Magnesium in PDB 3r3s: Structure of the Ygha Oxidoreductase From Salmonella Enterica

The structure of Structure of the Ygha Oxidoreductase From Salmonella Enterica, PDB code: 3r3s was solved by S.M.Anderson, Z.Wawrzak, O.Onopriyenko, S.N.Peterson, W.F.Anderson, A.Savchenko, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.34 / 1.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	75.728, 80.673, 96.168, 90.00, 100.96, 90.00
R / Rfree (%)	12.9 / 15.3

The binding sites of Magnesium atom in the Structure of the Ygha Oxidoreductase From Salmonella Enterica (pdb code 3r3s). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of the Ygha Oxidoreductase From Salmonella Enterica, PDB code: 3r3s:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of the Ygha Oxidoreductase From Salmonella Enterica


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Ygha Oxidoreductase From Salmonella Enterica within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg296 b:5.1 occ:1.00 OE2 A:GLU84 2.1 6.2 1.0 OD1 A:ASP58 2.1 6.3 1.0 O A:HOH298 2.1 7.4 1.0 O A:HOH297 2.1 6.2 1.0 OG A:SER59 2.1 5.0 1.0 O3B A:NAD300 2.2 5.6 1.0 CD A:GLU84 3.0 6.3 1.0 CG A:ASP58 3.0 5.9 1.0 CB A:SER59 3.2 5.1 1.0 C3B A:NAD300 3.2 5.9 1.0 OD2 A:ASP58 3.4 5.8 1.0 OE1 A:GLU84 3.7 7.6 1.0 CG A:GLU84 3.8 6.9 1.0 C2B A:NAD300 4.0 5.5 1.0 O A:GLY25 4.1 9.9 1.0 O2B A:NAD300 4.1 6.6 1.0 O2A A:NAD300 4.2 5.8 1.0 O1A A:NAD300 4.2 5.5 1.0 CB A:GLU84 4.3 7.5 1.0 N A:SER59 4.3 4.6 1.0 CA A:SER59 4.3 4.6 1.0 CB A:ASP58 4.4 5.6 1.0 OD2 A:ASP87 4.4 10.6 1.0 C4B A:NAD300 4.5 5.3 1.0 PA A:NAD300 4.5 5.4 1.0 O5B A:NAD300 4.6 5.5 1.0 O A:PRO24 4.6 7.2 1.0 C A:ASP58 4.8 5.4 1.0 CB A:PRO24 4.9 8.4 1.0 C5B A:NAD300 5.0 5.8 1.0

Magnesium binding site 2 out of 4 in the Structure of the Ygha Oxidoreductase From Salmonella Enterica


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Ygha Oxidoreductase From Salmonella Enterica within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg296 b:5.4 occ:1.00 OD1 B:ASP58 2.0 7.3 1.0 O B:HOH301 2.1 7.8 1.0 OE2 B:GLU84 2.1 7.3 1.0 O B:HOH299 2.1 7.1 1.0 OG B:SER59 2.1 6.0 1.0 O3B B:NAD300 2.1 6.1 1.0 CD B:GLU84 2.9 7.0 1.0 CG B:ASP58 3.0 7.2 1.0 C3B B:NAD300 3.2 6.1 1.0 CB B:SER59 3.2 5.3 1.0 OD2 B:ASP58 3.3 6.4 1.0 CG B:GLU84 3.7 7.6 1.0 OE1 B:GLU84 3.7 7.9 1.0 C2B B:NAD300 4.0 6.9 1.0 O B:GLY25 4.0 9.4 1.0 O2B B:NAD300 4.0 7.4 1.0 O2A B:NAD300 4.2 5.5 1.0 O1A B:NAD300 4.2 6.6 1.0 CB B:GLU84 4.2 8.1 1.0 CA B:SER59 4.3 5.4 1.0 N B:SER59 4.3 5.7 1.0 OD2 B:ASP87 4.3 8.9 1.0 CB B:ASP58 4.4 6.5 1.0 C4B B:NAD300 4.4 6.1 1.0 PA B:NAD300 4.5 5.7 1.0 O5B B:NAD300 4.5 5.9 1.0 O B:PRO24 4.6 8.3 1.0 C B:ASP58 4.8 5.9 1.0 CB B:PRO24 4.9 8.6 1.0 C5B B:NAD300 5.0 6.2 1.0

