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Calcium in PDB 1i75: Crystal Structure of Cyclodextrin Glucanotransferase From Alkalophilic Bacillus Sp.#1011 Complexed with 1-Deoxynojirimycin

Enzymatic activity of Crystal Structure of Cyclodextrin Glucanotransferase From Alkalophilic Bacillus Sp.#1011 Complexed with 1-Deoxynojirimycin

All present enzymatic activity of Crystal Structure of Cyclodextrin Glucanotransferase From Alkalophilic Bacillus Sp.#1011 Complexed with 1-Deoxynojirimycin:
2.4.1.19;

Protein crystallography data

The structure of Crystal Structure of Cyclodextrin Glucanotransferase From Alkalophilic Bacillus Sp.#1011 Complexed with 1-Deoxynojirimycin, PDB code: 1i75 was solved by R.Kanai, K.Haga, K.Yamane, K.Harata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 64.780, 74.240, 79.030, 85.03, 104.88, 101.02
R / Rfree (%) 15.4 / 21.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Cyclodextrin Glucanotransferase From Alkalophilic Bacillus Sp.#1011 Complexed with 1-Deoxynojirimycin (pdb code 1i75). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Cyclodextrin Glucanotransferase From Alkalophilic Bacillus Sp.#1011 Complexed with 1-Deoxynojirimycin, PDB code: 1i75:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1i75

Go back to Calcium Binding Sites List in 1i75
Calcium binding site 1 out of 4 in the Crystal Structure of Cyclodextrin Glucanotransferase From Alkalophilic Bacillus Sp.#1011 Complexed with 1-Deoxynojirimycin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Cyclodextrin Glucanotransferase From Alkalophilic Bacillus Sp.#1011 Complexed with 1-Deoxynojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1687

b:7.8
occ:1.00
 OD1 A:ASN33 2.1 10.9 1.0
OD1 A:ASN32 2.1 6.3 1.0
O A:HOH1184 2.2 4.3 1.0
O A:GLY51 2.4 9.1 1.0
O A:ASN29 2.4 11.1 1.0
OD1 A:ASP53 2.4 9.7 1.0
OD2 A:ASP27 2.6 6.5 1.0
CG A:ASN32 3.3 7.5 1.0
CG A:ASN33 3.4 9.0 1.0
CG A:ASP53 3.5 9.2 1.0
C A:ASN29 3.5 9.7 1.0
C A:GLY51 3.5 5.8 1.0
CG A:ASP27 3.5 7.2 1.0
CB A:ASP53 4.0 7.2 1.0
ND2 A:ASN32 4.0 5.7 1.0
CA A:GLY51 4.0 6.1 1.0
N A:ASN33 4.1 6.5 1.0
OD1 A:ASP27 4.1 7.2 1.0
O A:ALA111 4.2 8.4 1.0
ND2 A:ASN33 4.2 8.3 1.0
N A:PRO30 4.2 12.9 1.0
CA A:ASN33 4.3 8.0 1.0
N A:ASN29 4.3 10.4 1.0
C A:ASN32 4.3 10.0 1.0
CA A:PRO30 4.3 12.8 1.0
CA A:ASN29 4.4 7.8 1.0
CB A:ASN33 4.4 7.0 1.0
OD2 A:ASP53 4.5 6.2 1.0
CB A:ASP27 4.5 7.5 1.0
CB A:ASN32 4.5 8.3 1.0
CA A:ASP27 4.6 7.5 1.0
N A:GLY52 4.6 8.3 1.0
C A:GLY52 4.7 5.7 1.0
O A:ASN32 4.7 11.5 1.0
N A:ASN32 4.7 13.1 1.0
CB A:ASN29 4.7 8.2 1.0
O A:GLY52 4.8 6.4 1.0
CA A:ASN32 4.8 9.8 1.0
C A:PRO30 4.8 11.2 1.0
N A:ASP53 4.9 4.1 1.0
O A:HOH723 4.9 9.4 1.0
O A:PRO30 4.9 12.4 1.0
C A:ASP27 5.0 11.0 1.0

Calcium binding site 2 out of 4 in 1i75

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Calcium binding site 2 out of 4 in the Crystal Structure of Cyclodextrin Glucanotransferase From Alkalophilic Bacillus Sp.#1011 Complexed with 1-Deoxynojirimycin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Cyclodextrin Glucanotransferase From Alkalophilic Bacillus Sp.#1011 Complexed with 1-Deoxynojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1688

b:10.1
occ:1.00
 O A:HOH1137 2.1 13.8 1.0
O A:HOH751 2.3 8.6 1.0
O A:HOH739 2.3 9.3 1.0
OD1 A:ASN139 2.3 5.8 1.0
O A:HIS233 2.4 5.0 1.0
O A:ILE190 2.5 5.0 1.0
OD1 A:ASP199 2.6 13.4 1.0
OD2 A:ASP199 2.8 12.3 1.0
CG A:ASP199 3.1 11.6 1.0
CG A:ASN139 3.5 7.2 1.0
C A:ILE190 3.6 6.2 1.0
C A:HIS233 3.7 5.8 1.0
ND2 A:ASN139 4.0 7.2 1.0
CA A:ILE190 4.2 5.6 1.0
O A:ASN139 4.4 7.6 1.0
CA A:MET234 4.5 5.5 1.0
O A:GLY189 4.5 8.5 1.0
O A:LYS192 4.5 12.4 1.0
O A:HOH1149 4.5 17.3 1.0
CB A:HIS233 4.5 5.0 1.0
N A:MET234 4.5 4.6 1.0
CB A:ASP199 4.6 8.5 1.0
CA A:HIS233 4.6 4.7 1.0
CG A:MET234 4.7 6.1 1.0
N A:TYR191 4.7 6.8 1.0
ND1 A:HIS176 4.7 7.5 1.0
CB A:ASN139 4.7 4.2 1.0
CG2 A:ILE190 4.8 4.4 1.0
O A:LEU200 4.9 9.8 1.0
CE1 A:HIS176 4.9 7.9 1.0
CA A:TYR191 4.9 7.5 1.0

