Calcium in PDB 3wn6: Crystal Structure of Alpha-Amylase Amyi-1 From Oryza Sativa
Enzymatic activity of Crystal Structure of Alpha-Amylase Amyi-1 From Oryza Sativa
All present enzymatic activity of Crystal Structure of Alpha-Amylase Amyi-1 From Oryza Sativa:
3.2.1.1;
Protein crystallography data
The structure of Crystal Structure of Alpha-Amylase Amyi-1 From Oryza Sativa, PDB code: 3wn6
was solved by
A.Ochiai,
H.Sugai,
K.Harada,
S.Tanaka,
Y.Ishiyama,
K.Ito,
T.Tanaka,
T.Uchiumi,
M.Taniguchi,
T.Mitsui,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
48.32 /
2.16
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
70.917,
125.277,
96.642,
90.00,
90.20,
90.00
|
|
R / Rfree (%)
|
19.9 /
24.3
|
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Calcium atom in the Crystal Structure of Alpha-Amylase Amyi-1 From Oryza Sativa
(pdb code 3wn6). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the
Crystal Structure of Alpha-Amylase Amyi-1 From Oryza Sativa, PDB code: 3wn6:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 12 in 3wn6
Go back to
Calcium Binding Sites List in 3wn6
Calcium binding site 1 out
of 12 in the Crystal Structure of Alpha-Amylase Amyi-1 From Oryza Sativa
 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 Alpha-Amylase Amyi-1 From Oryza Sativa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca501
b:14.7
occ:1.00
|
O
|
A:HOH750
|
2.2
|
22.6
|
1.0
|
|
O
|
A:HOH624
|
2.4
|
6.8
|
1.0
|
|
OD2
|
A:ASP142
|
2.4
|
16.8
|
1.0
|
|
O
|
A:ASP138
|
2.4
|
24.6
|
1.0
|
|
OE2
|
A:GLU133
|
2.4
|
16.2
|
1.0
|
|
O
|
A:THR136
|
2.5
|
24.2
|
1.0
|
|
OD1
|
A:ASP142
|
2.7
|
14.8
|
1.0
|
|
OE1
|
A:GLU133
|
2.7
|
16.3
|
1.0
|
|
CG
|
A:ASP142
|
2.9
|
16.2
|
1.0
|
|
CD
|
A:GLU133
|
2.9
|
17.6
|
1.0
|
|
C
|
A:ASP138
|
3.6
|
25.2
|
1.0
|
|
C
|
A:THR136
|
3.7
|
24.2
|
1.0
|
|
N
|
A:GLY134
|
4.2
|
17.5
|
1.0
|
|
N
|
A:THR136
|
4.2
|
21.8
|
1.0
|
|
C
|
A:PRO137
|
4.2
|
29.9
|
1.0
|
|
O
|
A:PRO137
|
4.3
|
36.8
|
1.0
|
|
CB
|
A:ASP142
|
4.4
|
17.1
|
1.0
|
|
N
|
A:ASP138
|
4.4
|
27.6
|
1.0
|
|
O
|
A:ARG140
|
4.4
|
11.6
|
1.0
|
|
O
|
A:HOH693
|
4.4
|
28.2
|
1.0
|
|
CG
|
A:GLU133
|
4.4
|
17.8
|
1.0
|
|
OG1
|
A:THR136
|
4.5
|
24.0
|
1.0
|
|
CA
|
A:SER139
|
4.5
|
22.9
|
1.0
|
|
N
|
A:SER139
|
4.5
|
23.4
|
1.0
|
|
CA
|
A:THR136
