Atomistry » Magnesium » PDB 5xlh-5xut » 5xq2
Atomistry »
  Magnesium »
    PDB 5xlh-5xut »
      5xq2 »

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

Protein crystallography data

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

Magnesium Binding Sites:

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 5xq2

Go back to Magnesium Binding Sites List in 5xq2
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 5xq2

Go back to Magnesium Binding Sites List in 5xq2
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

Reference:

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
Page generated: Tue Aug 12 23:57:40 2025

Last articles

Mg in 6LU1
Mg in 6LT4
Mg in 6LY7
Mg in 6LY6
Mg in 6LY3
Mg in 6LX1
Mg in 6LTW
Mg in 6LVW
Mg in 6LUH
Mg in 6LTS
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy