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Calcium in PDB 1d7f: Crystal Structure of Asparagine 233-Replaced Cyclodextrin Glucanotransferase From Alkalophilic Bacillus Sp. 1011 Determined at 1.9 A Resolution

Enzymatic activity of Crystal Structure of Asparagine 233-Replaced Cyclodextrin Glucanotransferase From Alkalophilic Bacillus Sp. 1011 Determined at 1.9 A Resolution

All present enzymatic activity of Crystal Structure of Asparagine 233-Replaced Cyclodextrin Glucanotransferase From Alkalophilic Bacillus Sp. 1011 Determined at 1.9 A Resolution:
2.4.1.19;

Protein crystallography data

The structure of Crystal Structure of Asparagine 233-Replaced Cyclodextrin Glucanotransferase From Alkalophilic Bacillus Sp. 1011 Determined at 1.9 A Resolution, PDB code: 1d7f 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 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 64.860, 74.460, 79.100, 85.10, 105.00, 100.90
R / Rfree (%) 15.6 / 20.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Asparagine 233-Replaced Cyclodextrin Glucanotransferase From Alkalophilic Bacillus Sp. 1011 Determined at 1.9 A Resolution (pdb code 1d7f). 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 Asparagine 233-Replaced Cyclodextrin Glucanotransferase From Alkalophilic Bacillus Sp. 1011 Determined at 1.9 A Resolution, PDB code: 1d7f:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1d7f

Go back to Calcium Binding Sites List in 1d7f
Calcium binding site 1 out of 4 in the Crystal Structure of Asparagine 233-Replaced Cyclodextrin Glucanotransferase From Alkalophilic Bacillus Sp. 1011 Determined at 1.9 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 Asparagine 233-Replaced Cyclodextrin Glucanotransferase From Alkalophilic Bacillus Sp. 1011 Determined at 1.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca5001

b:14.2
occ:1.00
 OD1 A:ASN33 2.1 16.6 1.0
OD1 A:ASN32 2.2 14.2 1.0
O A:HOH5023 2.2 14.6 1.0
O A:GLY51 2.3 13.5 1.0
O A:ASN29 2.4 18.7 1.0
OD2 A:ASP53 2.5 14.6 1.0
OD2 A:ASP27 2.5 9.3 1.0
CG A:ASN33 3.3 14.1 1.0
CG A:ASP27 3.4 11.9 1.0
CG A:ASN32 3.4 11.1 1.0
C A:GLY51 3.5 11.1 1.0
CG A:ASP53 3.5 13.5 1.0
C A:ASN29 3.5 16.6 1.0
OD1 A:ASP27 4.0 11.7 1.0
CB A:ASP53 4.0 13.5 1.0
CA A:GLY51 4.0 9.1 1.0
N A:ASN33 4.1 14.5 1.0
O A:ALA111 4.1 12.2 1.0
ND2 A:ASN33 4.1 15.0 1.0
ND2 A:ASN32 4.1 12.0 1.0
CA A:ASN33 4.3 17.5 1.0
N A:PRO30 4.3 17.7 1.0
N A:ASN29 4.3 14.0 1.0
CA A:PRO30 4.3 16.9 1.0
C A:ASN32 4.3 14.5 1.0
CB A:ASN33 4.4 14.1 1.0
CB A:ASP27 4.4 9.2 1.0
CA A:ASN29 4.4 15.0 1.0
OD1 A:ASP53 4.5 10.2 1.0
CA A:ASP27 4.6 12.7 1.0
N A:GLY52 4.6 13.3 1.0
CB A:ASN32 4.6 15.3 1.0
C A:GLY52 4.7 8.5 1.0
N A:ASN32 4.7 16.5 1.0
O A:HOH5066 4.8 17.6 1.0
O A:ASN32 4.8 10.7 1.0
CA A:ASN32 4.8 13.8 1.0
C A:PRO30 4.8 16.1 1.0
CB A:ASN29 4.8 17.4 1.0
O A:PRO30 4.9 14.1 1.0
N A:ASP53 4.9 9.0 1.0
O A:GLY52 4.9 9.6 1.0
CA A:GLY52 4.9 12.1 1.0
C A:ASP27 5.0 15.3 1.0

