Magnesium in PDB 7did: Mycoplasma Genitalium Rnase R in Complex with Ribose Methylated Single-Stranded Rna

All present enzymatic activity of Mycoplasma Genitalium Rnase R in Complex with Ribose Methylated Single-Stranded Rna:
3.1.13.1;

The structure of Mycoplasma Genitalium Rnase R in Complex with Ribose Methylated Single-Stranded Rna, PDB code: 7did was solved by A.Abula, X.Quan, X.Li, T.Yang, T.Li, Q.Chen, X.Ji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.98 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.286, 80.784, 175.735, 90, 90, 90
R / Rfree (%)	18.8 / 22.2

The binding sites of Magnesium atom in the Mycoplasma Genitalium Rnase R in Complex with Ribose Methylated Single-Stranded Rna (pdb code 7did). 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 Mycoplasma Genitalium Rnase R in Complex with Ribose Methylated Single-Stranded Rna, PDB code: 7did:

Magnesium binding site 1 out of 1 in the Mycoplasma Genitalium Rnase R in Complex with Ribose Methylated Single-Stranded Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mycoplasma Genitalium Rnase R in Complex with Ribose Methylated Single-Stranded Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:39.6 occ:1.00 O A:HOH976 1.8 46.4 1.0 OD2 A:ASP276 2.2 41.9 1.0 OD1 A:ASP285 2.2 46.2 1.0 O3' C:A8 2.3 91.1 1.0 O A:HOH979 2.4 34.1 1.0 O2' C:A8 2.5 95.1 1.0 O A:HOH997 2.6 40.6 1.0 CG A:ASP276 3.2 36.6 1.0 C3' C:A8 3.2 93.4 1.0 CG A:ASP285 3.4 44.0 1.0 C2' C:A8 3.4 95.8 1.0 OD1 A:ASP276 3.6 38.4 1.0 C4' C:A8 3.8 93.5 1.0 O C:HOH101 3.9 63.4 1.0 N A:ALA284 3.9 38.3 1.0 OD2 A:ASP285 4.0 46.9 1.0 O C:HOH104 4.1 45.6 1.0 N A:ASP285 4.2 37.5 1.0 O A:ASP282 4.2 58.7 1.0 O C:HOH102 4.3 42.5 1.0 CA A:LEU283 4.4 45.6 1.0 O A:ASP285 4.5 34.7 1.0 CB A:ASP285 4.5 42.2 1.0 CB A:ASP276 4.5 33.9 1.0 C1' C:A8 4.6 95.0 1.0 O A:HOH1134 4.6 54.9 1.0 C A:LEU283 4.7 39.5 1.0 O A:VAL275 4.7 34.9 1.0 O4' C:A8 4.7 93.9 1.0 CA A:ALA284 4.8 42.8 1.0 CA A:ASP285 4.8 37.4 1.0 CB A:ALA284 4.9 41.2 1.0 C5' C:A8 4.9 88.6 1.0 C A:ALA284 5.0 41.8 1.0 O A:HOH1176 5.0 41.9 1.0

A.Abula, X.Quan, X.Li, T.Yang, T.Li, Q.Chen, X.Ji. Molecular Mechanism of Rnase R Substrate Sensitivity For Rna Ribose Methylation To Be Published.