Zinc in PDB 5wzp: Alpha-N-Acetylgalactosaminidase Nagbb From Bifidobacterium Bifidum - Ligand Free

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

The structure of Alpha-N-Acetylgalactosaminidase Nagbb From Bifidobacterium Bifidum - Ligand Free, PDB code: 5wzp 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)	103.55 / 2.64
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.637, 127.764, 176.756, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 31.1

The structure of Alpha-N-Acetylgalactosaminidase Nagbb From Bifidobacterium Bifidum - Ligand Free 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 - Ligand Free (pdb code 5wzp). 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 - Ligand Free, PDB code: 5wzp:
Jump to Zinc binding site number: 1; 2;

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


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 - Ligand Free within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:51.4 occ:1.00 SG A:CYS407 1.9 62.3 1.0 ND1 A:HIS450 2.1 40.9 1.0 SG A:CYS445 2.1 75.8 1.0 O A:HIS450 2.2 41.3 1.0 CB A:CYS407 2.7 48.6 1.0 CE1 A:HIS450 2.9 44.3 1.0 CB A:CYS445 3.0 52.0 1.0 CG A:HIS450 3.1 44.5 1.0 C A:HIS450 3.3 43.6 1.0 CB A:HIS450 3.5 43.2 1.0 CA A:HIS450 4.0 43.5 1.0 NE2 A:HIS450 4.1 46.1 1.0 CB A:HIS447 4.1 46.4 1.0 CA A:CYS407 4.1 50.8 1.0 CD2 A:HIS450 4.1 47.0 1.0 CA A:CYS445 4.3 43.5 1.0 N A:ARG451 4.3 49.7 1.0 O A:ALA384 4.6 43.7 1.0 N A:HIS450 4.6 43.5 1.0 CB A:GLU409 4.6 39.2 1.0 C A:CYS445 4.7 44.6 1.0 N A:HIS447 4.7 47.8 1.0 CA A:ARG451 4.7 47.5 1.0 O A:HIS447 4.7 46.5 1.0 CG A:GLU409 4.8 40.2 1.0 CD1 A:ILE385 4.8 39.4 1.0 CB A:MET452 4.9 41.9 1.0 CA A:HIS447 4.9 49.2 1.0 O A:CYS445 4.9 48.9 1.0 N A:MET452 4.9 48.8 1.0 C A:ARG451 5.0 49.9 1.0 C A:CYS407 5.0 46.6 1.0 CA A:ILE385 5.0 40.6 1.0

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


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 - Ligand Free within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:57.4 occ:1.00 O B:HIS450 2.0 59.1 1.0 ND1 B:HIS450 2.2 51.0 1.0 SG B:CYS445 2.4 48.9 1.0 CB B:CYS407 3.0 52.9 1.0 SG B:CYS407 3.1 50.7 1.0 CB B:CYS445 3.1 57.6 1.0 CE1 B:HIS450 3.1 54.4 1.0 C B:HIS450 3.2 53.8 1.0 CG B:HIS450 3.2 53.8 1.0 CB B:HIS450 3.5 52.0 1.0 CA B:HIS450 3.9 51.8 1.0 CB B:HIS447 4.1 52.3 1.0 NE2 B:HIS450 4.2 52.2 1.0 N B:ARG451 4.3 59.4 1.0 CA B:CYS407 4.3 54.7 1.0 CD2 B:HIS450 4.3 54.1 1.0 CA B:CYS445 4.5 62.0 1.0 CA B:ARG451 4.5 53.4 1.0 O B:HIS447 4.6 58.8 1.0 N B:HIS447 4.6 57.9 1.0 O B:ALA384 4.6 57.2 1.0 N B:HIS450 4.6 47.6 1.0 CG B:GLU409 4.7 43.7 1.0 C B:ARG451 4.7 50.2 1.0 C B:CYS445 4.7 64.1 1.0 CD1 B:ILE385 4.8 38.2 1.0 CB B:MET452 4.8 44.8 1.0 CA B:HIS447 4.9 56.7 1.0 N B:MET452 5.0 48.6 1.0 CB B:GLU409 5.0 42.9 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