Calcium in PDB 5yot: Isoprimeverose-Producing Enzyme From Aspergillus Oryzae in Complex with Isoprimeverose

The structure of Isoprimeverose-Producing Enzyme From Aspergillus Oryzae in Complex with Isoprimeverose, PDB code: 5yot was solved by T.Matsuzawa, M.Watanabe, Y.Nakamichi, K.Yaoi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	70.141, 130.454, 94.836, 90.00, 94.46, 90.00
R / Rfree (%)	16.7 / 21.1

The binding sites of Calcium atom in the Isoprimeverose-Producing Enzyme From Aspergillus Oryzae in Complex with Isoprimeverose (pdb code 5yot). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Isoprimeverose-Producing Enzyme From Aspergillus Oryzae in Complex with Isoprimeverose, PDB code: 5yot:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Isoprimeverose-Producing Enzyme From Aspergillus Oryzae in Complex with Isoprimeverose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Isoprimeverose-Producing Enzyme From Aspergillus Oryzae in Complex with Isoprimeverose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:25.5 occ:1.00 O A:VAL708 2.2 23.8 1.0 O A:HOH943 2.3 22.4 1.0 OD1 A:ASP706 2.3 23.1 1.0 O A:HOH942 2.3 24.0 1.0 O A:HOH966 2.3 23.7 1.0 O A:HOH967 2.4 22.0 1.0 CG A:ASP706 3.3 25.3 1.0 C A:VAL708 3.4 25.4 1.0 OD2 A:ASP706 3.7 31.0 1.0 N A:VAL708 4.0 23.9 1.0 O A:ALA758 4.2 22.6 1.0 CA A:VAL708 4.3 25.5 1.0 N A:ALA709 4.3 24.5 1.0 O A:PRO756 4.3 21.6 1.0 CA A:ALA709 4.3 24.3 1.0 O A:GLU755 4.4 27.6 1.0 N A:GLU707 4.6 25.4 1.0 CB A:ASP706 4.6 22.3 1.0 OE1 A:GLU755 4.7 22.8 1.0 CB A:GLU755 4.7 27.1 1.0 CB A:VAL708 4.7 30.9 1.0 N A:ALA758 4.7 24.2 1.0 CA A:GLY757 4.8 24.6 1.0 C A:ASP706 4.8 23.9 1.0 C A:GLY757 4.8 26.2 1.0 CB A:ALA709 4.9 25.8 1.0 C A:PRO756 4.9 25.8 1.0 CA A:ASP706 4.9 21.5 1.0

Calcium binding site 2 out of 2 in the Isoprimeverose-Producing Enzyme From Aspergillus Oryzae in Complex with Isoprimeverose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Isoprimeverose-Producing Enzyme From Aspergillus Oryzae in Complex with Isoprimeverose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca801 b:26.0 occ:1.00 O B:HOH1146 2.2 27.7 1.0 O B:VAL708 2.2 23.7 1.0 O B:HOH1028 2.2 23.2 1.0 O B:HOH979 2.2 23.2 1.0 OD1 B:ASP706 2.3 24.8 1.0 O B:HOH1086 2.4 23.9 1.0 C B:VAL708 3.3 25.5 1.0 CG B:ASP706 3.3 26.4 1.0 OD2 B:ASP706 3.7 30.4 1.0 N B:VAL708 4.0 22.5 1.0 CA B:VAL708 4.2 25.8 1.0 N B:ALA709 4.2 25.8 1.0 O B:ALA758 4.2 25.4 1.0 CA B:ALA709 4.3 24.3 1.0 O B:GLU755 4.4 27.3 1.0 O B:PRO756 4.4 25.7 1.0 N B:GLU707 4.5 25.1 1.0 CB B:GLU755 4.6 23.8 1.0 CB B:VAL708 4.6 29.2 1.0 CB B:ASP706 4.6 24.2 1.0 CA B:GLY757 4.7 24.4 1.0 OE1 B:GLU755 4.7 24.0 1.0 C B:ASP706 4.7 23.9 1.0 N B:ALA758 4.8 27.5 1.0 CB B:ALA709 4.8 28.9 1.0 C B:GLY757 4.8 26.9 1.0 CA B:ASP706 4.9 22.8 1.0 C B:PRO756 4.9 24.7 1.0 O B:HOH1213 5.0 25.0 1.0

T.Matsuzawa, M.Watanabe, Y.Nakamichi, Z.Fujimoto, K.Yaoi. Crystal Structure and Substrate Recognition Mechanism of Aspergillus Oryzae Isoprimeverose-Producing Enzyme. J.Struct.Biol. V. 205 84 2019.
ISSN: ESSN 1095-8657
PubMed: 30445155
DOI: 10.1016/J.JSB.2018.11.005