|
4.5
|
22.8
|
1.0
|
|
O
|
A:HOH794
|
4.6
|
35.7
|
1.0
|
|
N
|
A:GLY135
|
4.6
|
17.3
|
1.0
|
|
CA
|
A:ASP138
|
4.6
|
25.5
|
1.0
|
|
N
|
A:PRO137
|
4.7
|
25.9
|
1.0
|
|
CA
|
A:PRO137
|
4.7
|
27.2
|
1.0
|
|
O
|
A:HOH902
|
4.8
|
25.9
|
1.0
|
|
C
|
A:SER139
|
4.8
|
20.0
|
1.0
|
|
CA
|
A:GLY134
|
4.9
|
15.8
|
1.0
|
|
CA
|
A:GLU133
|
4.9
|
17.5
|
1.0
|
|
Calcium binding site 2 out
of 12 in 3wn6
Go back to
Calcium Binding Sites List in 3wn6
Calcium binding site 2 out
of 12 in the Crystal Structure of Alpha-Amylase Amyi-1 From Oryza Sativa
 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 Alpha-Amylase Amyi-1 From Oryza Sativa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca502
b:24.3
occ:1.00
|
OD2
|
A:ASP152
|
2.2
|
17.0
|
1.0
|
|
O
|
A:PHE167
|
2.3
|
23.1
|
1.0
|
|
OD1
|
A:ASP172
|
2.3
|
22.1
|
1.0
|
|
O
|
A:ALA170
|
2.4
|
17.7
|
1.0
|
|
O
|
A:HOH629
|
2.5
|
14.0
|
1.0
|
|
OD1
|
A:ASP166
|
2.7
|
22.5
|
1.0
|
|
CG
|
A:ASP152
|
3.2
|
20.9
|
1.0
|
|
C
|
A:PHE167
|
3.4
|
21.3
|
1.0
|
|
CG
|
A:ASP172
|
3.4
|
19.8
|
1.0
|
|
N
|
A:ASP172
|
3.4
|
21.6
|
1.0
|
|
C
|
A:ALA170
|
3.5
|
20.0
|
1.0
|
|
CG
|
A:ASP166
|
3.5
|
24.1
|
1.0
|
|
OD2
|
A:ASP166
|
3.7
|
26.5
|
1.0
|
|
OD1
|
A:ASP152
|
3.8
|
21.0
|
1.0
|
|
CB
|
A:ASP172
|
3.9
|
20.3
|
1.0
|
|
O
|
A:HOH774
|
3.9
|
13.1
|
1.0
|
|
N
|
A:PHE167
|
3.9
|
20.3
|
1.0
|
|
C
|
A:PRO171
|
3.9
|
21.0
|
1.0
|
|
CA
|
A:PRO171
|
4.1
|
21.0
|
1.0
|
|
CA
|
A:ASP172
|
4.2
|
20.0
|
1.0
|
|
CA
|
A:PHE167
|
4.2
|
20.2
|
1.0
|
|
N
|
A:PRO171
|
4.2
|
21.4
|
1.0
|
|
CA
|
A:ALA168
|
4.2
|
21.2
|
1.0
|
|
N
|
A:ALA168
|
4.3
|
21.1
|
1.0
|
|
OD2
|
A:ASP172
|
4.4
|
20.4
|
1.0
|
|
C
|
A:ALA168
|
4.4
|
22.1
|
1.0
|
|
CB
|
A:ASP152
|
4.4
|
19.9
|
1.0
|
|
N
|
A:ALA170
|
4.5
|
20.8
|
1.0
|
|
O
|
A:ALA168
|
4.5
|
24.8
|
1.0
|
|
O
|
A:HOH981
|
4.6
|
26.8
|
1.0
|
|
CA
|
A:ALA170
|
4.7
|
19.5
|
1.0
|
|
O
|
A:HOH692
|
4.7
|
27.2
|
1.0
|
|
CB
|
A:PHE167
|
4.7
|
20.3
|
1.0
|
|
O
|
A:PRO171
|
4.8
|
20.0
|
1.0
|
|
CB
|
A:ASP166
|
4.9
|
21.1
|
1.0
|
|
CD2
|
A:TYR154
|
4.9
|
24.8
|
1.0
|
|
C
|
A:ASP166
|
4.9
|
21.1
|
1.0
|
|
N
|
A:ALA169
|
5.0
|
21.0
|
1.0
|
|
Calcium binding site 3 out
of 12 in 3wn6
Go back to
Calcium Binding Sites List in 3wn6
Calcium binding site 3 out
of 12 in the Crystal Structure of Alpha-Amylase Amyi-1 From Oryza Sativa
