Magnesium in PDB 5o6b: Structure of SCPIF1 in Complex with Gggtttt and Adp-ALF4

All present enzymatic activity of Structure of SCPIF1 in Complex with Gggtttt and Adp-ALF4:
3.6.4.12;

The structure of Structure of SCPIF1 in Complex with Gggtttt and Adp-ALF4, PDB code: 5o6b was solved by K.Y.Lu, W.F.Chen, S.Rety, N.N.Liu, X.G.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.71 / 2.03
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.246, 88.373, 187.703, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 23.8

The structure of Structure of SCPIF1 in Complex with Gggtttt and Adp-ALF4 also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Structure of SCPIF1 in Complex with Gggtttt and Adp-ALF4 (pdb code 5o6b). 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 SCPIF1 in Complex with Gggtttt and Adp-ALF4, PDB code: 5o6b:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of SCPIF1 in Complex with Gggtttt and Adp-ALF4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of SCPIF1 in Complex with Gggtttt and Adp-ALF4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1003 b:26.1 occ:1.00 F2 A:ALF1002 1.9 27.4 1.0 O A:HOH1207 2.0 24.0 1.0 O1B A:ADP1001 2.1 26.6 1.0 OG A:SER265 2.1 29.6 1.0 O A:HOH1157 2.2 24.0 1.0 O A:HOH1173 2.2 24.6 1.0 CB A:SER265 3.1 24.2 1.0 PB A:ADP1001 3.3 26.9 1.0 O2B A:ADP1001 3.5 26.1 1.0 AL A:ALF1002 3.5 29.5 1.0 F4 A:ALF1002 3.6 31.3 1.0 OE2 A:GLU342 3.8 26.2 1.0 N A:SER265 3.9 30.1 1.0 OD2 A:ASP341 4.0 25.6 1.0 CA A:SER265 4.1 25.2 1.0 O A:HOH1160 4.1 28.3 1.0 O A:HOH1176 4.1 34.0 1.0 F3 A:ALF1002 4.2 31.1 1.0 O2A A:ADP1001 4.2 26.3 1.0 OD1 A:ASP341 4.2 31.3 1.0 CA A:GLY709 4.3 19.8 1.0 O3A A:ADP1001 4.3 28.9 1.0 O3B A:ADP1001 4.4 28.2 1.0 O A:HOH1150 4.4 26.9 1.0 ND2 A:ASN296 4.5 27.2 1.0 O A:GLY709 4.5 27.5 1.0 CG A:ASP341 4.5 28.3 1.0 CD A:GLU342 4.6 29.2 1.0 PA A:ADP1001 4.6 26.1 1.0 O1A A:ADP1001 4.7 29.7 1.0 CB A:LYS264 4.8 25.1 1.0 C A:LYS264 4.9 32.3 1.0 C A:GLY709 4.9 27.5 1.0 O A:HOH1241 5.0 37.3 1.0

Magnesium binding site 2 out of 2 in the Structure of SCPIF1 in Complex with Gggtttt and Adp-ALF4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of SCPIF1 in Complex with Gggtttt and Adp-ALF4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1003 b:30.7 occ:1.00 F2 B:ALF1002 1.9 32.4 1.0 O B:HOH1199 2.0 28.0 1.0 O1B B:ADP1001 2.0 31.6 1.0 OG B:SER265 2.1 26.5 1.0 O B:HOH1161 2.2 21.5 1.0 CB B:SER265 3.0 25.4 1.0 PB B:ADP1001 3.2 33.6 1.0 AL B:ALF1002 3.5 32.2 1.0 O2B B:ADP1001 3.6 36.7 1.0 F4 B:ALF1002 3.7 29.1 1.0 N B:SER265 3.8 32.2 1.0 OE1 B:GLU342 3.9 28.0 1.0 CA B:SER265 4.0 30.6 1.0 OD2 B:ASP341 4.0 30.7 1.0 O2A B:ADP1001 4.2 34.5 1.0 F3 B:ALF1002 4.2 29.9 1.0 O B:HOH1158 4.2 29.9 1.0 OD1 B:ASP341 4.2 30.7 1.0 O3A B:ADP1001 4.3 32.8 1.0 O3B B:ADP1001 4.3 34.9 1.0 O B:HOH1176 4.3 28.9 1.0 CA B:GLY709 4.4 25.4 1.0 PA B:ADP1001 4.4 32.3 1.0 O1A B:ADP1001 4.4 37.6 1.0 O B:GLY709 4.5 31.2 1.0 CG B:ASP341 4.6 26.5 1.0 CD B:GLU342 4.6 33.6 1.0 OD1 B:ASN296 4.6 32.8 1.0 O B:HOH1129 4.6 24.8 1.0 CB B:LYS264 4.8 29.0 1.0 C B:LYS264 4.8 37.4 1.0 C B:GLY709 5.0 31.4 1.0

K.Y.Lu, W.F.Chen, S.Rety, N.N.Liu, W.Q.Wu, Y.X.Dai, D.Li, H.Y.Ma, S.X.Dou, X.G.Xi. Insights Into the Structural and Mechanistic Basis of Multifunctional S. Cerevisiae PIF1P Helicase. Nucleic Acids Res. V. 46 1486 2018.
ISSN: ESSN 1362-4962
PubMed: 29202194
DOI: 10.1093/NAR/GKX1217