A:GLU342 3.9 13.8 1.0 OD1 A:ASP341 4.0 16.1 1.0 O2B A:ADP1001 4.0 29.7 1.0 CA A:SER265 4.0 32.4 1.0 CG A:ASP341 4.0 25.2 1.0 F4 A:ALF1002 4.1 24.0 1.0 O1B A:ADP1001 4.2 31.8 1.0 AL A:ALF1002 4.2 22.2 1.0 CA A:GLY709 4.4 21.1 1.0 ND2 A:ASN296 4.5 20.0 1.0 O2A A:ADP1001 4.5 29.9 1.0 CB A:LYS264 4.6 30.3 1.0 CD A:GLU342 4.6 23.1 1.0 O3A A:ADP1001 4.7 32.5 1.0 C A:LYS264 4.7 25.9 1.0 CE A:LYS264 4.8 36.3 1.0 O A:GLY709 4.8 23.2 1.0 F3 A:ALF1002 4.9 23.8 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of PIF1-G4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1003 b:30.9 occ:1.00 OG C:SER265 1.9 25.0 1.0 O1B C:ADP1001 2.1 33.5 1.0 CB C:SER265 2.7 30.5 1.0 F2 C:ALF1002 2.9 26.8 1.0 PB C:ADP1001 3.4 33.8 1.0 O2B C:ADP1001 3.7 33.0 1.0 OD2 C:ASP341 3.8 28.7 1.0 O1A C:ADP1001 3.8 33.2 1.0 N C:SER265 3.8 35.5 1.0 CA C:SER265 3.8 31.4 1.0 CA C:GLY709 4.0 22.9 1.0 OE2 C:GLU342 4.1 47.7 1.0 O C:GLY709 4.2 23.0 1.0 ND2 C:ASN296 4.2 25.1 1.0 F4 C:ALF1002 4.4 30.7 1.0 AL C:ALF1002 4.4 29.0 1.0 O3A C:ADP1001 4.4 35.9 1.0 PA C:ADP1001 4.4 33.1 1.0 O3B C:ADP1001 4.4 35.2 1.0 C C:GLY709 4.6 22.4 1.0 CG C:ASP341 4.6 25.4 1.0 O2A C:ADP1001 4.7 36.6 1.0 OD1 C:ASP341 4.7 23.1 1.0 CD C:GLU342 5.0 43.7 1.0 C C:LYS264 5.0 27.3 1.0 C C:SER265 5.0 29.4 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