Zinc in PDB 5wzn: Alpha-N-Acetylgalactosaminidase Nagbb From Bifidobacterium Bifidum - Galnac Complex

All present enzymatic activity of Alpha-N-Acetylgalactosaminidase Nagbb From Bifidobacterium Bifidum - Galnac Complex:
3.2.1.49;

The structure of Alpha-N-Acetylgalactosaminidase Nagbb From Bifidobacterium Bifidum - Galnac Complex, PDB code: 5wzn was solved by M.Sato, T.Arakawa, H.Ashida, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.29 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.636, 127.620, 176.817, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 24.6

The structure of Alpha-N-Acetylgalactosaminidase Nagbb From Bifidobacterium Bifidum - Galnac Complex also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Alpha-N-Acetylgalactosaminidase Nagbb From Bifidobacterium Bifidum - Galnac Complex (pdb code 5wzn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Alpha-N-Acetylgalactosaminidase Nagbb From Bifidobacterium Bifidum - Galnac Complex, PDB code: 5wzn:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Alpha-N-Acetylgalactosaminidase Nagbb From Bifidobacterium Bifidum - Galnac Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Alpha-N-Acetylgalactosaminidase Nagbb From Bifidobacterium Bifidum - Galnac Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:27.2 occ:1.00 SG A:CYS407 1.8 41.2 1.0 O A:HIS450 2.0 22.9 1.0 ND1 A:HIS450 2.0 22.1 1.0 SG A:CYS445 2.0 28.0 1.0 CG A:HIS450 3.0 23.8 1.0 CE1 A:HIS450 3.0 26.6 1.0 CB A:CYS445 3.0 26.6 1.0 C A:HIS450 3.1 26.3 1.0 CB A:CYS407 3.1 26.1 1.0 CB A:HIS450 3.3 26.2 1.0 CA A:HIS450 3.7 26.7 1.0 CB A:HIS447 4.1 29.4 1.0 NE2 A:HIS450 4.1 26.7 1.0 CD2 A:HIS450 4.1 23.7 1.0 N A:ARG451 4.2 26.9 1.0 N A:HIS450 4.4 26.7 1.0 CA A:CYS445 4.4 24.1 1.0 CA A:CYS407 4.5 25.9 1.0 CG A:GLU409 4.5 24.6 1.0 CA A:ARG451 4.5 29.9 1.0 O A:HIS447 4.7 28.5 1.0 CD1 A:ILE385 4.7 27.1 1.0 O A:ALA384 4.7 26.0 1.0 C A:ARG451 4.7 25.6 1.0 CB A:MET452 4.7 24.8 1.0 C A:CYS445 4.7 23.2 1.0 O A:CYS445 4.7 23.2 1.0 N A:HIS447 4.8 28.1 1.0 N A:MET452 4.8 24.6 1.0 CB A:GLU409 4.9 27.5 1.0 CA A:HIS447 4.9 29.4 1.0

Zinc binding site 2 out of 2 in the Alpha-N-Acetylgalactosaminidase Nagbb From Bifidobacterium Bifidum - Galnac Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Alpha-N-Acetylgalactosaminidase Nagbb From Bifidobacterium Bifidum - Galnac Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:33.0 occ:1.00 SG B:CYS407 1.7 35.5 1.0 SG B:CYS445 2.0 37.0 1.0 O B:HIS450 2.0 29.8 1.0 ND1 B:HIS450 2.1 34.5 1.0 CB B:CYS407 3.0 33.0 1.0 CB B:CYS445 3.0 34.9 1.0 C B:HIS450 3.0 32.5 1.0 CE1 B:HIS450 3.0 33.8 1.0 CG B:HIS450 3.0 34.3 1.0 CB B:HIS450 3.4 34.8 1.0 CA B:HIS450 3.7 31.9 1.0 CB B:HIS447 4.1 36.8 1.0 N B:ARG451 4.1 31.5 1.0 NE2 B:HIS450 4.1 33.6 1.0 CD2 B:HIS450 4.2 32.7 1.0 CA B:CYS407 4.4 32.7 1.0 N B:HIS450 4.4 30.1 1.0 CA B:CYS445 4.5 31.7 1.0 CA B:ARG451 4.5 32.5 1.0 O B:HIS447 4.6 36.0 1.0 CG B:GLU409 4.7 28.6 1.0 C B:ARG451 4.7 32.1 1.0 N B:HIS447 4.7 33.8 1.0 C B:CYS445 4.8 33.0 1.0 CB B:MET452 4.8 29.7 1.0 O B:CYS445 4.8 26.9 1.0 O B:ALA384 4.9 32.0 1.0 CD1 B:ILE385 4.9 36.3 1.0 CA B:HIS447 4.9 37.1 1.0 N B:MET452 4.9 31.8 1.0 CA B:ILE385 5.0 30.9 1.0

M.Sato, D.Liebschner, Y.Yamada, N.Matsugaki, T.Arakawa, S.S.Wills, M.Hattie, K.A.Stubbs, T.Ito, T.Senda, H.Ashida, S.Fushinobu. The First Crystal Structure of A Family 129 Glycoside Hydrolase From A Probiotic Bacterium Reveals Critical Residues and Metal Cofactors J. Biol. Chem. V. 292 12126 2017.
ISSN: ESSN 1083-351X
PubMed: 28546425
DOI: 10.1074/JBC.M117.777391