Calcium 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:

Zinc

(Zn)

2 atoms

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Alpha-N-Acetylgalactosaminidase Nagbb From Bifidobacterium Bifidum - Ligand Free, PDB code: 5wzp:
Jump to Calcium binding site number: 1; 2;

Calcium 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 Calcium with other atoms in the Ca 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:Ca702 b:36.3 occ:1.00 OD1 A:ASP322 1.9 35.5 1.0 O A:HOH811 2.1 46.2 1.0 ND1 A:HIS366 2.2 53.6 1.0 O A:HOH801 2.3 33.9 1.0 NE2 A:HIS320 2.3 49.3 1.0 NE2 A:HIS271 2.4 53.4 1.0 CG A:ASP322 2.7 42.5 1.0 OD2 A:ASP322 2.8 35.9 1.0 CE1 A:HIS366 2.9 45.6 1.0 CE1 A:HIS320 3.0 51.1 1.0 CD2 A:HIS320 3.2 52.8 1.0 CE1 A:HIS271 3.3 51.2 1.0 CG A:HIS366 3.3 55.0 1.0 CD2 A:HIS271 3.3 52.2 1.0 CB A:HIS366 3.8 52.8 1.0 ND1 A:HIS320 4.1 53.7 1.0 NE2 A:HIS366 4.1 46.9 1.0 CB A:ASP322 4.2 41.8 1.0 CG A:HIS320 4.2 53.8 1.0 CD2 A:HIS366 4.3 51.8 1.0 O A:HOH836 4.4 41.2 1.0 ND1 A:HIS271 4.4 55.5 1.0 CG A:HIS271 4.5 55.7 1.0 CE1 A:TYR329 4.5 42.7 1.0 OH A:TYR329 4.6 39.6 1.0 CE1 A:TYR433 4.6 44.9 1.0 CA A:ASP322 4.6 46.1 1.0 CD2 A:HIS492 4.7 53.4 1.0 NE2 A:HIS492 4.7 53.1 1.0 CD1 A:TYR433 4.7 49.9 1.0 N A:ASP322 4.9 52.1 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca702 b:55.8 occ:1.00 NE2 B:HIS271 2.2 97.5 1.0 NE2 B:HIS320 2.3 72.6 1.0 ND1 B:HIS366 2.4 63.2 1.0 OD1 B:ASP322 2.4 67.0 1.0 O B:HOH809 2.5 62.1 1.0 O B:HOH833 2.5 47.3 1.0 CE1 B:HIS320 3.0 69.8 1.0 CE1 B:HIS271 3.0 96.1 1.0 CE1 B:HIS366 3.1 61.8 1.0 CG B:ASP322 3.2 64.5 1.0 CD2 B:HIS271 3.2 0.3 1.0 OD2 B:ASP322 3.3 65.7 1.0 CD2 B:HIS320 3.3 74.5 1.0 CG B:HIS366 3.4 61.8 1.0 CB B:HIS366 3.8 61.1 1.0 ND1 B:HIS320 4.1 71.4 1.0 ND1 B:HIS271 4.2 92.0 1.0 NE2 B:HIS366 4.3 62.2 1.0 CG B:HIS320 4.3 68.4 1.0 CG B:HIS271 4.3 88.5 1.0 CD2 B:HIS366 4.4 61.6 1.0 CE1 B:TYR433 4.5 46.5 1.0 CE1 B:TYR329 4.6 56.0 1.0 CB B:ASP322 4.6 57.4 1.0 OH B:TYR329 4.6 56.1 1.0 CD2 B:HIS492 4.6 85.2 1.0 NE2 B:HIS492 4.7 85.0 1.0 CD1 B:TYR433 4.7 51.5 1.0 CZ B:TYR433 4.8 49.0 1.0 O B:HOH834 4.9 48.6 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