Zinc 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:

Sodium

(Na)

1 atom

The binding sites of Zinc atom in the GH29A Alpha-L-Fucosidase (pdb code 9eu2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the GH29A Alpha-L-Fucosidase, PDB code: 9eu2:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the GH29A Alpha-L-Fucosidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of GH29A Alpha-L-Fucosidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:28.6 occ:0.50 OD2 A:ASP140 2.0 31.9 1.0 NE2 A:HIS136 2.3 34.1 1.0 CG A:ASP140 2.8 32.7 1.0 OD1 A:ASP140 3.0 30.3 1.0 CD2 A:HIS136 3.0 33.2 1.0 HD2 A:HIS136 3.0 39.9 1.0 CE1 A:HIS136 3.4 38.5 1.0 HE1 A:HIS136 3.7 46.2 1.0 O A:HOH797 3.9 32.9 1.0 CG A:HIS136 4.2 31.7 1.0 CB A:ASP140 4.2 28.7 1.0 ND1 A:HIS136 4.4 36.8 1.0 HB2 A:ASP140 4.5 34.4 1.0 HB3 A:ASP140 4.5 34.4 1.0 HH12 A:ARG143 4.9 57.2 1.0 O A:HOH937 4.9 38.7 1.0

Zinc binding site 2 out of 3 in the GH29A Alpha-L-Fucosidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of GH29A Alpha-L-Fucosidase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:173.8 occ:1.00 HE2 C:HIS136 1.9 64.5 1.0 NE2 C:HIS136 2.3 53.8 1.0 HE1 C:HIS136 2.4 58.4 1.0 CE1 C:HIS136 2.5 48.6 1.0 OD2 C:ASP140 2.7 43.8 1.0 OD1 C:ASP140 2.8 39.9 1.0 CG C:ASP140 3.1 39.5 1.0 CD2 C:HIS136 3.5 49.7 1.0 O C:HOH969 3.7 50.0 1.0 ND1 C:HIS136 3.7 48.7 1.0 O C:HOH809 3.9 48.3 1.0 HD2 C:HIS136 4.0 59.6 1.0 HH12 C:ARG143 4.1 58.5 1.0 CG C:HIS136 4.2 37.9 1.0 CB C:ASP140 4.7 32.2 1.0 O C:HOH616 4.8 39.5 1.0 NH1 C:ARG143 4.9 48.7 1.0 O C:HOH1033 5.0 54.8 1.0

Zinc binding site 3 out of 3 in the GH29A Alpha-L-Fucosidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of GH29A Alpha-L-Fucosidase within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:249.8 occ:1.00 NE2 D:HIS136 2.3 60.5 1.0 HE1 D:HIS136 2.4 66.8 1.0 OD1 D:ASP140 2.5 51.2 1.0 CE1 D:HIS136 2.5 55.6 1.0 OD2 D:ASP140 3.0 48.6 1.0 CG D:ASP140 3.1 47.8 1.0 CD2 D:HIS136 3.5 52.6 1.0 ND1 D:HIS136 3.7 53.2 1.0 HD2 D:HIS136 4.0 63.1 1.0 CG D:HIS136 4.2 41.9 1.0 HD1 D:HIS136 4.3 63.8 1.0 O D:HOH610 4.4 46.3 1.0 O D:HOH896 4.5 50.4 1.0 O D:HOH843 4.6 52.8 1.0 HH12 D:ARG143 4.6 62.6 1.0 CB D:ASP140 4.6 40.1 1.0 HB2 D:ASP140 4.9 48.2 1.0 HB3 D:ASP140 5.0 48.2 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