Magnesium in PDB 8iu7: Structure of Staphylococcus Aureus Nrna (PDE2) in Complex with MG2+

The structure of Structure of Staphylococcus Aureus Nrna (PDE2) in Complex with MG2+, PDB code: 8iu7 was solved by K.Cheng, Y.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.32 / 1.86
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.91, 119.67, 119.57, 90, 91.37, 90
R / Rfree (%)	22.7 / 25.4

The binding sites of Magnesium atom in the Structure of Staphylococcus Aureus Nrna (PDE2) in Complex with MG2+ (pdb code 8iu7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Structure of Staphylococcus Aureus Nrna (PDE2) in Complex with MG2+, PDB code: 8iu7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Structure of Staphylococcus Aureus Nrna (PDE2) 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 Structure of Staphylococcus Aureus Nrna (PDE2) in Complex with MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:40.0 occ:1.00 O A:HOH536 1.9 45.6 1.0 OD2 A:ASP83 2.1 40.3 1.0 OD2 A:ASP27 2.1 54.5 1.0 NE2 A:HIS23 2.3 43.0 1.0 OD1 A:ASP27 2.6 46.0 1.0 CG A:ASP27 2.7 44.0 1.0 MG A:MG402 2.9 46.8 1.0 CG A:ASP83 3.1 40.6 1.0 CD2 A:HIS23 3.2 40.2 1.0 CE1 A:HIS23 3.3 41.9 1.0 OD1 A:ASP83 3.5 39.9 1.0 O A:HOH550 3.7 51.7 1.0 CB A:ASP27 4.2 42.8 1.0 N A:ALA30 4.2 40.7 1.0 O A:ASP83 4.3 39.4 1.0 CB A:ASP83 4.4 42.2 1.0 CG A:HIS23 4.4 40.4 1.0 ND1 A:HIS23 4.4 45.4 1.0 OD1 A:ASP158 4.4 47.1 1.0 CB A:ALA30 4.5 41.0 1.0 CB A:ASP29 4.5 40.3 1.0 OD2 A:ASP29 4.7 40.8 1.0 CA A:ALA30 4.8 43.1 1.0 NE2 A:HIS107 4.8 48.7 1.0 N A:ASP27 4.9 45.9 1.0 OD2 A:ASP158 4.9 47.8 1.0 C A:ASP29 5.0 39.8 1.0

Magnesium binding site 2 out of 8 in the Structure of Staphylococcus Aureus Nrna (PDE2) 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 Structure of Staphylococcus Aureus Nrna (PDE2) in Complex with MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:46.8 occ:1.00 OD2 A:ASP158 2.3 47.8 1.0 OD1 A:ASP83 2.4 39.9 1.0 OD2 A:ASP29 2.5 40.8 1.0 CE1 A:HIS106 2.8 40.6 1.0 O A:HOH550 2.9 51.7 1.0 MG A:MG401 2.9 40.0 1.0 OD2 A:ASP83 3.0 40.3 1.0 CG A:ASP83 3.1 40.6 1.0 CG A:ASP158 3.1 44.7 1.0 OD1 A:ASP158 3.1 47.1 1.0 O A:HOH536 3.3 45.6 1.0 CG A:ASP29 3.4 42.0 1.0 CB A:ASP29 3.4 40.3 1.0 NE2 A:HIS106 3.5 42.5 1.0 ND1 A:HIS106 3.9 41.7 1.0 NE2 A:HIS107 4.1 48.7 1.0 OD1 A:ASP27 4.2 46.0 1.0 OD2 A:ASP27 4.4 54.5 1.0 CB A:ASP158 4.5 41.1 1.0 OG1 A:THR126 4.6 42.7 1.0 CB A:ASP83 4.6 42.2 1.0 OD1 A:ASP29 4.6 40.2 1.0 CG A:ASP27 4.7 44.0 1.0 CA A:ASP29 4.7 41.0 1.0 N A:THR126 4.8 38.9 1.0 CD2 A:HIS106 4.8 40.0 1.0 CE1 A:HIS107 4.9 42.9 1.0 C A:ASP29 5.0 39.8 1.0 CD2 A:HIS107 5.0 40.8 1.0