Magnesium binding site 3 out of 4 in the Structure of the Ygha Oxidoreductase From Salmonella Enterica


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Ygha Oxidoreductase From Salmonella Enterica within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg296 b:5.1 occ:1.00 O C:HOH303 2.0 6.8 1.0 OD1 C:ASP58 2.1 5.5 1.0 O C:HOH297 2.1 5.5 1.0 OE2 C:GLU84 2.1 6.2 1.0 OG C:SER59 2.1 4.5 1.0 O3B C:NAD300 2.1 5.3 1.0 CD C:GLU84 3.0 6.0 1.0 CG C:ASP58 3.0 5.1 1.0 C3B C:NAD300 3.2 5.6 1.0 CB C:SER59 3.2 4.8 1.0 OD2 C:ASP58 3.4 5.3 1.0 OE1 C:GLU84 3.7 6.6 1.0 CG C:GLU84 3.8 6.5 1.0 C2B C:NAD300 4.0 5.8 1.0 O2B C:NAD300 4.0 6.2 1.0 O C:GLY25 4.1 9.1 1.0 O2A C:NAD300 4.2 4.8 1.0 O1A C:NAD300 4.2 5.1 1.0 CB C:GLU84 4.3 6.3 1.0 CA C:SER59 4.3 4.5 1.0 N C:SER59 4.3 4.2 1.0 CB C:ASP58 4.4 5.0 1.0 OD2 C:ASP87 4.4 10.9 1.0 C4B C:NAD300 4.5 5.3 1.0 PA C:NAD300 4.5 5.0 1.0 O5B C:NAD300 4.6 4.8 1.0 O C:PRO24 4.6 5.7 1.0 C C:ASP58 4.8 4.7 1.0 CB C:PRO24 4.9 7.7 1.0 C5B C:NAD300 5.0 5.3 1.0

Magnesium binding site 4 out of 4 in the Structure of the Ygha Oxidoreductase From Salmonella Enterica


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Ygha Oxidoreductase From Salmonella Enterica within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg296 b:5.5 occ:1.00 O D:HOH298 2.0 7.7 1.0 OD1 D:ASP58 2.0 6.7 1.0 O D:HOH297 2.1 5.7 1.0 OE2 D:GLU84 2.1 5.7 1.0 O3B D:NAD300 2.2 6.1 1.0 OG D:SER59 2.2 5.9 1.0 CD D:GLU84 3.0 6.1 1.0 CG D:ASP58 3.0 7.0 1.0 C3B D:NAD300 3.2 5.7 1.0 CB D:SER59 3.2 5.5 1.0 OD2 D:ASP58 3.3 6.7 1.0 OE1 D:GLU84 3.7 6.2 1.0 CG D:GLU84 3.8 6.6 1.0 C2B D:NAD300 4.0 6.0 1.0 O2B D:NAD300 4.1 6.8 1.0 O1A D:NAD300 4.2 5.8 1.0 O2A D:NAD300 4.2 5.5 1.0 O D:GLY25 4.3 9.1 1.0 OD2 D:ASP87 4.3 7.4 1.0 CB D:GLU84 4.3 7.5 1.0 N D:SER59 4.3 5.4 1.0 CA D:SER59 4.3 5.4 1.0 CB D:ASP58 4.4 6.4 1.0 C4B D:NAD300 4.5 5.5 1.0 PA D:NAD300 4.5 5.4 1.0 O D:PRO24 4.6 7.3 1.0 O5B D:NAD300 4.6 4.7 1.0 C D:ASP58 4.8 5.7 1.0 C5B D:NAD300 4.9 5.5 1.0 CB D:PRO24 4.9 7.5 1.0

S.M.Anderson, Z.Wawrzak, O.Onopriyenko, S.N.Peterson, W.F.Anderson, A.Savchenko, Center For Structural Genomics Of Infectious Diseases(Csgid). Structure of the Ygha Oxidoreductase From Salmonella Enterica To Be Published.