Calcium in PDB 2j7h: Beta-Glucosidase From Thermotoga Maritima in Complex with Azafagomine

All present enzymatic activity of Beta-Glucosidase From Thermotoga Maritima in Complex with Azafagomine:
3.2.1.21;

The structure of Beta-Glucosidase From Thermotoga Maritima in Complex with Azafagomine, PDB code: 2j7h was solved by T.M.Gloster, P.Meloncelli, R.V.Stick, D.Zechel, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.83 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	94.229, 94.478, 113.285, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 23.8

The binding sites of Calcium atom in the Beta-Glucosidase From Thermotoga Maritima in Complex with Azafagomine (pdb code 2j7h). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Beta-Glucosidase From Thermotoga Maritima in Complex with Azafagomine, PDB code: 2j7h:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Beta-Glucosidase From Thermotoga Maritima in Complex with Azafagomine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Beta-Glucosidase From Thermotoga Maritima in Complex with Azafagomine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1447 b:27.5 occ:1.00 OD2 A:ASP52 1.9 27.6 1.0 OXT A:ACT1448 2.0 46.4 1.0 NE2 A:HIS40 2.0 27.6 1.0 CG A:ASP52 2.8 26.0 1.0 O A:HOH2055 2.8 48.0 1.0 OD1 A:ASP52 3.0 25.1 1.0 CD2 A:HIS40 3.0 27.6 1.0 CE1 A:HIS40 3.0 26.6 1.0 C A:ACT1448 3.2 47.1 1.0 O A:ACT1448 3.9 47.5 1.0 O A:HOH2076 4.1 50.4 1.0 ND1 A:HIS40 4.1 26.4 1.0 CG A:HIS40 4.1 24.8 1.0 CB A:ASP52 4.2 23.8 1.0 CH3 A:ACT1448 4.3 46.6 1.0 CE1 A:HIS36 4.5 25.6 1.0 OG1 A:THR50 4.5 24.3 1.0 CG2 A:THR50 5.0 21.9 1.0 O A:HOH2071 5.0 39.1 1.0

Calcium binding site 2 out of 3 in the Beta-Glucosidase From Thermotoga Maritima in Complex with Azafagomine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Beta-Glucosidase From Thermotoga Maritima in Complex with Azafagomine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1446 b:36.3 occ:1.00 O B:ACT1448 1.8 47.3 1.0 OD2 B:ASP52 1.9 36.4 1.0 NE2 B:HIS40 2.1 37.1 1.0 O B:HOH2022 2.5 53.2 1.0 CG B:ASP52 2.8 36.6 1.0 OD1 B:ASP52 3.0 33.6 1.0 C B:ACT1448 3.1 48.5 1.0 CD2 B:HIS40 3.1 34.3 1.0 CE1 B:HIS40 3.1 35.4 1.0 CH3 B:ACT1448 3.9 48.8 1.0 OXT B:ACT1448 3.9 48.6 1.0 CB B:ASP52 4.2 36.0 1.0 ND1 B:HIS40 4.2 33.7 1.0 CG B:HIS40 4.2 32.1 1.0 OG1 B:THR50 4.5 35.8 1.0 CE1 B:HIS36 4.5 34.6 1.0 CG2 B:THR50 4.9 34.5 1.0

Calcium binding site 3 out of 3 in the Beta-Glucosidase From Thermotoga Maritima in Complex with Azafagomine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Beta-Glucosidase From Thermotoga Maritima in Complex with Azafagomine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1447 b:60.6 occ:1.00 O B:HOH2167 1.9 21.3 1.0 O B:ASP278 2.5 27.9 1.0 O B:HOH2161 2.9 29.0 1.0 OE1 B:GLU282 3.1 41.4 1.0 OG B:SER281 3.5 37.4 1.0 C B:ASP278 3.6 27.4 1.0 CD B:GLU282 4.0 40.4 1.0 O B:HOH2165 4.1 46.1 1.0 OE2 B:GLU282 4.1 43.7 1.0 CA B:ASP278 4.1 26.9 1.0 CB B:SER281 4.1 31.5 1.0 N B:SER281 4.6 28.5 1.0 N B:ASP279 4.7 26.1 1.0 CB B:ASP278 4.8 27.2 1.0 CA B:SER281 4.9 30.4 1.0 O B:LYS277 4.9 27.1 1.0 CA B:ASP279 5.0 24.8 1.0

T.M.Gloster, P.Meloncelli, R.V.Stick, D.Zechel, A.Vasella, G.J.Davies. Glycosidase Inhibition: An Assessment of the Binding of 18 Putative Transition-State Mimics. J.Am.Chem.Soc. V. 129 2345 2007.
ISSN: ISSN 0002-7863
PubMed: 17279749
DOI: 10.1021/JA066961G