Magnesium in PDB 6z2b: Toprim Domain of Rnase M5 Bound with Two MG2+ Ions

All present enzymatic activity of Toprim Domain of Rnase M5 Bound with Two MG2+ Ions:
3.1.26.8;

The structure of Toprim Domain of Rnase M5 Bound with Two MG2+ Ions, PDB code: 6z2b was solved by S.Oerum, M.Catala, C.Tisne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.68 / 2.14
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	87.7, 30.32, 158.31, 90, 100.89, 90
R / Rfree (%)	19.9 / 28.4

The binding sites of Magnesium atom in the Toprim Domain of Rnase M5 Bound with Two MG2+ Ions (pdb code 6z2b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Toprim Domain of Rnase M5 Bound with Two MG2+ Ions, PDB code: 6z2b:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Toprim Domain of Rnase M5 Bound with Two MG2+ Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Toprim Domain of Rnase M5 Bound with Two MG2+ Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:57.7 occ:1.00 O B:HOH305 1.9 45.8 1.0 O B:HOH303 2.0 48.9 1.0 OE1 B:GLU10 2.0 52.6 1.0 OD2 B:ASP56 2.2 43.7 1.0 O B:HOH336 2.4 48.5 1.0 O B:HOH337 2.7 74.1 1.0 CD B:GLU10 2.9 49.7 1.0 OE2 B:GLU10 3.1 54.1 1.0 CG B:ASP56 3.3 48.6 1.0 CB B:ASP56 3.8 43.5 1.0 OD2 B:ASP58 4.0 54.7 1.0 O B:ILE93 4.1 44.0 1.0 O B:HOH302 4.1 53.5 1.0 MG B:MG202 4.2 72.6 1.0 OD1 B:ASP58 4.2 38.1 1.0 CG B:GLU10 4.3 46.5 1.0 OD1 B:ASP56 4.3 45.7 1.0 CG B:ASP58 4.5 46.0 1.0 CB B:GLU10 4.6 41.0 1.0

Magnesium binding site 2 out of 2 in the Toprim Domain of Rnase M5 Bound with Two MG2+ Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Toprim Domain of Rnase M5 Bound with Two MG2+ Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:72.6 occ:1.00 O B:HOH302 2.0 53.5 1.0 OE2 B:GLU96 2.0 92.7 1.0 O B:HOH336 2.3 48.5 1.0 CD B:GLU96 3.1 77.2 1.0 CG B:GLU96 3.7 65.4 1.0 OD2 B:ASP56 3.9 43.7 1.0 OD1 B:ASP14 3.9 54.2 1.0 OE1 B:GLU96 4.2 67.4 1.0 OD2 B:ASP14 4.2 51.2 1.0 MG B:MG201 4.2 57.7 1.0 O B:ILE93 4.4 44.0 1.0 O B:HOH332 4.4 55.1 1.0 O B:HOH303 4.5 48.9 1.0 CG B:ASP14 4.5 44.8 1.0 CB B:GLU96 4.6 55.3 1.0 CA B:GLY94 4.6 41.3 1.0 CG B:ASP56 4.9 48.6 1.0 OE1 B:GLU10 4.9 52.6 1.0

S.Oerum, M.Catala, M.Bourguet, L.Gilet, P.Barraud, S.Cianferani, C.Condon, C.Tisne. Structural Studies of Rnase M5 Reveal Two-Metal-Ion Supported Two-Step Dsrna Cleavage For 5S Rrna Maturation. Rna Biol. 1 2021.
ISSN: ESSN 1555-8584
PubMed: 33541205
DOI: 10.1080/15476286.2021.1885896