Calcium in PDB 5yqs: 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: 5yqs was solved by K.Yaoi, T.Matsuzawa, M.Watanabe, Y.Nakamichi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.787, 129.911, 95.162, 90.00, 94.44, 90.00
R / Rfree (%)	15.3 / 20.8

The binding sites of Calcium atom in the Isoprimeverose-Producing Enzyme From Aspergillus Oryzae in Complex with Isoprimeverose (pdb code 5yqs). 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: 5yqs:
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:Ca812 b:22.7 occ:1.00 O A:VAL708 2.3 22.2 1.0 O A:HOH1026 2.3 23.4 1.0 OD1 A:ASP706 2.3 20.2 1.0 O A:HOH973 2.3 21.4 1.0 O A:HOH947 2.3 18.8 1.0 O A:HOH941 2.4 15.7 1.0 CG A:ASP706 3.3 21.6 1.0 C A:VAL708 3.4 21.7 1.0 OD2 A:ASP706 3.6 22.1 1.0 N A:VAL708 4.1 22.9 1.0 O A:ALA758 4.2 23.1 1.0 CA A:VAL708 4.3 22.5 1.0 N A:ALA709 4.3 20.1 1.0 O A:GLU755 4.4 26.4 1.0 CA A:ALA709 4.4 20.4 1.0 CB A:GLU755 4.5 23.1 1.0 O A:PRO756 4.5 25.6 1.0 CA A:GLY757 4.5 24.9 1.0 OE1 A:GLU755 4.6 22.7 1.0 CB A:ASP706 4.7 21.9 1.0 O A:HOH1099 4.7 19.5 1.0 N A:GLU707 4.7 26.2 1.0 N A:ALA758 4.7 24.5 1.0 CB A:VAL708 4.7 25.1 1.0 C A:GLY757 4.7 24.9 1.0 C A:ASP706 4.8 23.1 1.0 CB A:ALA709 4.9 20.1 1.0 O A:HOH1111 5.0 16.8 1.0 C A:PRO756 5.0 25.2 1.0 CA A:ASP706 5.0 20.6 1.0 C A:GLU755 5.0 25.5 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:Ca811 b:22.7 occ:1.00 O B:VAL708 2.2 20.3 1.0 OD1 B:ASP706 2.3 22.3 1.0 O B:HOH936 2.3 22.8 1.0 O B:HOH970 2.4 17.1 1.0 O B:HOH912 2.5 20.4 1.0 O B:HOH961 2.5 22.0 1.0 CG B:ASP706 3.3 22.8 1.0 C B:VAL708 3.4 20.8 1.0 OD2 B:ASP706 3.6 24.6 1.0 N B:VAL708 4.0 22.4 1.0 O B:ALA758 4.1 24.1 1.0 CA B:VAL708 4.2 21.7 1.0 N B:ALA709 4.3 19.7 1.0 CA B:ALA709 4.4 19.0 1.0 O B:GLU755 4.5 25.6 1.0 O B:HOH1086 4.5 21.9 1.0 O B:PRO756 4.5 22.1 1.0 N B:GLU707 4.6 26.9 1.0 CB B:ASP706 4.6 21.4 1.0 CB B:VAL708 4.7 23.9 1.0 CB B:GLU755 4.7 24.1 1.0 OE1 B:GLU755 4.7 22.0 1.0 CA B:GLY757 4.7 20.2 1.0 C B:ASP706 4.8 23.3 1.0 O B:HOH1088 4.8 20.9 1.0 C B:GLY757 4.9 21.6 1.0 CA B:ASP706 4.9 22.2 1.0 N B:ALA758 4.9 21.6 1.0 CB B:ALA709 4.9 18.5 1.0 C B:PRO756 5.0 22.0 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