Magnesium in PDB 8anp: Legionella Effector LEM3 Mutant D190A in Complex with MG2+

The structure of Legionella Effector LEM3 Mutant D190A in Complex with MG2+, PDB code: 8anp was solved by M.S.Kaspers, V.Pogenberg, S.Ernst, F.Ecker, C.Pett, P.Ochtrop, C.Hedberg, M.Groll, A.Itzen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.72, 187.69, 193.03, 90, 90, 90
R / Rfree (%)	19 / 23

The binding sites of Magnesium atom in the Legionella Effector LEM3 Mutant D190A in Complex with MG2+ (pdb code 8anp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Legionella Effector LEM3 Mutant D190A in Complex with MG2+, PDB code: 8anp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Legionella Effector LEM3 Mutant D190A in Complex with MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Legionella Effector LEM3 Mutant D190A in Complex with MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:37.6 occ:1.00 O A:HOH625 2.0 43.8 1.0 OD2 A:ASP105 2.0 36.7 1.0 OD1 A:ASP254 2.1 31.9 1.0 O A:HOH617 2.2 36.0 1.0 O A:HOH632 2.2 36.1 1.0 OD2 A:ASP394 2.2 37.1 1.0 CG A:ASP105 3.0 36.0 1.0 CG A:ASP254 3.1 34.3 1.0 CG A:ASP394 3.3 36.3 1.0 OD1 A:ASP105 3.4 37.6 1.0 OD2 A:ASP254 3.5 36.2 1.0 OD1 A:ASP394 3.7 35.5 1.0 MG A:MG502 3.9 51.1 1.0 O A:HOH649 4.1 34.9 1.0 O A:CYS395 4.1 32.4 1.0 N A:GLY255 4.2 33.5 1.0 CB A:ASP105 4.3 34.5 1.0 O A:HOH615 4.4 40.9 1.0 N A:ASP254 4.4 31.3 1.0 CB A:ASP254 4.4 35.3 1.0 O A:HOH666 4.5 61.9 1.0 OD1 A:ASP82 4.5 33.1 1.0 CB A:ASP394 4.6 36.6 1.0 CB A:THR253 4.7 30.5 1.0 CA A:ASP254 4.8 33.6 1.0 C A:ASP254 4.8 34.6 1.0 CA A:GLY255 4.9 34.5 1.0 OG1 A:THR253 5.0 29.2 1.0

Magnesium binding site 2 out of 7 in the Legionella Effector LEM3 Mutant D190A in Complex with MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Legionella Effector LEM3 Mutant D190A in Complex with MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:51.1 occ:1.00 O A:HOH616 2.0 52.1 1.0 OD1 A:ASP105 2.2 37.6 1.0 O A:HOH632 2.2 36.1 1.0 O A:GLY106 2.2 37.9 1.0 O A:HOH615 2.5 40.9 1.0 O A:HOH666 2.5 61.9 1.0 CG A:ASP105 3.3 36.0 1.0 C A:GLY106 3.3 36.7 1.0 OD2 A:ASP105 3.7 36.7 1.0 MG A:MG501 3.9 37.6 1.0 O A:HOH625 4.0 43.8 1.0 N A:LEU107 4.1 37.6 1.0 CA A:LEU107 4.1 40.0 1.0 N A:GLY106 4.2 35.2 1.0 C A:ASP105 4.3 33.6 1.0 CA A:GLY106 4.3 36.1 1.0 O A:GLY108 4.3 47.3 1.0 O A:HOH667 4.4 57.2 1.0 OD1 A:ASP394 4.5 35.5 1.0 CB A:ASP105 4.5 34.5 1.0 O A:HOH617 4.6 36.0 1.0 O A:ASP105 4.7 32.4 1.0 N A:GLY108 4.7 42.4 1.0 C A:LEU107 4.7 40.5 1.0 CD2 A:LEU107 4.8 44.0 1.0 CA A:ASP105 4.8 33.8 1.0 OD2 A:ASP394 4.9 37.1 1.0 CB A:LEU81 4.9 38.0 1.0 O A:HOH656 4.9 62.8 1.0 OD1 A:ASP82 4.9 33.1 1.0

Magnesium binding site 3 out of 7 in the Legionella Effector LEM3 Mutant D190A in Complex with MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Legionella Effector LEM3 Mutant D190A in Complex with MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:35.2 occ:1.00 O B:HOH618 2.0 46.8 1.0 OD2 B:ASP105 2.1 36.9 1.0 OD2 B:ASP394 2.3 37.8 1.0 O B:HOH607 2.3 34.2 1.0 O B:HOH614 2.3 49.2 1.0 OD1 B:ASP254 2.4 32.4 1.0 CG B:ASP105 3.0 36.4 1.0 CG B:ASP394 3.2 35.5 1.0 OD1 B:ASP105 3.2 37.9 1.0 CG B:ASP254 3.3 34.5 1.0 OD1 B:ASP394 3.5 35.7 1.0 OD2 B:ASP254 3.6 39.5 1.0 O B:HOH610 4.1 36.5 1.0 O B:HOH646 4.2 31.7 1.0 O B:CYS395 4.3 29.4 1.0 CB B:ASP105 4.3 34.4 1.0 N B:GLY255 4.5 33.9 1.0 CB B:ASP394 4.6 35.3 1.0 OD1 B:ASP82 4.6 32.0 1.0 CB B:ASP254 4.7 34.5 1.0 N B:ASP254 4.7 31.1 1.0

