Calcium in PDB 1qho: Five-Domain Alpha-Amylase From Bacillus Stearothermophilus, Maltose/Acarbose Complex
Enzymatic activity of Five-Domain Alpha-Amylase From Bacillus Stearothermophilus, Maltose/Acarbose Complex
All present enzymatic activity of Five-Domain Alpha-Amylase From Bacillus Stearothermophilus, Maltose/Acarbose Complex:
3.2.1.133;
Protein crystallography data
The structure of Five-Domain Alpha-Amylase From Bacillus Stearothermophilus, Maltose/Acarbose Complex, PDB code: 1qho
was solved by
Z.Dauter,
M.Dauter,
A.M.Brzozowski,
S.Christensen,
T.V.Borchert,
L.Beier,
K.S.Wilson,
G.J.Davies,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
1.70
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
89.820,
89.820,
185.750,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
15.1 /
17.5
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Five-Domain Alpha-Amylase From Bacillus Stearothermophilus, Maltose/Acarbose Complex
(pdb code 1qho). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the
Five-Domain Alpha-Amylase From Bacillus Stearothermophilus, Maltose/Acarbose Complex, PDB code: 1qho:
Jump to Calcium binding site number:
1;
2;
3;
Calcium binding site 1 out
of 3 in 1qho
Go back to
Calcium Binding Sites List in 1qho
Calcium binding site 1 out
of 3 in the Five-Domain Alpha-Amylase From Bacillus Stearothermophilus, Maltose/Acarbose Complex
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Five-Domain Alpha-Amylase From Bacillus Stearothermophilus, Maltose/Acarbose Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca696
b:11.7
occ:1.00
|
OD1
|
A:ASP79
|
2.5
|
12.0
|
1.0
|
OD1
|
A:ASP76
|
2.5
|
12.0
|
1.0
|
OE1
|
A:GLU101
|
2.5
|
11.4
|
1.0
|
O
|
A:ASN77
|
2.6
|
9.8
|
1.0
|
O
|
A:HOH1231
|
2.6
|
11.4
|
1.0
|
OE2
|
A:GLU102
|
2.6
|
16.2
|
1.0
|
OE1
|
A:GLU102
|
2.8
|
13.7
|
1.0
|
CD
|
A:GLU102
|
3.1
|
14.0
|
1.0
|
OE2
|
A:GLU101
|
3.2
|
12.0
|
1.0
|
CD
|
A:GLU101
|
3.2
|
11.9
|
1.0
|
C
|
A:ASN77
|
3.6
|
10.7
|
1.0
|
N
|
A:ASN77
|
3.6
|
9.6
|
1.0
|
CG
|
A:ASP79
|
3.7
|
14.4
|
1.0
|
CG
|
A:ASP76
|
3.7
|
12.9
|
1.0
|
NZ
|
A:LYS31
|
3.7
|
11.8
|
1.0
|
O
|
A:LEU78
|
4.2
|
11.6
|
1.0
|
CA
|
A:ASN77
|
4.2
|
9.6
|
1.0
|
OD2
|
A:ASP79
|
4.3
|
11.7
|
1.0
|
C
|
A:ASP76
|
4.3
|
9.8
|
1.0
|
C
|
