Calcium in PDB 1d3c: Michaelis Complex of Bacillus Circulans Strain 251 Cyclodextrin Glycosyltransferase with Gamma-Cyclodextrin

All present enzymatic activity of Michaelis Complex of Bacillus Circulans Strain 251 Cyclodextrin Glycosyltransferase with Gamma-Cyclodextrin:
2.4.1.19;

The structure of Michaelis Complex of Bacillus Circulans Strain 251 Cyclodextrin Glycosyltransferase with Gamma-Cyclodextrin, PDB code: 1d3c was solved by J.C.M.Uitdehaag, K.H.Kalk, B.A.Van Der Veen, L.Dijkhuizen, B.W.Dijkstra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 1.78
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	117.791, 109.532, 65.223, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 25.8

The binding sites of Calcium atom in the Michaelis Complex of Bacillus Circulans Strain 251 Cyclodextrin Glycosyltransferase with Gamma-Cyclodextrin (pdb code 1d3c). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Michaelis Complex of Bacillus Circulans Strain 251 Cyclodextrin Glycosyltransferase with Gamma-Cyclodextrin, PDB code: 1d3c:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Michaelis Complex of Bacillus Circulans Strain 251 Cyclodextrin Glycosyltransferase with Gamma-Cyclodextrin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Michaelis Complex of Bacillus Circulans Strain 251 Cyclodextrin Glycosyltransferase with Gamma-Cyclodextrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca687 b:19.7 occ:1.00 OD1 A:ASN33 2.2 16.4 1.0 OD1 A:ASP27 2.2 17.3 1.0 OD2 A:ASP53 2.4 23.4 1.0 O A:GLY51 2.4 13.0 1.0 OD1 A:ASN32 2.5 20.0 1.0 O A:HOH950 2.5 12.5 1.0 O A:ASN29 2.6 22.0 1.0 CG A:ASP27 3.1 16.4 1.0 CG A:ASP53 3.4 22.9 1.0 C A:ASN29 3.4 23.1 1.0 CG A:ASN33 3.4 25.5 1.0 C A:GLY51 3.5 15.5 1.0 CG A:ASN32 3.6 28.3 1.0 OD2 A:ASP27 3.7 16.5 1.0 CB A:ASP53 3.8 16.0 1.0 CA A:GLY51 3.9 12.8 1.0 ND2 A:ASN32 4.1 20.4 1.0 N A:ASN33 4.1 16.3 1.0 N A:ASN29 4.1 19.5 1.0 N A:PRO30 4.1 21.1 1.0 CB A:ASP27 4.2 15.0 1.0 ND2 A:ASN33 4.2 22.7 1.0 CA A:PRO30 4.2 20.8 1.0 CA A:ASN29 4.3 19.1 1.0 O A:ALA111 4.4 18.9 1.0 OD1 A:ASP53 4.4 23.4 1.0 CA A:ASN33 4.4 16.0 1.0 CA A:ASP27 4.4 13.8 1.0 C A:ASN32 4.4 20.7 1.0 CB A:ASN33 4.5 13.7 1.0 N A:GLY52 4.6 12.7 1.0 N A:ASP53 4.6 15.4 1.0 C A:GLY52 4.7 17.5 1.0 C A:PRO30 4.7 24.3 1.0 N A:ASN32 4.7 20.9 1.0 C A:ASP27 4.7 18.8 1.0 CB A:ASN29 4.7 17.8 1.0 O A:HOH777 4.8 14.3 1.0 CB A:ASN32 4.8 18.7 1.0 N A:GLY28 4.8 16.5 1.0 CA A:ASN32 4.9 19.4 1.0 CA A:ASP53 4.9 15.0 1.0 O A:ASN32 4.9 22.1 1.0 O A:GLY52 4.9 16.3 1.0 O A:PRO30 4.9 22.8 1.0

