Calcium in PDB 1j12: Beta-Amylase From Bacillus Cereus Var. Mycoides in Complex with Alpha-Ebg
Enzymatic activity of Beta-Amylase From Bacillus Cereus Var. Mycoides in Complex with Alpha-Ebg
All present enzymatic activity of Beta-Amylase From Bacillus Cereus Var. Mycoides in Complex with Alpha-Ebg:
3.2.1.2;
Protein crystallography data
The structure of Beta-Amylase From Bacillus Cereus Var. Mycoides in Complex with Alpha-Ebg, PDB code: 1j12
was solved by
T.Oyama,
H.Miyake,
M.Kusunoki,
Y.Nitta,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
8.00 /
2.10
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
177.900,
112.900,
146.200,
90.00,
105.80,
90.00
|
R / Rfree (%)
|
19.8 /
25.3
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Beta-Amylase From Bacillus Cereus Var. Mycoides in Complex with Alpha-Ebg
(pdb code 1j12). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Beta-Amylase From Bacillus Cereus Var. Mycoides in Complex with Alpha-Ebg, PDB code: 1j12:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 1j12
Go back to
Calcium Binding Sites List in 1j12
Calcium binding site 1 out
of 4 in the Beta-Amylase From Bacillus Cereus Var. Mycoides in Complex with Alpha-Ebg
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Beta-Amylase From Bacillus Cereus Var. Mycoides in Complex with Alpha-Ebg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca701
b:10.5
occ:1.00
|
OE1
|
A:GLU144
|
2.3
|
6.9
|
1.0
|
OE2
|
A:GLU56
|
2.4
|
13.0
|
1.0
|
OD1
|
A:ASP60
|
2.4
|
13.4
|
1.0
|
OE1
|
A:GLU141
|
2.6
|
11.4
|
1.0
|
O
|
A:HOH752
|
2.6
|
10.6
|
1.0
|
OE1
|
A:GLN61
|
2.6
|
13.7
|
1.0
|
CD
|
A:GLU56
|
3.4
|
11.8
|
1.0
|
CD
|
A:GLU144
|
3.5
|
9.8
|
1.0
|
CD
|
A:GLN61
|
3.6
|
16.5
|
1.0
|
CG
|
A:ASP60
|
3.7
|
3.2
|
1.0
|
OE1
|
A:GLU56
|
3.7
|
16.4
|
1.0
|
CD
|
A:GLU141
|
3.7
|
21.8
|
1.0
|
CB
|
A:GLU144
|
3.9
|
8.3
|
1.0
|
N
|
A:GLN61
|
3.9
|
13.5
|
1.0
|
NZ
|
A:LYS140
|
4.0
|
6.8
|
1.0
|
CH2
|
A:TRP106
|
4.1
|
9.1
|
1.0
|
CG
|
A:GLN61
|
4.2
|
5.9
|
1.0
|
OE2
|
A:GLU141
|
4.3
|
22.1
|
1.0
|
CG
|
A:GLU144
|
4.3
|
2.5
|
1.0
|
OE2
|
A:GLU144
|
4.3
|
10.7
|
1.0
|
OD2
|
A:ASP60
|
4.4
|
9.4
|
1.0
|
CA
|
A:ASP60
|
4.5
|
7.0
|
1.0
|
CA
|
A:GLU141
|
4.5
|
7.0
|
1.0
|
CA
|
A:GLN61
|
4.6
|
10.7
|
1.0
|
CZ
|
A:PHE63
|
4.6
|
9.8
|
1.0
|
C
|
A:ASP60
|
4.6
|
13.7
|
1.0
|
CB
|
A:ASP60
|
4.6
|
6.7
|
1.0
|
O
|
A:GLU141
|
4.6
|
15.0
|
1.0
|
NE2
|
A:GLN61
|
4.7
|
15.1
|
1.0
|
CZ2
|
A:TRP106
|
4.7
|
5.0
|
1.0
|
CG
|
A:GLU56
|
4.8
|
7.9
|
1.0
|
CB
|
A:GLU141
|
4.9
|
9.0
|
1.0
|
CG
|
A:GLU141
|
4.9
|
12.1
|
1.0
|
CB
|
A:GLN61
|
5.0
|
8.0
|
1.0
|
|
