Magnesium in PDB 5ls0: Crystal Structure of Inorganic Pyrophosphatase PPA1 From Arabidopsis Thaliana

All present enzymatic activity of Crystal Structure of Inorganic Pyrophosphatase PPA1 From Arabidopsis Thaliana:
3.6.1.1;

The structure of Crystal Structure of Inorganic Pyrophosphatase PPA1 From Arabidopsis Thaliana, PDB code: 5ls0 was solved by M.Grzechowiak, M.Sikorski, M.Jaskolski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.41 / 1.83
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	81.130, 81.130, 174.660, 90.00, 90.00, 120.00
R / Rfree (%)	15.4 / 19

The binding sites of Magnesium atom in the Crystal Structure of Inorganic Pyrophosphatase PPA1 From Arabidopsis Thaliana (pdb code 5ls0). 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 Inorganic Pyrophosphatase PPA1 From Arabidopsis Thaliana, PDB code: 5ls0:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Inorganic Pyrophosphatase PPA1 From Arabidopsis Thaliana


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 Inorganic Pyrophosphatase PPA1 From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:61.7 occ:1.00 OD1 A:ASP103 2.1 47.0 1.0 O A:HOH413 2.1 38.9 1.0 O A:HOH402 2.1 37.8 1.0 O A:HOH446 2.2 39.1 1.0 O A:HOH431 2.2 32.4 0.5 O A:HOH456 2.3 56.2 1.0 CG A:ASP103 3.1 42.2 1.0 O A:HOH431 3.3 41.3 0.5 OD2 A:ASP103 3.6 43.0 1.0 O A:HOH458 3.8 44.2 1.0 O A:HOH462 3.9 70.6 1.0 OH A:TYR88 4.1 40.0 1.0 OE1 A:GLU54 4.2 35.8 1.0 O A:HOH463 4.2 49.6 1.0 CB A:ASP103 4.2 37.5 1.0 OD2 A:ASP100 4.3 65.1 1.0 O A:PRO101 4.4 41.2 1.0 OE2 A:GLU54 4.6 30.1 1.0 CE1 A:TYR88 4.6 33.5 1.0 CZ A:TYR88 4.7 35.0 1.0 CA A:ASP103 4.7 35.7 1.0 CB A:ASP100 4.7 61.0 1.0 O A:HOH437 4.8 36.0 1.0 CD A:GLU54 4.8 33.8 1.0 CG A:ASP100 4.9 62.0 1.0 O A:GLY89 5.0 30.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Inorganic Pyrophosphatase PPA1 From Arabidopsis Thaliana


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 Inorganic Pyrophosphatase PPA1 From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:33.7 occ:1.00 O B:HOH452 2.1 28.5 1.0 O B:HOH478 2.1 39.2 1.0 OD1 B:ASP103 2.1 35.8 1.0 O B:HOH470 2.1 29.8 1.0 O B:HOH423 2.1 25.8 1.0 O B:HOH410 2.2 25.0 1.0 CG B:ASP103 3.1 37.0 1.0 OD2 B:ASP103 3.6 30.8 1.0 O B:HOH471 3.7 41.6 1.0 O B:HOH484 3.9 35.0 1.0 O B:HOH459 4.1 41.0 1.0 OE1 B:GLU54 4.1 26.1 1.0 OH B:TYR88 4.2 37.4 1.0 CB B:ASP103 4.3 34.2 1.0 O B:HOH450 4.3 35.3 1.0 O B:PRO101 4.3 26.9 1.0 OD2 B:ASP100 4.4 43.8 1.0 OE2 B:GLU54 4.5 23.9 1.0 CA B:ASP103 4.7 29.1 1.0 CE2 B:TYR88 4.7 27.4 1.0 CB B:ASP100 4.7 31.8 1.0 CD B:GLU54 4.8 24.6 1.0 O B:HOH436 4.8 27.2 1.0 CZ B:TYR88 4.8 30.3 1.0 O B:GLY89 4.9 25.3 1.0 CG B:ASP100 5.0 37.8 1.0 CB B:PHE90 5.0 24.4 1.0

M.Grzechowiak, M.Ruszkowski, J.Sliwiak, K.Szpotkowski, M.Sikorski, M.Jaskolski. Crystal Structures of Plant Inorganic Pyrophosphatase, An Enzyme with A Moonlighting Autoproteolytic Activity. Biochem.J. V. 476 2297 2019.
ISSN: ESSN 1470-8728
PubMed: 31371393
DOI: 10.1042/BCJ20190427