Calcium in PDB 6k0n: Catalytic Domain of GH87 Alpha-1,3-Glucanase in Complex with Nigerose

The structure of Catalytic Domain of GH87 Alpha-1,3-Glucanase in Complex with Nigerose, PDB code: 6k0n was solved by T.Itoh, R.Intuy, W.Suyotha, J.Hayashi, S.Yano, K.Makabe, M.Wakayama, T.Hibi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.82 / 1.60
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	132.656, 132.656, 76.236, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / 17.2

The binding sites of Calcium atom in the Catalytic Domain of GH87 Alpha-1,3-Glucanase in Complex with Nigerose (pdb code 6k0n). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Catalytic Domain of GH87 Alpha-1,3-Glucanase in Complex with Nigerose, PDB code: 6k0n:

Calcium binding site 1 out of 1 in the Catalytic Domain of GH87 Alpha-1,3-Glucanase in Complex with Nigerose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Catalytic Domain of GH87 Alpha-1,3-Glucanase in Complex with Nigerose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2006 b:8.0 occ:1.00 OD1 A:ASP882 2.3 8.0 1.0 OE1 A:GLU737 2.3 9.2 1.0 O A:SER764 2.4 8.3 1.0 O A:SER767 2.4 9.7 1.0 OE1 A:GLU739 2.4 9.6 1.0 OE2 A:GLU739 2.5 8.8 1.0 O A:ASP882 2.6 7.9 1.0 CD A:GLU739 2.8 9.5 1.0 C A:SER764 3.5 7.6 1.0 CD A:GLU737 3.5 12.0 1.0 C A:ASP882 3.5 7.6 1.0 CG A:ASP882 3.5 9.5 1.0 C A:SER767 3.6 9.3 1.0 CA A:ASP882 3.9 6.2 1.0 CB A:SER764 4.0 10.5 1.0 CA A:SER764 4.1 8.1 1.0 CB A:GLU737 4.2 10.1 1.0 OE2 A:GLU737 4.2 13.1 1.0 N A:SER764 4.3 7.2 1.0 CB A:ASP882 4.3 7.0 1.0 CG A:GLU739 4.4 9.3 1.0 CG A:GLU737 4.4 9.8 1.0 OD2 A:ASP882 4.4 8.7 1.0 CA A:SER768 4.4 8.8 0.5 N A:SER767 4.4 7.8 1.0 N A:SER768 4.4 8.3 1.0 CA A:SER768 4.5 8.8 0.5 N A:ALA738 4.5 7.5 1.0 CB A:ALA763 4.5 7.8 1.0 OG A:SER768 4.5 8.4 0.5 N A:GLY765 4.5 8.0 1.0 CA A:SER767 4.5 7.9 1.0 CA A:GLU737 4.5 8.3 1.0 N A:LEU883 4.6 8.4 1.0 CA A:GLY765 4.7 8.9 1.0 OG A:SER764 4.8 9.1 1.0 C A:ALA763 4.9 7.5 1.0 CB A:SER768 4.9 10.8 0.5 CB A:LEU883 4.9 8.8 1.0 O A:HOH2230 4.9 19.3 1.0 C A:GLU737 5.0 8.4 1.0

T.Itoh, R.Intuy, W.Suyotha, J.Hayashi, S.Yano, K.Makabe, M.Wakayama, T.Hibi. 28STRUCTURAL Insights Into Substrate Recognition and Catalysis By Glycoside Hydrolase Family 87 Alpha-1,3-Glucanase From Paenibacillus Glycanilyticus FH11. Febs J. 2019.
ISSN: ISSN 1742-464X
PubMed: 31788942
DOI: 10.1111/FEBS.15161