Calcium 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:

Zinc

(Zn)

2 atoms

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

Calcium 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 Calcium with other atoms in the Ca 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:Ca703 b:37.3 occ:1.00 O A:HOH802 1.8 52.5 1.0 OD1 A:ASP322 1.9 40.6 1.0 NE2 A:HIS271 2.1 71.2 1.0 ND1 A:HIS366 2.3 45.4 1.0 NE2 A:HIS320 2.4 67.1 1.0 O A:HOH801 2.4 48.7 1.0 CG A:ASP322 2.7 45.7 1.0 OD2 A:ASP322 2.8 43.1 1.0 CE1 A:HIS366 2.9 48.7 1.0 CE1 A:HIS271 2.9 71.0 1.0 CE1 A:HIS320 3.0 64.8 1.0 CD2 A:HIS271 3.1 74.8 1.0 CD2 A:HIS320 3.4 68.0 1.0 CG A:HIS366 3.5 54.8 1.0 O7 A:DJN702 3.6 58.7 1.0 ND1 A:HIS320 4.0 65.5 1.0 CB A:HIS366 4.0 58.2 1.0 ND1 A:HIS271 4.0 71.3 1.0 NE2 A:HIS366 4.1 50.5 1.0 CG A:HIS271 4.2 70.0 1.0 CG A:HIS320 4.3 66.7 1.0 CB A:ASP322 4.3 45.0 1.0 OH A:TYR329 4.3 47.3 1.0 CE2 A:TYR433 4.3 51.7 1.0 CD2 A:HIS492 4.4 58.5 1.0 CD2 A:HIS366 4.4 53.6 1.0 CD2 A:TYR433 4.5 54.4 1.0 CE1 A:TYR329 4.5 51.8 1.0 NE2 A:HIS492 4.6 57.0 1.0 C7 A:DJN702 4.7 58.4 1.0 CA A:ASP322 4.8 47.6 1.0 CZ A:TYR329 4.9 48.8 1.0 CZ A:TYR433 5.0 50.3 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca703 b:50.0 occ:1.00 O B:HOH802 2.0 50.4 1.0 O B:HOH801 2.1 54.8 1.0 OD1 B:ASP322 2.3 67.2 1.0 ND1 B:HIS366 2.3 72.1 1.0 NE2 B:HIS320 2.5 74.1 1.0 NE2 B:HIS271 2.6 95.9 1.0 OD2 B:ASP322 2.9 62.7 1.0 CG B:ASP322 3.0 67.2 1.0 CE1 B:HIS366 3.0 73.1 1.0 CE1 B:HIS320 3.2 77.8 1.0 CG B:HIS366 3.3 74.7 1.0 CE1 B:HIS271 3.4 96.7 1.0 CD2 B:HIS320 3.5 76.5 1.0 O7 B:DJN702 3.6 56.3 1.0 CD2 B:HIS271 3.6 97.7 1.0 CB B:HIS366 3.8 79.9 1.0 NE2 B:HIS366 4.1 74.0 1.0 CD2 B:HIS366 4.3 73.7 1.0 OH B:TYR329 4.3 61.2 1.0 CE1 B:TYR329 4.3 60.1 1.0 ND1 B:HIS320 4.4 78.5 1.0 CE2 B:TYR433 4.4 59.6 1.0 CB B:ASP322 4.4 66.4 1.0 C7 B:DJN702 4.5 64.9 1.0 ND1 B:HIS271 4.5 98.0 1.0 CG B:HIS320 4.6 76.7 1.0 CG B:HIS271 4.6 90.9 1.0 CD2 B:HIS492 4.7 0.2 1.0 CD2 B:TYR433 4.7 58.3 1.0 CZ B:TYR329 4.8 61.2 1.0 NE2 B:HIS492 4.8 0.5 1.0 C8 B:DJN702 4.9 64.1 1.0 CZ B:TYR433 4.9 58.4 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