Magnesium in PDB 5o6d: Structure of SCPIF1 in Complex with Polydt and Atpgs

All present enzymatic activity of Structure of SCPIF1 in Complex with Polydt and Atpgs:
3.6.4.12;

The structure of Structure of SCPIF1 in Complex with Polydt and Atpgs, PDB code: 5o6d 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)	65.00 / 3.28
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.406, 90.783, 186.169, 90.00, 90.00, 90.00
R / Rfree (%)	25.2 / 32.2

The binding sites of Magnesium atom in the Structure of SCPIF1 in Complex with Polydt and Atpgs (pdb code 5o6d). 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 Polydt and Atpgs, PDB code: 5o6d:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of SCPIF1 in Complex with Polydt and Atpgs


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 Polydt and Atpgs within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:19.5 occ:1.00 OG A:SER265 2.0 59.6 1.0 O2B A:AGS1001 2.3 0.3 1.0 S1G A:AGS1001 2.5 0.4 1.0 CB A:SER265 2.9 60.8 1.0 ND2 A:ASN296 3.1 43.0 1.0 O A:GLY709 3.3 54.8 1.0 CA A:GLY709 3.7 53.7 1.0 PB A:AGS1001 3.7 0.8 1.0 O1A A:AGS1001 3.7 92.1 1.0 PG A:AGS1001 3.8 0.6 1.0 OD2 A:ASP341 3.9 44.9 1.0 C A:GLY709 3.9 54.2 1.0 O3B A:AGS1001 4.1 0.8 1.0 O3G A:AGS1001 4.2 0.4 1.0 CA A:SER265 4.2 61.5 1.0 CG A:ASN296 4.4 36.9 1.0 N A:SER265 4.5 63.3 1.0 PA A:AGS1001 4.6 70.0 1.0 O3A A:AGS1001 4.6 91.3 1.0 OE2 A:GLU342 4.6 71.3 1.0 O2A A:AGS1001 4.7 68.2 1.0 O1B A:AGS1001 4.7 0.2 1.0 CG A:ASP341 4.8 45.8 1.0 OD1 A:ASP341 4.8 38.4 1.0 N A:GLY709 5.0 54.2 1.0

Magnesium binding site 2 out of 2 in the Structure of SCPIF1 in Complex with Polydt and Atpgs


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 Polydt and Atpgs within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:49.4 occ:1.00 OG B:SER265 2.0 70.2 1.0 S1G B:AGS1001 2.4 0.2 1.0 ND2 B:ASN296 2.4 37.6 1.0 CB B:SER265 3.0 70.2 1.0 O2B B:AGS1001 3.5 80.5 1.0 OD2 B:ASP341 3.6 36.0 1.0 O B:GLY709 3.7 41.5 1.0 CA B:GLY709 3.7 37.3 1.0 CG B:ASN296 3.7 31.4 1.0 PG B:AGS1001 4.1 0.6 1.0 C B:GLY709 4.2 39.2 1.0 OE2 B:GLU342 4.3 53.8 1.0 CA B:SER265 4.4 59.1 1.0 CB B:ASN296 4.4 31.2 1.0 O3G B:AGS1001 4.4 0.7 1.0 CG B:ASP341 4.5 33.4 1.0 O2A B:AGS1001 4.5 32.7 1.0 OD1 B:ASP341 4.6 34.9 1.0 OD1 B:ASN296 4.7 24.6 1.0 PB B:AGS1001 4.8 71.3 1.0 N B:SER265 4.8 50.4 1.0 O3B B:AGS1001 5.0 0.1 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