 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 Alpha-Amylase Amyi-1 From Oryza Sativa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca503
b:26.1
occ:1.00
|
O
|
A:HOH683
|
2.2
|
27.7
|
1.0
|
|
O
|
A:GLY207
|
2.2
|
14.3
|
1.0
|
|
OD1
|
A:ASN116
|
2.3
|
21.8
|
1.0
|
|
O
|
A:ALA165
|
2.4
|
18.6
|
1.0
|
|
OD1
|
A:ASP162
|
2.5
|
17.9
|
1.0
|
|
OD2
|
A:ASP172
|
2.5
|
20.4
|
1.0
|
|
OD2
|
A:ASP162
|
2.5
|
19.9
|
1.0
|
|
CG
|
A:ASP162
|
2.8
|
21.6
|
1.0
|
|
C
|
A:GLY207
|
3.2
|
15.7
|
1.0
|
|
CG
|
A:ASN116
|
3.4
|
21.1
|
1.0
|
|
C
|
A:ALA165
|
3.5
|
18.8
|
1.0
|
|
CG
|
A:ASP172
|
3.6
|
19.8
|
1.0
|
|
CA
|
A:GLY207
|
3.7
|
16.7
|
1.0
|
|
ND2
|
A:ASN116
|
3.9
|
20.9
|
1.0
|
|
CB
|
A:ASP172
|
4.0
|
20.3
|
1.0
|
|
C
|
A:GLY164
|
4.2
|
18.2
|
1.0
|
|
O
|
A:GLY164
|
4.2
|
19.5
|
1.0
|
|
N
|
A:TYR208
|
4.3
|
16.6
|
1.0
|
|
O
|
A:ASN116
|
4.3
|
18.1
|
1.0
|
|
N
|
A:ASP166
|
4.4
|
20.1
|
1.0
|
|
CB
|
A:ASP162
|
4.4
|
23.4
|
1.0
|
|
N
|
A:ALA165
|
4.4
|
18.2
|
1.0
|
|
CA
|
A:ASP166
|
4.4
|
20.7
|
1.0
|
|
CA
|
A:ALA165
|
4.6
|
18.8
|
1.0
|
|
O
|
A:HOH672
|
4.7
|
17.0
|
1.0
|
|
CB
|
A:ASN116
|
4.7
|
19.8
|
1.0
|
|
OD1
|
A:ASP172
|
4.7
|
22.1
|
1.0
|
|
N
|
A:GLY164
|
4.7
|
19.6
|
1.0
|
|
CA
|
A:GLY164
|
4.7
|
18.6
|
1.0
|
|
CA
|
A:TYR208
|
4.8
|
17.4
|
1.0
|
|
O
|
A:HOH692
|
4.8
|
27.2
|
1.0
|
|
C
|
A:ASN116
|
5.0
|
18.3
|
1.0
|
|
CA
|
A:ASN116
|
5.0
|
18.9
|
1.0
|
|
Calcium binding site 4 out
of 12 in 3wn6
Go back to
Calcium Binding Sites List in 3wn6
Calcium binding site 4 out
of 12 in the Crystal Structure of Alpha-Amylase Amyi-1 From Oryza Sativa
 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 Alpha-Amylase Amyi-1 From Oryza Sativa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca501
b:22.0
occ:1.00
|
O
|
B:HOH667
|
2.2
|
20.4
|
1.0
|
|
O
|
B:GLY207
|
2.3
|
15.6
|
1.0
|
|
ND2
|
B:ASN116
|
2.4
|
18.0
|
1.0
|
|
OD1
|
B:ASP162
|
2.4
|
16.5
|
1.0
|
|
OD2
|
B:ASP162
|
2.4
|
15.8
|
1.0
|
|
O
|
B:ALA165
|
2.5
|
18.0
|
1.0
|
|
OD1
|
B:ASP172
|
2.5
|
21.2
|
1.0
|
|
CG
|
B:ASP162
|
2.8
|
19.4
|
1.0
|
|
C
|
B:GLY207
|
3.3
|
14.5
|
1.0
|
|
CG
|
B:ASN116
|
3.5
|
18.0
|
1.0
|
|
CG
|
B:ASP172
|
3.5
|
19.1
|
1.0
|
|
C
|
B:ALA165
|
3.6
|
19.0
|
1.0
|
|
CA
|
B:GLY207
|
3.8
|
14.7
|
1.0
|
|
OD1
|
B:ASN116