Magnesium binding site 4 out of 7 in the Legionella Effector LEM3 Mutant D190A in Complex with MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Legionella Effector LEM3 Mutant D190A in Complex with MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:58.5 occ:1.00 O B:HOH659 2.0 39.0 1.0 O B:HOH626 2.1 44.4 1.0 O B:HOH673 2.1 45.2 1.0 O B:HOH606 2.1 44.1 1.0 O B:HOH609 2.2 42.4 1.0 O B:HOH683 2.2 50.7 1.0 CE B:LYS469 4.0 50.3 1.0 O B:HOH642 4.1 40.1 1.0 OE1 B:GLU439 4.2 47.5 1.0 OD1 B:ASP473 4.3 39.0 1.0 NZ B:LYS469 4.3 52.1 1.0 OE2 B:GLU439 4.3 45.9 1.0 OE1 B:GLN476 4.4 37.4 1.0 OG B:SER446 4.6 40.7 1.0 CD B:GLU439 4.7 45.9 1.0

Magnesium binding site 5 out of 7 in the Legionella Effector LEM3 Mutant D190A in Complex with MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Legionella Effector LEM3 Mutant D190A in Complex with MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:36.3 occ:1.00 OD2 C:ASP105 2.1 36.4 1.0 OD2 C:ASP394 2.2 40.1 1.0 O C:HOH608 2.3 54.7 1.0 OD1 C:ASP254 2.3 36.0 1.0 O C:HOH604 2.3 31.1 1.0 O C:HOH616 2.5 46.0 1.0 CG C:ASP105 2.9 36.4 1.0 CG C:ASP254 3.1 36.5 1.0 OD1 C:ASP105 3.2 36.1 1.0 CG C:ASP394 3.2 38.2 1.0 OD2 C:ASP254 3.3 38.0 1.0 OD1 C:ASP394 3.6 39.6 1.0 O C:HOH627 4.2 33.1 1.0 O C:HOH629 4.3 32.5 1.0 O C:CYS395 4.3 35.2 1.0 CB C:ASP105 4.3 35.0 1.0 N C:GLY255 4.5 34.8 1.0 CB C:ASP394 4.5 37.4 1.0 CB C:ASP254 4.6 36.5 1.0 OD1 C:ASP82 4.6 32.8 1.0 N C:ASP254 4.7 33.4 1.0

Magnesium binding site 6 out of 7 in the Legionella Effector LEM3 Mutant D190A in Complex with MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Legionella Effector LEM3 Mutant D190A in Complex with MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:76.2 occ:1.00 O C:HOH659 1.9 46.4 1.0 O C:HOH625 2.0 46.5 1.0 O C:HOH630 2.5 54.5 1.0 OE2 C:GLU439 3.0 51.2 1.0 O C:HOH619 3.2 49.1 1.0 OE1 C:GLU439 3.8 50.9 1.0 CD C:GLU439 3.8 49.9 1.0 O C:HOH621 4.7 43.0 1.0 OE1 C:GLN476 4.7 44.6 1.0 NZ C:LYS469 4.7 56.9 1.0 CA C:HIS443 4.8 39.7 1.0 OG C:SER446 4.9 49.3 1.0 N C:HIS443 4.9 38.3 1.0 CE C:LYS469 5.0 54.8 1.0

Magnesium binding site 7 out of 7 in the Legionella Effector LEM3 Mutant D190A in Complex with MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Legionella Effector LEM3 Mutant D190A in Complex with MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:33.7 occ:1.00 OD2 D:ASP105 2.0 40.1 1.0 OD2 D:ASP394 2.2 42.8 1.0 O D:HOH603 2.2 48.3 1.0 O D:HOH611 2.3 39.6 1.0 OD1 D:ASP254 2.4 41.9 1.0 O D:HOH606 2.7 50.5 1.0 CG D:ASP105 2.8 40.3 1.0 OD1 D:ASP105 3.0 40.8 1.0 CG D:ASP394 3.2 42.7 1.0 CG D:ASP254 3.2 41.3 1.0 OD2 D:ASP254 3.4 42.6 1.0 OD1 D:ASP394 3.6 43.9 1.0 O D:HOH620 4.2 34.4 1.0 CB D:ASP105 4.2 39.1 1.0 O D:CYS395 4.4 39.9 1.0 CB D:ASP394 4.5 43.8 1.0 O D:HOH617 4.5 35.2 1.0 N D:GLY255 4.6 41.1 1.0 OD1 D:ASP82 4.7 36.4 1.0 CB D:ASP254 4.7 42.2 1.0 N D:ASP254 4.8 39.4 1.0

M.S.Kaspers, V.Pogenberg, S.Ernst, F.Ecker, C.Pett, P.Ochtrop, C.Hedberg, M.Groll, A.Itzen. Legionella Effector LEM3 Displaces the Switch II Region of RAB1B For Dephosphocholination To Be Published.
DOI: 10.1038/S41467-023-37621-7