A:LEU78
|
4.4
|
9.4
|
1.0
|
OD2
|
A:ASP76
|
4.4
|
12.1
|
1.0
|
CA
|
A:ASP76
|
4.5
|
9.5
|
1.0
|
CA
|
A:ASP79
|
4.5
|
10.3
|
1.0
|
CG
|
A:GLU102
|
4.5
|
12.3
|
1.0
|
OG
|
A:SER32
|
4.5
|
13.1
|
1.0
|
CB
|
A:SER32
|
4.5
|
12.6
|
1.0
|
CD
|
A:ARG95
|
4.5
|
12.5
|
1.0
|
N
|
A:ASP79
|
4.6
|
11.2
|
1.0
|
N
|
A:GLU102
|
4.6
|
12.2
|
1.0
|
CG
|
A:GLU101
|
4.6
|
9.6
|
1.0
|
OH
|
A:TYR46
|
4.6
|
11.7
|
1.0
|
CB
|
A:ASP76
|
4.7
|
9.1
|
1.0
|
CB
|
A:ASP79
|
4.7
|
13.2
|
1.0
|
N
|
A:LEU78
|
4.7
|
10.3
|
1.0
|
CB
|
A:ASN77
|
4.8
|
9.4
|
1.0
|
ND1
|
A:HIS103
|
4.9
|
12.8
|
1.0
|
CA
|
A:GLU101
|
4.9
|
11.5
|
1.0
|
|
Calcium binding site 2 out
of 3 in 1qho
Go back to
Calcium Binding Sites List in 1qho
Calcium binding site 2 out
of 3 in the Five-Domain Alpha-Amylase From Bacillus Stearothermophilus, Maltose/Acarbose Complex
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Five-Domain Alpha-Amylase From Bacillus Stearothermophilus, Maltose/Acarbose Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca697
b:10.4
occ:1.00
|
O
|
A:HIS232
|
2.5
|
9.3
|
1.0
|
OD1
|
A:ASN131
|
2.5
|
9.6
|
1.0
|
O
|
A:HOH1204
|
2.5
|
9.2
|
1.0
|
O
|
A:HOH1207
|
2.5
|
10.3
|
1.0
|
O
|
A:HOH1213
|
2.6
|
10.7
|
1.0
|
O
|
A:GLN184
|
2.6
|
10.2
|
1.0
|
OD2
|
A:ASP198
|
2.6
|
10.4
|
1.0
|
OD1
|
A:ASP198
|
2.7
|
10.7
|
1.0
|
CG
|
A:ASP198
|
3.0
|
12.3
|
1.0
|
CG
|
A:ASN131
|
3.6
|
10.7
|
1.0
|
C
|
A:GLN184
|
3.6
|
10.5
|
1.0
|
C
|
A:HIS232
|
3.7
|
12.0
|
1.0
|
ND2
|
A:ASN131
|
4.0
|
9.2
|
1.0
|
CA
|
A:GLN184
|
4.1
|
9.7
|
1.0
|
CA
|
A:PHE233
|
4.2
|
10.6
|
1.0
|
O
|
A:ASN131
|
4.3
|
11.2
|
1.0
|
ND1
|
A:HIS169
|
4.3
|
11.2
|
1.0
|
CB
|
A:PHE233
|
4.3
|
9.2
|
1.0
|
N
|
A:PHE233
|
4.4
|
10.0
|
1.0
|
CE1
|
A:HIS169
|
4.4
|
11.4
|
1.0
|
CB
|
A:ASP198
|
4.5
|
11.4
|
1.0
|
O
|
A:LYS186
|
4.6
|
12.1
|
1.0
|
CB
|
A:HIS232
|
4.6
|
9.9
|
1.0
|
O
|
A:ALA183
|
4.6
|
10.5
|
1.0
|
O
|
A:LEU199
|
4.6
|
10.9
|
1.0
|
N
|
A:TRP185
|
4.6
|
10.9
|
1.0
|
CA
|
A:HIS232
|
4.6
|
11.8
|
1.0
|
OE1
|
A:GLN201
|
4.7
|
11.2
|
1.0
|
CB
|
A:ASN131
|
4.8
|
10.2
|
1.0
|
NE2
|
A:GLN201
|
4.9
|
9.6
|
1.0
|
O
|
A:HOH1249
|
4.9
|
12.1
|
1.0
|
CA
|
A:TRP185
|
4.9
|
9.9
|
1.0
|
|
Calcium binding site 3 out
of 3 in 1qho
Go back to
Calcium Binding Sites List in 1qho
Calcium binding site 3 out
