Magnesium in PDB 4fyp: Crystal Structure of Plant Vegetative Storage Protein

The structure of Crystal Structure of Plant Vegetative Storage Protein, PDB code: 4fyp was solved by Y.Chen, J.Wei, M.Wang, W.Gong, M.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.46 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	122.328, 49.182, 84.905, 90.00, 116.09, 90.00
R / Rfree (%)	18.1 / 22.4

The binding sites of Magnesium atom in the Crystal Structure of Plant Vegetative Storage Protein (pdb code 4fyp). 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 Plant Vegetative Storage Protein, PDB code: 4fyp:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Plant Vegetative Storage Protein


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 Plant Vegetative Storage Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:26.4 occ:1.00 OD2 A:ASP124 2.0 27.4 1.0 O A:HOH557 2.0 30.1 1.0 O A:HOH556 2.0 22.6 1.0 O A:ASP126 2.1 24.2 1.0 O A:HOH437 2.1 22.3 1.0 OD1 A:ASP245 2.2 24.0 1.0 CG A:ASP124 3.0 24.8 1.0 CG A:ASP245 3.2 23.2 1.0 C A:ASP126 3.3 26.9 1.0 OD1 A:ASP124 3.4 26.6 1.0 OD2 A:ASP245 3.5 23.3 1.0 OD2 A:ASP249 4.0 29.7 1.0 CA A:ASP126 4.1 25.1 1.0 O A:HOH436 4.1 46.0 1.0 N A:ASP126 4.1 24.8 1.0 OG1 A:THR128 4.2 24.2 1.0 CB A:ASP126 4.3 27.8 1.0 OH A:TYR266 4.3 26.4 1.0 CB A:ASP124 4.3 24.3 1.0 N A:ASP127 4.3 24.3 1.0 O A:HOH569 4.4 44.2 1.0 CB A:ASP127 4.5 27.1 1.0 CB A:ASP245 4.5 22.2 1.0 CG A:GLN246 4.6 19.3 1.0 N A:ASP245 4.6 21.6 1.0 CA A:ASP127 4.7 24.1 1.0 C A:ASP127 4.7 24.4 1.0 N A:THR128 4.7 23.7 1.0 C A:LEU125 4.8 23.5 1.0 O A:HOH426 4.8 34.7 1.0 CG A:ASP249 4.8 29.6 1.0 OD1 A:ASP249 4.9 32.1 1.0 N A:LEU125 5.0 24.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Plant Vegetative Storage Protein


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 Plant Vegetative Storage Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:26.8 occ:1.00 OD2 B:ASP124 2.1 23.7 1.0 O B:HOH500 2.1 24.9 1.0 OD1 B:ASP245 2.1 24.8 1.0 O B:ASP126 2.1 24.2 1.0 O B:HOH558 2.2 23.6 1.0 O B:HOH559 2.2 21.8 1.0 CG B:ASP124 3.0 24.5 1.0 CG B:ASP245 3.1 24.1 1.0 OD1 B:ASP124 3.2 26.3 1.0 C B:ASP126 3.3 22.3 1.0 OD2 B:ASP245 3.4 24.1 1.0 CA B:ASP126 4.0 24.7 1.0 N B:ASP126 4.1 24.6 1.0 OD2 B:ASP249 4.1 24.0 1.0 OG1 B:THR128 4.1 21.3 1.0 CB B:ASP126 4.3 24.7 1.0 O B:HOH423 4.3 42.0 1.0 CB B:ASP124 4.3 22.8 1.0 N B:ASP127 4.3 22.2 1.0 CB B:ASP127 4.4 21.8 1.0 OH B:TYR266 4.4 28.5 1.0 CB B:ASP245 4.5 23.3 1.0 C B:ASP127 4.6 23.9 1.0 CA B:ASP127 4.6 22.7 1.0 O B:HOH424 4.6 41.8 1.0 N B:ASP245 4.6 22.8 1.0 N B:THR128 4.7 21.1 1.0 CG B:GLN246 4.7 24.2 1.0 O B:HOH560 4.7 41.4 1.0 C B:LEU125 4.8 24.9 1.0 OD1 B:ASP249 4.9 26.0 1.0 CG B:ASP249 5.0 24.4 1.0 N B:LEU125 5.0 25.1 1.0

Y.Chen, J.Wei, M.Wang, Z.Shi, W.Gong, M.Zhang. The Crystal Structure of Arabidopsis VSP1 Reveals the Plant Class C-Like Phosphatase Structure of the Dddd Superfamily of Phosphohydrolases Plos One V. 7 49421 2012.
ISSN: ESSN 1932-6203
PubMed: 23166664
DOI: 10.1371/JOURNAL.PONE.0049421