Magnesium in PDB 9b20: Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Amp Bound)

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

The structure of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Amp Bound), PDB code: 9b20 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)	45.16 / 1.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.91, 68.79, 56.663, 90, 115.2, 90
R / Rfree (%)	16.4 / 20.3

The binding sites of Magnesium atom in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Amp Bound) (pdb code 9b20). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Amp Bound), PDB code: 9b20:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Amp 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 (Amp Bound) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:23.8 occ:1.00 OE2 A:GLU116 2.1 20.5 1.0 O A:HOH456 2.2 24.9 1.0 O A:HOH410 2.2 27.3 1.0 O A:ALA96 2.2 16.3 1.0 O A:HOH404 2.2 25.7 1.0 O A:HOH499 2.3 23.8 1.0 CD A:GLU116 3.1 19.3 1.0 OE1 A:GLU116 3.3 24.2 1.0 C A:ALA96 3.3 17.4 1.0 O A:HOH542 3.8 44.2 1.0 O1P A:AMP301 3.9 41.0 1.0 O3P A:AMP301 3.9 37.3 1.0 N A:ALA96 4.1 16.1 1.0 CA A:ALA96 4.2 15.4 1.0 N A:GLY97 4.2 15.2 1.0 NH2 A:ARG79 4.3 24.9 1.0 CA A:GLY97 4.3 16.1 1.0 NE2 A:GLN77 4.4 27.1 1.0 O A:HOH411 4.4 24.6 1.0 P A:AMP301 4.4 41.2 1.0 CG A:GLU116 4.4 20.1 1.0 O A:HOH403 4.4 29.4 1.0 CB A:ALA96 4.5 15.8 1.0 O A:HOH550 4.5 32.4 1.0 OE1 A:GLU112 4.6 28.6 1.0 CD A:GLU112 4.8 43.8 1.0 OE1 A:GLN77 4.8 30.6 1.0 OE2 A:GLU112 4.9 32.9 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Amp 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 (Amp Bound) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:26.3 occ:1.00 OE2 B:GLU116 2.2 26.6 1.0 O B:ALA96 2.2 16.4 1.0 O B:HOH416 2.2 29.6 1.0 O B:HOH459 2.4 22.9 1.0 O B:HOH443 2.4 23.6 1.0 O B:HOH494 2.5 30.1 1.0 CD B:GLU116 3.1 22.4 1.0 OE1 B:GLU116 3.3 23.3 1.0 C B:ALA96 3.3 14.9 1.0 MG B:MG303 3.3 31.9 1.0 O1P B:AMP301 3.5 59.3 1.0 OE2 B:GLU164 3.7 26.7 1.0 N B:ALA96 4.0 15.1 1.0 NH2 B:ARG79 4.0 28.4 1.0 OE1 B:GLU112 4.1 33.2 1.0 CA B:ALA96 4.1 14.7 1.0 O3P B:AMP301 4.1 61.2 1.0 NE2 B:GLN77 4.3 29.5 1.0 N B:GLY97 4.3 14.5 1.0 P B:AMP301 4.3 74.5 1.0 CA B:GLY97 4.4 14.5 1.0 CB B:ALA96 4.4 18.5 1.0 OE1 B:GLN77 4.5 20.3 1.0 CG B:GLU116 4.5 20.3 1.0 CD B:GLN77 4.8 24.6 1.0 CD B:GLU112 4.8 27.2 1.0 O B:HOH483 4.9 29.5 1.0 CD B:GLU164 4.9 44.9 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (Amp 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 (Amp Bound) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:31.9 occ:1.00 O B:HOH406 1.9 27.1 1.0 O B:HOH459 2.0 22.9 1.0 OE2 B:GLU164 2.0 26.7 1.0 OE2 B:GLU116 2.2 26.6 1.0 OE1 B:GLU112 2.2 33.2 1.0 O B:HOH505 2.3 31.8 1.0 CD B:GLU164 2.9 44.9 1.0 CD B:GLU116 3.1 22.4 1.0 OE1 B:GLU164 3.2 32.0 1.0 CD B:GLU112 3.2 27.2 1.0 MG B:MG302 3.3 26.3 1.0 CG B:GLU116 3.5 20.3 1.0 OE2 B:GLU112 3.5 30.2 1.0 O B:HOH416 3.6 29.6 1.0 O B:ALA96 3.9 16.4 1.0 OE1 B:GLU116 4.2 23.3 1.0 OE1 B:GLU115 4.3 40.0 1.0 CG B:GLU164 4.4 41.1 1.0 O1P B:AMP301 4.4 59.3 1.0 O B:HOH483 4.5 29.5 1.0 O3P B:AMP301 4.6 61.2 1.0 CG B:GLU112 4.6 19.7 1.0 CB B:GLU112 4.9 20.5 1.0 P B:AMP301 5.0 74.5 1.0

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