Calcium in PDB 3a24: Crystal Structure of BT1871 Retaining Glycosidase

The structure of Crystal Structure of BT1871 Retaining Glycosidase, PDB code: 3a24 was solved by M.Okuyama, M.Kitamura, H.Hondoh, I.Tanaka, M.Yao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.94 / 2.30
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	122.962, 167.100, 192.182, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 21.8

The binding sites of Calcium atom in the Crystal Structure of BT1871 Retaining Glycosidase (pdb code 3a24). 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 BT1871 Retaining Glycosidase, PDB code: 3a24:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of BT1871 Retaining Glycosidase


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 BT1871 Retaining Glycosidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1268 b:23.0 occ:1.00 OE2 A:GLU470 2.4 28.4 1.0 OE2 A:GLU174 2.5 27.3 1.0 O A:HOH1131 2.5 24.8 1.0 O A:HOH1130 2.5 30.9 1.0 OE1 A:GLU464 2.6 28.6 1.0 O A:HOH1129 2.6 36.8 1.0 OE2 A:GLU464 2.8 27.0 1.0 O A:HOH1132 3.0 38.5 1.0 CD A:GLU464 3.0 25.5 1.0 CD A:GLU470 3.3 27.0 1.0 CD A:GLU174 3.5 28.9 1.0 OE1 A:GLU470 3.5 27.2 1.0 OE1 A:GLU174 3.8 28.7 1.0 O A:HOH783 4.1 23.6 1.0 O A:HOH779 4.1 22.2 1.0 CG A:GLU464 4.5 22.8 1.0 ND1 A:HIS445 4.6 29.5 1.0 OD2 A:ASP415 4.7 32.6 1.0 O A:HOH729 4.7 24.8 1.0 N A:GLY446 4.7 29.9 1.0 CG A:GLU470 4.8 25.4 1.0 OD1 A:ASP415 4.8 33.2 1.0 CG A:GLU174 4.8 27.3 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of BT1871 Retaining Glycosidase


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 BT1871 Retaining Glycosidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1269 b:15.3 occ:1.00 O B:HOH1175 2.4 21.0 1.0 OE2 B:GLU470 2.5 24.5 1.0 O B:HOH1173 2.5 18.4 1.0 OE2 B:GLU174 2.6 23.3 1.0 OE1 B:GLU464 2.6 22.9 1.0 OE2 B:GLU464 2.7 26.0 1.0 O B:HOH1176 2.8 32.3 1.0 CD B:GLU464 3.0 23.1 1.0 O B:HOH1174 3.0 34.3 1.0 CD B:GLU470 3.4 22.9 1.0 OE1 B:GLU470 3.5 27.5 1.0 CD B:GLU174 3.5 22.2 1.0 OE1 B:GLU174 3.8 25.1 1.0 O B:HOH702 4.3 23.4 1.0 O B:HOH700 4.3 14.0 1.0 ND1 B:HIS445 4.4 16.4 1.0 CG B:GLU464 4.4 20.8 1.0 N B:GLY446 4.6 18.1 1.0 OD2 B:ASP415 4.6 16.6 1.0 O B:HOH873 4.7 14.6 1.0 O B:HOH1201 4.8 26.4 1.0 OD1 B:ASP415 4.8 19.6 1.0 CG B:GLU470 4.8 21.1 1.0 CG B:GLU174 4.9 22.2 1.0

M.Okuyama, M.Kitamura, H.Hondoh, M.S.Kang, H.Mori, A.Kimura, I.Tanaka, M.Yao. Catalytic Mechanism of Retaining Alpha-Galactosidase Belonging to Glycoside Hydrolase Family 97. J.Mol.Biol. V. 392 1232 2009.
ISSN: ISSN 0022-2836
PubMed: 19646996
DOI: 10.1016/J.JMB.2009.07.068