Sodium in PDB 7e9u: Trehalase of Arabidopsis Thaliana

All present enzymatic activity of Trehalase of Arabidopsis Thaliana:
3.2.1.28;

The structure of Trehalase of Arabidopsis Thaliana, PDB code: 7e9u was solved by Y.Taguchi, W.Saburi, J.Yu, R.Imai, M.Yao, H.Mori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.22 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.981, 129.813, 155.802, 90, 90, 90
R / Rfree (%)	20.9 / 25.8

The binding sites of Sodium atom in the Trehalase of Arabidopsis Thaliana (pdb code 7e9u). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Trehalase of Arabidopsis Thaliana, PDB code: 7e9u:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Trehalase of Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Trehalase of Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ A:Na703 b:39.5 occ:0.97 OD1 A:ASP380 2.3 37.6 1.0 O A:HOH931 2.5 38.6 1.0 O A:GLY378 2.5 37.7 1.0 O A:HOH868 2.5 32.9 1.0 O A:HOH807 2.5 34.1 1.0 O3 A:GOL701 2.7 40.1 1.0 C A:GLY378 3.3 33.9 1.0 O A:HOH813 3.4 39.4 1.0 CG A:ASP380 3.5 40.7 1.0 C3 A:GOL701 3.7 41.0 1.0 CA A:GLY378 3.7 30.5 1.0 O1 A:GOL701 3.9 38.1 1.0 OD2 A:ASP380 4.0 37.6 1.0 N A:ASP380 4.2 35.1 1.0 NE1 A:TRP528 4.2 36.9 1.0 N A:CYS379 4.3 30.8 1.0 NE2 A:GLN279 4.5 36.3 1.0 O2 A:PO4702 4.5 49.0 0.7 CB A:ASP380 4.7 37.6 1.0 C2 A:GOL701 4.7 41.0 1.0 CA A:CYS379 4.7 34.3 1.0 C1 A:GOL701 4.8 38.5 1.0 NE1 A:TRP231 4.8 32.5 1.0 N A:GLY378 4.9 34.8 1.0 O A:ALA375 4.9 32.6 1.0 CE2 A:TRP528 4.9 32.9 1.0 CZ2 A:TRP528 5.0 35.8 1.0

Sodium binding site 2 out of 2 in the Trehalase of Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Trehalase of Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ B:Na703 b:45.6 occ:1.00 O B:HOH847 2.2 38.1 1.0 OD1 B:ASP380 2.3 43.9 1.0 O B:HOH875 2.5 40.2 1.0 O B:GLY378 2.6 36.8 1.0 O B:HOH844 2.7 41.3 1.0 O1 B:GOL701 2.9 44.8 1.0 C B:GLY378 3.3 37.3 1.0 CG B:ASP380 3.4 46.6 1.0 C1 B:GOL701 3.4 49.1 1.0 CA B:GLY378 3.7 35.9 1.0 O B:HOH822 3.7 47.9 1.0 OD2 B:ASP380 3.9 46.3 1.0 O3 B:GOL701 4.2 44.2 1.0 O3 B:PO4702 4.2 52.4 0.6 N B:CYS379 4.3 38.1 1.0 NE2 B:GLN279 4.3 38.7 1.0 N B:ASP380 4.3 44.7 1.0 NE1 B:TRP528 4.3 39.6 1.0 CB B:ASP380 4.6 42.8 1.0 NE1 B:TRP231 4.7 35.0 1.0 O B:ALA375 4.7 41.3 1.0 C2 B:GOL701 4.7 46.5 1.0 N B:GLY378 4.8 40.4 1.0 CA B:CYS379 4.8 40.3 1.0 C3 B:GOL701 4.9 45.7 1.0 CZ2 B:TRP528 4.9 40.8 1.0 CE2 B:TRP528 5.0 38.4 1.0

Y.Taguchi, W.Saburi, J.Yu, R.Imai, M.Yao, H.Mori. pH-Dependent Alteration of Substrate Specificity of Plant Trehalase and Its Molecular Mechanism To Be Published.