Calcium in PDB 1p6w: Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) in Complex with the Substrate Analogue, Methyl 4I,4II,4III- Tri-Thiomaltotetraoside (Thio-DP4)
Enzymatic activity of Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) in Complex with the Substrate Analogue, Methyl 4I,4II,4III- Tri-Thiomaltotetraoside (Thio-DP4)
All present enzymatic activity of Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) in Complex with the Substrate Analogue, Methyl 4I,4II,4III- Tri-Thiomaltotetraoside (Thio-DP4):
3.2.1.1;
Protein crystallography data
The structure of Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) in Complex with the Substrate Analogue, Methyl 4I,4II,4III- Tri-Thiomaltotetraoside (Thio-DP4), PDB code: 1p6w
was solved by
X.Robert,
R.Haser,
N.Aghajari,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.52 /
2.00
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
93.430,
72.100,
60.880,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17 /
21.6
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) in Complex with the Substrate Analogue, Methyl 4I,4II,4III- Tri-Thiomaltotetraoside (Thio-DP4)
(pdb code 1p6w). 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 Barley Alpha-Amylase Isozyme 1 (AMY1) in Complex with the Substrate Analogue, Methyl 4I,4II,4III- Tri-Thiomaltotetraoside (Thio-DP4), PDB code: 1p6w:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 1p6w
Go back to
Calcium Binding Sites List in 1p6w
Calcium binding site 1 out
of 4 in the Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) in Complex with the Substrate Analogue, Methyl 4I,4II,4III- Tri-Thiomaltotetraoside (Thio-DP4)
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 Barley Alpha-Amylase Isozyme 1 (AMY1) in Complex with the Substrate Analogue, Methyl 4I,4II,4III- Tri-Thiomaltotetraoside (Thio-DP4) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca500
b:7.4
occ:1.00
|
OD2
|
A:ASP149
|
2.3
|
8.8
|
1.0
|
O
|
A:GLY184
|
2.4
|
6.0
|
1.0
|
OD2
|
A:ASP139
|
2.4
|
13.2
|
1.0
|
OD1
|
A:ASN92
|
2.4
|
7.2
|
1.0
|
O
|
A:ALA142
|
2.4
|
9.4
|
1.0
|
O
|
A:HOH630
|
2.5
|
1.2
|
1.0
|
OD1
|
A:ASP139
|
2.6
|
10.9
|
1.0
|
CG
|
A:ASP139
|
2.8
|
11.7
|
1.0
|
C
|
A:GLY184
|
3.4
|
6.7
|
1.0
|
CG
|
A:ASN92
|
3.4
|
7.9
|
1.0
|
CG
|
A:ASP149
|
3.4
|
8.1
|
1.0
|
C
|
A:ALA142
|
3.6
|
10.4
|
1.0
|
ND2
|
A:ASN92
|
3.8
|
5.3
|
1.0
|
CA
|
A:GLY184
|
3.8
|
5.6
|
1.0
|
O
|
A:GLY141
|
3.9
|
10.1
|
1.0
|
CB
|
A:ASP149
|
3.9
|
7.7
|
1.0
|
C
|
A:GLY141
|
4.0
|
11.1
|
1.0
|
CA
|
A:ASP143
|
4.3
|
10.1
|
1.0
|
CB
|
A:ASP139
|
4.3
|
9.0
|
1.0
|
N
|
A:ASP143
|
4.3
|
10.1
|
1.0
|
N
|
A:ALA142
|
4.4
|
11.4
|
1.0
|
O
|
A:ASN92
|
4.4
|
8.4
|
1.0
|
N
|
A:TYR185
|
4.5