Calcium binding site 3 out of 4 in 1i75

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Calcium binding site 3 out of 4 in the Crystal Structure of Cyclodextrin Glucanotransferase From Alkalophilic Bacillus Sp.#1011 Complexed with 1-Deoxynojirimycin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Cyclodextrin Glucanotransferase From Alkalophilic Bacillus Sp.#1011 Complexed with 1-Deoxynojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1689

b:11.9
occ:1.00
 OD1 B:ASN33 2.1 12.9 1.0
O B:HOH1095 2.2 17.8 1.0
O B:GLY51 2.2 11.6 1.0
OD1 B:ASN32 2.2 11.8 1.0
O B:ASN29 2.4 20.3 1.0
OD2 B:ASP53 2.4 9.2 1.0
OD2 B:ASP27 2.5 9.9 1.0
CG B:ASN33 3.3 11.1 1.0
C B:GLY51 3.4 10.9 1.0
CG B:ASP53 3.4 12.2 1.0
CG B:ASN32 3.5 10.2 1.0
CG B:ASP27 3.5 9.2 1.0
C B:ASN29 3.5 16.5 1.0
CB B:ASP53 3.9 10.7 1.0
CA B:GLY51 3.9 8.8 1.0
ND2 B:ASN32 4.1 14.1 1.0
ND2 B:ASN33 4.1 10.0 1.0
OD1 B:ASP27 4.1 14.8 1.0
O B:ALA111 4.1 13.1 1.0
N B:ASN33 4.2 11.3 1.0
N B:PRO30 4.3 19.6 1.0
CA B:PRO30 4.3 20.2 1.0
N B:ASN29 4.3 15.0 1.0
OD1 B:ASP53 4.3 11.1 1.0
CA B:ASN33 4.4 12.6 1.0
CA B:ASN29 4.4 13.3 1.0
CB B:ASN33 4.4 10.3 1.0
CB B:ASP27 4.5 10.8 1.0
C B:ASN32 4.5 14.3 1.0
N B:GLY52 4.5 11.3 1.0
CA B:ASP27 4.5 12.4 1.0
C B:GLY52 4.6 10.7 1.0
CB B:ASN32 4.7 14.1 1.0
CB B:ASN29 4.8 12.3 1.0
C B:PRO30 4.8 20.0 1.0
N B:ASP53 4.8 7.3 1.0
O B:GLY52 4.8 11.8 1.0
N B:ASN32 4.8 16.4 1.0
O B:ASN32 4.9 15.3 1.0
O B:PRO30 4.9 23.0 1.0
O B:HOH860 4.9 14.9 1.0
CA B:GLY52 4.9 10.4 1.0
C B:ASP27 4.9 11.5 1.0
CA B:ASN32 4.9 14.9 1.0
N B:GLY28 5.0 12.5 1.0
CA B:ASP53 5.0 7.6 1.0

Calcium binding site 4 out of 4 in 1i75

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Calcium binding site 4 out of 4 in the Crystal Structure of Cyclodextrin Glucanotransferase From Alkalophilic Bacillus Sp.#1011 Complexed with 1-Deoxynojirimycin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Cyclodextrin Glucanotransferase From Alkalophilic Bacillus Sp.#1011 Complexed with 1-Deoxynojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1690

b:13.0
occ:1.00
 O B:HOH784 2.1 13.6 1.0
O B:HOH1082 2.2 12.4 1.0
OD1 B:ASN139 2.3 12.4 1.0
O B:HOH1071 2.3 10.5 1.0
O B:HIS233 2.3 10.4 1.0
O B:ILE190 2.6 12.4 1.0
OD2 B:ASP199 2.8 18.5 1.0
OD1 B:ASP199 2.8 15.0 1.0
CG B:ASP199 3.1 16.9 1.0
CG B:ASN139 3.5 9.3 1.0
C B:HIS233 3.6 11.1 1.0
C B:ILE190 3.7 12.3 1.0
ND2 B:ASN139 4.0 11.7 1.0
CA B:ILE190 4.3 10.2 1.0
CA B:MET234 4.4 9.9 1.0
N B:MET234 4.4 6.7 1.0
O B:ASN139 4.5 10.3 1.0
CB B:HIS233 4.5 7.6 1.0
O B:GLY189 4.5 13.7 1.0
CA B:HIS233 4.5 9.8 1.0
O B:HOH1066 4.6 14.3 1.0
O B:LYS192 4.6 14.2 1.0
CG B:MET234 4.6 6.0 1.0
CB B:ASP199 4.6 12.8 1.0
CB B:ASN139 4.7 7.3 1.0
N B:TYR191 4.8 13.7 1.0
CG2 B:ILE190 4.9 8.7 1.0
O B:LEU200 4.9 11.5 1.0

Reference:

R.Kanai, K.Haga, K.Yamane, K.Harata. Crystal Structure of Cyclodextrin Glucanotransferase From Alkalophilic Bacillus Sp. 1011 Complexed with 1-Deoxynojirimycin at 2.0 A Resolution. J.Biochem.(Tokyo) V. 129 593 2001.
ISSN: ISSN 0021-924X
PubMed: 11275559
Page generated: Mon Jul 7 15:47:13 2025

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