Calcium 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:

Zinc

(Zn)

2 atoms

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

Calcium 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 Calcium with other atoms in the Ca 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:Ca703 b:21.7 occ:1.00 OD1 A:ASP322 2.0 25.6 1.0 O A:HOH930 2.0 24.2 1.0 NE2 A:HIS320 2.1 30.3 1.0 ND1 A:HIS366 2.2 27.4 1.0 NE2 A:HIS271 2.3 38.8 1.0 O A:HOH831 2.4 28.8 1.0 CG A:ASP322 2.9 30.4 1.0 CE1 A:HIS366 3.0 24.5 1.0 CE1 A:HIS320 3.0 29.7 1.0 OD2 A:ASP322 3.1 35.3 1.0 CE1 A:HIS271 3.2 34.1 1.0 CD2 A:HIS320 3.2 28.5 1.0 CD2 A:HIS271 3.3 31.6 1.0 CG A:HIS366 3.3 27.3 1.0 CB A:HIS366 3.7 26.5 1.0 O7 A:A2G702 4.1 42.5 1.0 ND1 A:HIS320 4.1 29.4 1.0 NE2 A:HIS366 4.2 23.8 1.0 CG A:HIS320 4.3 28.4 1.0 ND1 A:HIS271 4.3 34.5 1.0 CD2 A:HIS366 4.3 25.4 1.0 CB A:ASP322 4.4 26.5 1.0 CG A:HIS271 4.4 34.4 1.0 OH A:TYR329 4.5 25.6 1.0 CE2 A:TYR433 4.5 26.5 1.0 CE1 A:TYR329 4.6 26.1 1.0 O A:HOH943 4.6 42.7 1.0 CD2 A:TYR433 4.7 24.4 1.0 ND1 A:HIS492 4.7 27.0 1.0 CA A:ASP322 4.8 29.7 1.0 CE1 A:HIS492 4.9 27.0 1.0 CA A:HIS366 4.9 27.1 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca703 b:31.9 occ:1.00 NE2 B:HIS320 2.2 50.1 1.0 O B:HOH909 2.2 42.7 1.0 OD1 B:ASP322 2.2 49.3 1.0 O B:HOH877 2.3 39.1 1.0 NE2 B:HIS271 2.3 57.0 1.0 ND1 B:HIS366 2.3 32.9 1.0 CE1 B:HIS320 2.9 50.4 1.0 CG B:ASP322 3.1 49.7 1.0 CE1 B:HIS366 3.1 32.8 1.0 CD2 B:HIS320 3.2 52.6 1.0 CE1 B:HIS271 3.2 55.0 1.0 OD2 B:ASP322 3.3 43.5 1.0 CD2 B:HIS271 3.3 57.7 1.0 CG B:HIS366 3.4 28.7 1.0 CB B:HIS366 3.8 35.0 1.0 O7 B:A2G702 4.1 45.1 1.0 ND1 B:HIS320 4.1 47.8 1.0 CG B:HIS320 4.3 47.2 1.0 CE2 B:TYR433 4.3 35.0 1.0 NE2 B:HIS366 4.3 35.1 1.0 ND1 B:HIS271 4.3 53.4 1.0 CG B:HIS271 4.4 52.9 1.0 CD2 B:HIS366 4.4 34.9 1.0 CB B:ASP322 4.5 39.5 1.0 O B:HOH913 4.5 46.2 1.0 CD2 B:TYR433 4.6 35.7 1.0 CE1 B:TYR329 4.6 36.9 1.0 OH B:TYR329 4.7 42.5 1.0 ND1 B:HIS492 4.8 41.5 1.0 CE1 B:HIS492 4.8 43.0 1.0 CZ B:TYR433 4.9 34.5 1.0 C7 B:A2G702 5.0 43.2 1.0 CA B:ASP322 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