Magnesium in PDB 4kyi: Legionella Pneumophila Effector

The structure of Legionella Pneumophila Effector, PDB code: 4kyi was solved by M.Lucas, A.H.Gaspar, C.Pallara, A.L.Rojas, J.Fernandez-Recio, M.P.Machner, A.Hierro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.83 / 3.08
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	94.275, 97.976, 109.849, 76.57, 80.71, 78.91
R / Rfree (%)	23.3 / 28

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

Magnesium binding site 1 out of 4 in the Legionella Pneumophila Effector


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Legionella Pneumophila Effector within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg304 b:36.3 occ:1.00 OG B:SER35 2.0 78.6 1.0 OG1 B:THR53 2.0 36.3 1.0 O2G B:GNP301 2.0 72.8 1.0 O2B B:GNP301 2.2 72.8 1.0 O3G B:GNP301 2.7 72.8 1.0 PG B:GNP301 2.7 72.8 1.0 CB B:THR53 3.0 36.3 1.0 CB B:SER35 3.2 78.6 1.0 PB B:GNP301 3.3 72.8 1.0 OD2 B:ASP76 3.3 56.2 1.0 N3B B:GNP301 3.4 72.8 1.0 N B:THR53 3.8 36.3 1.0 O B:THR77 3.9 27.3 1.0 N B:SER35 3.9 78.6 1.0 CA B:THR53 4.0 36.3 1.0 CG2 B:THR53 4.1 36.3 1.0 OD1 B:ASP76 4.1 56.2 1.0 CG B:ASP76 4.1 56.2 1.0 CA B:SER35 4.1 78.6 1.0 O1B B:GNP301 4.1 72.8 1.0 O1G B:GNP301 4.1 72.8 1.0 O2A B:GNP301 4.2 72.8 1.0 O3A B:GNP301 4.5 72.8 1.0 CE B:LYS34 4.6 56.4 1.0 CB B:LYS34 4.7 56.4 1.0 O1 B:EDO302 4.7 45.4 1.0 PA B:GNP301 4.7 72.8 1.0 O1A B:GNP301 4.8 72.8 1.0 C B:LYS34 4.9 56.4 1.0 NZ B:LYS34 5.0 56.4 1.0 C B:THR77 5.0 27.3 1.0 C B:SER52 5.0 35.3 1.0

Magnesium binding site 2 out of 4 in the Legionella Pneumophila Effector


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Legionella Pneumophila Effector within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg302 b:36.6 occ:1.00 OG D:SER35 2.0 41.5 1.0 O2B D:GNP301 2.0 80.9 1.0 OG1 D:THR53 2.0 59.8 1.0 O2G D:GNP301 2.0 80.9 1.0 CB D:SER35 3.1 41.5 1.0 PG D:GNP301 3.1 80.9 1.0 PB D:GNP301 3.2 80.9 1.0 CB D:THR53 3.3 59.8 1.0 N3B D:GNP301 3.4 80.9 1.0 O3G D:GNP301 3.7 80.9 1.0 N D:SER35 3.8 41.5 1.0 OD2 D:ASP76 3.8 47.8 1.0 CA D:SER35 4.0 41.5 1.0 O1B D:GNP301 4.0 80.9 1.0 N D:THR53 4.1 59.8 1.0 O2A D:GNP301 4.1 80.9 1.0 CG2 D:THR53 4.2 59.8 1.0 O D:THR77 4.2 36.5 1.0 OD1 D:ASP76 4.2 47.8 1.0 CA D:THR53 4.3 59.8 1.0 O3A D:GNP301 4.3 80.9 1.0 CG D:ASP76 4.4 47.8 1.0 O1G D:GNP301 4.5 80.9 1.0 O1A D:GNP301 4.5 80.9 1.0 PA D:GNP301 4.5 80.9 1.0 CB D:LYS34 4.7 77.0 1.0 NZ D:LYS34 4.7 77.0 1.0 CE D:LYS34 4.8 77.0 1.0 C D:LYS34 4.8 77.0 1.0 C D:SER52 4.9 24.9 1.0

