Calcium in PDB 1tcm: Cyclodextrin Glycosyltransferase W616A Mutant From Bacillus Circulans Strain 251
Enzymatic activity of Cyclodextrin Glycosyltransferase W616A Mutant From Bacillus Circulans Strain 251
All present enzymatic activity of Cyclodextrin Glycosyltransferase W616A Mutant From Bacillus Circulans Strain 251:
2.4.1.19;
Protein crystallography data
The structure of Cyclodextrin Glycosyltransferase W616A Mutant From Bacillus Circulans Strain 251, PDB code: 1tcm
was solved by
R.M.A.Knegtel,
B.W.Dijkstra,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
6.50 /
2.20
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
73.700,
84.800,
118.300,
90.00,
107.00,
90.00
|
R / Rfree (%)
|
19.3 /
25
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Cyclodextrin Glycosyltransferase W616A Mutant From Bacillus Circulans Strain 251
(pdb code 1tcm). 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 Glycosyltransferase W616A Mutant From Bacillus Circulans Strain 251, PDB code: 1tcm:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 1tcm
Go back to
Calcium Binding Sites List in 1tcm
Calcium binding site 1 out
of 4 in the Cyclodextrin Glycosyltransferase W616A Mutant From Bacillus Circulans Strain 251
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Cyclodextrin Glycosyltransferase W616A Mutant From Bacillus Circulans Strain 251 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca687
b:23.5
occ:1.00
|
OD2
|
A:ASP53
|
2.4
|
26.8
|
1.0
|
OD1
|
A:ASN32
|
2.5
|
14.4
|
1.0
|
OD1
|
A:ASP27
|
2.6
|
20.5
|
1.0
|
O
|
A:GLY51
|
2.6
|
21.5
|
1.0
|
O
|
A:ASN29
|
2.7
|
26.1
|
1.0
|
OD1
|
A:ASN33
|
2.8
|
26.9
|
1.0
|
CG
|
A:ASP53
|
3.5
|
21.4
|
1.0
|
CG
|
A:ASN32
|
3.5
|
30.1
|
1.0
|
CG
|
A:ASP27
|
3.5
|
24.2
|
1.0
|
C
|
A:GLY51
|
3.6
|
20.8
|
1.0
|
C
|
A:ASN29
|
3.7
|
25.2
|
1.0
|
CB
|
A:ASP53
|
3.9
|
13.4
|
1.0
|
CG
|
A:ASN33
|
3.9
|
30.0
|
1.0
|
CA
|
A:GLY51
|
4.0
|
23.1
|
1.0
|
ND2
|
A:ASN32
|
4.0
|
18.5
|
1.0
|
N
|
A:ASN33
|
4.1
|
21.7
|
1.0
|
OD2
|
A:ASP27
|
4.2
|
23.1
|
1.0
|
C
|
A:ASN32
|
4.3
|
24.2
|
1.0
|
CA
|
A:ASN33
|
4.4
|
20.8
|
1.0
|
O
|
A:HOH767
|
4.4
|
93.6
|
1.0
|
CA
|
A:PRO30
|
4.4
|
19.2
|
1.0
|
N
|
A:PRO30
|
4.4
|
19.7
|
1.0
|
OD1
|
A:ASP53
|
4.5
|
21.6
|
1.0
|
N
|
A:ASN29
|
4.5
|
23.2
|
1.0
|
CB
|
A:ASP27
|
4.5
|
20.7
|
1.0
|
O
|
A:ALA111
|
4.6
|
16.9
|
1.0
|
CA
|
A:ASN29
|
4.6
|
22.1
|
1.0
|
CB
|
A:ASN32
|
4.6
|
13.5
|
1.0
|
CB
|
A:ASN33
|
4.7
|
17.0
|
1.0
|
O
|
A:ASN32
|
4.7
|
23.4
|
1.0
|
CA
|
A:ASP27
|
4.7
|
20.1
|
1.0
|
N
|
A:ASN32
|
4.7
|
20.2
|
1.0
|
C
|
A:PRO30
|