|
3.9
|
18.7
|
1.0
|
|
CB
|
B:ASP172
|
3.9
|
18.0
|
1.0
|
|
O
|
B:GLY164
|
4.3
|
19.4
|
1.0
|
|
CB
|
B:ASP162
|
4.3
|
20.1
|
1.0
|
|
O
|
B:ASN116
|
4.3
|
18.4
|
1.0
|
|
C
|
B:GLY164
|
4.3
|
18.8
|
1.0
|
|
CA
|
B:ASP166
|
4.4
|
21.1
|
1.0
|
|
N
|
B:TYR208
|
4.4
|
14.9
|
1.0
|
|
N
|
B:ASP166
|
4.4
|
19.6
|
1.0
|
|
N
|
B:ALA165
|
4.5
|
17.9
|
1.0
|
|
O
|
B:HOH624
|
4.6
|
11.9
|
1.0
|
|
OD2
|
B:ASP172
|
4.6
|
23.0
|
1.0
|
|
CA
|
B:ALA165
|
4.6
|
17.8
|
1.0
|
|
O
|
B:HOH764
|
4.7
|
28.8
|
1.0
|
|
CB
|
B:ASN116
|
4.7
|
17.6
|
1.0
|
|
N
|
B:GLY164
|
4.7
|
18.6
|
1.0
|
|
CA
|
B:GLY164
|
4.8
|
18.0
|
1.0
|
|
CA
|
B:TYR208
|
4.8
|
16.4
|
1.0
|
|
O
|
B:ILE173
|
4.9
|
13.2
|
1.0
|
|
SG
|
B:CYS149
|
4.9
|
20.6
|
1.0
|
|
C
|
B:ASN116
|
5.0
|
17.4
|
1.0
|
|
CA
|
B:ASP172
|
5.0
|
17.7
|
1.0
|
|
Calcium binding site 5 out
of 12 in 3wn6
Go back to
Calcium Binding Sites List in 3wn6
Calcium binding site 5 out
of 12 in the Crystal Structure of Alpha-Amylase Amyi-1 From Oryza Sativa
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Crystal Structure of Alpha-Amylase Amyi-1 From Oryza Sativa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca502
b:16.7
occ:1.00
|
O
|
B:HOH644
|
2.2
|
11.2
|
1.0
|
|
O
|
B:HOH710
|
2.3
|
29.9
|
1.0
|
|
O
|
B:ASP138
|
2.4
|
21.4
|
1.0
|
|
OD2
|
B:ASP142
|
2.4
|
15.8
|
1.0
|
|
OE2
|
B:GLU133
|
2.5
|
17.6
|
1.0
|
|
O
|
B:THR136
|
2.5
|
21.1
|
1.0
|
|
OD1
|
B:ASP142
|
2.6
|
11.9
|
1.0
|
|
OE1
|
B:GLU133
|
2.8
|
18.0
|
1.0
|
|
CG
|
B:ASP142
|
2.8
|
15.2
|
1.0
|
|
CD
|
B:GLU133
|
3.0
|
16.6
|
1.0
|
|
C
|
B:ASP138
|
3.6
|
23.1
|
1.0
|
|
C
|
B:THR136
|
3.7
|
22.4
|
1.0
|
|
N
|
B:GLY134
|
4.2
|
14.9
|
1.0
|
|
N
|
B:THR136
|
4.2
|
19.6
|
1.0
|
|
O
|
B:HOH757
|
4.3
|
28.7
|
1.0
|
|
C
|
B:PRO137
|
4.3
|
26.6
|
1.0
|
|
O
|
B:PRO137
|
4.3
|
35.5
|
1.0
|
|
CB
|
B:ASP142
|
4.3
|
17.8
|
1.0
|
|
O
|
B:ARG140
|
4.3
|
12.2
|
1.0
|
|
N
|
B:ASP138
|
4.4
|
25.9
|
1.0
|
|
CA
|
B:SER139
|
4.4
|
21.9
|
0.5
|
|
OG1
|
B:THR136
|
4.4
|
22.4
|
1.0
|
|
N
|
B:SER139
|
4.4
|
22.0
|
0.5
|
|
N
|
B:SER139
|
4.4
|
22.9
|
0.5
|
|
CA
|
B:SER139
|
4.4
|
23.4
|
0.5
|
|
CG
|
B:GLU133
|
4.5
|
16.7
|
1.0
|
|
CA
|
B:THR136
|
4.5
|
20.7
|
1.0
|
|
O
|
B:HOH775
|
4.6
|
27.1
|
1.0
|
|
CA
|
B:ASP138
|
4.6
|
24.1
|
1.0
|
|
N
|
B:GLY135
|
4.6
|
15.8
|