Magnesium binding site 3 out of 4 in the Legionella Pneumophila Effector


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Legionella Pneumophila Effector within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg302 b:54.5 occ:1.00 OG1 F:THR53 2.0 58.7 1.0 O2B F:GNP301 2.0 81.4 1.0 O2G F:GNP301 2.1 81.4 1.0 OG F:SER35 2.2 54.3 1.0 O3G F:GNP301 2.7 81.4 1.0 PG F:GNP301 2.7 81.4 1.0 CB F:THR53 3.0 58.7 1.0 PB F:GNP301 3.2 81.4 1.0 N3B F:GNP301 3.2 81.4 1.0 CB F:SER35 3.4 54.3 1.0 N F:THR53 3.7 58.7 1.0 O2A F:GNP301 3.8 81.4 1.0 CA F:THR53 3.9 58.7 1.0 N F:SER35 3.9 54.3 1.0 OD2 F:ASP76 4.0 41.9 1.0 O1B F:GNP301 4.1 81.4 1.0 CG2 F:THR53 4.2 58.7 1.0 OD1 F:ASP76 4.2 41.9 1.0 O1G F:GNP301 4.2 81.4 1.0 CA F:SER35 4.2 54.3 1.0 O3A F:GNP301 4.3 81.4 1.0 O F:THR77 4.3 51.4 1.0 PA F:GNP301 4.4 81.4 1.0 CG F:ASP76 4.5 41.9 1.0 O1A F:GNP301 4.6 81.4 1.0 C F:SER52 4.7 57.0 1.0 CB F:LYS34 4.8 62.8 1.0 O F:GLU51 4.9 73.5 1.0

Magnesium binding site 4 out of 4 in the Legionella Pneumophila Effector


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Legionella Pneumophila Effector within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg302 b:35.3 occ:1.00 OG1 H:THR53 2.0 41.0 1.0 O2B H:GNP301 2.0 63.3 1.0 OG H:SER35 2.1 26.4 1.0 O2G H:GNP301 2.4 63.3 1.0 CB H:SER35 3.2 26.4 1.0 CB H:THR53 3.3 41.0 1.0 PB H:GNP301 3.3 63.3 1.0 PG H:GNP301 3.4 63.3 1.0 N3B H:GNP301 3.6 63.3 1.0 OD2 H:ASP76 3.6 47.6 1.0 N H:SER35 3.7 26.4 1.0 O3G H:GNP301 3.8 63.3 1.0 OD1 H:ASP76 4.0 47.6 1.0 N H:THR53 4.0 41.0 1.0 CA H:SER35 4.0 26.4 1.0 O2A H:GNP301 4.0 63.3 1.0 O1B H:GNP301 4.1 63.3 1.0 CG H:ASP76 4.2 47.6 1.0 CG2 H:THR53 4.2 41.0 1.0 CA H:THR53 4.2 41.0 1.0 O H:THR77 4.2 28.9 1.0 O1A H:GNP301 4.3 63.3 1.0 O3A H:GNP301 4.3 63.3 1.0 PA H:GNP301 4.4 63.3 1.0 CB H:LYS34 4.4 47.5 1.0 CE H:LYS34 4.5 47.5 1.0 C H:LYS34 4.6 47.5 1.0 NZ H:LYS34 4.7 47.5 1.0 O1G H:GNP301 4.8 63.3 1.0 CA H:LYS34 4.9 47.5 1.0 N H:LYS34 4.9 47.5 1.0

M.Lucas, A.H.Gaspar, C.Pallara, A.L.Rojas, J.Fernandez-Recio, M.P.Machner, A.Hierro. Structural Basis For the Recruitment and Activation of the Legionella Phospholipase Vipd By the Host Gtpase RAB5. Proc.Natl.Acad.Sci.Usa V. 111 E3514 2014.
ISSN: ISSN 0027-8424
PubMed: 25114243
DOI: 10.1073/PNAS.1405391111