Zinc in PDB 8k7y: Crystal Structure of GH146 Beta-L-Arabinofuranosidase BLL3HYPBA1 (Amino Acids 380-1051), Ligand-Free Form

All present enzymatic activity of Crystal Structure of GH146 Beta-L-Arabinofuranosidase BLL3HYPBA1 (Amino Acids 380-1051), Ligand-Free Form:
3.2.1.185;

The structure of Crystal Structure of GH146 Beta-L-Arabinofuranosidase BLL3HYPBA1 (Amino Acids 380-1051), Ligand-Free Form, PDB code: 8k7y was solved by S.Maruyama, L.Pan, M.Miyake, K.Fujita, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.57 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	75.231, 83.51, 102.034, 90, 90.66, 90
R / Rfree (%)	22 / 25.9

The binding sites of Zinc atom in the Crystal Structure of GH146 Beta-L-Arabinofuranosidase BLL3HYPBA1 (Amino Acids 380-1051), Ligand-Free Form (pdb code 8k7y). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of GH146 Beta-L-Arabinofuranosidase BLL3HYPBA1 (Amino Acids 380-1051), Ligand-Free Form, PDB code: 8k7y:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of GH146 Beta-L-Arabinofuranosidase BLL3HYPBA1 (Amino Acids 380-1051), Ligand-Free Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of GH146 Beta-L-Arabinofuranosidase BLL3HYPBA1 (Amino Acids 380-1051), Ligand-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:16.1 occ:1.00 OE2 A:GLU723 2.0 15.8 1.0 SG A:CYS805 2.3 15.0 1.0 SG A:CYS725 2.4 17.0 1.0 SG A:CYS804 2.4 14.2 1.0 CD A:GLU723 3.0 16.2 1.0 N A:CYS805 3.1 14.0 1.0 CB A:CYS725 3.3 16.2 1.0 CB A:CYS805 3.3 15.4 1.0 CG A:GLU723 3.4 16.2 1.0 CA A:CYS805 3.4 15.0 1.0 CB A:CYS804 3.5 13.0 1.0 C A:CYS804 3.7 14.6 1.0 N A:CYS725 4.0 14.8 1.0 O A:HOH2303 4.1 27.9 1.0 CZ A:TYR771 4.1 17.1 1.0 CA A:CYS804 4.1 13.9 1.0 CA A:CYS725 4.2 15.6 1.0 OE1 A:GLU723 4.2 17.3 1.0 CE2 A:TYR771 4.2 17.3 1.0 OH A:TYR771 4.3 17.2 1.0 CE1 A:TYR771 4.5 17.3 1.0 O A:CYS804 4.5 13.0 1.0 CD2 A:TYR771 4.6 16.3 1.0 N A:CYS804 4.7 14.6 1.0 CB A:GLU723 4.9 15.4 1.0 C A:CYS805 4.9 15.0 1.0 CD1 A:TYR771 4.9 16.1 1.0 ND2 A:ASN630 4.9 18.0 1.0 N A:THR724 5.0 13.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of GH146 Beta-L-Arabinofuranosidase BLL3HYPBA1 (Amino Acids 380-1051), Ligand-Free Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of GH146 Beta-L-Arabinofuranosidase BLL3HYPBA1 (Amino Acids 380-1051), Ligand-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn2001 b:14.8 occ:1.00 OE1 E:GLU723 2.1 14.4 1.0 SG E:CYS805 2.2 14.8 1.0 SG E:CYS804 2.3 15.1 1.0 SG E:CYS725 2.3 12.4 1.0 N E:CYS805 3.1 13.2 1.0 CD E:GLU723 3.1 16.1 1.0 CB E:CYS804 3.2 12.5 1.0 CB E:CYS725 3.2 13.2 1.0 CB E:CYS805 3.4 13.4 1.0 CG E:GLU723 3.4 16.6 1.0 CA E:CYS805 3.5 13.8 1.0 C E:CYS804 3.6 12.7 1.0 CA E:CYS804 3.9 13.4 1.0 N E:CYS725 4.0 13.7 1.0 O E:HOH2314 4.0 22.8 1.0 CZ E:TYR771 4.1 16.9 1.0 CA E:CYS725 4.1 13.3 1.0 CE2 E:TYR771 4.2 17.3 1.0 OE2 E:GLU723 4.2 15.8 1.0 O E:CYS804 4.3 12.1 1.0 OH E:TYR771 4.3 17.8 1.0 CE1 E:TYR771 4.5 16.8 1.0 N E:CYS804 4.6 13.8 1.0 CD2 E:TYR771 4.6 17.1 1.0 O E:HOH2258 4.8 12.9 1.0 ND2 E:ASN630 4.9 14.1 1.0 CB E:GLU723 4.9 16.8 1.0 C E:CYS805 5.0 14.1 1.0 N E:THR724 5.0 14.6 1.0 CD1 E:TYR771 5.0 16.6 1.0

K.Fujita, H.Tsunomachi, P.Lixia, S.Maruyama, M.Miyake, A.Dakeshita, K.Kitahara, K.Tanaka, Y.Ito, A.Ishiwata, S.Fushinobu. Bifidobacterial GH146 Beta-L-Arabinofuranosidase For the Removal of Beta 1,3-L-Arabinofuranosides on Plant Glycans. Appl.Microbiol.Biotechnol. V. 108 199 2024.
ISSN: ESSN 1432-0614
PubMed: 38324037
DOI: 10.1007/S00253-024-13014-8