1.0
|
|
N
|
B:PRO137
|
4.7
|
26.2
|
1.0
|
|
C
|
B:SER139
|
4.7
|
21.5
|
0.5
|
|
C
|
B:SER139
|
4.7
|
22.2
|
0.5
|
|
CA
|
B:PRO137
|
4.8
|
26.7
|
1.0
|
|
CA
|
B:GLY134
|
4.8
|
14.6
|
1.0
|
|
N
|
B:ARG140
|
4.9
|
20.7
|
1.0
|
|
CA
|
B:GLU133
|
4.9
|
15.7
|
1.0
|
|
Calcium binding site 6 out
of 12 in 3wn6
Go back to
Calcium Binding Sites List in 3wn6
Calcium binding site 6 out
of 12 in the Crystal Structure of Alpha-Amylase Amyi-1 From Oryza Sativa
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Crystal Structure of Alpha-Amylase Amyi-1 From Oryza Sativa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca503
b:21.3
occ:1.00
|
O
|
B:PHE167
|
2.2
|
21.6
|
1.0
|
|
OD2
|
B:ASP152
|
2.3
|
16.5
|
1.0
|
|
OD2
|
B:ASP172
|
2.4
|
23.0
|
1.0
|
|
O
|
B:ALA170
|
2.4
|
17.2
|
1.0
|
|
O
|
B:HOH654
|
2.5
|
12.9
|
1.0
|
|
OD1
|
B:ASP166
|
2.7
|
22.1
|
1.0
|
|
CG
|
B:ASP152
|
3.3
|
20.1
|
1.0
|
|
C
|
B:PHE167
|
3.3
|
21.4
|
1.0
|
|
CG
|
B:ASP172
|
3.4
|
19.1
|
1.0
|
|
CG
|
B:ASP166
|
3.5
|
22.4
|
1.0
|
|
N
|
B:ASP172
|
3.5
|
18.4
|
1.0
|
|
C
|
B:ALA170
|
3.6
|
19.9
|
1.0
|
|
OD2
|
B:ASP166
|
3.7
|
24.3
|
1.0
|
|
OD1
|
B:ASP152
|
3.8
|
20.8
|
1.0
|
|
O
|
B:HOH788
|
3.9
|
18.9
|
1.0
|
|
N
|
B:PHE167
|
3.9
|
21.0
|
1.0
|
|
CB
|
B:ASP172
|
3.9
|
18.0
|
1.0
|
|
C
|
B:PRO171
|
4.0
|
18.6
|
1.0
|
|
CA
|
B:PRO171
|
4.2
|
19.6
|
1.0
|
|
CA
|
B:PHE167
|
4.2
|
20.5
|
1.0
|
|
CA
|
B:ALA168
|
4.2
|
23.3
|
1.0
|
|
N
|
B:ALA168
|
4.2
|
22.6
|
1.0
|
|
CA
|
B:ASP172
|
4.2
|
17.7
|
1.0
|
|
N
|
B:PRO171
|
4.3
|
19.6
|
1.0
|
|
OD1
|
B:ASP172
|
4.4
|
21.2
|
1.0
|
|
C
|
B:ALA168
|
4.4
|
23.2
|
1.0
|
|
N
|
B:ALA170
|
4.4
|
21.6
|
1.0
|
|
O
|
B:ALA168
|
4.5
|
25.3
|
1.0
|
|
CB
|
B:ASP152
|
4.5
|
20.5
|
1.0
|
|
CA
|
B:ALA170
|
4.7
|
19.9
|
1.0
|
|
CB
|
B:PHE167
|
4.7
|
20.8
|
1.0
|
|
O
|
B:HOH764
|
4.7
|
28.8
|
1.0
|
|
CB
|
B:ASP166
|
4.8
|
20.7
|
1.0
|
|
C
|
B:ASP166
|
4.8
|
20.5
|
1.0
|
|
CD2
|
B:TYR154
|
4.9
|
25.2
|
1.0
|
|
O
|
B:PRO171
|
4.9
|
18.9
|
1.0
|
|
N
|
B:ALA169
|
4.9
|
22.2
|
1.0
|
|
Calcium binding site 7 out
of 12 in 3wn6
Go back to
Calcium Binding Sites List in 3wn6
Calcium binding site 7 out
of 12 in the Crystal Structure of Alpha-Amylase Amyi-1 From Oryza Sativa
