Magnesium in PDB 7bil: Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Oligo Ggtttggtttggtt

The structure of Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Oligo Ggtttggtttggtt, PDB code: 7bil was solved by Y.X.Dai, W.F.Chen, F.Y.Teng, N.N.Liu, X.M.Hou, S.X.Dou, S.Rety, X.G.Xi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.02 / 2.21
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	88.052, 103.438, 251.566, 90, 90, 90
R / Rfree (%)	17.9 / 22

The structure of Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Oligo Ggtttggtttggtt also contains other interesting chemical elements:

Aluminium	(Al)	2 atoms
Potassium	(K)	1 atom
Fluorine	(F)	8 atoms

The binding sites of Magnesium atom in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Oligo Ggtttggtttggtt (pdb code 7bil). 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 Oligo Ggtttggtttggtt, PDB code: 7bil:
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 Oligo Ggtttggtttggtt


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 Oligo Ggtttggtttggtt within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:36.9 occ:1.00 F2 A:ALF1003 1.9 44.0 1.0 O2B A:ADP1001 1.9 40.3 1.0 O A:HOH1140 2.0 35.0 1.0 O A:HOH1153 2.1 40.4 1.0 O A:HOH1131 2.1 39.8 1.0 OG1 A:THR98 2.2 36.6 1.0 CB A:THR98 3.2 38.8 1.0 PB A:ADP1001 3.2 39.6 1.0 AL A:ALF1003 3.4 36.6 1.0 O3B A:ADP1001 3.4 33.5 1.0 F4 A:ALF1003 3.6 38.3 1.0 N A:THR98 3.8 39.7 1.0 OE1 A:GLU172 4.0 40.0 1.0 OD2 A:ASP171 4.0 39.0 1.0 O A:HOH1136 4.1 37.5 1.0 F3 A:ALF1003 4.1 37.0 1.0 CA A:THR98 4.1 37.1 1.0 O2A A:ADP1001 4.1 34.6 1.0 O3A A:ADP1001 4.1 31.1 1.0 O1B A:ADP1001 4.3 34.7 1.0 CG2 A:THR98 4.3 38.0 1.0 OD1 A:ASP171 4.3 39.2 1.0 O A:GLY436 4.4 37.5 1.0 CA A:GLY436 4.5 38.3 1.0 PA A:ADP1001 4.5 35.3 1.0 O A:HOH1137 4.5 39.8 1.0 O A:HOH1108 4.6 38.5 1.0 CG A:ASP171 4.6 39.7 1.0 CB A:LYS97 4.6 34.3 1.0 CD A:GLU172 4.7 48.8 1.0 O1A A:ADP1001 4.8 44.2 1.0 C A:LYS97 4.9 44.0 1.0 CE A:LYS97 4.9 37.3 1.0 C A:GLY436 5.0 41.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Oligo Ggtttggtttggtt


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 Oligo Ggtttggtttggtt within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:62.3 occ:1.00 F2 B:ALF1003 1.8 52.9 1.0 O B:HOH1111 2.1 59.6 1.0 OG1 B:THR98 2.1 65.6 1.0 O B:HOH1115 2.1 60.9 1.0 O B:HOH1107 2.2 58.3 1.0 O3B B:ADP1001 2.3 62.7 1.0 CB B:THR98 3.2 65.5 1.0 PB B:ADP1001 3.4 58.0 1.0 AL B:ALF1003 3.5 57.7 1.0 O1B B:ADP1001 3.6 62.2 1.0 F3 B:ALF1003 3.6 53.7 1.0 OE1 B:GLU172 3.9 58.1 1.0 OD2 B:ASP171 3.9 63.3 1.0 N B:THR98 3.9 66.5 1.0 CA B:THR98 4.1 66.0 1.0 F4 B:ALF1003 4.2 57.8 1.0 O B:HOH1104 4.2 58.5 1.0 OD1 B:ASP171 4.2 66.4 1.0 CG2 B:THR98 4.3 63.4 1.0 O1A B:ADP1001 4.4 61.3 1.0 O B:GLY436 4.4 59.0 1.0 CA B:GLY436 4.4 54.1 1.0 O2B B:ADP1001 4.4 57.6 1.0 O3A B:ADP1001 4.5 64.6 1.0 CG B:ASP171 4.5 67.3 1.0 CD B:GLU172 4.5 64.0 1.0 O B:HOH1102 4.6 53.7 1.0 PA B:ADP1001 4.7 62.4 1.0 O2A B:ADP1001 4.8 61.1 1.0 C B:GLY436 4.9 54.7 1.0 CB B:LYS97 4.9 62.6 1.0 CG B:GLU172 5.0 58.9 1.0 C B:LYS97 5.0 68.0 1.0

Y.X.Dai, W.F.Chen, N.N.Liu, F.Y.Teng, H.L.Guo, X.M.Hou, S.X.Dou, S.Rety, X.G.Xi. Structural and Functional Studies of SF1B PIF1 From Thermus Oshimai Reveal Dimerization-Induced Helicase Inhibition. Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962
PubMed: 33784404
DOI: 10.1093/NAR/GKAB188