4.7
|
25.7
|
1.0
|
CA
|
A:ASN32
|
4.7
|
19.2
|
1.0
|
C
|
A:GLY52
|
4.8
|
18.4
|
1.0
|
N
|
A:ASP53
|
4.8
|
14.3
|
1.0
|
N
|
A:GLY52
|
4.8
|
13.5
|
1.0
|
ND2
|
A:ASN33
|
4.9
|
17.2
|
1.0
|
O
|
A:PRO30
|
4.9
|
26.7
|
1.0
|
CA
|
A:ASP53
|
5.0
|
13.0
|
1.0
|
|
Calcium binding site 2 out
of 4 in 1tcm
Go back to
Calcium Binding Sites List in 1tcm
Calcium binding site 2 out
of 4 in the Cyclodextrin Glycosyltransferase W616A Mutant From Bacillus Circulans Strain 251
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Cyclodextrin Glycosyltransferase W616A Mutant From Bacillus Circulans Strain 251 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca688
b:12.6
occ:1.00
|
OD1
|
A:ASP199
|
2.3
|
11.4
|
1.0
|
O
|
A:HIS233
|
2.5
|
19.0
|
1.0
|
OD1
|
A:ASN139
|
2.6
|
18.6
|
1.0
|
OD2
|
A:ASP199
|
2.7
|
19.9
|
1.0
|
CG
|
A:ASP199
|
2.8
|
13.5
|
1.0
|
O
|
A:ILE190
|
2.9
|
7.6
|
1.0
|
O
|
A:HOH698
|
3.1
|
35.9
|
1.0
|
C
|
A:HIS233
|
3.7
|
17.7
|
1.0
|
CG
|
A:ASN139
|
3.8
|
24.9
|
1.0
|
C
|
A:ILE190
|
4.0
|
10.1
|
1.0
|
O
|
A:ASN139
|
4.2
|
27.2
|
1.0
|
CB
|
A:ASP199
|
4.3
|
5.1
|
1.0
|
CA
|
A:MET234
|
4.4
|
13.3
|
1.0
|
CG
|
A:MET234
|
4.4
|
18.3
|
1.0
|
N
|
A:MET234
|
4.5
|
12.7
|
1.0
|
ND2
|
A:ASN139
|
4.6
|
13.3
|
1.0
|
CA
|
A:ILE190
|
4.6
|
1.0
|
1.0
|
O
|
A:LEU200
|
4.6
|
2.2
|
1.0
|
CB
|
A:HIS233
|
4.6
|
14.8
|
1.0
|
O
|
A:HOH694
|
4.6
|
25.8
|
1.0
|
CA
|
A:HIS233
|
4.7
|
13.6
|
1.0
|
CE1
|
A:HIS202
|
4.9
|
1.6
|
1.0
|
CG2
|
A:ILE190
|
4.9
|
2.2
|
1.0
|
C
|
A:ASN139
|
4.9
|
24.8
|
1.0
|
CB
|
A:ASN139
|
4.9
|
17.9
|
1.0
|
ND1
|
A:HIS176
|
4.9
|
4.0
|
1.0
|
CD
|
A:PRO235
|
4.9
|
13.6
|
1.0
|
CA
|
A:ASN139
|
5.0
|
19.0
|
1.0
|
|
Calcium binding site 3 out
of 4 in 1tcm
Go back to
Calcium Binding Sites List in 1tcm
Calcium binding site 3 out
of 4 in the Cyclodextrin Glycosyltransferase W616A Mutant From Bacillus Circulans Strain 251
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Cyclodextrin Glycosyltransferase W616A Mutant From Bacillus Circulans Strain 251 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca687
b:16.0
occ:1.00
|
OD1
|
B:ASP27
|
2.2
|
20.5
|
1.0
|
OD1
|
B:ASN33
|
2.2
|
19.1
|
1.0
|
O
|
B:GLY51
|
2.5
|
20.9
|
1.0
|
OD2
|
B:ASP53
|
2.6
|
15.3
|
1.0
|
OD1
|
B:ASN32
|
2.6
|
23.7
|
1.0
|
O
|
B:ASN29
|
2.9
|
18.3
|
1.0
|
CG
|
B:ASP27
|
3.1
|
18.7
|
1.0
|
CG
|
B:ASN33
|
3.4
|
16.1
|
1.0
|
C
|
B:GLY51
|
3.5
|
18.2
|
1.0
|
OD2
|
B:ASP27
|
3.6
|
20.0
|
1.0
|
C
|
B:ASN29
|
3.6
|
20.9
|
1.0
|
CG
|
B:ASN32
|
3.7
|
31.3
|
1.0
|
CG
|
B:ASP53
|
3.7
|
20.1
|
1.0
|
CA
|
B:GLY51
|
4.0
|
12.4
|
