Calcium in PDB 2cxg: Cyclodextrin Glycosyltransferase Complexed to the Inhibitor Acarbose

All present enzymatic activity of Cyclodextrin Glycosyltransferase Complexed to the Inhibitor Acarbose:
2.4.1.19;

The structure of Cyclodextrin Glycosyltransferase Complexed to the Inhibitor Acarbose, PDB code: 2cxg was solved by B.V.Strokopytov, J.C.M.Uitdehaag, R.Ruiterkamp, B.W.Dijkstra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	120.887, 111.903, 65.748, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 23.7

The binding sites of Calcium atom in the Cyclodextrin Glycosyltransferase Complexed to the Inhibitor Acarbose (pdb code 2cxg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Cyclodextrin Glycosyltransferase Complexed to the Inhibitor Acarbose, PDB code: 2cxg:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Cyclodextrin Glycosyltransferase Complexed to the Inhibitor Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cyclodextrin Glycosyltransferase Complexed to the Inhibitor Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca688 b:14.4 occ:1.00 OD1 A:ASN33 2.2 28.1 1.0 OD1 A:ASN32 2.4 18.9 1.0 O A:HOH728 2.5 9.9 1.0 O A:ASN29 2.5 16.1 1.0 OD2 A:ASP53 2.5 24.1 1.0 O A:GLY51 2.5 15.3 1.0 OD1 A:ASP27 2.6 17.1 1.0 CG A:ASP27 3.3 17.0 1.0 CG A:ASN33 3.4 36.0 1.0 C A:ASN29 3.5 16.4 1.0 CG A:ASP53 3.5 20.0 1.0 CG A:ASN32 3.5 27.4 1.0 C A:GLY51 3.6 15.4 1.0 OD2 A:ASP27 3.7 18.0 1.0 CB A:ASP53 3.9 8.7 1.0 CA A:GLY51 4.0 13.3 1.0 N A:ASN33 4.0 13.5 1.0 ND2 A:ASN32 4.1 17.9 1.0 CA A:PRO30 4.2 12.1 1.0 ND2 A:ASN33 4.2 33.4 1.0 N A:PRO30 4.2 12.3 1.0 CA A:ASN33 4.3 14.5 1.0 O A:ALA111 4.3 11.2 1.0 C A:ASN32 4.4 16.3 1.0 N A:ASN29 4.4 14.1 1.0 CB A:ASP27 4.4 12.6 1.0 OD1 A:ASP53 4.4 21.4 1.0 CB A:ASN33 4.4 11.8 1.0 CA A:ASN29 4.4 12.9 1.0 CA A:ASP27 4.6 11.2 1.0 O A:GLY52 4.6 12.5 1.0 O A:HOH748 4.7 21.7 1.0 C A:GLY52 4.7 12.4 1.0 C A:PRO30 4.7 16.9 1.0 CB A:ASN32 4.8 9.5 1.0 N A:GLY52 4.8 10.2 1.0 N A:ASN32 4.8 12.6 1.0 O A:ASN32 4.8 16.7 1.0 CA A:ASN32 4.8 11.4 1.0 N A:ASP53 4.9 8.4 1.0 CB A:ASN29 4.9 8.3 1.0 O A:PRO30 5.0 17.7 1.0 C A:ASP27 5.0 16.5 1.0

Calcium binding site 2 out of 2 in the Cyclodextrin Glycosyltransferase Complexed to the Inhibitor Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cyclodextrin Glycosyltransferase Complexed to the Inhibitor Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca689 b:12.5 occ:1.00 O A:HOH790 2.4 36.1 1.0 O A:HIS233 2.4 7.6 1.0 OD1 A:ASP199 2.4 16.7 1.0 O A:ILE190 2.6 9.0 1.0 OD2 A:ASP199 2.6 9.6 1.0 OD1 A:ASN139 2.7 5.2 1.0 O A:HOH706 2.8 5.2 1.0 CG A:ASP199 2.9 14.0 1.0 C A:HIS233 3.6 8.0 1.0 C A:ILE190 3.6 8.6 1.0 CG A:ASN139 3.8 15.3 1.0 ND2 A:ASN139 4.2 5.0 1.0 CA A:ILE190 4.3 4.5 1.0 CB A:ASP199 4.4 7.4 1.0 O A:LYS192 4.4 10.3 1.0 CB A:HIS233 4.5 3.0 1.0 O A:ASN139 4.5 13.3 1.0 N A:MET234 4.5 3.8 1.0 CA A:HIS233 4.6 3.3 1.0 CA A:MET234 4.6 3.0 1.0 O A:HOH780 4.6 27.0 1.0 N A:TYR191 4.7 4.4 1.0 ND1 A:HIS176 4.7 11.3 1.0 CG2 A:ILE190 4.7 5.4 1.0 O A:LEU200 4.7 10.4 1.0 O A:GLY189 4.8 12.1 1.0 O A:HOH732 4.9 12.3 1.0 CG A:MET234 4.9 6.9 1.0 CA A:TYR191 4.9 3.7 1.0

B.Strokopytov, D.Penninga, H.J.Rozeboom, K.H.Kalk, L.Dijkhuizen, B.W.Dijkstra. X-Ray Structure of Cyclodextrin Glycosyltransferase Complexed with Acarbose. Implications For the Catalytic Mechanism of Glycosidases. Biochemistry V. 34 2234 1995.
ISSN: ISSN 0006-2960
PubMed: 7857935
DOI: 10.1021/BI00007A018