Magnesium in PDB 5xou: Crystal Structure of T. Thermophilus Argonaute Protein Complexed with A Bulge 7T8 on the Guide Strand

The structure of Crystal Structure of T. Thermophilus Argonaute Protein Complexed with A Bulge 7T8 on the Guide Strand, PDB code: 5xou was solved by G.Sheng, J.Wang, H.Zhao, Y.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.17 / 2.63
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	112.747, 114.982, 160.441, 90.00, 90.00, 90.00
R / Rfree (%)	23.5 / 27.6

The binding sites of Magnesium atom in the Crystal Structure of T. Thermophilus Argonaute Protein Complexed with A Bulge 7T8 on the Guide Strand (pdb code 5xou). 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 7T8 on the Guide Strand, PDB code: 5xou:
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 7T8 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 7T8 on the Guide Strand within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:63.4 occ:1.00 OP1 C:DA3 2.1 62.3 1.0 OP2 C:DT1 2.2 64.9 1.0 OXT A:VAL685 2.3 65.7 1.0 O A:VAL685 2.4 73.7 1.0 C A:VAL685 2.7 63.5 1.0 OE1 A:GLN433 3.2 35.2 1.0 P C:DA3 3.4 57.4 1.0 O3' C:DG2 3.6 47.7 1.0 P C:DT1 3.6 57.1 1.0 NE2 A:GLN433 3.8 38.7 1.0 CD A:GLN433 3.9 40.7 1.0 O5' C:DT1 4.1 54.0 1.0 CA A:VAL685 4.1 42.4 1.0 OP1 C:DT1 4.2 45.8 1.0 O5' C:DA3 4.3 62.5 1.0 C5' C:DA3 4.3 69.7 1.0 CG2 A:VAL685 4.3 46.4 1.0 CB A:VAL685 4.5 60.9 1.0 CE A:LYS457 4.5 46.8 1.0 OP2 C:DA3 4.6 58.9 1.0 NZ A:LYS457 4.6 61.2 1.0 OP3 C:DT1 4.7 59.1 1.0 C3' C:DG2 4.7 51.1 1.0 C5' C:DT1 4.8 49.4 1.0 CA A:GLY453 5.0 55.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of T. Thermophilus Argonaute Protein Complexed with A Bulge 7T8 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 7T8 on the Guide Strand within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:57.0 occ:1.00 OP2 E:DT1 2.1 47.5 1.0 OP1 E:DA3 2.2 37.8 1.0 O B:VAL685 2.3 83.2 1.0 O E:HOH801 2.7 44.1 1.0 OXT B:VAL685 2.8 65.4 1.0 C B:VAL685 3.0 68.9 1.0 OP3 E:DT1 3.1 46.3 1.0 P E:DT1 3.1 45.1 1.0 O B:HOH803 3.3 60.2 1.0 NH1 B:ARG661 3.4 0.1 1.0 P E:DA3 3.4 45.9 1.0 O B:HOH808 3.7 55.4 1.0 OP2 E:DA3 3.9 58.9 1.0 O5' E:DT1 4.2 55.0 1.0 C5' E:DT1 4.2 58.9 1.0 OP1 E:DT1 4.2 48.3 1.0 O3' E:DG2 4.3 51.5 1.0 CZ B:ARG661 4.4 93.2 1.0 CA B:VAL685 4.4 56.9 1.0 O B:PHE684 4.6 76.5 1.0 O5' E:DA3 4.6 50.0 1.0 NE B:ARG661 4.8 86.2 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