Magnesium in PDB 9dud: Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Fad Bound)

All present enzymatic activity of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Fad Bound):
3.6.1.13;

The structure of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Fad Bound), PDB code: 9dud was solved by Seattle Structural Genomics Center For Infectious Disease, Seattlestructural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.23 / 1.32
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.351, 79.69, 91.973, 90, 90, 90
R / Rfree (%)	14.4 / 17

The binding sites of Magnesium atom in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Fad Bound) (pdb code 9dud). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Fad Bound), PDB code: 9dud:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Fad Bound)


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 Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Fad Bound) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:24.8 occ:1.00 O A:HOH417 2.0 32.4 1.0 O A:HOH423 2.0 21.9 1.0 O A:HOH472 2.1 24.8 1.0 OE2 A:GLU116 2.1 22.2 1.0 OE1 A:GLU112 2.2 23.2 1.0 OE2 A:GLU164 2.2 35.2 1.0 CD A:GLU116 3.1 21.9 1.0 CD A:GLU112 3.2 22.6 1.0 CD A:GLU164 3.2 35.5 1.0 CG A:GLU116 3.5 20.3 1.0 OE1 A:GLU164 3.5 35.6 1.0 MG A:MG303 3.5 24.8 1.0 OE2 A:GLU112 3.6 23.7 1.0 O A:HOH407 3.7 22.2 1.0 O4' A:FAD301 3.7 67.1 1.0 O A:ALA96 3.9 17.9 1.0 O1A A:FAD301 4.0 48.0 1.0 O A:HOH403 4.1 33.3 1.0 OE1 A:GLU116 4.2 22.7 1.0 OE1 A:GLU115 4.3 29.2 1.0 O3P A:FAD301 4.4 51.9 1.0 CG A:GLU112 4.5 21.2 1.0 CG A:GLU164 4.6 35.2 1.0 C4' A:FAD301 4.7 67.0 1.0 O5' A:FAD301 4.7 62.2 1.0 PA A:FAD301 4.8 46.4 1.0 CB A:GLU112 4.8 20.4 1.0 CB A:GLU116 5.0 21.0 1.0 C A:ALA96 5.0 16.7 1.0 CD1 A:ILE166 5.0 22.8 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Fad Bound)


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 Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Fad Bound) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:24.8 occ:1.00 OE2 A:GLU116 2.3 22.2 1.0 O A:HOH407 2.3 22.2 1.0 O A:HOH486 2.4 24.5 1.0 O A:HOH523 2.4 22.8 1.0 O A:ALA96 2.4 17.9 1.0 O A:HOH423 2.6 21.9 1.0 CD A:GLU116 3.0 21.9 1.0 OE1 A:GLU116 3.1 22.7 1.0 C A:ALA96 3.5 16.7 1.0 MG A:MG302 3.5 24.8 1.0 O3P A:FAD301 3.8 51.9 1.0 NH2 A:ARG79 3.9 21.8 1.0 OE2 A:GLU164 3.9 35.2 1.0 N A:ALA96 3.9 14.6 1.0 CA A:ALA96 4.1 15.6 1.0 O1A A:FAD301 4.2 48.0 1.0 NE2 A:GLN77 4.2 25.0 1.0 PA A:FAD301 4.3 46.4 1.0 OE1 A:GLU112 4.3 23.2 1.0 CB A:ALA96 4.3 15.1 1.0 CG A:GLU116 4.5 20.3 1.0 N A:GLY97 4.5 16.5 1.0 OE1 A:GLN77 4.5 24.7 1.0 CA A:GLY97 4.7 17.4 1.0 O2A A:FAD301 4.7 44.7 1.0 CD A:GLN77 4.8 23.3 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Fad Bound)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Fad Bound) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:21.4 occ:1.00 O B:HOH402 2.3 21.3 1.0 OE2 B:GLU116 2.3 18.2 1.0 O B:HOH511 2.3 19.6 1.0 O B:HOH470 2.4 19.8 1.0 O B:ALA96 2.4 15.3 1.0 O B:HOH468 2.5 19.4 1.0 CD B:GLU116 3.1 17.9 1.0 OE1 B:GLU116 3.1 19.9 1.0 C B:ALA96 3.5 13.1 1.0 MG B:MG303 3.5 19.1 1.0 NH2 B:ARG79 3.9 19.6 1.0 O1A B:FAD301 3.9 49.2 1.0 O3P B:FAD301 3.9 46.6 1.0 N B:ALA96 4.0 12.3 1.0 OE2 B:GLU164 4.0 28.5 1.0 CA B:ALA96 4.2 12.8 1.0 PA B:FAD301 4.3 46.9 1.0 NE2 B:GLN77 4.3 23.6 1.0 OE1 B:GLU112 4.4 18.2 1.0 OE1 B:GLN77 4.4 22.1 1.0 CB B:ALA96 4.5 14.0 1.0 CG B:GLU116 4.5 16.1 1.0 N B:GLY97 4.5 13.5 1.0 CA B:GLY97 4.7 14.4 1.0 O B:HOH622 4.8 28.2 1.0 CD B:GLN77 4.8 21.1 1.0 O2A B:FAD301 5.0 48.8 1.0 CZ B:ARG79 5.0 18.2 1.0 CD B:GLU112 5.0 18.0 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Fad Bound)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Fad Bound) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:19.1 occ:1.00 O B:HOH532 2.1 25.3 1.0 OE2 B:GLU116 2.1 18.2 1.0 O B:HOH468 2.1 19.4 1.0 OE1 B:GLU112 2.1 18.2 1.0 O B:HOH420 2.1 19.8 1.0 OE2 B:GLU164 2.2 28.5 1.0 CD B:GLU116 3.1 17.9 1.0 CD B:GLU112 3.1 18.0 1.0 CD B:GLU164 3.2 27.1 1.0 CG B:GLU116 3.5 16.1 1.0 OE2 B:GLU112 3.5 19.5 1.0 MG B:MG302 3.5 21.4 1.0 OE1 B:GLU164 3.5 25.8 1.0 O B:HOH402 3.8 21.3 1.0 O B:ALA96 3.9 15.3 1.0 O B:HOH407 4.2 31.0 1.0 OE1 B:GLU116 4.2 19.9 1.0 OE1 B:GLU115 4.2 23.2 1.0 O B:HOH569 4.3 38.4 1.0 O1A B:FAD301 4.3 49.2 1.0 CG B:GLU112 4.4 17.0 1.0 CG B:GLU164 4.5 27.4 1.0 O3P B:FAD301 4.6 46.6 1.0 O B:HOH459 4.7 24.8 1.0 CB B:GLU112 4.7 16.0 1.0 CB B:GLU116 5.0 16.1 1.0

P.Enayati, L.Liu, S.Lovell, G.W.Buchko, K.P.Battaile. Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Fad Bound) To Be Published.