Calcium binding site 2 out of 3 in the Michaelis Complex of Bacillus Circulans Strain 251 Cyclodextrin Glycosyltransferase with Gamma-Cyclodextrin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Michaelis Complex of Bacillus Circulans Strain 251 Cyclodextrin Glycosyltransferase with Gamma-Cyclodextrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca688 b:12.6 occ:1.00 O A:HOH867 2.4 11.5 1.0 O A:HOH866 2.4 12.7 1.0 O A:HIS233 2.4 14.7 1.0 OD2 A:ASP199 2.4 10.5 1.0 O A:HOH915 2.4 12.4 1.0 O A:ILE190 2.5 16.1 1.0 OD1 A:ASP199 2.5 14.2 1.0 OD1 A:ASN139 2.5 11.5 1.0 CG A:ASP199 2.8 11.9 1.0 CG A:ASN139 3.6 17.8 1.0 C A:HIS233 3.6 15.2 1.0 C A:ILE190 3.7 16.9 1.0 ND2 A:ASN139 4.1 18.1 1.0 O A:ASN139 4.3 13.6 1.0 CA A:ILE190 4.3 9.5 1.0 CB A:ASP199 4.3 5.2 1.0 O A:LYS192 4.4 22.6 1.0 CA A:MET234 4.5 8.7 1.0 N A:MET234 4.5 10.3 1.0 CB A:HIS233 4.5 10.3 1.0 O A:HOH788 4.5 14.0 1.0 O A:GLY189 4.5 10.5 1.0 CA A:HIS233 4.6 9.5 1.0 ND1 A:HIS176 4.6 16.7 1.0 O A:LEU200 4.7 16.9 1.0 N A:TYR191 4.7 15.6 1.0 CG A:MET234 4.7 11.9 1.0 CB A:ASN139 4.9 10.1 1.0 CE1 A:HIS176 4.9 15.9 1.0 CG2 A:ILE190 4.9 11.3 1.0 O A:HOH736 5.0 13.8 1.0 CA A:TYR191 5.0 15.5 1.0

Calcium binding site 3 out of 3 in the Michaelis Complex of Bacillus Circulans Strain 251 Cyclodextrin Glycosyltransferase with Gamma-Cyclodextrin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Michaelis Complex of Bacillus Circulans Strain 251 Cyclodextrin Glycosyltransferase with Gamma-Cyclodextrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca689 b:22.1 occ:1.00 O A:ALA315 2.3 9.7 1.0 O A:HOH806 2.4 8.6 1.0 O A:HOH978 2.4 15.6 1.0 O A:HOH1057 2.4 17.5 1.0 O A:HOH1344 2.5 39.5 1.0 O A:HOH927 2.6 28.9 1.0 OD1 A:ASP577 2.7 26.6 1.0 C A:ALA315 3.4 12.4 1.0 CG A:ASP577 3.8 27.4 1.0 CA A:ALA315 4.1 11.7 1.0 O A:HOH889 4.2 12.2 1.0 OD2 A:ASP577 4.3 34.3 1.0 O A:HOH1240 4.4 43.9 1.0 OE1 A:GLN316 4.5 11.4 1.0 O A:ASP577 4.5 12.8 1.0 N A:GLN316 4.5 9.5 1.0 CB A:ALA315 4.6 11.5 1.0 O A:HOH724 4.6 34.6 1.0 O A:HOH905 4.7 13.8 1.0 N A:ASP577 4.7 14.0 1.0 CA A:GLN316 4.8 6.9 1.0 O A:HOH822 4.8 12.7 1.0 C A:ASP577 4.9 13.8 1.0 CG A:GLN316 5.0 5.3 1.0

J.C.Uitdehaag, K.H.Kalk, B.A.Van Der Veen, L.Dijkhuizen, B.W.Dijkstra. The Cyclization Mechanism of Cyclodextrin Glycosyltransferase (Cgtase) As Revealed By A Gamma-Cyclodextrin-Cgtase Complex at 1.8-A Resolution. J.Biol.Chem. V. 274 34868 1999.
ISSN: ISSN 0021-9258
PubMed: 10574960
DOI: 10.1074/JBC.274.49.34868