Sodium in PDB 9eu2: GH29A Alpha-L-Fucosidase

All present enzymatic activity of GH29A Alpha-L-Fucosidase:
3.2.1.51;

The structure of GH29A Alpha-L-Fucosidase, PDB code: 9eu2 was solved by Y.Y.Yang, B.Zeuner, J.P.Morth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.02 / 1.84
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	147.912, 147.912, 197.086, 90, 90, 120
R / Rfree (%)	16.2 / 18.8

The structure of GH29A Alpha-L-Fucosidase also contains other interesting chemical elements:

Zinc

(Zn)

3 atoms

The binding sites of Sodium atom in the GH29A Alpha-L-Fucosidase (pdb code 9eu2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the GH29A Alpha-L-Fucosidase, PDB code: 9eu2:

Sodium binding site 1 out of 1 in the GH29A Alpha-L-Fucosidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of GH29A Alpha-L-Fucosidase within 5.0Å range: probe atom residue distance (Å) B Occ C:Na505 b:43.6 occ:1.00 OD2 C:ASP387 2.3 37.6 1.0 HB2 C:ASP387 2.6 44.6 1.0 O B:HOH943 2.7 41.4 1.0 O C:HOH634 2.8 30.9 1.0 O B:HOH772 2.9 30.6 1.0 HD13 C:LEU385 3.0 40.4 1.0 CG C:ASP387 3.1 44.2 1.0 CB C:ASP387 3.1 37.2 1.0 HB3 C:ASP387 3.3 44.6 1.0 HD2 B:PHE391 3.4 36.7 1.0 HD11 C:LEU385 3.6 40.4 1.0 HE B:ARG366 3.6 41.2 1.0 CD1 C:LEU385 3.7 33.6 1.0 O B:HOH923 3.9 48.7 1.0 HE1 B:TRP368 3.9 32.1 1.0 HD3 B:PRO393 4.1 33.0 1.0 HD12 C:LEU385 4.1 40.4 1.0 HD2 B:ARG366 4.3 43.4 1.0 H C:ASP387 4.3 41.0 1.0 CD2 B:PHE391 4.3 30.6 1.0 OD1 C:ASP387 4.3 42.8 1.0 HG3 B:PRO393 4.3 36.9 1.0 NE B:ARG366 4.4 34.3 1.0 HG3 B:ARG366 4.5 38.6 1.0 HE2 B:PHE391 4.5 36.1 1.0 CA C:ASP387 4.5 36.7 1.0 O C:HOH749 4.6 46.1 1.0 HB3 B:PHE391 4.6 30.9 1.0 O B:PHE391 4.6 25.5 1.0 O C:ALA389 4.7 27.8 1.0 NE1 B:TRP368 4.7 26.8 1.0 CD B:ARG366 4.7 36.1 1.0 N C:ASP387 4.8 34.2 1.0 HD1 B:TRP368 4.8 32.7 1.0 CE2 B:PHE391 4.9 30.1 1.0 CG C:LEU385 5.0 28.8 1.0 HG C:LEU385 5.0 34.5 1.0 CD B:PRO393 5.0 27.5 1.0 HB3 B:ARG366 5.0 33.3 1.0

Y.Yang, J.Holck, A.T.Thorhallsson, C.J.Hunt, H.Yang, J.P.Morth, A.S.Meyer, B.Zeuner. Structural Elucidation and Characterization of GH29A Alpha-L-Fucosidases and the Effect of pH on Their Transglycosylation. Febs J. V. 292 653 2025.
ISSN: ISSN 1742-464X
PubMed: 39658312
DOI: 10.1111/FEBS.17347