Magnesium in PDB 5xgu: Escherichia Coli. Rnase R

All present enzymatic activity of Escherichia Coli. Rnase R:
3.1.13.1;

The structure of Escherichia Coli. Rnase R, PDB code: 5xgu was solved by L.Y.Chu, T.J.Hsieh, H.S.Yuan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.67 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.691, 120.863, 83.626, 90.00, 91.61, 90.00
R / Rfree (%)	18.7 / 23.6

The binding sites of Magnesium atom in the Escherichia Coli. Rnase R (pdb code 5xgu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Escherichia Coli. Rnase R, PDB code: 5xgu:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Escherichia Coli. Rnase R


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Escherichia Coli. Rnase R within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:18.9 occ:1.00 O B:HOH1093 2.0 28.2 1.0 O B:HOH952 2.2 19.6 1.0 OD2 B:ASP195 2.3 23.2 1.0 OD1 B:ASP186 2.4 19.1 1.0 O B:HOH917 2.4 17.7 1.0 O B:HOH1395 2.6 34.0 1.0 CG B:ASP195 3.1 21.9 1.0 OD1 B:ASP195 3.4 23.4 1.0 CG B:ASP186 3.4 21.0 1.0 O B:HOH1290 3.4 39.8 1.0 OD2 B:ASP186 3.7 16.3 1.0 O B:HOH957 3.9 32.8 1.0 O B:HOH926 4.0 36.9 1.0 OD1 B:ASP194 4.1 40.6 1.0 O B:HOH835 4.1 14.3 1.0 N B:ASP195 4.2 15.4 1.0 O B:ILE185 4.3 12.8 1.0 CB B:ASP195 4.4 12.2 1.0 O B:ASP195 4.4 14.2 1.0 N B:ASP194 4.5 18.8 1.0 CB B:ASP186 4.7 17.4 1.0 CA B:ASP195 4.8 11.1 1.0 CA B:PHE193 4.8 15.3 1.0 O B:HOH1163 4.9 17.6 1.0 O B:ASP192 5.0 33.5 1.0

Magnesium binding site 2 out of 2 in the Escherichia Coli. Rnase R


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Escherichia Coli. Rnase R within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:22.1 occ:1.00 O A:HOH1016 2.1 27.4 1.0 OD1 A:ASP186 2.2 18.0 1.0 O A:HOH954 2.3 16.5 1.0 O A:HOH951 2.3 19.4 1.0 OD1 A:ASP195 2.4 19.7 1.0 O A:HOH1323 2.7 38.0 1.0 CG A:ASP186 3.2 18.7 1.0 CG A:ASP195 3.2 20.8 1.0 OD2 A:ASP195 3.5 19.4 1.0 OD2 A:ASP186 3.5 16.4 1.0 O A:HOH1282 3.7 39.4 1.0 O A:HOH1218 3.9 42.5 1.0 N A:ASP194 3.9 19.0 1.0 O A:HOH911 4.0 31.4 1.0 N A:ASP195 4.0 14.6 1.0 O A:ILE185 4.3 15.6 1.0 O A:ASP195 4.4 13.9 1.0 CB A:ASP195 4.5 18.5 1.0 CB A:ASP194 4.5 14.7 1.0 CB A:ASP186 4.6 15.7 1.0 CA A:ASP194 4.6 24.7 1.0 CA A:PHE193 4.6 17.3 1.0 C A:PHE193 4.7 16.9 1.0 CA A:ASP195 4.7 14.3 1.0 O A:HOH1035 4.7 17.6 1.0 C A:ASP194 4.8 15.1 1.0 O A:ASP192 4.9 27.4 1.0 O A:HOH955 5.0 30.6 1.0 C A:ASP195 5.0 16.2 1.0

L.Y.Chu, T.J.Hsieh, B.Golzarroshan, Y.P.Chen, S.Agrawal, H.S.Yuan. Structural Insights Into Rna Unwinding and Degradation By Rnase R. Nucleic Acids Res. V. 45 12015 2017.
ISSN: ESSN 1362-4962
PubMed: 29036353
DOI: 10.1093/NAR/GKX880