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Calcium in PDB 1ded: Crystal Structure of Alkalophilic Asparagine 233-Replaced Cyclodextrin Glucanotransferase Complexed with An Inhibitor, Acarbose, at 2.0 A Resolution

Enzymatic activity of Crystal Structure of Alkalophilic Asparagine 233-Replaced Cyclodextrin Glucanotransferase Complexed with An Inhibitor, Acarbose, at 2.0 A Resolution

All present enzymatic activity of Crystal Structure of Alkalophilic Asparagine 233-Replaced Cyclodextrin Glucanotransferase Complexed with An Inhibitor, Acarbose, at 2.0 A Resolution:
2.4.1.19;

Protein crystallography data

The structure of Crystal Structure of Alkalophilic Asparagine 233-Replaced Cyclodextrin Glucanotransferase Complexed with An Inhibitor, Acarbose, at 2.0 A Resolution, PDB code: 1ded was solved by N.Ishii, 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 (°) 64.930, 73.830, 79.050, 85.10, 105.40, 100.50
R / Rfree (%) 16.3 / 22.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Alkalophilic Asparagine 233-Replaced Cyclodextrin Glucanotransferase Complexed with An Inhibitor, Acarbose, at 2.0 A Resolution (pdb code 1ded). 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 Alkalophilic Asparagine 233-Replaced Cyclodextrin Glucanotransferase Complexed with An Inhibitor, Acarbose, at 2.0 A Resolution, PDB code: 1ded:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1ded

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Calcium binding site 1 out of 4 in the Crystal Structure of Alkalophilic Asparagine 233-Replaced Cyclodextrin Glucanotransferase Complexed with An Inhibitor, Acarbose, at 2.0 A Resolution


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 Alkalophilic Asparagine 233-Replaced Cyclodextrin Glucanotransferase Complexed with An Inhibitor, Acarbose, at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca5001

b:20.0
occ:1.00
 OD1 A:ASN33 2.1 26.0 1.0
O A:GLY51 2.2 10.2 1.0
OD1 A:ASN32 2.2 6.6 1.0
O A:ASN29 2.2 26.7 1.0
O A:HOH1911 2.2 13.8 1.0
OD2 A:ASP53 2.6 17.1 1.0
OD2 A:ASP27 2.9 2.0 1.0
H2 A:HOH1911 2.9 0.0 0.0
H1 A:HOH1911 3.0 0.0 0.0
CG A:ASN33 3.3 20.7 1.0
C A:GLY51 3.3 7.9 1.0
CG A:ASN32 3.4 9.5 1.0
C A:ASN29 3.5 22.1 1.0
CG A:ASP53 3.6 15.5 1.0
H A:ASN29 3.6 0.0 0.0
CG A:ASP27 3.7 9.7 1.0
CA A:GLY51 3.9 6.7 1.0
HD21 A:ASN32 4.0 0.0 0.0
O A:ALA111 4.0 14.3 1.0
CB A:ASP53 4.0 15.5 1.0
N A:ASN33 4.1 18.4 1.0
HD21 A:ASN33 4.1 0.0 0.0
ND2 A:ASN33 4.2 18.0 1.0
ND2 A:ASN32 4.2 7.5 1.0
CA A:ASN33 4.2 22.8 1.0
N A:PRO30 4.3 22.3 1.0
H A:ASN32 4.3 0.0 0.0
C A:ASN32 4.3 17.6 1.0
CA A:PRO30 4.3 20.2 1.0
N A:ASN29 4.3 17.4 1.0
OD1 A:ASP27 4.3 13.3 1.0
CB A:ASN33 4.3 19.1 1.0
CA A:ASN29 4.4 19.2 1.0
N A:GLY52 4.5 8.3 1.0
H A:ASN33 4.5 0.0 0.0
O A:ASN32 4.5 21.1 1.0
CB A:ASP27 4.6 8.7 1.0
CB A:ASN32 4.6 12.1 1.0
OD1 A:ASP53 4.6 10.4 1.0
C A:GLY52 4.6 15.0 1.0
CA A:ASP27 4.7 8.2 1.0
O A:GLY52 4.7 7.4 1.0
O A:HOH778 4.7 16.9 1.0
N A:ASN32 4.8 15.3 1.0
C A:PRO30 4.8 19.3 1.0
CA A:ASN32 4.8 15.5 1.0
O A:PRO30 4.8 21.0 1.0
CB A:ASN29 4.8 14.5 1.0
CA A:GLY52 4.9 10.1 1.0
N A:ASP53 5.0 12.7 1.0