Calcium binding site 2 out of 4 in 1d7f

Go back to Calcium Binding Sites List in 1d7f
Calcium binding site 2 out of 4 in the Crystal Structure of Asparagine 233-Replaced Cyclodextrin Glucanotransferase From Alkalophilic Bacillus Sp. 1011 Determined at 1.9 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 Asparagine 233-Replaced Cyclodextrin Glucanotransferase From Alkalophilic Bacillus Sp. 1011 Determined at 1.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca5003

b:30.2
occ:1.00
 O A:HOH5320 2.2 21.3 1.0
OD1 A:ASN139 2.3 15.5 1.0
O A:HOH5109 2.3 17.7 1.0
O A:HOH5056 2.3 24.6 1.0
O A:ASN233 2.4 16.7 1.0
O A:ILE190 2.4 13.1 1.0
OD1 A:ASP199 2.9 21.8 1.0
OD2 A:ASP199 3.1 24.6 1.0
CG A:ASP199 3.4 23.5 1.0
CG A:ASN139 3.5 12.2 1.0
C A:ILE190 3.5 14.4 1.0
C A:ASN233 3.6 15.3 1.0
ND2 A:ASN139 3.9 14.3 1.0
CA A:ILE190 4.1 12.1 1.0
CA A:MET234 4.4 14.8 1.0
N A:MET234 4.4 14.5 1.0
O A:GLY189 4.5 13.4 1.0
O A:ASN139 4.6 13.8 1.0
CG A:MET234 4.6 10.7 1.0
CA A:ASN233 4.6 14.5 1.0
N A:TYR191 4.7 14.9 1.0
O A:LYS192 4.7 19.6 1.0
CB A:ASN233 4.7 15.8 1.0
O A:HOH5362 4.7 27.9 1.0
CB A:ASN139 4.7 12.3 1.0
ND1 A:HIS176 4.8 17.1 1.0
CG2 A:ILE190 4.8 10.8 1.0
CB A:ASP199 4.8 19.4 1.0
O A:LEU200 5.0 16.4 1.0
CA A:TYR191 5.0 12.9 1.0
CE1 A:HIS176 5.0 18.0 1.0

Calcium binding site 3 out of 4 in 1d7f

Go back to Calcium Binding Sites List in 1d7f
Calcium binding site 3 out of 4 in the Crystal Structure of Asparagine 233-Replaced Cyclodextrin Glucanotransferase From Alkalophilic Bacillus Sp. 1011 Determined at 1.9 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 Asparagine 233-Replaced Cyclodextrin Glucanotransferase From Alkalophilic Bacillus Sp. 1011 Determined at 1.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca5002

