Magnesium in PDB 6rre: Sidd, Deampylase From Legionella Pneumophila

The structure of Sidd, Deampylase From Legionella Pneumophila, PDB code: 6rre was solved by I.Tascon, M.Lucas, A.L.Rojas, A.Hierro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.81 / 3.59
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.570, 141.643, 234.298, 90.00, 92.75, 90.00
R / Rfree (%)	29.5 / 33.8

The binding sites of Magnesium atom in the Sidd, Deampylase From Legionella Pneumophila (pdb code 6rre). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Sidd, Deampylase From Legionella Pneumophila, PDB code: 6rre:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Sidd, Deampylase From Legionella Pneumophila


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Sidd, Deampylase From Legionella Pneumophila within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:1.0 occ:1.00 OD1 B:ASP110 2.4 0.6 1.0 OD1 B:ASP326 2.7 0.4 1.0 OD2 B:ASP326 2.8 0.2 1.0 OD2 B:ASP110 3.0 99.8 1.0 CG B:ASP110 3.0 0.6 1.0 CG B:ASP326 3.1 0.5 1.0 O B:GLY111 3.6 0.1 1.0 OD1 B:ASP92 3.7 0.7 1.0 OD1 B:ASP91 3.9 1.0 1.0 OD2 B:ASP91 4.3 0.4 1.0 CG B:ASP91 4.5 0.9 1.0 CB B:ASP110 4.6 89.0 1.0 CG B:ASP92 4.6 0.5 1.0 CB B:ASP326 4.6 0.8 1.0 OD2 B:ASP92 4.6 97.4 1.0 N B:ASP327 4.6 0.5 1.0 CB B:ASP327 4.7 0.1 1.0 C B:GLY111 4.7 0.1 1.0 OD2 B:ASP327 4.8 0.6 1.0 N B:GLY111 4.9 99.4 1.0 CG B:ASP327 5.0 0.5 1.0 O B:ASP327 5.0 0.1 1.0

Magnesium binding site 2 out of 4 in the Sidd, Deampylase From Legionella Pneumophila


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Sidd, Deampylase From Legionella Pneumophila within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:0.1 occ:1.00 OD2 C:ASP326 2.0 0.4 1.0 OD2 C:ASP110 2.0 0.9 1.0 O C:HOH701 2.0 0.1 1.0 CG C:ASP326 2.4 0.8 1.0 OD1 C:ASP326 2.5 0.7 1.0 CG C:ASP110 2.8 0.9 1.0 OD1 C:ASP110 2.9 1.0 1.0 OD2 C:ASP192 3.5 0.9 1.0 CB C:ASP326 3.7 0.5 1.0 CB C:ASP110 4.3 0.5 1.0 N C:ASP327 4.3 0.3 1.0 OD1 C:ASP92 4.4 0.6 1.0 CG C:ASP192 4.5 0.4 1.0 O C:ASP327 4.6 0.4 1.0 NZ C:LYS217 4.6 0.1 1.0 OD2 C:ASP92 4.6 0.6 1.0 CB C:TYR253 4.7 0.5 1.0 O C:GLY111 4.8 0.1 1.0 CA C:ASP326 4.8 0.0 1.0 CB C:ASP327 4.9 0.1 1.0 OD1 C:ASP192 5.0 0.8 1.0 CG C:ASP92 5.0 0.9 1.0

Magnesium binding site 3 out of 4 in the Sidd, Deampylase From Legionella Pneumophila


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Sidd, Deampylase From Legionella Pneumophila within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:0.0 occ:1.00 OD2 D:ASP326 2.1 0.2 1.0 OD2 D:ASP110 2.1 0.6 1.0 CG D:ASP326 2.4 0.8 1.0 OD1 D:ASP326 2.5 0.2 1.0 CG D:ASP110 2.8 1.0 1.0 OD1 D:ASP110 2.8 0.0 1.0 OD2 D:ASP192 3.4 0.3 1.0 CB D:ASP326 3.7 0.5 1.0 NZ D:LYS217 4.2 0.0 1.0 CB D:ASP110 4.2 0.3 1.0 N D:ASP327 4.3 0.8 1.0 CG D:ASP192 4.3 0.5 1.0 OD1 D:ASP92 4.5 0.7 1.0 O D:ASP327 4.6 0.9 1.0 OD2 D:ASP92 4.6 0.5 1.0 O D:GLY111 4.7 0.6 1.0 OD1 D:ASP192 4.8 0.5 1.0 CA D:ASP326 4.8 0.4 1.0 CB D:ASP327 4.9 0.7 1.0 CG D:ASP92 5.0 0.3 1.0

Magnesium binding site 4 out of 4 in the Sidd, Deampylase From Legionella Pneumophila


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Sidd, Deampylase From Legionella Pneumophila within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg601 b:0.2 occ:1.00 OD2 F:ASP91 2.9 0.2 1.0 OD1 F:ASP91 3.4 0.1 1.0 CG F:ASP91 3.5 0.4 1.0 CA F:GLY114 4.1 0.9 1.0 N F:GLY114 4.3 0.9 1.0

I.Tascon, X.Li, M.Lucas, D.Nelson, A.Vidaurrazaga, Y.H.Lin, A.L.Rojas, A.Hierro, M.P.Machner. Structural Insight Into the Membrane Targeting Domain of the Legionella Deampylase Sidd. Plos Pathog. V. 16 08734 2020.
ISSN: ESSN 1553-7374
PubMed: 32853279
DOI: 10.1371/JOURNAL.PPAT.1008734