Calcium binding site 2 out
of 4 in 1j12
Go back to
Calcium Binding Sites List in 1j12
Calcium binding site 2 out
of 4 in the Beta-Amylase From Bacillus Cereus Var. Mycoides in Complex with Alpha-Ebg
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Beta-Amylase From Bacillus Cereus Var. Mycoides in Complex with Alpha-Ebg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca701
b:11.9
occ:1.00
|
OE1
|
B:GLU144
|
2.4
|
13.0
|
1.0
|
OD1
|
B:ASP60
|
2.4
|
13.1
|
1.0
|
OE2
|
B:GLU56
|
2.4
|
8.7
|
1.0
|
O
|
B:HOH773
|
2.5
|
12.9
|
1.0
|
OE1
|
B:GLU141
|
2.6
|
5.4
|
1.0
|
OE1
|
B:GLN61
|
2.6
|
22.1
|
1.0
|
CD
|
B:GLU144
|
3.4
|
12.2
|
1.0
|
CD
|
B:GLU56
|
3.5
|
14.9
|
1.0
|
CD
|
B:GLN61
|
3.6
|
11.2
|
1.0
|
CG
|
B:ASP60
|
3.7
|
10.0
|
1.0
|
CD
|
B:GLU141
|
3.7
|
9.5
|
1.0
|
OE1
|
B:GLU56
|
3.7
|
13.6
|
1.0
|
CB
|
B:GLU144
|
3.8
|
10.2
|
1.0
|
N
|
B:GLN61
|
3.9
|
9.1
|
1.0
|
NZ
|
B:LYS140
|
4.0
|
13.2
|
1.0
|
CH2
|
B:TRP106
|
4.1
|
7.3
|
1.0
|
OE2
|
B:GLU141
|
4.2
|
14.4
|
1.0
|
CG
|
B:GLU144
|
4.2
|
9.7
|
1.0
|
OE2
|
B:GLU144
|
4.2
|
17.7
|
1.0
|
CG
|
B:GLN61
|
4.2
|
8.9
|
1.0
|
OD2
|
B:ASP60
|
4.4
|
5.5
|
1.0
|
CA
|
B:ASP60
|
4.5
|
11.2
|
1.0
|
CA
|
B:GLU141
|
4.5
|
5.8
|
1.0
|
CZ
|
B:PHE63
|
4.6
|
10.8
|
1.0
|
CA
|
B:GLN61
|
4.6
|
12.4
|
1.0
|
C
|
B:ASP60
|
4.6
|
13.0
|
1.0
|
CB
|
B:ASP60
|
4.7
|
7.9
|
1.0
|
O
|
B:GLU141
|
4.7
|
17.1
|
1.0
|
NE2
|
B:GLN61
|
4.7
|
10.5
|
1.0
|
CG
|
B:GLU56
|
4.8
|
3.0
|
1.0
|
CZ2
|
B:TRP106
|
4.8
|
9.0
|
1.0
|
CG
|
B:GLU141
|
4.8
|
7.0
|
1.0
|
CB
|
B:GLU141
|
4.9
|
8.4
|
1.0
|
CE2
|
B:PHE63
|
4.9
|
7.1
|
1.0
|
CZ3
|
B:TRP106
|
5.0
|
8.2
|
1.0
|
|
Calcium binding site 3 out
of 4 in 1j12
Go back to
Calcium Binding Sites List in 1j12
Calcium binding site 3 out
of 4 in the Beta-Amylase From Bacillus Cereus Var. Mycoides in Complex with Alpha-Ebg
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Beta-Amylase From Bacillus Cereus Var. Mycoides in Complex with Alpha-Ebg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca701
b:14.9
occ:1.00
|
OD1
|
C:ASP60
|
2.4
|
11.9
|
1.0
|
OE1
|
C:GLU144
|
2.4
|
11.5
|
1.0
|
OE1
|
C:GLN61
|
2.6
|
17.8
|
1.0
|
OE2
|
C:GLU56
|
2.6
|
9.4
|
1.0
|
O
|
C:HOH771
|
2.6
|
14.0
|
1.0
|
OE1
|
C:GLU141
|
2.6
|
13.2
|
1.0
|
CD
|
C:GLU144
|
3.4
|
8.2
|
1.0
|
CD
|
C:GLU56
|
3.6
|
9.8
|
1.0
|
CG
|
C:ASP60
|
3.6
|
9.0
|
1.0
|
CD
|
C:GLU141
|
3.6
|
17.0
|
1.0
|
CD
|
C:GLN61
|
3.6
|
15.7
|
1.0
|
CB
|
C:GLU144
|
3.8
|
10.3
|
1.0
|
OE1
|
C:GLU56
|
3.8
|
14.2
|
1.0
|
N
|
C:GLN61
|
3.8
|
9.8
|
1.0
|
NZ
|
C:LYS140
|
3.9
|
8.3
|
1.0
|
OE2
|
C:GLU141
|
4.1
|
12.7
|
1.0
|
CH2
|
C:TRP106