1.0
|
CB
|
B:ASP53
|
4.1
|
15.1
|
1.0
|
N
|
B:ASN33
|
4.1
|
13.6
|
1.0
|
CA
|
B:PRO30
|
4.1
|
18.3
|
1.0
|
ND2
|
B:ASN32
|
4.2
|
13.5
|
1.0
|
N
|
B:PRO30
|
4.2
|
18.8
|
1.0
|
ND2
|
B:ASN33
|
4.2
|
1.0
|
1.0
|
CA
|
B:ASN33
|
4.3
|
11.6
|
1.0
|
CB
|
B:ASP27
|
4.3
|
16.4
|
1.0
|
O
|
B:ALA111
|
4.3
|
21.3
|
1.0
|
CB
|
B:ASN33
|
4.5
|
2.3
|
1.0
|
CA
|
B:ASP27
|
4.5
|
13.2
|
1.0
|
N
|
B:ASN29
|
4.5
|
16.1
|
1.0
|
CA
|
B:ASN29
|
4.5
|
16.6
|
1.0
|
O
|
B:HOH767
|
4.6
|
48.3
|
1.0
|
N
|
B:GLY52
|
4.7
|
13.5
|
1.0
|
N
|
B:ASP53
|
4.7
|
13.4
|
1.0
|
C
|
B:ASN32
|
4.7
|
18.0
|
1.0
|
C
|
B:PRO30
|
4.7
|
19.3
|
1.0
|
OD1
|
B:ASP53
|
4.8
|
22.5
|
1.0
|
C
|
B:GLY52
|
4.8
|
15.2
|
1.0
|
N
|
B:ASN32
|
4.9
|
14.7
|
1.0
|
C
|
B:ASP27
|
4.9
|
14.1
|
1.0
|
CB
|
B:ASN32
|
4.9
|
15.3
|
1.0
|
|
Calcium binding site 4 out
of 4 in 1tcm
Go back to
Calcium Binding Sites List in 1tcm
Calcium binding site 4 out
of 4 in the Cyclodextrin Glycosyltransferase W616A Mutant From Bacillus Circulans Strain 251
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Cyclodextrin Glycosyltransferase W616A Mutant From Bacillus Circulans Strain 251 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca688
b:11.4
occ:1.00
|
O
|
B:ILE190
|
2.5
|
11.3
|
1.0
|
OD2
|
B:ASP199
|
2.7
|
13.7
|
1.0
|
O
|
B:HIS233
|
2.8
|
13.6
|
1.0
|
C
|
B:ILE190
|
3.5
|
11.4
|
1.0
|
CG2
|
B:ILE190
|
3.7
|
6.0
|
1.0
|
OD1
|
B:ASN139
|
3.8
|
10.7
|
1.0
|
C
|
B:HIS233
|
3.9
|
12.9
|
1.0
|
CA
|
B:MET234
|
4.0
|
6.3
|
1.0
|
CG
|
B:ASP199
|
4.0
|
11.3
|
1.0
|
CD
|
B:PRO235
|
4.0
|
12.5
|
1.0
|
CA
|
B:ILE190
|
4.2
|
6.3
|
1.0
|
ND1
|
B:HIS176
|
4.2
|
21.0
|
1.0
|
O
|
B:LEU200
|
4.3
|
13.5
|
1.0
|
CE1
|
B:HIS176
|
4.3
|
19.8
|
1.0
|
N
|
B:MET234
|
4.4
|
7.2
|
1.0
|
CG
|
B:MET234
|
4.4
|
8.0
|
1.0
|
N
|
B:TYR191
|
4.4
|
5.9
|
1.0
|
CB
|
B:ILE190
|
4.6
|
7.9
|
1.0
|
OD1
|
B:ASP199
|
4.6
|
12.8
|
1.0
|
CA
|
B:TYR191
|
4.7
|
5.3
|
1.0
|
CD1
|
B:TYR191
|
4.7
|
1.0
|
1.0
|
ND1
|
B:HIS202
|
4.7
|
13.7
|
1.0
|
C
|
B:MET234
|
4.8
|
14.4
|
1.0
|
N
|
B:PRO235
|
4.8
|
12.2
|
1.0
|
CG
|
B:PRO235
|
4.8
|
17.5
|
1.0
|
CB
|
B:MET234
|
4.8
|
6.7
|
1.0
|
CB
|
B:ASP199
|
4.9
|
1.0
|
1.0
|
CE1
|
B:HIS202
|
4.9
|
13.0
|
1.0
|
|
Reference:
D.Penninga,
B.A.Van Der Veen,
R.M.Knegtel,
S.A.Van Hijum,
H.J.Rozeboom,
K.H.Kalk,
B.W.Dijkstra,
L.Dijkhuizen.
The Raw Starch Binding Domain of Cyclodextrin Glycosyltransferase From Bacillus Circulans Strain 251. J.Biol.Chem. V. 271 32777 1996.
ISSN: ISSN 0021-9258
PubMed: 8955113
DOI: 10.1074/JBC.271.51.32777
Page generated: Thu Jul 11 22:59:28 2024
|