Calcium in PDB 5e1q: Mutant (D415G) GH97 Alpha-Galactosidase in Complex with Gal-Lac

All present enzymatic activity of Mutant (D415G) GH97 Alpha-Galactosidase in Complex with Gal-Lac:
3.2.1.22;

The structure of Mutant (D415G) GH97 Alpha-Galactosidase in Complex with Gal-Lac, PDB code: 5e1q was solved by K.Matsunaga, K.Yamashita, T.Tagami, M.Yao, M.Okuyama, A.Kimura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.44 / 1.94
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.620, 100.624, 237.079, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 22.3

The binding sites of Calcium atom in the Mutant (D415G) GH97 Alpha-Galactosidase in Complex with Gal-Lac (pdb code 5e1q). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Mutant (D415G) GH97 Alpha-Galactosidase in Complex with Gal-Lac, PDB code: 5e1q:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Mutant (D415G) GH97 Alpha-Galactosidase in Complex with Gal-Lac


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mutant (D415G) GH97 Alpha-Galactosidase in Complex with Gal-Lac within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:28.9 occ:1.00 O2 A:GLA703 2.3 33.7 1.0 OE2 A:GLU470 2.3 30.5 1.0 OE2 A:GLU174 2.4 35.0 1.0 OE2 A:GLU464 2.5 29.0 1.0 O2' A:LAT702 2.5 30.0 1.0 OE1 A:GLU464 2.7 29.1 1.0 O A:HOH1107 2.7 32.3 1.0 CD A:GLU464 2.9 28.1 1.0 O1' A:LAT702 3.0 32.2 1.0 CD A:GLU470 3.2 31.5 1.0 C2' A:LAT702 3.4 31.0 1.0 CD A:GLU174 3.4 35.0 1.0 C2 A:GLA703 3.4 31.7 1.0 OE1 A:GLU470 3.5 33.1 1.0 C1 A:GLA703 3.6 31.1 1.0 C1' A:LAT702 3.7 31.8 1.0 OE1 A:GLU174 3.8 35.9 1.0 O A:HOH1001 4.1 28.0 1.0 O A:HOH886 4.1 30.7 1.0 C3 A:GLA703 4.2 29.9 1.0 ND1 A:HIS445 4.4 29.6 1.0 CG A:GLU464 4.4 25.8 1.0 O A:HOH1077 4.5 32.9 1.0 CG A:GLU470 4.6 29.6 1.0 O A:HOH850 4.6 26.5 1.0 O A:HOH962 4.7 38.3 1.0 CG A:GLU174 4.8 34.1 1.0 O3 A:GLA703 4.8 27.8 1.0 O A:HOH908 4.8 31.9 1.0 C3' A:LAT702 4.8 30.9 1.0 N A:GLY446 4.9 30.9 1.0 O5 A:GLA703 5.0 29.1 1.0

Calcium binding site 2 out of 2 in the Mutant (D415G) GH97 Alpha-Galactosidase in Complex with Gal-Lac


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mutant (D415G) GH97 Alpha-Galactosidase in Complex with Gal-Lac within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca701 b:26.4 occ:1.00 OE2 B:GLU470 2.3 28.9 1.0 OE2 B:GLU464 2.3 30.2 1.0 OE2 B:GLU174 2.3 31.0 1.0 O2 B:GLA703 2.4 28.2 1.0 O B:HOH968 2.4 38.8 1.0 O2' B:LAT702 2.5 31.0 1.0 OE1 B:GLU464 2.7 30.8 1.0 CD B:GLU464 2.9 30.5 1.0 O1' B:LAT702 3.0 28.5 1.0 CD B:GLU470 3.2 29.5 1.0 CD B:GLU174 3.3 30.9 1.0 C2' B:LAT702 3.4 30.4 1.0 C2 B:GLA703 3.5 28.4 1.0 OE1 B:GLU470 3.5 31.5 1.0 C1 B:GLA703 3.5 28.6 1.0 OE1 B:GLU174 3.6 31.4 1.0 C1' B:LAT702 3.7 29.0 1.0 O B:HOH872 4.0 35.0 1.0 O B:HOH932 4.1 30.8 1.0 C3 B:GLA703 4.3 28.2 1.0 CG B:GLU464 4.3 28.5 1.0 O B:HOH813 4.4 33.7 1.0 ND1 B:HIS445 4.4 27.6 1.0 CG B:GLU470 4.6 26.5 1.0 O B:HOH928 4.6 32.3 1.0 O B:HOH973 4.7 25.5 1.0 CG B:GLU174 4.7 29.7 1.0 C3' B:LAT702 4.8 31.4 1.0 O B:HOH939 4.8 26.5 1.0 O3 B:GLA703 4.8 28.6 1.0 O5 B:GLA703 5.0 29.1 1.0 O B:HOH920 5.0 30.4 1.0 N B:GLY446 5.0 29.3 1.0

M.Okuyama, K.Matsunaga, K.I.Watanabe, K.Yamashita, T.Tagami, A.Kikuchi, M.Ma, P.Klahan, H.Mori, M.Yao, A.Kimura. Efficient Synthesis of Alpha-Galactosyl Oligosaccharides Using A Mutant Bacteroides Thetaiotaomicron Retaining Alpha-Galactosidase (BTGH97B). Febs J. V. 284 766 2017.
ISSN: ISSN 1742-4658
PubMed: 28103425
DOI: 10.1111/FEBS.14018