|
7.1
|
1.0
|
OD1
|
A:ASP149
|
4.5
|
10.4
|
1.0
|
N
|
A:GLY141
|
4.5
|
11.7
|
1.0
|
CA
|
A:GLY141
|
4.6
|
11.5
|
1.0
|
CA
|
A:ALA142
|
4.6
|
9.6
|
1.0
|
O
|
A:HOH809
|
4.7
|
14.2
|
1.0
|
CB
|
A:ASN92
|
4.8
|
7.9
|
1.0
|
O
|
A:HOH754
|
4.8
|
10.2
|
1.0
|
SG
|
A:CYS125
|
4.8
|
9.4
|
1.0
|
CA
|
A:TYR185
|
4.9
|
7.1
|
1.0
|
CA
|
A:ASP149
|
5.0
|
9.0
|
1.0
|
|
Calcium binding site 2 out
of 4 in 1p6w
Go back to
Calcium Binding Sites List in 1p6w
Calcium binding site 2 out
of 4 in the Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) in Complex with the Substrate Analogue, Methyl 4I,4II,4III- Tri-Thiomaltotetraoside (Thio-DP4)
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 Barley Alpha-Amylase Isozyme 1 (AMY1) in Complex with the Substrate Analogue, Methyl 4I,4II,4III- Tri-Thiomaltotetraoside (Thio-DP4) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca501
b:15.2
occ:1.00
|
O
|
A:ASP114
|
2.3
|
15.6
|
1.0
|
O
|
A:HOH656
|
2.5
|
14.7
|
1.0
|
O
|
A:HOH604
|
2.5
|
9.7
|
1.0
|
OE2
|
A:GLU109
|
2.5
|
12.9
|
1.0
|
OD2
|
A:ASP118
|
2.5
|
13.3
|
1.0
|
O
|
A:THR112
|
2.6
|
17.6
|
1.0
|
OD1
|
A:ASP118
|
2.6
|
12.2
|
1.0
|
CG
|
A:ASP118
|
2.9
|
13.3
|
1.0
|
OE1
|
A:GLU109
|
2.9
|
15.9
|
1.0
|
CD
|
A:GLU109
|
3.0
|
13.2
|
1.0
|
C
|
A:ASP114
|
3.6
|
18.1
|
1.0
|
C
|
A:THR112
|
3.7
|
17.8
|
1.0
|
N
|
A:THR112
|
4.1
|
14.3
|
1.0
|
C
|
A:SER113
|
4.2
|
19.0
|
1.0
|
OG1
|
A:THR112
|
4.2
|
15.3
|
1.0
|
N
|
A:ASP114
|
4.3
|
19.0
|
1.0
|
O
|
A:HOH1636
|
4.3
|
24.6
|
1.0
|
O
|
A:SER113
|
4.4
|
20.7
|
1.0
|
N
|
A:GLY110
|
4.4
|
10.1
|
1.0
|
CB
|
A:ASP118
|
4.4
|
12.7
|
1.0
|
O
|
A:ARG116
|
4.4
|
11.7
|
1.0
|
CA
|
A:GLY115
|
4.4
|
16.7
|
1.0
|
N
|
A:GLY115
|
4.5
|
16.8
|
1.0
|
CA
|
A:THR112
|
4.5
|
15.8
|
1.0
|
CG
|
A:GLU109
|
4.5
|
13.7
|
1.0
|
CA
|
A:ASP114
|
4.5
|
18.9
|
1.0
|
N
|
A:GLY111
|
4.5
|
11.4
|
1.0
|
O
|
A:HOH1090
|
4.6
|
27.8
|
1.0
|
O
|
A:HOH843
|
4.6
|
11.6
|
1.0
|
N
|
A:SER113
|
4.6
|
18.0
|
1.0
|
N
|
A:ARG116
|
4.7
|
15.0
|
1.0
|
C
|
A:GLY115
|
4.7
|
16.1
|
1.0
|
CA
|
A:SER113
|
4.7
|
19.7
|
1.0
|
O
|
A:HOH1530
|
4.9
|
23.1
|
1.0
|
|
Calcium binding site 3 out
of 4 in 1p6w
Go back to
Calcium Binding Sites List in 1p6w
Calcium binding site 3 out
of 4 in the Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) in Complex with the Substrate Analogue, Methyl 4I,4II,4III- Tri-Thiomaltotetraoside (Thio-DP4)
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 Barley Alpha-Amylase Isozyme 1 (AMY1) in Complex with the Substrate Analogue, Methyl 4I,4II,4III- Tri-Thiomaltotetraoside (Thio-DP4) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca502
b:12.3
occ:1.00
|
O
|
A:PHE144
|
2.3
|
9.1
|
1.0
|
O
|
A:ALA147
|
2.3
|
11.2
|
1.0
|
O
|
