Magnesium in PDB 5xq2: Crystal Structure of T. Thermophilus Argonaute Protein Complexed with A Bulge 5A6 on the Guide Strand

The structure of Crystal Structure of T. Thermophilus Argonaute Protein Complexed with A Bulge 5A6 on the Guide Strand, PDB code: 5xq2 was solved by G.Sheng, T.Gogakos, J.Wang, H.Zhao, A.Serganov, S.Juranek, T.Tuschl, D.Patel, Y.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.95 / 3.33
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	201.843, 201.843, 201.843, 90.00, 90.00, 90.00
R / Rfree (%)	25.2 / 29.4

The binding sites of Magnesium atom in the Crystal Structure of T. Thermophilus Argonaute Protein Complexed with A Bulge 5A6 on the Guide Strand (pdb code 5xq2). 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 T. Thermophilus Argonaute Protein Complexed with A Bulge 5A6 on the Guide Strand, PDB code: 5xq2:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of T. Thermophilus Argonaute Protein Complexed with A Bulge 5A6 on the Guide Strand


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 T. Thermophilus Argonaute Protein Complexed with A Bulge 5A6 on the Guide Strand within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg101 b:51.1 occ:1.00 N7 X:DG4 2.9 20.0 1.0 C8 X:DG4 3.5 20.0 1.0 OP2 X:DG4 3.9 23.2 1.0 C5 X:DG4 4.1 20.0 1.0 N7 X:DG5 4.3 37.5 1.0 O6 X:DG4 4.6 20.0 1.0 O5' X:DG4 4.7 32.7 1.0 C6 X:DG4 4.7 20.0 1.0 N9 X:DG4 4.7 20.0 1.0 O6 X:DG5 4.8 47.8 1.0 P X:DG4 4.9 33.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of T. Thermophilus Argonaute Protein Complexed with A Bulge 5A6 on the Guide Strand


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 T. Thermophilus Argonaute Protein Complexed with A Bulge 5A6 on the Guide Strand within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg101 b:35.9 occ:1.00 N7 E:DG4 2.9 20.0 1.0 C8 E:DG4 3.7 20.0 1.0 C5 E:DG4 3.8 20.0 1.0 N7 E:DG5 3.9 34.0 1.0 O6 E:DG4 4.0 20.0 1.0 O6 E:DG5 4.0 55.0 1.0 C6 E:DG4 4.2 20.0 1.0 C5 E:DG5 4.6 38.1 1.0 C6 E:DG5 4.7 48.0 1.0 OP2 E:DG4 4.7 17.5 1.0 C8 E:DG5 4.9 30.2 1.0 N9 E:DG4 4.9 20.0 1.0 N6 E:DA6 4.9 53.5 1.0 C4 E:DG4 4.9 20.0 1.0

G.Sheng, T.Gogakos, J.Wang, H.Zhao, A.Serganov, S.Juranek, T.Tuschl, D.J.Patel, Y.Wang. Structure/Cleavage-Based Insights Into Helical Perturbations at Bulge Sites Within T. Thermophilus Argonaute Silencing Complexes Nucleic Acids Res. V. 45 9149 2017.
ISSN: ESSN 1362-4962
PubMed: 28911094
DOI: 10.1093/NAR/GKX547