Magnesium in PDB 5xp8: Crystal Structure of T. Thermophilus Argonaute Protein Complexed with A Bulge 4A5 on the Guide Strand

The structure of Crystal Structure of T. Thermophilus Argonaute Protein Complexed with A Bulge 4A5 on the Guide Strand, PDB code: 5xp8 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)	45.20 / 3.10
Space group	P 41 3 2
Cell size a, b, c (Å), α, β, γ (°)	202.140, 202.140, 202.140, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 27.6

The binding sites of Magnesium atom in the Crystal Structure of T. Thermophilus Argonaute Protein Complexed with A Bulge 4A5 on the Guide Strand (pdb code 5xp8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of T. Thermophilus Argonaute Protein Complexed with A Bulge 4A5 on the Guide Strand, PDB code: 5xp8:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of T. Thermophilus Argonaute Protein Complexed with A Bulge 4A5 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 4A5 on the Guide Strand within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:13.0 occ:1.00 OD1 A:ASP660 1.9 90.6 1.0 OD2 A:ASP478 2.3 34.3 1.0 CG A:ASP660 2.4 72.5 1.0 OD2 A:ASP660 3.0 70.1 1.0 CB A:ASP660 3.2 51.0 1.0 OP1 F:DT9 3.2 57.8 1.0 CG A:ASP478 3.5 36.0 1.0 P F:DT9 3.7 38.9 1.0 O5' F:DT9 3.7 73.9 1.0 NZ A:LYS664 3.7 66.2 1.0 OP2 F:DA10 3.8 46.8 1.0 OP2 F:DT9 3.8 38.8 1.0 CA A:ASP660 4.0 38.8 1.0 OD1 A:ASP478 4.1 30.7 1.0 C3' F:DT9 4.4 69.8 1.0 C5' F:DT9 4.5 73.4 1.0 OD2 A:ASP546 4.5 99.6 1.0 MG A:MG703 4.5 28.4 1.0 CB A:ASP478 4.7 13.2 1.0 O A:ALA479 4.8 39.0 1.0 O A:ASP660 4.8 50.4 1.0 C A:ASP660 4.9 42.7 1.0 CG A:ASP546 4.9 94.5 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of T. Thermophilus Argonaute Protein Complexed with A Bulge 4A5 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 4A5 on the Guide Strand within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:29.0 occ:0.00 OP2 E:DT1 1.9 57.5 1.0 O A:VAL685 2.0 33.1 1.0 OP1 E:DA3 2.0 23.6 1.0 OXT A:VAL685 2.0 55.3 1.0 OP3 E:DT1 2.1 23.6 1.0 C A:VAL685 2.3 54.0 1.0 P E:DT1 2.5 56.6 1.0 P E:DA3 3.3 40.5 1.0 OP1 E:DT1 3.6 43.7 1.0 O5' E:DT1 3.8 24.0 1.0 CA A:VAL685 3.8 39.1 1.0 NH2 A:ARG661 3.8 0.9 1.0 OP2 E:DA3 3.9 29.5 1.0 O3' E:DG2 4.3 51.9 1.0 C5' E:DT1 4.3 34.8 1.0 NZ A:LYS457 4.4 37.8 1.0 O A:PHE684 4.4 67.1 1.0 O5' E:DA3 4.5 24.4 1.0 N A:VAL685 4.6 33.3 1.0 NE2 A:GLN433 4.8 50.3 1.0 OE1 A:GLN433 4.8 54.3 1.0 C A:PHE684 4.8 46.8 1.0 CB A:VAL685 4.9 37.6 1.0 CZ A:ARG661 4.9 99.2 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of T. Thermophilus Argonaute Protein Complexed with A Bulge 4A5 on the Guide Strand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of T. Thermophilus Argonaute Protein Complexed with A Bulge 4A5 on the Guide Strand within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:28.4 occ:1.00 OP1 F:DT9 1.5 57.8 1.0 OD2 A:ASP546 2.2 99.6 1.0 OD1 A:ASP478 2.3 30.7 1.0 P F:DT9 2.4 38.9 1.0 O3' F:DC8 2.4 93.4 1.0 CG A:ASP478 3.4 36.0 1.0 CG A:ASP546 3.4 94.5 1.0 O5' F:DT9 3.4 73.9 1.0 OP2 F:DT9 3.6 38.8 1.0 C5' F:DT9 3.6 73.4 1.0 OE2 A:GLU512 3.6 72.3 1.0 OD2 A:ASP478 3.7 34.3 1.0 C3' F:DC8 3.8 93.7 1.0 OE1 A:GLU512 3.9 73.0 1.0 O A:ASP546 4.0 43.2 1.0 CD A:GLU512 4.1 74.2 1.0 CB A:ASP546 4.2 79.0 1.0 O A:ALA479 4.3 39.0 1.0 OD1 A:ASP546 4.4 99.8 1.0 C A:ASP546 4.4 39.3 1.0 C4' F:DC8 4.5 94.3 1.0 MG A:MG701 4.5 13.0 1.0 N A:ALA479 4.6 18.8 1.0 C2' F:DC8 4.7 80.6 1.0 NH1 A:ARG545 4.7 40.0 1.0 CB A:ASP478 4.8 13.2 1.0 N A:GLY547 5.0 35.8 1.0 NZ A:LYS575 5.0 49.7 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