Calcium in PDB 1pam: Cyclodextrin Glucanotransferase

All present enzymatic activity of Cyclodextrin Glucanotransferase:
2.4.1.19;

The structure of Cyclodextrin Glucanotransferase, PDB code: 1pam was solved by K.Harata, K.Haga, A.Nakamura, M.Aoyagi, K.Yamane, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	64.930, 74.450, 79.120, 85.20, 105.00, 101.00
R / Rfree (%)	16.1 / 21.1

The binding sites of Calcium atom in the Cyclodextrin Glucanotransferase (pdb code 1pam). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Cyclodextrin Glucanotransferase, PDB code: 1pam:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Cyclodextrin Glucanotransferase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cyclodextrin Glucanotransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca687 b:15.1 occ:1.00 OD1 A:ASN33 2.1 17.5 1.0 OD1 A:ASN32 2.2 15.4 1.0 O A:HOH732 2.2 17.8 1.0 O A:ASN29 2.3 21.1 1.0 O A:GLY51 2.3 15.0 1.0 OD1 A:ASP27 2.4 15.0 1.0 OD2 A:ASP53 2.5 18.0 1.0 CG A:ASN33 3.3 16.5 1.0 CG A:ASP27 3.4 14.8 1.0 C A:ASN29 3.4 18.6 1.0 CG A:ASN32 3.5 15.1 1.0 C A:GLY51 3.5 11.1 1.0 CG A:ASP53 3.5 17.0 1.0 OD2 A:ASP27 4.0 16.0 1.0 CB A:ASP53 4.0 13.4 1.0 CA A:GLY51 4.0 12.2 1.0 ND2 A:ASN33 4.1 18.5 1.0 N A:ASN33 4.1 13.7 1.0 ND2 A:ASN32 4.2 14.4 1.0 N A:PRO30 4.2 19.8 1.0 N A:ASN29 4.3 18.8 1.0 O A:ALA111 4.3 16.0 1.0 CA A:PRO30 4.3 20.7 1.0 CA A:ASN33 4.3 15.6 1.0 CA A:ASN29 4.3 17.7 1.0 C A:ASN32 4.3 13.5 1.0 CB A:ASP27 4.4 12.8 1.0 CB A:ASN33 4.4 15.7 1.0 CA A:ASP27 4.5 14.6 1.0 OD1 A:ASP53 4.5 11.8 1.0 N A:GLY52 4.6 13.7 1.0 CB A:ASN32 4.6 15.8 1.0 CB A:ASN29 4.7 19.2 1.0 C A:GLY52 4.7 12.4 1.0 N A:ASN32 4.7 17.4 1.0 C A:PRO30 4.7 18.0 1.0 O A:PRO30 4.7 19.4 1.0 O A:ASN32 4.8 15.1 1.0 CA A:ASN32 4.8 13.7 1.0 O A:HOH743 4.9 18.9 1.0 O A:GLY52 4.9 13.1 1.0 N A:ASP53 4.9 11.3 1.0 C A:ASP27 4.9 15.0 1.0 CA A:GLY52 5.0 11.8 1.0

Calcium binding site 2 out of 4 in the Cyclodextrin Glucanotransferase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cyclodextrin Glucanotransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca688 b:26.3 occ:1.00 O A:HOH746 2.3 19.2 1.0 OD1 A:ASN139 2.3 18.4 1.0 O A:ILE190 2.4 14.6 1.0 O A:HIS233 2.4 13.8 1.0 O A:HOH725 2.4 16.9 1.0 O A:HOH815 2.4 26.0 1.0 OD2 A:ASP199 2.7 24.4 1.0 OD1 A:ASP199 3.1 21.8 1.0 CG A:ASP199 3.3 23.1 1.0 CG A:ASN139 3.4 15.5 1.0 C A:ILE190 3.5 15.0 1.0 C A:HIS233 3.6 14.4 1.0 ND2 A:ASN139 3.9 19.1 1.0 CA A:ILE190 4.1 14.2 1.0 O A:ASN139 4.5 14.1 1.0 CA A:MET234 4.5 14.0 1.0 O A:GLY189 4.5 14.5 1.0 N A:MET234 4.5 13.5 1.0 CB A:HIS233 4.5 14.8 1.0 CA A:HIS233 4.6 13.9 1.0 O A:LYS192 4.6 21.4 1.0 N A:TYR191 4.6 17.2 1.0 CG A:MET234 4.6 11.9 1.0 ND1 A:HIS176 4.7 16.6 1.0 CB A:ASN139 4.7 13.7 1.0 CB A:ASP199 4.7 18.1 1.0 CG2 A:ILE190 4.8 11.6 1.0 CE1 A:HIS176 4.9 19.1 1.0 O A:HOH808 4.9 25.6 1.0 CA A:TYR191 5.0 15.6 1.0

