Zinc in PDB 5wzr: Alpha-N-Acetylgalactosaminidase Nagbb From Bifidobacterium Bifidum - Gal-Nhac-Dnj Complex

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

The structure of Alpha-N-Acetylgalactosaminidase Nagbb From Bifidobacterium Bifidum - Gal-Nhac-Dnj Complex, PDB code: 5wzr 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)	103.95 / 2.79
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.628, 128.478, 176.885, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 31.3

The structure of Alpha-N-Acetylgalactosaminidase Nagbb From Bifidobacterium Bifidum - Gal-Nhac-Dnj 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 - Gal-Nhac-Dnj Complex (pdb code 5wzr). 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 - Gal-Nhac-Dnj Complex, PDB code: 5wzr:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Alpha-N-Acetylgalactosaminidase Nagbb From Bifidobacterium Bifidum - Gal-Nhac-Dnj 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 - Gal-Nhac-Dnj Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:50.9 occ:1.00 SG A:CYS407 2.0 46.5 1.0 O A:HIS450 2.0 43.6 1.0 ND1 A:HIS450 2.1 47.0 1.0 SG A:CYS445 2.1 44.7 1.0 CG A:HIS450 3.0 45.8 1.0 C A:HIS450 3.0 48.4 1.0 CB A:CYS407 3.0 48.4 1.0 CB A:CYS445 3.1 46.3 1.0 CE1 A:HIS450 3.1 48.8 1.0 CB A:HIS450 3.2 47.2 1.0 CA A:HIS450 3.6 47.2 1.0 N A:ARG451 4.0 48.7 1.0 CD2 A:HIS450 4.1 43.5 1.0 NE2 A:HIS450 4.2 44.5 1.0 CB A:HIS447 4.2 54.6 1.0 N A:HIS450 4.3 48.9 1.0 CA A:CYS407 4.4 48.7 1.0 CA A:CYS445 4.5 46.7 1.0 CA A:ARG451 4.5 46.2 1.0 O A:HIS447 4.5 51.3 1.0 CD1 A:ILE385 4.7 48.3 1.0 C A:ARG451 4.7 45.7 1.0 C A:CYS445 4.8 51.2 1.0 N A:MET452 4.8 47.5 1.0 CB A:MET452 4.8 49.3 1.0 CG A:GLU409 4.8 57.7 1.0 N A:HIS447 4.9 53.2 1.0 O A:ALA384 4.9 47.6 1.0 CB A:GLU409 5.0 54.6 1.0

Zinc binding site 2 out of 2 in the Alpha-N-Acetylgalactosaminidase Nagbb From Bifidobacterium Bifidum - Gal-Nhac-Dnj 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 - Gal-Nhac-Dnj Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:56.5 occ:1.00 SG B:CYS407 2.0 58.2 1.0 SG B:CYS445 2.1 53.5 1.0 O B:HIS450 2.2 58.7 1.0 ND1 B:HIS450 2.4 60.5 1.0 CB B:CYS445 3.0 58.0 1.0 CB B:CYS407 3.0 57.0 1.0 CG B:HIS450 3.2 61.4 1.0 C B:HIS450 3.2 61.1 1.0 CE1 B:HIS450 3.3 59.6 1.0 CB B:HIS450 3.4 62.7 1.0 CA B:HIS450 3.9 63.1 1.0 N B:ARG451 4.3 60.5 1.0 CA B:CYS407 4.3 57.9 1.0 CB B:HIS447 4.4 71.4 1.0 CD2 B:HIS450 4.4 60.1 1.0 NE2 B:HIS450 4.4 61.6 1.0 CA B:CYS445 4.4 57.9 1.0 O B:HIS447 4.5 68.5 1.0 N B:HIS450 4.6 62.5 1.0 CG B:GLU409 4.7 58.9 1.0 CA B:ARG451 4.7 61.8 1.0 CB B:MET452 4.7 54.9 1.0 C B:ARG451 4.7 57.7 1.0 N B:HIS447 4.8 63.0 1.0 C B:CYS445 4.8 59.2 1.0 CD1 B:ILE385 4.8 54.8 1.0 N B:MET452 4.9 52.7 1.0 CA B:ILE385 4.9 53.6 1.0 CB B:GLU409 5.0 60.9 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