Magnesium binding site 3 out of 8 in the Structure of Staphylococcus Aureus Nrna (PDE2) 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 Structure of Staphylococcus Aureus Nrna (PDE2) in Complex with MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:53.7 occ:1.00 OD2 C:ASP27 2.0 47.5 1.0 OD1 C:ASP27 2.0 49.2 1.0 OD2 C:ASP83 2.1 45.5 1.0 O C:HOH526 2.2 53.8 1.0 NE2 C:HIS23 2.3 46.9 1.0 CG C:ASP27 2.3 47.0 1.0 MG C:MG402 3.0 61.5 1.0 CE1 C:HIS23 3.1 55.7 1.0 CG C:ASP83 3.2 47.1 1.0 CD2 C:HIS23 3.3 48.0 1.0 OD1 C:ASP83 3.7 48.4 1.0 CB C:ASP27 3.8 48.3 1.0 N C:ALA30 4.1 45.8 1.0 CB C:ALA30 4.1 45.5 1.0 ND1 C:HIS23 4.3 47.1 1.0 CB C:ASP29 4.4 47.0 1.0 N C:ASP27 4.4 51.8 1.0 CG C:HIS23 4.4 48.5 1.0 CB C:ASP83 4.4 47.2 1.0 CA C:ALA30 4.5 47.3 1.0 CA C:ASP27 4.6 47.2 1.0 O C:ASP83 4.6 48.3 1.0 OD1 C:ASP158 4.7 49.5 1.0 C C:ASP29 4.8 47.5 1.0 OD2 C:ASP29 4.9 45.8 1.0 O C:HOH523 5.0 47.6 1.0 CA C:ASP29 5.0 46.0 1.0 N C:ASP29 5.0 45.6 1.0 C C:ASP27 5.0 45.8 1.0

Magnesium binding site 4 out of 8 in the Structure of Staphylococcus Aureus Nrna (PDE2) 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 Structure of Staphylococcus Aureus Nrna (PDE2) in Complex with MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:61.5 occ:1.00 OD1 C:ASP83 2.6 48.4 1.0 OD2 C:ASP158 2.7 55.4 1.0 OD2 C:ASP29 2.8 45.8 1.0 OD1 C:ASP158 2.9 49.5 1.0 CE1 C:HIS106 2.9 46.3 1.0 MG C:MG401 3.0 53.7 1.0 O C:HOH526 3.1 53.8 1.0 OD2 C:ASP83 3.1 45.5 1.0 CG C:ASP158 3.1 56.9 1.0 CG C:ASP83 3.2 47.1 1.0 CB C:ASP29 3.5 47.0 1.0 CG C:ASP29 3.6 48.5 1.0 NE2 C:HIS106 3.6 52.5 1.0 OD2 C:ASP27 4.0 47.5 1.0 ND1 C:HIS106 4.1 47.6 1.0 CE1 C:HIS107 4.1 49.2 1.0 OD1 C:ASP27 4.2 49.2 1.0 NE2 C:HIS107 4.3 54.1 1.0 CG C:ASP27 4.5 47.0 1.0 CB C:ASP158 4.5 43.6 1.0 CB C:ASP83 4.6 47.2 1.0 CA C:ASP29 4.8 46.0 1.0 OD1 C:ASP29 4.8 46.7 1.0 O C:HOH523 4.8 47.6 1.0 CD2 C:HIS106 4.9 46.8 1.0 OG1 C:THR126 4.9 50.7 1.0 NE2 C:HIS23 5.0 46.9 1.0

Magnesium binding site 5 out of 8 in the Structure of Staphylococcus Aureus Nrna (PDE2) 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 Structure of Staphylococcus Aureus Nrna (PDE2) in Complex with MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:63.6 occ:1.00 OD2 D:ASP83 2.1 48.6 1.0 OD2 D:ASP27 2.1 56.8 1.0 MG D:MG402 2.4 58.5 1.0 NE2 D:HIS23 2.5 55.9 1.0 OD1 D:ASP27 2.6 60.7 1.0 CG D:ASP27 2.7 56.6 1.0 CG D:ASP83 3.0 48.2 1.0 CD2 D:HIS23 3.1 63.3 1.0 OD1 D:ASP83 3.4 47.9 1.0 CE1 D:HIS23 3.5 57.9 1.0 NE2 D:HIS107 4.1 62.0 1.0 O D:ASP83 4.2 51.4 1.0 CB D:ASP27 4.2 51.6 1.0 CB D:ASP83 4.3 50.2 1.0 CG D:HIS23 4.3 57.1 1.0 N D:ALA30 4.5 49.7 1.0 ND1 D:HIS23 4.5 53.6 1.0 CB D:ASP29 4.5 47.1 1.0 CB D:ALA30 4.6 51.8 1.0 OD1 D:ASP158 4.6 52.9 1.0 OD2 D:ASP29 4.6 47.5 1.0 OD2 D:ASP158 4.7 59.5 1.0 CE1 D:HIS107 4.7 62.6 1.0 CA D:ALA30 4.9 56.1 1.0