Calcium binding site 3 out of 4 in the Cyclodextrin Glucanotransferase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cyclodextrin Glucanotransferase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca687 b:19.0 occ:1.00 OD1 B:ASN33 2.1 20.0 1.0 OD1 B:ASN32 2.1 25.1 1.0 O B:HOH746 2.2 21.8 1.0 O B:ASN29 2.3 23.4 1.0 O B:GLY51 2.4 18.3 1.0 OD1 B:ASP27 2.5 18.9 1.0 OD2 B:ASP53 2.5 18.2 1.0 CG B:ASN32 3.4 24.0 1.0 CG B:ASN33 3.4 19.1 1.0 C B:ASN29 3.4 20.0 1.0 CG B:ASP27 3.5 19.5 1.0 CG B:ASP53 3.5 19.3 1.0 C B:GLY51 3.5 15.9 1.0 CB B:ASP53 3.9 15.1 1.0 CA B:GLY51 4.0 15.6 1.0 ND2 B:ASN32 4.0 27.7 1.0 OD2 B:ASP27 4.1 20.9 1.0 ND2 B:ASN33 4.1 18.5 1.0 N B:ASN33 4.1 19.3 1.0 O B:ALA111 4.2 17.4 1.0 N B:PRO30 4.2 23.3 1.0 N B:ASN29 4.3 21.1 1.0 CA B:ASN33 4.3 20.9 1.0 CA B:PRO30 4.3 24.8 1.0 C B:ASN32 4.4 19.9 1.0 CA B:ASN29 4.4 20.8 1.0 CB B:ASP27 4.4 18.3 1.0 CB B:ASN33 4.5 18.4 1.0 OD1 B:ASP53 4.5 17.8 1.0 CA B:ASP27 4.5 19.3 1.0 CB B:ASN32 4.6 24.2 1.0 N B:GLY52 4.6 17.8 1.0 C B:GLY52 4.7 15.2 1.0 CB B:ASN29 4.7 19.5 1.0 O B:HOH726 4.7 20.1 1.0 N B:ASN32 4.8 22.6 1.0 O B:ASN32 4.8 20.6 1.0 C B:PRO30 4.8 24.8 1.0 CA B:ASN32 4.8 21.9 1.0 N B:ASP53 4.9 14.0 1.0 O B:GLY52 4.9 14.8 1.0 O B:PRO30 4.9 26.4 1.0 C B:ASP27 4.9 18.9 1.0

Calcium binding site 4 out of 4 in the Cyclodextrin Glucanotransferase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cyclodextrin Glucanotransferase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca688 b:27.1 occ:1.00 O B:HOH785 2.2 26.2 1.0 O B:HOH700 2.3 15.6 1.0 OD1 B:ASN139 2.3 17.8 1.0 O B:ILE190 2.4 17.6 1.0 O B:HIS233 2.4 15.4 1.0 O B:HOH754 2.5 22.7 1.0 OD2 B:ASP199 2.8 29.9 1.0 OD1 B:ASP199 2.9 28.0 1.0 CG B:ASP199 3.2 27.1 1.0 CG B:ASN139 3.4 15.8 1.0 C B:ILE190 3.5 18.5 1.0 C B:HIS233 3.7 18.1 1.0 ND2 B:ASN139 4.0 20.6 1.0 CA B:ILE190 4.2 18.4 1.0 O B:ASN139 4.4 17.9 1.0 CB B:HIS233 4.4 14.3 1.0 O B:GLY189 4.5 19.4 1.0 CA B:MET234 4.5 16.0 1.0 N B:MET234 4.5 15.4 1.0 CA B:HIS233 4.6 16.5 1.0 O B:LYS192 4.6 23.2 1.0 CG B:MET234 4.6 16.2 1.0 N B:TYR191 4.7 18.1 1.0 CB B:ASP199 4.7 21.6 1.0 CB B:ASN139 4.7 14.6 1.0 ND1 B:HIS176 4.8 21.1 1.0 CG2 B:ILE190 4.8 16.7 1.0 O B:LEU200 4.9 15.8 1.0 CA B:TYR191 5.0 20.8 1.0

K.Harata, K.Haga, A.Nakamura, M.Aoyagi, K.Yamane. X-Ray Structure of Cyclodextrin Glucanotransferase From Alkalophilic Bacillus Sp. 1011. Comparison of Two Independent Molecules at 1.8 A Resolution. Acta Crystallogr.,Sect.D V. 52 1136 1996.
ISSN: ISSN 0907-4449
PubMed: 15299574
DOI: 10.1107/S0907444996008438