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Crystal Structure of Alpha-Amylase Amyi-1 From Oryza Sativa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca501
b:16.6
occ:1.00
|
O
|
C:HOH674
|
2.3
|
8.6
|
1.0
|
|
OD2
|
C:ASP172
|
2.4
|
19.7
|
1.0
|
|
OD2
|
C:ASP162
|
2.4
|
23.6
|
1.0
|
|
OD1
|
C:ASP162
|
2.4
|
21.1
|
1.0
|
|
O
|
C:GLY207
|
2.4
|
21.0
|
1.0
|
|
ND2
|
C:ASN116
|
2.5
|
13.1
|
1.0
|
|
O
|
C:ALA165
|
2.5
|
21.8
|
1.0
|
|
CG
|
C:ASP162
|
2.7
|
23.5
|
1.0
|
|
CG
|
C:ASP172
|
3.4
|
19.3
|
1.0
|
|
C
|
C:GLY207
|
3.4
|
20.6
|
1.0
|
|
CG
|
C:ASN116
|
3.5
|
14.9
|
1.0
|
|
C
|
C:ALA165
|
3.6
|
21.9
|
1.0
|
|
CB
|
C:ASP172
|
3.8
|
20.8
|
1.0
|
|
OD1
|
C:ASN116
|
3.9
|
15.1
|
1.0
|
|
CA
|
C:GLY207
|
3.9
|
19.4
|
1.0
|
|
CB
|
C:ASP162
|
4.2
|
25.6
|
1.0
|
|
O
|
C:GLY164
|
4.2
|
22.5
|
1.0
|
|
C
|
C:GLY164
|
4.3
|
21.9
|
1.0
|
|
CA
|
C:ASP166
|
4.3
|
24.2
|
1.0
|
|
O
|
C:ASN116
|
4.3
|
16.7
|
1.0
|
|
O
|
C:HOH653
|
4.3
|
20.2
|
1.0
|
|
N
|
C:ASP166
|
4.4
|
21.9
|
1.0
|
|
N
|
C:ALA165
|
4.5
|
20.3
|
1.0
|
|
OD1
|
C:ASP172
|
4.5
|
19.3
|
1.0
|
|
N
|
C:TYR208
|
4.5
|
20.1
|
1.0
|
|
CA
|
C:ALA165
|
4.6
|
22.2
|
1.0
|
|
CB
|
C:ASN116
|
4.8
|
14.2
|
1.0
|
|
N
|
C:GLY164
|
4.8
|
22.4
|
1.0
|
|
O
|
C:HOH731
|
4.8
|
25.4
|
1.0
|
|
SG
|
C:CYS149
|
4.8
|
24.5
|
1.0
|
|
CA
|
C:GLY164
|
4.9
|
21.9
|
1.0
|
|
CA
|
C:ASP172
|
4.9
|
20.5
|
1.0
|
|
O
|
C:ILE173
|
4.9
|
17.7
|
1.0
|
|
CA
|
C:TYR208
|
4.9
|
20.8
|
1.0
|
|
C
|
C:ASN116
|
5.0
|
15.8
|
1.0
|
|
Calcium binding site 8 out
of 12 in 3wn6
Go back to
Calcium Binding Sites List in 3wn6
Calcium binding site 8 out
of 12 in the Crystal Structure of Alpha-Amylase Amyi-1 From Oryza Sativa
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Crystal Structure of Alpha-Amylase Amyi-1 From Oryza Sativa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca502
b:24.8
occ:1.00
|
O
|
C:ASP138
|
2.3
|
24.8
|
1.0
|
|
OE2
|
C:GLU133
|
2.4
|
20.2
|
1.0
|
|
O
|
C:HOH614
|
2.5
|
6.8
|
1.0
|
|
O
|
C:THR136
|
2.5
|
22.3
|
1.0
|
|
OD2
|
C:ASP142
|
2.5
|
16.8
|
1.0
|
|
O
|
C:HOH646
|
2.5
|
16.1
|
1.0
|
|
OD1
|
C:ASP142
|
2.7
|
16.6
|
1.0
|
|
OE1
|
C:GLU133
|
2.8
|
20.1
|
1.0
|
|
CG
|
C:ASP142
|
2.9
|
17.8
|
1.0
|
|
CD
|
C:GLU133
|
3.0
|
19.4
|
1.0
|
|
C
|
C:ASP138
|
3.6
|
22.6
|
1.0
|
|
C
|
C:THR136
|
3.7
|
22.4
|
1.0
|
|
N
|
C:GLY134
|
4.2
|
18.1
|
1.0
|
|
N
|
C:THR136
