Magnesium in PDB 2dsc: Crystal Structure of Human Adp-Ribose Pyrophosphatase NUDT5 in Complex with Magnesium and Adp-Ribose

All present enzymatic activity of Crystal Structure of Human Adp-Ribose Pyrophosphatase NUDT5 in Complex with Magnesium and Adp-Ribose:
3.6.1.13;

The structure of Crystal Structure of Human Adp-Ribose Pyrophosphatase NUDT5 in Complex with Magnesium and Adp-Ribose, PDB code: 2dsc was solved by M.Zha, C.Zhong, J.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.41 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	112.466, 40.623, 99.685, 90.00, 121.44, 90.00
R / Rfree (%)	19.3 / 22.8

The binding sites of Magnesium atom in the Crystal Structure of Human Adp-Ribose Pyrophosphatase NUDT5 in Complex with Magnesium and Adp-Ribose (pdb code 2dsc). 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 Human Adp-Ribose Pyrophosphatase NUDT5 in Complex with Magnesium and Adp-Ribose, PDB code: 2dsc:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human Adp-Ribose Pyrophosphatase NUDT5 in Complex with Magnesium and Adp-Ribose


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 Human Adp-Ribose Pyrophosphatase NUDT5 in Complex with Magnesium and Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:9.6 occ:0.50 O A:ALA96 2.3 24.0 1.0 O A:HOH409 2.4 28.5 1.0 O1A B:APR401 2.4 32.3 1.0 O2B B:APR401 2.5 34.1 1.0 OE2 A:GLU116 2.5 41.6 1.0 O A:HOH433 2.5 34.3 1.0 C A:ALA96 3.5 23.4 1.0 CD A:GLU116 3.5 38.8 1.0 PA B:APR401 3.7 35.7 1.0 OE2 A:GLU166 3.7 0.1 1.0 PB B:APR401 3.7 35.2 1.0 OE2 A:GLU112 3.8 48.0 1.0 OE1 A:GLU116 3.9 38.8 1.0 O A:HOH486 3.9 72.6 1.0 O3A B:APR401 3.9 34.7 1.0 N A:ALA96 4.3 18.9 1.0 CA A:GLY97 4.3 29.3 1.0 N A:GLY97 4.3 27.0 1.0 O A:HOH406 4.3 21.1 1.0 NH2 A:ARG84 4.3 26.6 1.0 CA A:ALA96 4.4 20.7 1.0 O B:HOH485 4.4 36.7 1.0 CD A:GLU112 4.5 45.1 1.0 NE2 A:GLN82 4.5 33.8 1.0 OE1 A:GLN82 4.6 32.4 1.0 O1B B:APR401 4.6 34.3 1.0 O2A B:APR401 4.6 35.2 1.0 O5' B:APR401 4.7 35.1 1.0 CG A:GLU116 4.7 35.7 1.0 CD A:GLU166 4.8 0.4 1.0 CB A:ALA96 4.9 18.3 1.0 O5D B:APR401 4.9 37.5 1.0 CG A:GLU112 4.9 40.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Adp-Ribose Pyrophosphatase NUDT5 in Complex with Magnesium and Adp-Ribose


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 Human Adp-Ribose Pyrophosphatase NUDT5 in Complex with Magnesium and Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:26.3 occ:0.50 O B:HOH418 2.4 29.1 1.0 OE1 B:GLU116 2.5 66.5 1.0 O1A A:APR402 2.5 53.7 1.0 O2B A:APR402 2.6 52.4 1.0 O B:ALA96 2.6 27.5 1.0 O B:HOH448 2.7 39.2 1.0 CD B:GLU116 3.6 62.0 1.0 OE1 B:GLU112 3.6 61.0 1.0 C B:ALA96 3.7 27.8 1.0 PA A:APR402 3.8 54.6 1.0 PB A:APR402 3.9 55.6 1.0 OE2 B:GLU116 4.0 60.3 1.0 OE1 B:GLU166 4.1 0.3 1.0 O3A A:APR402 4.1 55.9 1.0 O B:HOH407 4.3 27.4 1.0 O B:HOH547 4.4 41.7 1.0 NH2 B:ARG84 4.4 21.3 1.0 N B:ALA96 4.5 21.7 1.0 OE1 B:GLN82 4.6 28.3 1.0 NE2 B:GLN82 4.6 27.0 1.0 N B:GLY97 4.6 29.2 1.0 CA B:GLY97 4.6 33.9 1.0 CA B:ALA96 4.6 24.9 1.0 O A:HOH444 4.7 39.9 1.0 O1B A:APR402 4.7 53.5 1.0 CD B:GLU112 4.7 57.6 1.0 O2A A:APR402 4.8 53.6 1.0 O5' A:APR402 4.8 54.2 1.0 CG B:GLU116 4.9 55.4 1.0 O5D A:APR402 5.0 57.9 1.0

M.Zha, C.Zhong, Y.Peng, H.Hu, J.Ding. Crystal Structures of Human NUDT5 Reveal Insights Into the Structural Basis of the Substrate Specificity J.Mol.Biol. V. 364 1021 2006.
ISSN: ISSN 0022-2836
PubMed: 17052728
DOI: 10.1016/J.JMB.2006.09.078