b:19.1
occ:1.00
 OD1 B:ASN33 2.1 15.5 1.0
O B:HOH5279 2.2 20.0 1.0
OD1 B:ASN32 2.2 27.0 1.0
O B:GLY51 2.3 18.8 1.0
O B:ASN29 2.3 23.7 1.0
OD2 B:ASP27 2.5 15.3 1.0
OD2 B:ASP53 2.5 15.0 1.0
CG B:ASN33 3.3 15.3 1.0
CG B:ASP53 3.4 18.8 1.0
CG B:ASN32 3.5 24.4 1.0
C B:GLY51 3.5 16.5 1.0
CG B:ASP27 3.5 15.5 1.0
C B:ASN29 3.5 21.6 1.0
CB B:ASP53 3.8 16.8 1.0
CA B:GLY51 4.0 11.0 1.0
N B:ASN33 4.1 18.4 1.0
ND2 B:ASN33 4.1 15.6 1.0
OD1 B:ASP27 4.1 19.1 1.0
O B:ALA111 4.1 16.2 1.0
ND2 B:ASN32 4.2 28.3 1.0
N B:PRO30 4.2 21.7 1.0
CA B:PRO30 4.3 24.4 1.0
CA B:ASN33 4.3 18.2 1.0
C B:ASN32 4.4 19.2 1.0
N B:ASN29 4.4 22.9 1.0
CB B:ASN33 4.4 15.9 1.0
OD1 B:ASP53 4.4 18.8 1.0
CB B:ASP27 4.4 15.4 1.0
CA B:ASN29 4.4 21.6 1.0
CA B:ASP27 4.5 16.5 1.0
N B:GLY52 4.6 11.4 1.0
CB B:ASN32 4.6 25.0 1.0
O B:HOH5091 4.6 19.6 1.0
C B:GLY52 4.7 12.2 1.0
C B:PRO30 4.8 23.1 1.0
N B:ASP53 4.8 12.8 1.0
N B:ASN32 4.8 24.6 1.0
O B:ASN32 4.8 22.2 1.0
CA B:ASN32 4.8 22.0 1.0
O B:GLY52 4.8 12.9 1.0
CB B:ASN29 4.9 20.0 1.0
C B:ASP27 4.9 17.4 1.0
O B:PRO30 5.0 22.5 1.0
CA B:ASP53 5.0 13.4 1.0
CA B:GLY52 5.0 13.0 1.0

Calcium binding site 4 out of 4 in 1d7f

Go back to Calcium Binding Sites List in 1d7f
Calcium binding site 4 out of 4 in the Crystal Structure of Asparagine 233-Replaced Cyclodextrin Glucanotransferase From Alkalophilic Bacillus Sp. 1011 Determined at 1.9 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 Asparagine 233-Replaced Cyclodextrin Glucanotransferase From Alkalophilic Bacillus Sp. 1011 Determined at 1.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca5004

b:29.9
occ:1.00
 O B:HOH5028 2.2 19.9 1.0
OD1 B:ASN139 2.3 18.8 1.0
O B:HOH5054 2.3 19.7 1.0
O B:ASN233 2.3 17.0 1.0
O B:ILE190 2.4 17.1 1.0
O B:HOH5280 2.4 26.1 1.0
OD2 B:ASP199 2.9 28.8 1.0
OD1 B:ASP199 3.0 26.7 1.0
CG B:ASP199 3.3 27.2 1.0
CG B:ASN139 3.4 15.3 1.0
C B:ILE190 3.5 17.4 1.0
C B:ASN233 3.6 17.0 1.0
ND2 B:ASN139 3.9 18.7 1.0
CA B:ILE190 4.1 19.2 1.0
O B:GLY189 4.3 18.9 1.0
CA B:MET234 4.4 14.4 1.0
N B:MET234 4.4 14.5 1.0
CB B:ASN233 4.5 17.5 1.0
O B:LYS192 4.5 25.1 1.0
CA B:ASN233 4.5 18.3 1.0
O B:ASN139 4.6 16.0 1.0
CG B:MET234 4.6 15.3 1.0
N B:TYR191 4.6 15.6 1.0
CB B:ASN139 4.7 11.4 1.0
O B:HOH5321 4.8 31.2 1.0
CB B:ASP199 4.8 21.0 1.0
CG2 B:ILE190 4.9 19.5 1.0
ND1 B:HIS176 4.9 20.7 1.0
CA B:TYR191 5.0 19.4 1.0

Reference:

N.Ishii, K.Haga, K.Yamane, K.Harata. Crystal Structure of Asparagine 233-Replaced Cyclodextrin Glucanotransferase From Alkalophilic Bacillus Sp. 1011 Determined at 1.9 A Resolution. J.Mol.Recog. V. 13 35 2000.
ISSN: ISSN 0952-3499
PubMed: 10679895
DOI: 10.1002/(SICI)1099-1352(200001/02)13:1<35::AID-JMR481>3.0.CO;2-J
Page generated: Thu Jul 11 07:24:37 2024

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