of 3 in the Five-Domain Alpha-Amylase From Bacillus Stearothermophilus, Maltose/Acarbose Complex
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Five-Domain Alpha-Amylase From Bacillus Stearothermophilus, Maltose/Acarbose Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca698
b:13.2
occ:1.00
|
OD1
|
A:ASN27
|
2.5
|
13.2
|
1.0
|
OD2
|
A:ASP50
|
2.5
|
11.6
|
1.0
|
O
|
A:GLY48
|
2.5
|
11.4
|
1.0
|
OD1
|
A:ASN26
|
2.5
|
12.5
|
1.0
|
OD1
|
A:ASP21
|
2.6
|
12.3
|
1.0
|
O
|
A:ASP23
|
2.6
|
13.2
|
1.0
|
O
|
A:HOH1277
|
2.6
|
13.4
|
1.0
|
CG
|
A:ASP21
|
3.5
|
16.5
|
1.0
|
CG
|
A:ASP50
|
3.5
|
13.3
|
1.0
|
C
|
A:ASP23
|
3.6
|
14.4
|
1.0
|
C
|
A:GLY48
|
3.6
|
11.1
|
1.0
|
CG
|
A:ASN27
|
3.7
|
16.1
|
1.0
|
CG
|
A:ASN26
|
3.7
|
15.5
|
1.0
|
CB
|
A:ASP50
|
4.0
|
10.8
|
1.0
|
OD2
|
A:ASP21
|
4.0
|
15.8
|
1.0
|
CA
|
A:GLY48
|
4.1
|
10.8
|
1.0
|
N
|
A:ASN27
|
4.2
|
14.0
|
1.0
|
ND2
|
A:ASN26
|
4.2
|
15.3
|
1.0
|
CA
|
A:THR24
|
4.3
|
16.2
|
1.0
|
O
|
A:HIS103
|
4.3
|
12.3
|
1.0
|
N
|
A:ASP23
|
4.3
|
13.7
|
1.0
|
ND2
|
A:ASN27
|
4.3
|
14.7
|
1.0
|
N
|
A:THR24
|
4.3
|
14.9
|
1.0
|
CA
|
A:ASN27
|
4.4
|
13.2
|
1.0
|
C
|
A:ASN26
|
4.4
|
13.0
|
1.0
|
CB
|
A:ASP21
|
4.4
|
13.9
|
1.0
|
CA
|
A:ASP23
|
4.4
|
14.7
|
1.0
|
OD1
|
A:ASP50
|
4.5
|
10.8
|
1.0
|
CA
|
A:ASP21
|
4.5
|
13.7
|
1.0
|
C
|
A:GLY49
|
4.6
|
10.5
|
1.0
|
N
|
A:ASN26
|
4.6
|
14.2
|
1.0
|
CB
|
A:ASN27
|
4.7
|
12.3
|
1.0
|
C
|
A:THR24
|
4.7
|
16.0
|
1.0
|
CB
|
A:ASP23
|
4.7
|
13.2
|
1.0
|
N
|
A:GLY49
|
4.7
|
11.8
|
1.0
|
O
|
A:HOH1225
|
4.8
|
11.0
|
1.0
|
N
|
A:ASP50
|
4.8
|
10.6
|
1.0
|
O
|
A:ASN26
|
4.8
|
11.7
|
1.0
|
O
|
A:GLY49
|
4.8
|
11.2
|
1.0
|
CB
|
A:ASN26
|
4.9
|
13.1
|
1.0
|
C
|
A:ASP21
|
4.9
|
13.9
|
1.0
|
CA
|
A:ASN26
|
4.9
|
12.6
|
1.0
|
N
|
A:GLY22
|
4.9
|
12.7
|
1.0
|
O
|
A:THR24
|
4.9
|
16.0
|
1.0
|
CA
|
A:GLY49
|
5.0
|
11.5
|
1.0
|
|
Reference:
Z.Dauter,
M.Dauter,
A.M.Brzozowski,
S.Christensen,
T.V.Borchert,
L.Beier,
K.S.Wilson,
G.J.Davies.
X-Ray Structure of Novamyl, the Five-Domain "Maltogenic" Alpha-Amylase From Bacillus Stearothermophilus: Maltose and Acarbose Complexes at 1.7A Resolution. Biochemistry V. 38 8385 1999.
ISSN: ISSN 0006-2960
PubMed: 10387084
DOI: 10.1021/BI990256L
Page generated: Thu Jul 11 21:45:29 2024
|