Magnesium in PDB 9dt7: Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (5-O-Phosphono-Alpha-D-Ribofuranose Bound)

All present enzymatic activity of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (5-O-Phosphono-Alpha-D-Ribofuranose Bound):
3.6.1.13;

The structure of Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (5-O-Phosphono-Alpha-D-Ribofuranose Bound), PDB code: 9dt7 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)	60.17 / 1.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.509, 79.74, 91.709, 90, 90, 90
R / Rfree (%)	13 / 15.3

The binding sites of Magnesium atom in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (5-O-Phosphono-Alpha-D-Ribofuranose Bound) (pdb code 9dt7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (5-O-Phosphono-Alpha-D-Ribofuranose Bound), PDB code: 9dt7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (5-O-Phosphono-Alpha-D-Ribofuranose 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 (5-O-Phosphono-Alpha-D-Ribofuranose Bound) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:44.2 occ:1.00 OE2 A:GLU116 2.0 32.0 1.0 O1X B:HSX303 2.1 17.2 0.5 O A:HOH499 2.2 33.3 1.0 O A:HOH424 2.6 34.9 1.0 O A:ALA96 2.8 19.4 1.0 CD A:GLU116 2.9 30.7 1.0 OE1 A:GLU116 3.2 29.9 1.0 P' B:HSX303 3.3 16.8 0.5 O A:HOH578 3.4 27.8 0.5 O3X B:HSX303 3.6 17.9 0.5 O A:HOH413 3.7 35.3 1.0 NH2 A:ARG79 3.7 20.1 1.0 C A:ALA96 3.8 17.9 1.0 O2X B:HSX303 4.2 17.2 0.5 OE1 A:GLN77 4.2 21.5 1.0 N A:ALA96 4.3 15.3 1.0 CG A:GLU116 4.3 30.1 1.0 O5 B:HSX303 4.4 15.9 0.5 CA A:ALA96 4.5 16.3 1.0 NE2 A:GLN77 4.5 17.4 1.0 C5 B:HSX303 4.5 15.1 0.5 O A:HOH409 4.5 46.3 1.0 OE2 A:GLU164 4.5 48.5 1.0 CB A:ALA96 4.7 17.2 1.0 OE1 A:GLU112 4.8 26.5 1.0 CD A:GLN77 4.8 18.2 1.0 CZ A:ARG79 4.8 17.5 1.0 N A:GLY97 4.8 18.3 1.0 NH1 A:ARG79 5.0 18.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (5-O-Phosphono-Alpha-D-Ribofuranose 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 (5-O-Phosphono-Alpha-D-Ribofuranose Bound) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:18.4 occ:1.00 OE2 B:GLU116 2.1 17.8 1.0 O B:HOH468 2.1 16.1 1.0 O B:HOH455 2.1 19.8 1.0 O2X B:HSX302 2.1 14.8 0.7 O B:HOH519 2.3 24.3 1.0 O B:ALA96 2.4 13.9 1.0 CD B:GLU116 3.1 15.7 1.0 P' B:HSX302 3.3 14.3 0.7 OE1 B:GLU116 3.4 15.4 1.0 C B:ALA96 3.5 11.5 1.0 O3X B:HSX302 3.6 15.7 0.7 O B:HOH401 3.6 32.9 1.0 NH2 B:ARG79 4.2 18.0 1.0 O1X B:HSX302 4.2 14.7 0.7 N B:ALA96 4.3 11.1 1.0 O B:HOH418 4.3 17.9 1.0 CA B:ALA96 4.3 11.1 1.0 OE1 B:GLU112 4.4 19.0 1.0 CG B:GLU116 4.4 13.8 1.0 N B:GLY97 4.4 12.0 1.0 O B:HOH646 4.4 44.9 1.0 OE1 B:GLN77 4.4 21.0 1.0 CA B:GLY97 4.4 12.9 1.0 O5 B:HSX302 4.5 13.9 0.7 C5 B:HSX302 4.6 13.6 0.7 O B:HOH409 4.6 43.1 1.0 NE2 B:GLN77 4.6 17.2 1.0 CB B:ALA96 4.6 12.3 1.0 O B:HOH564 4.7 45.1 1.0 CD B:GLU112 4.8 15.7 1.0 OE2 B:GLU112 5.0 17.3 1.0 CD B:GLN77 5.0 17.8 1.0

L.Liu, S.Lovell, G.W.Buchko, K.P.Battaile. Crystal Structure of Adp-Ribose Diphosphatase From Klebsiella Pneumoniae (5-O-Phosphono-Alpha-D-Ribofuranose Bound) To Be Published.