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Calcium in PDB 1ukq: Crystal Structure of Cyclodextrin Glucanotransferase Complexed with A Pseudo-Maltotetraose Derived From Acarbose

Enzymatic activity of Crystal Structure of Cyclodextrin Glucanotransferase Complexed with A Pseudo-Maltotetraose Derived From Acarbose

All present enzymatic activity of Crystal Structure of Cyclodextrin Glucanotransferase Complexed with A Pseudo-Maltotetraose Derived From Acarbose:
2.4.1.19;

Protein crystallography data

The structure of Crystal Structure of Cyclodextrin Glucanotransferase Complexed with A Pseudo-Maltotetraose Derived From Acarbose, PDB code: 1ukq was solved by K.Haga, R.Kanai, O.Sakamoto, K.Harata, K.Yamane, 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 (°) 64.940, 74.490, 79.100, 85.13, 105.02, 101.02
R / Rfree (%) 18.4 / 24.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Cyclodextrin Glucanotransferase Complexed with A Pseudo-Maltotetraose Derived From Acarbose (pdb code 1ukq). 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 Complexed with A Pseudo-Maltotetraose Derived From Acarbose, PDB code: 1ukq:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1ukq

Go back to Calcium Binding Sites List in 1ukq
Calcium binding site 1 out of 4 in the Crystal Structure of Cyclodextrin Glucanotransferase Complexed with A Pseudo-Maltotetraose Derived From Acarbose


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 Complexed with A Pseudo-Maltotetraose Derived From Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca687

b:9.5
occ:1.00
 OD1 A:ASN32 2.2 14.1 1.0
O A:HOH1444 2.2 10.5 1.0
OD1 A:ASN33 2.2 16.2 1.0
O A:GLY51 2.3 7.7 1.0
O A:ASN29 2.3 18.4 1.0
OD1 A:ASP53 2.4 10.4 1.0
OD2 A:ASP27 2.6 13.2 1.0
CG A:ASN32 3.4 13.7 1.0
CG A:ASP53 3.4 9.0 1.0
CG A:ASN33 3.4 19.8 1.0
CG A:ASP27 3.4 12.8 1.0
C A:GLY51 3.5 8.7 1.0
C A:ASN29 3.5 14.9 1.0
CB A:ASP53 3.9 7.4 1.0
OD1 A:ASP27 4.0 11.2 1.0
CA A:GLY51 4.1 5.6 1.0
N A:ASN33 4.1 14.0 1.0
ND2 A:ASN32 4.1 9.8 1.0
O A:ALA111 4.2 14.4 1.0
CA A:PRO30 4.2 19.2 1.0
N A:PRO30 4.2 17.6 1.0
ND2 A:ASN33 4.3 19.9 1.0
CA A:ASN33 4.3 14.9 1.0
C A:ASN32 4.3 14.1 1.0
CB A:ASP27 4.4 10.0 1.0
N A:ASN29 4.4 16.3 1.0
OD2 A:ASP53 4.4 7.3 1.0
CB A:ASN33 4.4 16.1 1.0
CA A:ASN29 4.5 16.8 1.0
CA A:ASP27 4.5 9.9 1.0
N A:GLY52 4.6 6.7 1.0
CB A:ASN32 4.6 14.1 1.0
C A:GLY52 4.6 5.5 1.0
C A:PRO30 4.7 17.3 1.0
O A:ASN32 4.8 10.6 1.0
O A:PRO30 4.8 18.5 1.0
N A:ASN32 4.8 17.2 1.0
O A:HOH1035 4.8 13.3 1.0
N A:ASP53 4.8 8.2 1.0
CA A:ASN32 4.8 13.5 1.0
O A:GLY52 4.8 8.2 1.0
CB A:ASN29 4.8 16.1 1.0
CA A:GLY52 4.9 8.0 1.0

Calcium binding site 2 out of 4 in 1ukq

Go back to Calcium Binding Sites List in 1ukq
Calcium binding site 2 out of 4 in the Crystal Structure of Cyclodextrin Glucanotransferase Complexed with A Pseudo-Maltotetraose Derived From Acarbose


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 Complexed with A Pseudo-Maltotetraose Derived From Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca688

b:18.0
occ:1.00
 O A:HOH1599 2.1 16.7 1.0
O A:HOH1289 2.2 10.5 1.0
OD1 A:ASN139 2.3 9.6 1.0
O A:ILE190 2.3 9.1 1.0
O A:HOH1456 2.3 7.2 1.0
O A:HIS233 2.3 10.2 1.0
OD2 A:ASP199 2.7 16.6 1.0
OD1 A:ASP199 3.0 11.9 1.0
CG A:ASP199 3.2 14.8 1.0
C A:ILE190 3.5 11.0 1.0
CG A:ASN139 3.5 6.9 1.0
C A:HIS233 3.6 11.7 1.0
ND2 A:ASN139 4.0 6.9 1.0
CA A:ILE190 4.0 11.2 1.0
N A:MET234 4.4 10.9 1.0
CA A:MET234 4.5 11.5 1.0
O A:ASN139 4.5 10.7 1.0
O A:HOH1348 4.5 16.9 1.0
CB A:HIS233 4.5 8.1 1.0
O A:GLY189 4.6 12.3 1.0
N A:TYR191 4.6 9.9 1.0
CA A:HIS233 4.6 9.1 1.0
O A:LYS192 4.6 17.1 1.0
CG2 A:ILE190 4.6 8.2 1.0
CG A:MET234 4.7 10.7 1.0
CB A:ASN139 4.7 6.0 1.0
CB A:ASP199 4.7 10.9 1.0
ND1 A:HIS176 4.7 15.7 1.0
O A:LEU200 4.8 19.9 1.0
CA A:TYR191 4.9 11.8 1.0
CE1 A:HIS176 5.0 16.1 1.0