Calcium binding site 2 out of 4 in 1ded

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Calcium binding site 2 out of 4 in the Crystal Structure of Alkalophilic Asparagine 233-Replaced Cyclodextrin Glucanotransferase Complexed with An Inhibitor, Acarbose, at 2.0 A Resolution


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 Alkalophilic Asparagine 233-Replaced Cyclodextrin Glucanotransferase Complexed with An Inhibitor, Acarbose, at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca5003

b:36.3
occ:1.00
 O A:HOH1933 2.2 22.7 1.0
OD1 A:ASN139 2.2 15.1 1.0
O A:HOH1931 2.2 24.9 1.0
O A:ASN233 2.4 10.7 1.0
O A:HOH1932 2.4 25.9 1.0
O A:ILE190 2.5 12.4 1.0
H1 A:HOH1931 2.9 0.0 0.0
H1 A:HOH1933 2.9 0.0 0.0
H2 A:HOH1933 2.9 0.0 0.0
OD2 A:ASP199 3.0 26.0 1.0
H2 A:HOH1931 3.0 0.0 0.0
OD1 A:ASP199 3.1 26.0 1.0
H1 A:HOH1932 3.1 0.0 0.0
H2 A:HOH1932 3.2 0.0 0.0
CG A:ASP199 3.4 23.8 1.0
CG A:ASN139 3.4 10.4 1.0
HD21 A:ASN139 3.5 0.0 0.0
C A:ILE190 3.6 15.9 1.0
C A:ASN233 3.6 10.3 1.0
ND2 A:ASN139 3.9 5.0 1.0
CA A:ILE190 4.1 11.7 1.0
HD1 A:HIS176 4.2 0.0 0.0
CA A:MET234 4.3 13.9 1.0
O A:ASN139 4.4 15.2 1.0
N A:MET234 4.4 13.4 1.0
O A:GLY189 4.5 14.9 1.0
CG A:MET234 4.5 8.3 1.0
ND1 A:HIS176 4.6 15.5 1.0
CE1 A:HIS176 4.6 17.8 1.0
HD1 A:HIS202 4.6 0.0 0.0
CG2 A:ILE190 4.6 11.8 1.0
CA A:ASN233 4.6 14.5 1.0
CB A:ASN139 4.6 9.0 1.0
O A:LYS192 4.7 25.7 1.0
N A:TYR191 4.7 15.8 1.0
O A:HOH3044 4.8 18.5 1.0
CB A:ASN233 4.8 6.9 1.0
CB A:ASP199 4.8 20.4 1.0
O A:LEU200 4.8 14.9 1.0
HD22 A:ASN139 4.9 0.0 0.0
CE1 A:HIS202 5.0 5.0 1.0
CA A:ASN139 5.0 10.8 1.0

Calcium binding site 3 out of 4 in 1ded

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Calcium binding site 3 out of 4 in the Crystal Structure of Alkalophilic Asparagine 233-Replaced Cyclodextrin Glucanotransferase Complexed with An Inhibitor, Acarbose, at 2.0 A Resolution


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 Alkalophilic Asparagine 233-Replaced Cyclodextrin Glucanotransferase Complexed with An Inhibitor, Acarbose, at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca5002