Magnesium binding site 6 out of 8 in the Structure of Staphylococcus Aureus Nrna (PDE2) 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 Structure of Staphylococcus Aureus Nrna (PDE2) in Complex with MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:58.5 occ:1.00 MG D:MG401 2.4 63.6 1.0 OD2 D:ASP158 2.4 59.5 1.0 OD2 D:ASP29 2.8 47.5 1.0 OD1 D:ASP83 3.0 47.9 1.0 CG D:ASP158 3.0 54.0 1.0 OD1 D:ASP158 3.0 52.9 1.0 OD2 D:ASP83 3.0 48.6 1.0 CB D:ASP29 3.3 47.1 1.0 CE1 D:HIS106 3.3 49.3 1.0 CG D:ASP83 3.4 48.2 1.0 OD2 D:ASP27 3.5 56.8 1.0 CG D:ASP29 3.5 51.6 1.0 OD1 D:ASP27 3.7 60.7 1.0 CG D:ASP27 3.9 56.6 1.0 NE2 D:HIS107 3.9 62.0 1.0 NE2 D:HIS106 4.1 48.4 1.0 CE1 D:HIS107 4.2 62.6 1.0 ND1 D:HIS106 4.4 49.9 1.0 CB D:ASP158 4.4 48.7 1.0 O D:HOH508 4.4 52.5 1.0 CA D:ASP29 4.6 50.7 1.0 OD1 D:ASP29 4.7 47.3 1.0 NE2 D:HIS23 4.8 55.9 1.0 N D:ALA30 4.9 49.7 1.0 C D:ASP29 4.9 53.0 1.0 CB D:ASP83 4.9 50.2 1.0 OG1 D:THR126 5.0 50.1 1.0

Magnesium binding site 7 out of 8 in the Structure of Staphylococcus Aureus Nrna (PDE2) 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 Structure of Staphylococcus Aureus Nrna (PDE2) in Complex with MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:64.0 occ:1.00 O B:HOH506 1.9 50.4 1.0 OD2 B:ASP29 2.1 42.3 1.0 OD1 B:ASP83 2.2 45.6 1.0 CE1 B:HIS106 2.6 41.8 1.0 OD2 B:ASP158 2.7 55.3 1.0 OD2 B:ASP83 2.8 43.9 1.0 CG B:ASP83 2.8 45.4 1.0 CG B:ASP29 3.0 41.2 1.0 CG B:ASP158 3.2 47.7 1.0 OD1 B:ASP158 3.3 48.9 1.0 MG B:MG402 3.3 48.3 1.0 CB B:ASP29 3.3 40.2 1.0 NE2 B:HIS106 3.5 47.1 1.0 ND1 B:HIS106 3.6 43.5 1.0 CE1 B:HIS107 3.9 45.3 1.0 OG1 B:THR126 4.1 40.9 1.0 OD2 B:ASP27 4.2 47.4 1.0 OD1 B:ASP29 4.2 39.4 1.0 CB B:ASP83 4.3 38.7 1.0 NE2 B:HIS107 4.3 51.6 1.0 OD1 B:ASP27 4.4 46.6 1.0 N B:THR126 4.4 38.8 1.0 CB B:ASP158 4.5 42.6 1.0 CA B:ASP29 4.7 40.9 1.0 CD2 B:HIS106 4.7 44.7 1.0 CG B:ASP27 4.7 47.1 1.0 CG B:HIS106 4.8 41.1 1.0 C B:ASP29 4.8 39.2 1.0 CB B:THR126 4.9 38.9 1.0 N B:ALA30 4.9 37.2 1.0 O B:ASP83 4.9 40.0 1.0 ND1 B:HIS107 5.0 48.8 1.0 O B:HOH507 5.0 45.6 1.0

Magnesium binding site 8 out of 8 in the Structure of Staphylococcus Aureus Nrna (PDE2) in Complex with MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Staphylococcus Aureus Nrna (PDE2) in Complex with MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:48.3 occ:1.00 O B:HOH506 1.8 50.4 1.0 OD2 B:ASP83 1.9 43.9 1.0 NE2 B:HIS23 2.1 44.6 1.0 OD1 B:ASP27 2.2 46.6 1.0 OD2 B:ASP27 2.2 47.4 1.0 CG B:ASP27 2.5 47.1 1.0 CD2 B:HIS23 2.9 41.1 1.0 CG B:ASP83 3.0 45.4 1.0 CE1 B:HIS23 3.2 50.4 1.0 MG B:MG401 3.3 64.0 1.0 OD1 B:ASP83 3.7 45.6 1.0 CB B:ALA30 3.9 40.2 1.0 N B:ALA30 4.0 37.2 1.0 CB B:ASP27 4.1 45.6 1.0 CB B:ASP83 4.1 38.7 1.0 CG B:HIS23 4.1 47.8 1.0 O B:ASP83 4.1 40.0 1.0 ND1 B:HIS23 4.2 48.2 1.0 CA B:ALA30 4.4 39.5 1.0 CB B:ASP29 4.5 40.2 1.0 N B:ASP27 4.7 49.4 1.0 OD2 B:ASP29 4.7 42.3 1.0 OD1 B:ASP158 4.7 48.9 1.0 CE1 B:HIS107 4.7 45.3 1.0 C B:ASP29 4.8 39.2 1.0 CA B:ASP27 4.9 43.3 1.0

K.Cheng, Y.Wang. Structure of Staphylococcus Aureus Nrna in Complex with MG2+. To Be Published.