Calcium binding site 3 out of 4 in 1ukq

Go back to Calcium Binding Sites List in 1ukq
Calcium binding site 3 out of 4 in the Crystal Structure of Cyclodextrin Glucanotransferase Complexed with A Pseudo-Maltotetraose Derived From Acarbose


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 Complexed with A Pseudo-Maltotetraose Derived From Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca689

b:16.3
occ:1.00
 OD1 B:ASN33 2.1 21.1 1.0
O B:HOH1625 2.1 16.1 1.0
OD1 B:ASN32 2.2 13.5 1.0
O B:GLY51 2.2 20.5 1.0
OD2 B:ASP27 2.4 21.0 1.0
O B:ASN29 2.4 20.8 1.0
OD2 B:ASP53 2.7 22.6 1.0
CG B:ASP53 3.3 20.5 1.0
CG B:ASN33 3.3 19.2 1.0
C B:GLY51 3.4 17.4 1.0
CG B:ASN32 3.4 13.1 1.0
CG B:ASP27 3.5 19.8 1.0
C B:ASN29 3.6 18.3 1.0
CB B:ASP53 3.7 18.8 1.0
O B:ALA111 3.9 9.6 1.0
CA B:GLY51 3.9 15.1 1.0
OD1 B:ASP53 4.1 24.0 1.0
ND2 B:ASN32 4.1 16.0 1.0
OD1 B:ASP27 4.1 20.5 1.0
N B:ASN33 4.1 13.0 1.0
ND2 B:ASN33 4.2 16.8 1.0
CA B:ASN33 4.3 16.1 1.0
N B:PRO30 4.4 19.2 1.0
N B:ASN29 4.4 16.7 1.0
CB B:ASN33 4.4 17.1 1.0
C B:ASN32 4.4 13.4 1.0
CA B:PRO30 4.5 19.8 1.0
CA B:ASN29 4.5 17.4 1.0
N B:GLY52 4.5 17.7 1.0
CB B:ASP27 4.5 16.3 1.0
O B:HOH1624 4.5 22.9 1.0
C B:GLY52 4.6 13.8 1.0
CB B:ASN32 4.6 14.4 1.0
CA B:ASP27 4.6 14.2 1.0
N B:ASP53 4.7 12.7 1.0
O B:PRO30 4.8 20.8 1.0
C B:PRO30 4.8 20.1 1.0
CB B:ASN29 4.8 18.0 1.0
O B:ASN32 4.8 14.2 1.0
O B:GLY52 4.8 12.8 1.0
N B:ASN32 4.8 16.1 1.0
CA B:ASN32 4.9 14.9 1.0
CA B:ASP53 4.9 14.7 1.0
CA B:GLY52 4.9 15.0 1.0

Calcium binding site 4 out of 4 in 1ukq

Go back to Calcium Binding Sites List in 1ukq
Calcium binding site 4 out of 4 in the Crystal Structure of Cyclodextrin Glucanotransferase Complexed with A Pseudo-Maltotetraose Derived From Acarbose


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 Complexed with A Pseudo-Maltotetraose Derived From Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca690

b:18.2
occ:1.00
 O B:HOH1579 2.0 15.5 1.0
OD1 B:ASN139 2.3 15.4 1.0
O B:HOH1297 2.3 14.6 1.0
O B:HOH1502 2.3 18.4 1.0
O B:HIS233 2.4 14.9 1.0
O B:ILE190 2.4 15.7 1.0
OD1 B:ASP199 2.8 17.3 1.0
OD2 B:ASP199 2.8 18.4 1.0
CG B:ASP199 3.2 18.1 1.0
CG B:ASN139 3.5 13.3 1.0
C B:ILE190 3.6 12.7 1.0
C B:HIS233 3.6 13.5 1.0
ND2 B:ASN139 4.0 15.7 1.0
CA B:ILE190 4.2 13.5 1.0
CA B:MET234 4.4 12.8 1.0
N B:MET234 4.4 12.4 1.0
O B:LYS192 4.4 18.3 1.0
O B:ASN139 4.5 12.7 1.0
CB B:HIS233 4.6 11.9 1.0
CA B:HIS233 4.6 12.6 1.0
CG B:MET234 4.6 11.9 1.0
N B:TYR191 4.7 12.9 1.0
CB B:ASP199 4.7 15.9 1.0
O B:HOH1580 4.7 32.8 1.0
CB B:ASN139 4.7 13.4 1.0
O B:GLY189 4.7 12.6 1.0
CG2 B:ILE190 4.8 12.8 1.0
O B:LEU200 4.9 15.1 1.0
ND1 B:HIS176 4.9 12.1 1.0
CA B:TYR191 4.9 16.2 1.0

Reference:

K.Haga, R.Kanai, O.Sakamoto, M.Aoyagi, K.Harata, K.Yamane. Effects of Essential Carbohydrate/Aromatic Stacking Interaction with TYR100 and PHE259 on Substrate Binding of Cyclodextrin Glycosyltransferase From Alkalophilic Bacillus Sp. 1011 J.Biochem.(Tokyo) V. 134 881 2003.
ISSN: ISSN 0021-924X
PubMed: 14769878
DOI: 10.1093/JB/MVG215
Page generated: Thu Jul 11 23:31:40 2024

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