Magnesium in PDB 6njd: Crystal Structure of Ravd (Residues 1-200) From Legionella Pneumophila (Strain Corby) Complexed with Met-1 Linked Di-Ubiquitin

The structure of Crystal Structure of Ravd (Residues 1-200) From Legionella Pneumophila (Strain Corby) Complexed with Met-1 Linked Di-Ubiquitin, PDB code: 6njd was solved by X.Wang, Y.Zhou, Y.Zhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.01 / 2.05
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	77.740, 102.090, 90.920, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 24.6

The binding sites of Magnesium atom in the Crystal Structure of Ravd (Residues 1-200) From Legionella Pneumophila (Strain Corby) Complexed with Met-1 Linked Di-Ubiquitin (pdb code 6njd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Ravd (Residues 1-200) From Legionella Pneumophila (Strain Corby) Complexed with Met-1 Linked Di-Ubiquitin, PDB code: 6njd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Ravd (Residues 1-200) From Legionella Pneumophila (Strain Corby) Complexed with Met-1 Linked Di-Ubiquitin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Ravd (Residues 1-200) From Legionella Pneumophila (Strain Corby) Complexed with Met-1 Linked Di-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:42.4 occ:1.00 O A:HOH307 2.0 44.2 1.0 O A:HOH316 2.1 36.0 1.0 OD1 A:ASP108 2.2 47.4 1.0 CG A:ASP108 3.1 46.1 1.0 OD2 A:ASP108 3.4 45.0 1.0 O A:ALA104 3.9 42.7 1.0 O A:HOH345 4.1 58.7 1.0 O A:HOH347 4.2 54.1 1.0 O B:HOH428 4.4 57.0 1.0 OE1 A:GLN107 4.5 49.5 1.0 CB A:ASP108 4.5 45.6 1.0 C A:ALA104 4.7 42.0 1.0 N A:ASP108 4.8 45.6 1.0 CB A:ALA104 4.9 41.2 1.0 CA A:ASP108 4.9 46.2 1.0 CB B:ALA138 5.0 42.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Ravd (Residues 1-200) From Legionella Pneumophila (Strain Corby) Complexed with Met-1 Linked Di-Ubiquitin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Ravd (Residues 1-200) From Legionella Pneumophila (Strain Corby) Complexed with Met-1 Linked Di-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:60.6 occ:1.00 O B:HOH481 2.2 50.8 1.0 OE2 B:GLU186 2.4 53.1 1.0 NE2 B:HIS185 2.9 48.2 1.0 CD B:GLU186 3.5 50.9 1.0 CD2 B:HIS185 3.7 46.6 1.0 CE1 B:HIS185 3.9 48.6 1.0 CG B:GLU186 4.1 48.1 1.0 OE1 B:GLU186 4.6 50.1 1.0 CG B:HIS185 4.9 47.3 1.0 ND1 B:HIS185 5.0 47.9 1.0

M.Wan, X.Wang, C.Huang, D.Xu, Z.Wang, Y.Zhou, Y.Zhu. A Bacterial Effector Deubiquitinase Specifically Hydrolyses Linear Ubiquitin Chains to Inhibit Host Inflammatory Signalling. Nat Microbiol V. 4 1282 2019.
ISSN: ESSN 2058-5276
PubMed: 31110362
DOI: 10.1038/S41564-019-0454-1