|
4.1
|
5.2
|
1.0
|
CG
|
C:GLU144
|
4.2
|
3.2
|
1.0
|
OE2
|
C:GLU144
|
4.2
|
7.2
|
1.0
|
CG
|
C:GLN61
|
4.2
|
5.5
|
1.0
|
OD2
|
C:ASP60
|
4.3
|
9.6
|
1.0
|
CA
|
C:ASP60
|
4.5
|
6.5
|
1.0
|
CA
|
C:GLU141
|
4.5
|
6.1
|
1.0
|
CA
|
C:GLN61
|
4.6
|
9.4
|
1.0
|
CZ
|
C:PHE63
|
4.6
|
9.2
|
1.0
|
C
|
C:ASP60
|
4.6
|
13.4
|
1.0
|
CB
|
C:ASP60
|
4.6
|
6.3
|
1.0
|
NE2
|
C:GLN61
|
4.7
|
12.7
|
1.0
|
O
|
C:GLU141
|
4.7
|
11.8
|
1.0
|
CG
|
C:GLU141
|
4.8
|
11.5
|
1.0
|
CB
|
C:GLU141
|
4.8
|
13.9
|
1.0
|
CZ2
|
C:TRP106
|
4.8
|
4.4
|
1.0
|
CG
|
C:GLU56
|
4.9
|
3.7
|
1.0
|
O
|
C:HOH735
|
5.0
|
12.9
|
1.0
|
CZ3
|
C:TRP106
|
5.0
|
9.6
|
1.0
|
|
Calcium binding site 4 out
of 4 in 1j12
Go back to
Calcium Binding Sites List in 1j12
Calcium binding site 4 out
of 4 in the Beta-Amylase From Bacillus Cereus Var. Mycoides in Complex with Alpha-Ebg
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Beta-Amylase From Bacillus Cereus Var. Mycoides in Complex with Alpha-Ebg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca701
b:14.5
occ:1.00
|
OE1
|
D:GLU144
|
2.3
|
11.4
|
1.0
|
OE2
|
D:GLU56
|
2.4
|
13.7
|
1.0
|
OD1
|
D:ASP60
|
2.4
|
20.3
|
1.0
|
OE1
|
D:GLN61
|
2.5
|
17.8
|
1.0
|
OE1
|
D:GLU141
|
2.5
|
18.0
|
1.0
|
CD
|
D:GLU56
|
3.3
|
13.3
|
1.0
|
CD
|
D:GLU144
|
3.4
|
3.0
|
1.0
|
OE1
|
D:GLU56
|
3.6
|
15.0
|
1.0
|
CG
|
D:ASP60
|
3.6
|
6.2
|
1.0
|
CD
|
D:GLN61
|
3.6
|
11.7
|
1.0
|
CB
|
D:GLU144
|
3.7
|
5.3
|
1.0
|
CD
|
D:GLU141
|
3.7
|
15.7
|
1.0
|
N
|
D:GLN61
|
3.8
|
12.0
|
1.0
|
CG
|
D:GLU144
|
4.1
|
4.0
|
1.0
|
NZ
|
D:LYS140
|
4.2
|
12.5
|
1.0
|
CG
|
D:GLN61
|
4.2
|
9.5
|
1.0
|
OE2
|
D:GLU144
|
4.3
|
9.9
|
1.0
|
CH2
|
D:TRP106
|
4.4
|
10.8
|
1.0
|
CA
|
D:GLU141
|
4.4
|
7.2
|
1.0
|
OD2
|
D:ASP60
|
4.4
|
10.3
|
1.0
|
OE2
|
D:GLU141
|
4.4
|
10.7
|
1.0
|
CZ
|
D:PHE63
|
4.4
|
7.9
|
1.0
|
CA
|
D:ASP60
|
4.4
|
6.8
|
1.0
|
CA
|
D:GLN61
|
4.5
|
12.4
|
1.0
|
C
|
D:ASP60
|
4.5
|
12.7
|
1.0
|
O
|
D:GLU141
|
4.6
|
14.0
|
1.0
|
CB
|
D:ASP60
|
4.6
|
5.1
|
1.0
|
NE2
|
D:GLN61
|
4.7
|
5.3
|
1.0
|
CG
|
D:GLU56
|
4.7
|
7.5
|
1.0
|
CB
|
D:GLU141
|
4.7
|
12.0
|
1.0
|
CG
|
D:GLU141
|
4.8
|
16.3
|
1.0
|
CE2
|
D:PHE63
|
4.9
|
7.0
|
1.0
|
CZ2
|
D:TRP106
|
5.0
|
6.2
|
1.0
|
CB
|
D:GLN61
|
5.0
|
10.9
|
1.0
|
C
|
D:GLU141
|
5.0
|
14.4
|
1.0
|
|
Reference:
T.Oyama,
H.Miyake,
M.Kusunoki,
Y.Nitta.
Crystal Structures of Beta-Amylase From Bacillus Cereus Var. Mycoides in Complexes with Substrate Analogs and Affinity-Labeling Reagents J.Biochem.(Tokyo) V. 133 467 2003.
ISSN: ISSN 0021-924X
PubMed: 12761294
DOI: 10.1093/JB/MVG061
Page generated: Thu Jul 11 10:31:12 2024
|