Magnesium in PDB 5xpa: Crystal Structure of T. Thermophilus Argonaute Protein Complexed with A Bulge 9'U10' on the Target Strand

The structure of Crystal Structure of T. Thermophilus Argonaute Protein Complexed with A Bulge 9'U10' on the Target Strand, PDB code: 5xpa was solved by G.Sheng, T.Gogakos, J.Wang, H.Zhao, A.Serganov, S.Juranek, T.Tuschl, J.D.Patel, Y.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.15 / 2.90
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	109.134, 109.134, 184.685, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 28.1

The binding sites of Magnesium atom in the Crystal Structure of T. Thermophilus Argonaute Protein Complexed with A Bulge 9'U10' on the Target Strand (pdb code 5xpa). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of T. Thermophilus Argonaute Protein Complexed with A Bulge 9'U10' on the Target Strand, PDB code: 5xpa:

Magnesium binding site 1 out of 1 in the Crystal Structure of T. Thermophilus Argonaute Protein Complexed with A Bulge 9'U10' on the Target 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 9'U10' on the Target Strand within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:68.2 occ:1.00 OP2 C:DT1 2.0 84.0 1.0 O A:VAL685 2.1 68.3 1.0 OP1 C:DA3 2.2 63.0 1.0 OXT A:VAL685 2.2 75.7 1.0 C A:VAL685 2.5 70.3 1.0 P C:DT1 3.1 68.8 1.0 OE1 A:GLN433 3.3 59.4 1.0 OP1 C:DT1 3.6 61.5 1.0 P C:DA3 3.6 67.8 1.0 NZ A:LYS457 3.6 67.1 1.0 OP3 C:DT1 3.8 74.3 1.0 NE2 A:GLN433 3.9 59.9 1.0 CD A:GLN433 4.0 60.1 1.0 O3' C:DG2 4.0 62.0 1.0 CA A:VAL685 4.1 66.6 1.0 O5' C:DT1 4.4 74.0 1.0 CE A:LYS457 4.4 56.1 1.0 OP2 C:DA3 4.5 66.8 1.0 C5' C:DT1 4.6 70.1 1.0 O5' C:DA3 4.7 71.0 1.0 CB A:VAL685 4.7 69.9 1.0 N A:VAL685 4.8 65.0 1.0 CG2 A:VAL685 4.9 62.0 1.0 C5' C:DA3 4.9 69.1 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