A:HOH788
|
2.3
|
8.8
|
1.0
|
OD2
|
A:ASP128
|
2.3
|
9.8
|
1.0
|
OD1
|
A:ASP143
|
2.4
|
13.8
|
1.0
|
OD1
|
A:ASP149
|
2.4
|
10.4
|
1.0
|
CG
|
A:ASP143
|
3.1
|
11.7
|
1.0
|
OD2
|
A:ASP143
|
3.2
|
13.6
|
1.0
|
CG
|
A:ASP128
|
3.3
|
12.9
|
1.0
|
C
|
A:PHE144
|
3.3
|
11.5
|
1.0
|
CG
|
A:ASP149
|
3.4
|
8.1
|
1.0
|
C
|
A:ALA147
|
3.5
|
10.9
|
1.0
|
N
|
A:ASP149
|
3.6
|
9.5
|
1.0
|
OD1
|
A:ASP128
|
3.7
|
11.0
|
1.0
|
N
|
A:PHE144
|
3.7
|
10.7
|
1.0
|
CB
|
A:ASP149
|
3.9
|
7.7
|
1.0
|
C
|
A:PRO148
|
4.0
|
9.4
|
1.0
|
CA
|
A:PHE144
|
4.1
|
11.3
|
1.0
|
CA
|
A:PRO148
|
4.2
|
10.0
|
1.0
|
N
|
A:ALA145
|
4.2
|
11.9
|
1.0
|
CA
|
A:ASP149
|
4.2
|
9.0
|
1.0
|
N
|
A:ALA147
|
4.3
|
12.2
|
1.0
|
N
|
A:PRO148
|
4.3
|
10.5
|
1.0
|
CA
|
A:ALA145
|
4.3
|
12.3
|
1.0
|
O
|
A:HOH1152
|
4.4
|
21.0
|
1.0
|
OD2
|
A:ASP149
|
4.4
|
8.8
|
1.0
|
CB
|
A:ASP143
|
4.5
|
11.0
|
1.0
|
C
|
A:ALA145
|
4.5
|
11.9
|
1.0
|
O
|
A:ALA145
|
4.5
|
12.7
|
1.0
|
CA
|
A:ALA147
|
4.5
|
11.8
|
1.0
|
CB
|
A:PHE144
|
4.5
|
13.8
|
1.0
|
CB
|
A:ASP128
|
4.6
|
11.8
|
1.0
|
O
|
A:HOH809
|
4.6
|
14.2
|
1.0
|
C
|
A:ASP143
|
4.7
|
10.9
|
1.0
|
O
|
A:PRO148
|
4.8
|
8.2
|
1.0
|
CA
|
A:ASP143
|
4.8
|
10.1
|
1.0
|
|
Calcium binding site 4 out
of 4 in 1p6w
Go back to
Calcium Binding Sites List in 1p6w
Calcium binding site 4 out
of 4 in the Crystal Structure of Barley Alpha-Amylase Isozyme 1 (AMY1) in Complex with the Substrate Analogue, Methyl 4I,4II,4III- Tri-Thiomaltotetraoside (Thio-DP4)
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 Barley Alpha-Amylase Isozyme 1 (AMY1) in Complex with the Substrate Analogue, Methyl 4I,4II,4III- Tri-Thiomaltotetraoside (Thio-DP4) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca503
b:15.8
occ:1.00
|
O
|
A:HOH1548
|
2.4
|
26.2
|
1.0
|
O
|
A:HOH1546
|
2.5
|
7.4
|
1.0
|
O
|
A:HOH1550
|
2.5
|
22.4
|
1.0
|
O
|
A:HOH1545
|
2.5
|
11.8
|
1.0
|
O
|
A:HOH1547
|
2.9
|
13.7
|
1.0
|
O
|
A:HOH1523
|
3.0
|
17.5
|
1.0
|
O
|
A:HOH1544
|
3.7
|
14.9
|
1.0
|
O
|
A:HOH641
|
4.1
|
9.1
|
1.0
|
O
|
A:HOH709
|
4.6
|
10.8
|
1.0
|
O
|
A:HOH676
|
4.6
|
20.4
|
1.0
|
OD1
|
A:ASP180
|
4.6
|
3.5
|
1.0
|
O
|
A:HOH1621
|
4.6
|
28.0
|
1.0
|
OD2
|
A:ASP291
|
4.7
|
10.8
|
1.0
|
OD1
|
A:ASP291
|
4.7
|
12.8
|
1.0
|
OE2
|
A:GLU205
|
4.8
|
15.5
|
1.0
|
OE1
|
A:GLU205
|
4.8
|
10.2
|
1.0
|
CG
|
A:ASP291
|
5.0
|
12.2
|
1.0
|
|
Reference:
X.Robert,
R.Haser,
T.E.Gottschalk,
F.Ratajczak,
H.Driguez,
B.Svensson,
N.Aghajari.
The Structure of Barley Alpha-Amylase Isozyme 1 Reveals A Novel Role of Domain C in Substrate Recognition and Binding: A Pair of Sugar Tongs Structure V. 11 973 2003.
ISSN: ISSN 0969-2126
PubMed: 12906828
DOI: 10.1016/S0969-2126(03)00151-5
Page generated: Thu Jul 11 13:39:50 2024
|