|
4.2
|
22.1
|
1.0
|
|
C
|
C:PRO137
|
4.3
|
27.5
|
1.0
|
|
O
|
C:ARG140
|
4.3
|
13.4
|
1.0
|
|
O
|
C:PRO137
|
4.3
|
36.9
|
1.0
|
|
OG1
|
C:THR136
|
4.3
|
26.4
|
1.0
|
|
N
|
C:ASP138
|
4.4
|
25.5
|
1.0
|
|
O
|
C:HOH688
|
4.4
|
20.4
|
1.0
|
|
N
|
C:SER139
|
4.4
|
20.8
|
1.0
|
|
CA
|
C:SER139
|
4.4
|
20.4
|
1.0
|
|
CB
|
C:ASP142
|
4.4
|
18.3
|
1.0
|
|
CA
|
C:THR136
|
4.5
|
22.8
|
1.0
|
|
CG
|
C:GLU133
|
4.5
|
18.7
|
1.0
|
|
CA
|
C:ASP138
|
4.6
|
22.7
|
1.0
|
|
N
|
C:GLY135
|
4.6
|
16.9
|
1.0
|
|
N
|
C:PRO137
|
4.6
|
25.1
|
1.0
|
|
C
|
C:SER139
|
4.7
|
18.8
|
1.0
|
|
CA
|
C:PRO137
|
4.7
|
26.6
|
1.0
|
|
CA
|
C:GLY134
|
4.8
|
16.5
|
1.0
|
|
N
|
C:ARG140
|
4.9
|
17.0
|
1.0
|
|
CA
|
C:GLU133
|
5.0
|
18.2
|
1.0
|
|
Calcium binding site 9 out
of 12 in 3wn6
Go back to
Calcium Binding Sites List in 3wn6
Calcium binding site 9 out
of 12 in the Crystal Structure of Alpha-Amylase Amyi-1 From Oryza Sativa
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Crystal Structure of Alpha-Amylase Amyi-1 From Oryza Sativa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca503
b:28.3
occ:1.00
|
OD2
|
C:ASP152
|
2.2
|
22.4
|
1.0
|
|
OD1
|
C:ASP172
|
2.2
|
19.3
|
1.0
|
|
O
|
C:PHE167
|
2.3
|
24.0
|
1.0
|
|
O
|
C:HOH610
|
2.3
|
29.1
|
1.0
|
|
O
|
C:ALA170
|
2.4
|
17.6
|
1.0
|
|
OD1
|
C:ASP166
|
2.6
|
25.1
|
1.0
|
|
CG
|
C:ASP152
|
3.3
|
25.8
|
1.0
|
|
CG
|
C:ASP172
|
3.3
|
19.3
|
1.0
|
|
C
|
C:PHE167
|
3.3
|
24.0
|
1.0
|
|
N
|
C:ASP172
|
3.4
|
22.2
|
1.0
|
|
CG
|
C:ASP166
|
3.5
|
26.0
|
1.0
|
|
C
|
C:ALA170
|
3.6
|
18.1
|
1.0
|
|
OD2
|
C:ASP166
|
3.7
|
28.2
|
1.0
|
|
CB
|
C:ASP172
|
3.8
|
20.8
|
1.0
|
|
OD1
|
C:ASP152
|
3.8
|
26.4
|
1.0
|
|
N
|
C:PHE167
|
3.9
|
22.6
|
1.0
|
|
C
|
C:PRO171
|
4.0
|
19.7
|
1.0
|
|
CA
|
C:PRO171
|
4.1
|
18.8
|
1.0
|
|
CA
|
C:ASP172
|
4.1
|
20.5
|
1.0
|
|
CA
|
C:PHE167
|
4.2
|
23.0
|
1.0
|
|
N
|
C:ALA168
|
4.2
|
22.6
|
1.0
|
|
CA
|
C:ALA168
|
4.3
|
23.8
|
1.0
|
|
O
|
C:HOH731
|
4.3
|
25.4
|
1.0
|
|
N
|
C:PRO171
|
4.3
|
19.5
|
1.0
|
|
OD2
|
C:ASP172
|
4.3
|
19.7
|
1.0
|
|
CB
|
C:ASP152
|
4.4
|
22.3
|
1.0
|
|
C
|
C:ALA168
|
4.5
|
23.8
|
1.0
|
|
N
|
C:ALA170
|
4.5
|
18.0
|
1.0
|
|
O
|
C:ALA168
|
4.6
|
24.5
|
1.0
|
|
CB
|
C:PHE167
|
4.7
|
22.9
|
1.0
|
|
CA
|
C:ALA170
|
4.7
|
18.5
|
1.0
|
|
CB
|
C:ASP166
|
4.8
|
