Calcium in PDB 5z06: Crystal Structure of Beta-1,2-Glucanase From Parabacteroides Distasonis

The structure of Crystal Structure of Beta-1,2-Glucanase From Parabacteroides Distasonis, PDB code: 5z06 was solved by H.Shimizu, M.Nakajima, A.Miyanaga, Y.Takahashi, N.Tanaka, K.Kobayashi, N.Sugimoto, H.Nakai, H.Taguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.73 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	130.080, 123.337, 101.376, 90.00, 107.88, 90.00
R / Rfree (%)	17.8 / 21.9

The binding sites of Calcium atom in the Crystal Structure of Beta-1,2-Glucanase From Parabacteroides Distasonis (pdb code 5z06). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Beta-1,2-Glucanase From Parabacteroides Distasonis, PDB code: 5z06:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Beta-1,2-Glucanase From Parabacteroides Distasonis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Beta-1,2-Glucanase From Parabacteroides Distasonis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:31.1 occ:1.00 O A:GLU29 2.3 32.4 1.0 O A:THR66 2.3 27.4 1.0 OG1 A:THR66 2.3 28.3 1.0 O A:ASN69 2.4 30.4 1.0 OD1 A:ASN30 2.5 33.0 1.0 OD1 A:ASP192 2.5 28.8 1.0 OD2 A:ASP192 2.6 28.0 1.0 CG A:ASP192 2.9 28.4 1.0 CG A:ASN30 3.3 32.9 1.0 C A:THR66 3.3 31.5 1.0 CB A:THR66 3.5 29.3 1.0 C A:GLU29 3.5 33.1 1.0 C A:ASN69 3.6 29.8 1.0 CA A:THR66 3.8 31.1 1.0 ND2 A:ASN30 3.8 32.4 1.0 N A:THR66 3.9 33.1 1.0 N A:ASN69 4.0 31.8 1.0 OD1 A:ASP193 4.1 43.7 1.0 CA A:ASN30 4.2 34.0 1.0 N A:ASN30 4.2 33.6 1.0 CE2 A:PHE28 4.3 32.2 1.0 CB A:ASN30 4.3 33.0 1.0 CB A:ALA64 4.3 32.3 1.0 CB A:ASP192 4.4 28.9 1.0 CA A:ASN69 4.4 30.2 1.0 O A:PRO67 4.4 33.7 1.0 N A:PRO67 4.5 33.2 1.0 CA A:GLU29 4.6 34.0 1.0 N A:SER70 4.6 29.8 1.0 OD1 A:ASN69 4.7 33.3 1.0 C A:PRO67 4.7 38.5 1.0 OD2 A:ASP193 4.7 45.1 1.0 CG A:ASP193 4.7 39.3 1.0 CG2 A:THR66 4.7 29.4 1.0 CA A:SER70 4.7 28.7 1.0 CG A:GLU29 4.9 42.3 1.0 C A:PHE65 4.9 33.9 1.0 N A:PHE65 5.0 35.4 1.0 CA A:PRO67 5.0 34.5 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Beta-1,2-Glucanase From Parabacteroides Distasonis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Beta-1,2-Glucanase From Parabacteroides Distasonis within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca801 b:30.6 occ:1.00 O B:GLU29 2.2 28.9 1.0 O B:THR66 2.3 26.7 1.0 OG1 B:THR66 2.3 30.5 1.0 O B:ASN69 2.3 29.9 1.0 OD1 B:ASN30 2.4 27.6 1.0 OD1 B:ASP192 2.5 27.8 1.0 OD2 B:ASP192 2.6 28.5 1.0 CG B:ASP192 2.9 27.7 1.0 CG B:ASN30 3.3 29.1 1.0 C B:THR66 3.3 30.1 1.0 CB B:THR66 3.4 31.6 1.0 C B:GLU29 3.4 29.8 1.0 C B:ASN69 3.6 30.5 1.0 CA B:THR66 3.7 31.6 1.0 ND2 B:ASN30 3.8 27.8 1.0 N B:THR66 3.8 32.5 1.0 N B:ASN69 4.0 33.2 1.0 OD1 B:ASP193 4.1 39.5 1.0 CA B:ASN30 4.2 29.2 1.0 N B:ASN30 4.2 29.0 1.0 CE2 B:PHE28 4.3 30.5 1.0 CB B:ALA64 4.3 33.3 1.0 CB B:ASN30 4.3 27.5 1.0 CB B:ASP192 4.4 27.8 1.0 O B:PRO67 4.4 29.1 1.0 CA B:ASN69 4.4 30.8 1.0 N B:PRO67 4.5 29.6 1.0 CA B:GLU29 4.5 31.8 1.0 N B:SER70 4.5 29.7 1.0 OD1 B:ASN69 4.6 34.0 1.0 C B:PRO67 4.6 33.5 1.0 CA B:SER70 4.7 30.1 1.0 CG2 B:THR66 4.7 33.9 1.0 CG B:ASP193 4.8 38.7 1.0 OD2 B:ASP193 4.8 45.4 1.0 CA B:PRO67 4.9 30.6 1.0 N B:PHE65 4.9 33.6 1.0 CG B:GLU29 4.9 38.7 1.0 C B:PHE65 4.9 33.1 1.0 CZ B:PHE28 5.0 30.0 1.0

H.Shimizu, M.Nakajima, A.Miyanaga, Y.Takahashi, N.Tanaka, K.Kobayashi, N.Sugimoto, H.Nakai, H.Taguchi. Characterization and Structural Analysis of A Novel Exo-Type Enzyme Acting on Beta-1,2-Glucooligosaccharides From Parabacteroides Distasonis Biochemistry V. 57 3849 2018.
ISSN: ISSN 1520-4995
PubMed: 29763309
DOI: 10.1021/ACS.BIOCHEM.8B00385