Calcium in PDB 5h40: Crystal Structure of 1,2-Beta-Oligoglucan Phosphorylase From Lachnoclostridium Phytofermentans in Complex with Sophorose

All present enzymatic activity of Crystal Structure of 1,2-Beta-Oligoglucan Phosphorylase From Lachnoclostridium Phytofermentans in Complex with Sophorose:
2.4.1.333;

The structure of Crystal Structure of 1,2-Beta-Oligoglucan Phosphorylase From Lachnoclostridium Phytofermentans in Complex with Sophorose, PDB code: 5h40 was solved by M.Nakajima, N.Tanaka, N.Furukawa, T.Nihira, Y.Kodutsumi, Y.Takahashi, N.Sugimoto, A.Miyanaga, S.Fushinobu, H.Taguchi, H.Nakai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	86.02 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.780, 94.330, 156.920, 90.00, 97.60, 90.00
R / Rfree (%)	17.9 / 21.1

The binding sites of Calcium atom in the Crystal Structure of 1,2-Beta-Oligoglucan Phosphorylase From Lachnoclostridium Phytofermentans in Complex with Sophorose (pdb code 5h40). 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 1,2-Beta-Oligoglucan Phosphorylase From Lachnoclostridium Phytofermentans in Complex with Sophorose, PDB code: 5h40:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of 1,2-Beta-Oligoglucan Phosphorylase From Lachnoclostridium Phytofermentans in Complex with Sophorose


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 1,2-Beta-Oligoglucan Phosphorylase From Lachnoclostridium Phytofermentans in Complex with Sophorose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1204 b:36.9 occ:1.00 O A:HOH1579 2.2 37.1 1.0 O A:ASP1040 2.2 20.6 1.0 O A:HOH1305 2.4 43.4 1.0 O A:HOH1441 2.5 23.9 1.0 C A:ASP1040 3.4 24.2 1.0 CA A:GLY1041 4.2 25.7 1.0 N A:GLY1041 4.2 24.1 1.0 OD1 A:ASP1040 4.3 23.5 1.0 CA A:ASP1040 4.4 25.4 1.0 CB A:ASP1040 4.4 24.1 1.0 OD2 A:ASP589 4.4 36.1 1.0 O A:GLU1038 4.5 27.3 1.0 N A:ASP1040 4.7 25.6 1.0 OD1 A:ASP589 4.7 31.8 1.0 C A:GLY1041 4.8 24.6 1.0 CG A:ASP1040 4.9 24.7 1.0 CG A:ASP589 5.0 38.3 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of 1,2-Beta-Oligoglucan Phosphorylase From Lachnoclostridium Phytofermentans in Complex with Sophorose


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 1,2-Beta-Oligoglucan Phosphorylase From Lachnoclostridium Phytofermentans in Complex with Sophorose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1205 b:33.0 occ:1.00 O B:ASP1040 2.2 16.6 1.0 O B:HOH1481 2.3 29.0 1.0 O B:HOH1575 2.4 31.8 1.0 O B:HOH1352 2.4 25.3 1.0 C B:ASP1040 3.3 18.6 1.0 CA B:GLY1041 4.2 18.9 1.0 N B:GLY1041 4.2 18.7 1.0 CA B:ASP1040 4.3 19.9 1.0 CB B:ASP1040 4.3 20.1 1.0 OD1 B:ASP1040 4.3 25.1 1.0 OD2 B:ASP589 4.4 36.5 1.0 O B:GLU1038 4.4 26.0 1.0 N B:ASP1040 4.6 22.5 1.0 OD1 B:ASP589 4.6 33.2 1.0 C B:GLY1041 4.7 20.8 1.0 CG B:ASP1040 4.9 22.0 1.0 CG B:ASP589 4.9 36.2 1.0

M.Nakajima, N.Tanaka, N.Furukawa, T.Nihira, Y.Kodutsumi, Y.Takahashi, N.Sugimoto, A.Miyanaga, S.Fushinobu, H.Taguchi, H.Nakai. Mechanistic Insight Into the Substrate Specificity of 1,2-Beta-Oligoglucan Phosphorylase From Lachnoclostridium Phytofermentans Sci Rep V. 7 42671 2017.
ISSN: ESSN 2045-2322
PubMed: 28198470
DOI: 10.1038/SREP42671