23.7
|
1.0
|
|
C
|
C:ASP166
|
4.8
|
23.8
|
1.0
|
|
O
|
C:PRO171
|
4.8
|
18.6
|
1.0
|
|
O
|
C:HOH838
|
4.9
|
29.9
|
1.0
|
|
CD2
|
C:TYR154
|
4.9
|
23.6
|
1.0
|
|
CA
|
C:ASP166
|
5.0
|
24.2
|
1.0
|
|
Calcium binding site 10 out
of 12 in 3wn6
Go back to
Calcium Binding Sites List in 3wn6
Calcium binding site 10 out
of 12 in the Crystal Structure of Alpha-Amylase Amyi-1 From Oryza Sativa
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Crystal Structure of Alpha-Amylase Amyi-1 From Oryza Sativa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca501
b:18.9
occ:1.00
|
OD2
|
D:ASP162
|
2.3
|
17.6
|
1.0
|
|
OD1
|
D:ASP162
|
2.3
|
19.0
|
1.0
|
|
O
|
D:HOH663
|
2.3
|
13.1
|
1.0
|
|
O
|
D:GLY207
|
2.4
|
22.6
|
1.0
|
|
OD1
|
D:ASP172
|
2.5
|
18.5
|
1.0
|
|
O
|
D:ALA165
|
2.5
|
21.5
|
1.0
|
|
ND2
|
D:ASN116
|
2.6
|
13.6
|
1.0
|
|
CG
|
D:ASP162
|
2.6
|
20.4
|
1.0
|
|
C
|
D:GLY207
|
3.4
|
19.1
|
1.0
|
|
CG
|
D:ASP172
|
3.5
|
16.8
|
1.0
|
|
C
|
D:ALA165
|
3.6
|
24.7
|
1.0
|
|
CG
|
D:ASN116
|
3.6
|
14.1
|
1.0
|
|
CB
|
D:ASP172
|
3.8
|
15.8
|
1.0
|
|
CA
|
D:GLY207
|
3.9
|
19.4
|
1.0
|
|
OD1
|
D:ASN116
|
4.0
|
15.1
|
1.0
|
|
CB
|
D:ASP162
|
4.2
|
19.8
|
1.0
|
|
O
|
D:GLY164
|
4.2
|
26.1
|
1.0
|
|
C
|
D:GLY164
|
4.3
|
22.3
|
1.0
|
|
CA
|
D:ASP166
|
4.3
|
27.3
|
1.0
|
|
O
|
D:ASN116
|
4.4
|
14.9
|
1.0
|
|
N
|
D:ASP166
|
4.4
|
24.5
|
1.0
|
|
N
|
D:ALA165
|
4.4
|
22.0
|
1.0
|
|
N
|
D:TYR208
|
4.5
|
18.3
|
1.0
|
|
O
|
D:HOH609
|
4.5
|
11.8
|
1.0
|
|
OD2
|
D:ASP172
|
4.6
|
18.7
|
1.0
|
|
CA
|
D:ALA165
|
4.6
|
23.2
|
1.0
|
|
O
|
D:HOH806
|
4.7
|
26.6
|
1.0
|
|
N
|
D:GLY164
|
4.7
|
20.3
|
1.0
|
|
SG
|
D:CYS149
|
4.8
|
20.6
|
1.0
|
|
CA
|
D:GLY164
|
4.8
|
22.2
|
1.0
|
|
CB
|
D:ASN116
|
4.8
|
13.8
|
1.0
|
|
O
|
D:ILE173
|
4.9
|
15.2
|
1.0
|
|
CA
|
D:TYR208
|
4.9
|
18.9
|
1.0
|
|
CA
|
D:ASP172
|
4.9
|
15.8
|
1.0
|
|
Reference:
A.Ochiai,
H.Sugai,
K.Harada,
S.Tanaka,
Y.Ishiyama,
K.Ito,
T.Tanaka,
T.Uchiumi,
M.Taniguchi,
T.Mitsui.
Crystal Structure of Alpha-Amylase From Oryza Sativa: Molecular Insights Into Enzyme Activity and Thermostability Biosci.Biotechnol.Biochem. V. 78 989 2014.
ISSN: ISSN 0916-8451
PubMed: 25036124
DOI: 10.1080/09168451.2014.917261
Page generated: Sat Dec 12 04:35:48 2020
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