Calcium in PDB 2j78: Beta-Glucosidase From Thermotoga Maritima in Complex with Gluco-Hydroximolactam

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

The structure of Beta-Glucosidase From Thermotoga Maritima in Complex with Gluco-Hydroximolactam, PDB code: 2j78 was solved by T.M.Gloster, D.Zechel, A.Vasella, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.55 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	96.950, 91.459, 111.527, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 20.1

The binding sites of Calcium atom in the Beta-Glucosidase From Thermotoga Maritima in Complex with Gluco-Hydroximolactam (pdb code 2j78). 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 Gluco-Hydroximolactam, PDB code: 2j78:
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 Gluco-Hydroximolactam


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 Gluco-Hydroximolactam within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1447 b:16.0 occ:1.00 OE2 A:GLU66 2.3 16.4 1.0 O A:HOH2173 2.4 14.5 1.0 OE1 A:GLU69 2.4 17.1 1.0 CD A:GLU66 3.4 18.2 1.0 CD A:GLU69 3.4 15.7 1.0 NZ A:LYS111 3.9 15.2 1.0 OE1 A:GLU66 4.0 18.7 1.0 O A:HOH2174 4.0 12.5 0.5 CG A:GLU69 4.1 14.6 1.0 OE2 A:GLU69 4.4 19.2 1.0 CB A:GLU69 4.5 13.5 1.0 CG A:GLU66 4.5 16.5 1.0 CB A:GLU66 4.6 13.0 1.0 O A:GLU66 4.8 13.8 1.0 CA A:GLU66 4.8 13.3 1.0 CE A:LYS111 5.0 16.0 1.0

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


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 Gluco-Hydroximolactam within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1448 b:27.3 occ:1.00 O A:HOH2489 2.3 31.6 1.0 O A:HOH2482 2.4 17.2 0.5 O A:HOH2490 2.4 24.8 1.0 O A:HOH2486 2.4 25.2 1.0 O A:ASP278 2.4 13.4 1.0 O A:HOH2478 2.7 19.3 1.0 OG A:SER281 2.7 21.2 1.0 C A:ASP278 3.5 13.4 1.0 OE1 A:GLU282 3.8 22.6 0.5 CB A:SER281 3.8 17.1 1.0 CA A:ASP278 4.0 14.6 1.0 O A:HOH2229 4.4 21.4 0.5 OE1 A:GLU282 4.5 26.3 0.5 N A:SER281 4.6 14.6 1.0 N A:ASP279 4.6 13.8 1.0 O A:LYS277 4.7 13.6 1.0 CB A:ASP278 4.7 15.1 1.0 CD A:GLU282 4.8 20.9 0.5 O A:HOH2491 4.8 20.4 0.5 CA A:SER281 4.8 16.5 1.0 O A:HOH2215 4.9 42.6 1.0

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


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 Gluco-Hydroximolactam within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1445 b:21.4 occ:1.00 O B:HOH2366 2.4 21.2 1.0 OD1 B:ASP278 2.4 24.4 1.0 O B:HOH2361 2.5 23.9 1.0 CG B:ASP278 3.5 21.6 1.0 CB B:ASP278 4.1 18.4 1.0 O B:HOH2369 4.2 29.3 0.5 CA B:ASP278 4.4 17.6 1.0 O B:HOH2359 4.5 31.9 1.0 OD2 B:ASP278 4.6 24.8 1.0 O B:HOH2367 4.8 25.0 1.0 ND2 B:ASN275 4.8 24.7 1.0 O B:HOH2368 4.9 39.7 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