b:27.1
occ:1.00
 OD1 B:ASN33 2.1 23.0 1.0
O B:HOH1921 2.1 28.0 1.0
OD1 B:ASN32 2.2 23.3 1.0
O B:GLY51 2.3 28.3 1.0
OD2 B:ASP53 2.5 23.5 1.0
O B:ASN29 2.5 34.0 1.0
OD2 B:ASP27 2.6 11.1 1.0
H1 B:HOH1921 2.8 0.0 0.0
H2 B:HOH1921 2.9 0.0 0.0
CG B:ASN33 3.3 21.4 1.0
C B:GLY51 3.4 22.6 1.0
CG B:ASN32 3.5 23.9 1.0
CG B:ASP53 3.5 25.5 1.0
C B:ASN29 3.7 24.9 1.0
CG B:ASP27 3.7 12.7 1.0
H B:ASN29 3.8 0.0 0.0
CB B:ASP53 3.9 18.6 1.0
CA B:GLY51 4.0 21.2 1.0
O B:ALA111 4.0 17.1 1.0
HD21 B:ASN32 4.0 0.0 0.0
N B:ASN33 4.0 20.6 1.0
H B:ASN32 4.1 0.0 0.0
CA B:ASN33 4.1 20.6 1.0
ND2 B:ASN32 4.2 19.1 1.0
ND2 B:ASN33 4.2 22.4 1.0
C B:ASN32 4.2 25.2 1.0
HD21 B:ASN33 4.2 0.0 0.0
CB B:ASN33 4.3 14.6 1.0
N B:PRO30 4.4 26.0 1.0
OD1 B:ASP27 4.4 17.3 1.0
O B:ASN32 4.4 28.4 1.0
CA B:PRO30 4.4 29.2 1.0
H B:ASN33 4.4 0.0 0.0
OD1 B:ASP53 4.5 28.1 1.0
N B:ASN29 4.5 25.9 1.0
N B:GLY52 4.6 19.6 1.0
CA B:ASN29 4.6 24.3 1.0
CB B:ASN32 4.7 22.7 1.0
CB B:ASP27 4.7 13.3 1.0
C B:GLY52 4.7 15.6 1.0
O B:PRO30 4.7 27.5 1.0
N B:ASN32 4.7 26.1 1.0
CA B:ASN32 4.8 24.2 1.0
C B:PRO30 4.8 24.7 1.0
N B:ASP53 4.8 13.4 1.0
CA B:ASP27 4.8 18.2 1.0
O B:GLY52 4.8 8.8 1.0
CB B:ASN29 4.9 20.9 1.0
CA B:ASP53 5.0 15.1 1.0

Calcium binding site 4 out of 4 in 1ded

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Calcium binding site 4 out of 4 in the Crystal Structure of Alkalophilic Asparagine 233-Replaced Cyclodextrin Glucanotransferase Complexed with An Inhibitor, Acarbose, at 2.0 A Resolution


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 Alkalophilic Asparagine 233-Replaced Cyclodextrin Glucanotransferase Complexed with An Inhibitor, Acarbose, at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca5004

b:32.1
occ:1.00
 OD1 B:ASN139 2.2 13.8 1.0
O B:ASN233 2.2 15.2 1.0
O B:HOH1942 2.2 33.1 1.0
O B:ILE190 2.3 15.1 1.0
O B:HOH1943 2.3 19.8 1.0
O B:HOH1941 2.3 13.9 1.0
OD1 B:ASP199 2.7 16.2 1.0
H2 B:HOH1943 2.8 0.0 0.0
H2 B:HOH1942 2.9 0.0 0.0
H1 B:HOH1942 3.0 0.0 0.0
H2 B:HOH1941 3.0 0.0 0.0
H1 B:HOH1941 3.0 0.0 0.0
H1 B:HOH1943 3.1 0.0 0.0
CG B:ASN139 3.3 14.6 1.0
CG B:ASP199 3.4 19.6 1.0
C B:ILE190 3.4 19.3 1.0
OD2 B:ASP199 3.4 19.9 1.0
C B:ASN233 3.5 17.0 1.0
HD21 B:ASN139 3.6 0.0 0.0
ND2 B:ASN139 3.9 11.7 1.0
CA B:ILE190 4.0 16.4 1.0
HD1 B:HIS176 4.1 0.0 0.0
CA B:MET234 4.3 6.4 1.0
N B:MET234 4.3 13.1 1.0
O B:GLY189 4.4 17.3 1.0
O B:ASN139 4.5 23.2 1.0
CA B:ASN233 4.5 19.6 1.0
CG B:MET234 4.5 13.2 1.0
CB B:ASN233 4.5 18.2 1.0
O B:LYS192 4.6 22.8 1.0
N B:TYR191 4.6 21.3 1.0
CB B:ASN139 4.6 11.5 1.0
HD1 B:HIS202 4.7 0.0 0.0
CG2 B:ILE190 4.7 16.8 1.0
CB B:ASP199 4.8 17.1 1.0
HD22 B:ASN139 4.9 0.0 0.0
O B:LEU200 5.0 14.7 1.0
CB B:ILE190 5.0 16.0 1.0
CB B:MET234 5.0 11.2 1.0
ND1 B:HIS176 5.0 11.4 1.0
CA B:TYR191 5.0 20.3 1.0

Reference:

N.Ishii, K.Haga, K.Yamane, K.Harata. Crystal Structure of Alkalophilic Asparagine 233-Replaced Cyclodextrin Glucanotransferase Complexed with An Inhibitor, Acarbose, at 2.0 A Resolution. J.Biochem.(Tokyo) V. 127 383 2000.
ISSN: ISSN 0021-924X
PubMed: 10731709
Page generated: Thu Jul 11 07:32:14 2024

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