Zinc in PDB 5wzq: Alpha-N-Acetylgalactosaminidase Nagbb From Bifidobacterium Bifidum - Quadruple Mutant

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

The structure of Alpha-N-Acetylgalactosaminidase Nagbb From Bifidobacterium Bifidum - Quadruple Mutant, PDB code: 5wzq 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)	103.51 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.885, 127.837, 176.364, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 22.5

The binding sites of Zinc atom in the Alpha-N-Acetylgalactosaminidase Nagbb From Bifidobacterium Bifidum - Quadruple Mutant (pdb code 5wzq). 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 - Quadruple Mutant, PDB code: 5wzq:
Jump to Zinc binding site number: 1; 2;

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


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 - Quadruple Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:11.7 occ:1.00 ND1 A:HIS450 2.0 12.2 1.0 O A:HIS450 2.0 13.5 1.0 SG A:CYS445 2.2 11.9 1.0 SG A:CYS407 2.3 10.4 1.0 CG A:HIS450 2.9 11.6 1.0 CE1 A:HIS450 3.0 12.8 1.0 CB A:CYS445 3.0 11.1 1.0 CB A:CYS407 3.1 9.2 1.0 C A:HIS450 3.1 14.4 1.0 CB A:HIS450 3.3 11.9 1.0 CA A:HIS450 3.7 12.7 1.0 CB A:HIS447 4.1 14.7 1.0 CD2 A:HIS450 4.1 12.4 1.0 NE2 A:HIS450 4.1 12.5 1.0 N A:ARG451 4.2 14.8 1.0 N A:HIS450 4.4 12.3 1.0 CA A:CYS407 4.4 9.3 1.0 CA A:CYS445 4.5 12.1 1.0 O A:HIS447 4.5 14.6 1.0 CA A:ARG451 4.5 14.8 1.0 CB A:MET452 4.6 11.5 1.0 CG A:GLU409 4.6 12.7 1.0 N A:HIS447 4.7 13.6 1.0 C A:ARG451 4.7 13.5 1.0 N A:MET452 4.8 12.0 1.0 C A:CYS445 4.8 12.3 1.0 CD1 A:ILE385 4.8 13.9 1.0 CA A:HIS447 4.9 14.8 1.0 O A:CYS445 4.9 11.7 1.0 O A:ALA384 4.9 12.2 1.0 CB A:GLU409 5.0 12.7 1.0

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


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 - Quadruple Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:13.8 occ:1.00 ND1 B:HIS450 2.0 12.6 1.0 O B:HIS450 2.1 14.6 1.0 SG B:CYS445 2.2 16.1 1.0 SG B:CYS407 2.3 12.4 1.0 CG B:HIS450 3.0 13.2 1.0 CE1 B:HIS450 3.0 14.5 1.0 CB B:CYS445 3.1 13.4 1.0 CB B:CYS407 3.1 11.1 1.0 C B:HIS450 3.1 16.8 1.0 CB B:HIS450 3.3 13.5 1.0 CA B:HIS450 3.7 15.1 1.0 CB B:HIS447 4.1 16.7 1.0 NE2 B:HIS450 4.1 13.7 1.0 CD2 B:HIS450 4.1 13.8 1.0 N B:ARG451 4.2 16.5 1.0 N B:HIS450 4.4 15.5 1.0 CA B:CYS407 4.4 11.3 1.0 CA B:CYS445 4.5 13.3 1.0 O B:HIS447 4.6 19.6 1.0 CB B:MET452 4.6 14.8 1.0 CA B:ARG451 4.6 17.7 1.0 CG B:GLU409 4.6 12.7 1.0 CD1 B:ILE385 4.7 14.2 1.0 C B:ARG451 4.7 15.6 1.0 N B:HIS447 4.8 15.7 1.0 CB B:GLU409 4.8 13.6 1.0 O B:ALA384 4.8 13.4 1.0 N B:MET452 4.8 13.2 1.0 C B:CYS445 4.8 13.0 1.0 CA B:HIS447 5.0 18.0 1.0 O B:CYS445 5.0 12.4 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