Magnesium in PDB 7dcy: Apo Form of Mycoplasma Genitalium Rnase R

All present enzymatic activity of Apo Form of Mycoplasma Genitalium Rnase R:
3.1.13.1;

The structure of Apo Form of Mycoplasma Genitalium Rnase R, PDB code: 7dcy 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)	47.55 / 1.97
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.652, 80.768, 176.476, 90, 90, 90
R / Rfree (%)	17.3 / 20

The binding sites of Magnesium atom in the Apo Form of Mycoplasma Genitalium Rnase R (pdb code 7dcy). 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 Apo Form of Mycoplasma Genitalium Rnase R, PDB code: 7dcy:

Magnesium binding site 1 out of 1 in the Apo Form of Mycoplasma Genitalium Rnase R


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Apo Form of Mycoplasma Genitalium Rnase R within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:49.3 occ:1.00 O A:HOH1013 1.9 36.9 1.0 OD2 A:ASP276 2.1 35.6 1.0 O A:HOH953 2.1 37.0 1.0 OD1 A:ASP285 2.2 45.9 1.0 O A:HOH934 2.2 36.8 1.0 O A:HOH1266 2.3 43.1 1.0 CG A:ASP285 2.9 43.8 1.0 CG A:ASP276 3.0 34.6 1.0 OD2 A:ASP285 3.2 49.1 1.0 OD1 A:ASP276 3.3 35.5 1.0 O A:HOH996 3.9 40.9 1.0 O A:HOH931 4.0 39.4 1.0 O A:VAL275 4.0 31.2 1.0 O A:ASP282 4.0 44.5 1.0 O A:ASP285 4.1 30.8 1.0 O A:HOH1315 4.3 50.3 1.0 CB A:ASP285 4.3 34.2 1.0 O A:HOH1132 4.3 43.0 1.0 N A:ASP285 4.4 29.8 1.0 CB A:ASP276 4.4 28.7 1.0 OD1 A:ASP284 4.7 39.0 1.0 CA A:ASP285 4.7 31.7 1.0 O A:HOH1070 4.8 41.5 1.0 C A:ASP285 4.8 34.6 1.0 C A:VAL275 4.9 32.4 1.0 N A:ASP284 4.9 28.7 1.0 CA A:ASP276 4.9 32.0 1.0

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