Calcium in PDB 5h3z: Crystal Structure of 1,2-Beta-Oligoglucan Phosphorylase From Lachnoclostridium Phytofermentans

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

The structure of Crystal Structure of 1,2-Beta-Oligoglucan Phosphorylase From Lachnoclostridium Phytofermentans, PDB code: 5h3z 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)	42.72 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	87.761, 94.784, 157.943, 90.00, 98.41, 90.00
R / Rfree (%)	16.8 / 20.4

The binding sites of Calcium atom in the Crystal Structure of 1,2-Beta-Oligoglucan Phosphorylase From Lachnoclostridium Phytofermentans (pdb code 5h3z). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of 1,2-Beta-Oligoglucan Phosphorylase From Lachnoclostridium Phytofermentans, PDB code: 5h3z:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of 1,2-Beta-Oligoglucan Phosphorylase From Lachnoclostridium Phytofermentans


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1205 b:39.7 occ:1.00 O A:ASP1040 2.2 20.8 1.0 O A:HOH1316 2.6 35.7 1.0 O A:HOH1671 2.7 39.9 1.0 C A:ASP1040 3.3 24.0 1.0 CA A:GLY1041 4.1 27.0 1.0 N A:GLY1041 4.2 26.6 1.0 OD1 A:ASP1040 4.3 33.8 1.0 CA A:ASP1040 4.3 27.7 1.0 CB A:ASP1040 4.3 31.6 1.0 OD2 A:ASP589 4.5 45.4 1.0 OD1 A:ASP589 4.6 40.4 1.0 N A:ASP1040 4.6 26.3 1.0 O A:GLU1038 4.6 33.8 1.0 C A:GLY1041 4.7 29.3 1.0 CG A:ASP1040 4.9 36.0 1.0 CG A:ASP589 5.0 46.8 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of 1,2-Beta-Oligoglucan Phosphorylase From Lachnoclostridium Phytofermentans


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1207 b:59.2 occ:1.00 O B:PRO502 2.3 29.2 1.0 O B:HOH1567 2.3 40.4 1.0 ND2 B:ASN498 2.6 38.4 1.0 O B:HOH1691 2.7 45.9 1.0 C B:PRO502 3.3 26.9 1.0 CG B:ASN498 3.9 40.8 1.0 CA B:PRO502 4.0 29.6 1.0 O B:LEU504 4.2 25.4 1.0 N B:GLU503 4.2 28.7 1.0 N B:LEU504 4.4 30.1 1.0 CA B:GLU503 4.4 33.4 1.0 OD1 B:ASN498 4.5 53.1 1.0 O B:HOH1724 4.5 42.9 1.0 O B:PRO491 4.6 33.1 1.0 CD B:PRO491 4.6 29.6 1.0 O B:TYR501 4.6 27.0 1.0 C B:GLU503 4.7 33.7 1.0 CB B:PRO502 4.9 29.9 1.0 CB B:SER490 4.9 30.9 1.0 CB B:ASN498 5.0 44.3 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of 1,2-Beta-Oligoglucan Phosphorylase From Lachnoclostridium Phytofermentans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of 1,2-Beta-Oligoglucan Phosphorylase From Lachnoclostridium Phytofermentans within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1208 b:37.2 occ:1.00 O B:ASP1040 2.1 22.4 1.0 O B:HOH1702 2.3 42.6 1.0 O B:HOH1433 2.4 35.8 1.0 O B:HOH1305 2.5 29.6 1.0 O B:HOH1490 2.7 28.1 1.0 C B:ASP1040 3.3 22.8 1.0 N B:GLY1041 4.2 21.6 1.0 CA B:GLY1041 4.2 21.2 1.0 CA B:ASP1040 4.3 24.5 1.0 OD2 B:ASP589 4.3 36.9 1.0 CB B:ASP1040 4.4 27.3 1.0 OD1 B:ASP589 4.5 29.6 1.0 OD1 B:ASP1040 4.5 29.1 1.0 N B:ASP1040 4.6 25.3 1.0 O B:GLU1038 4.6 29.3 1.0 C B:GLY1041 4.7 24.4 1.0 CG B:ASP589 4.9 34.6 1.0 CG B:ASP1040 5.0 28.7 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