Calcium in PDB 7w2a: Gliadinase BGA1903
Protein crystallography data
The structure of Gliadinase BGA1903, PDB code: 7w2a
was solved by
M.Meng,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
26.60 /
1.60
|
|
Space group
|
P 32
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
83.885,
83.885,
107.079,
90,
90,
120
|
|
R / Rfree (%)
|
14.7 /
17
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Gliadinase BGA1903
(pdb code 7w2a). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
Gliadinase BGA1903, PDB code: 7w2a:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 7w2a
Go back to
Calcium Binding Sites List in 7w2a
Calcium binding site 1 out
of 6 in the Gliadinase BGA1903
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Gliadinase BGA1903 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca501
b:8.0
occ:1.00
|
OD2
|
A:ASP118
|
2.3
|
8.3
|
1.0
|
|
O
|
A:VAL240
|
2.4
|
9.3
|
1.0
|
|
O
|
A:THR245
|
2.4
|
9.5
|
1.0
|
|
OD1
|
A:ASN243
|
2.4
|
9.3
|
1.0
|
|
O
|
A:VAL247
|
2.4
|
9.0
|
1.0
|
|
OD1
|
A:ASP163
|
2.5
|
9.6
|
1.0
|
|
OD2
|
A:ASP163
|
2.5
|
8.3
|
1.0
|
|
CG
|
A:ASP163
|
2.8
|
8.5
|
1.0
|
|
CG
|
A:ASN243
|
3.4
|
10.1
|
1.0
|
|
CG
|
A:ASP118
|
3.4
|
8.8
|
1.0
|
|
C
|
A:VAL240
|
3.6
|
8.5
|
1.0
|
|
C
|
A:VAL247
|
3.6
|
8.2
|
1.0
|
|
C
|
A:THR245
|
3.6
|
11.4
|
1.0
|
|
N
|
A:VAL247
|
3.7
|
9.4
|
1.0
|
|
ND2
|
A:ASN243
|
3.8
|
10.5
|
1.0
|
|
C
|
A:GLY246
|
4.0
|
10.2
|
1.0
|
|
CB
|
A:ASP118
|
4.0
|
8.3
|
1.0
|
|
CA
|
A:VAL247
|
4.3
|
7.7
|
1.0
|
|
CA
|
A:SER241
|
4.3
|
8.1
|
1.0
|
|
CA
|
A:GLY246
|
4.3
|
8.7
|
1.0
|
|
N
|
A:SER241
|
4.3
|
7.6
|
1.0
|
|
CB
|
A:ASP163
|
4.4
|
8.7
|
1.0
|
|
OD1
|
A:ASP118
|
4.4
|
8.6
|
1.0
|
|
N
|
A:GLY246
|
4.4
|
9.2
|
1.0
|
|
CG2
|
A:THR245
|
4.5
|
16.1
|
1.0
|
|
N
|
A:THR245
|
4.5
|
11.0
|
1.0
|
|
O
|
A:GLY246
|
4.6
|
9.0
|
1.0
|
|
CA
|
A:VAL240
|
4.6
|
7.4
|
1.0
|
|
CA
|
A:THR245
|
4.6
|
11.5
|
1.0
|
|
N
|
A:ALA248
|
4.6
|
7.1
|
1.0
|
|
N
|
A:ASN243
|
4.7
|
9.5
|
1.0
|
|
CB
|
A:ASN243
|
4.7
|
9.4
|
1.0
|
|
N
|
A:VAL240
|
4.8
|
7.4
|
1.0
|
|
C
|
A:SER241
|
4.8
|
8.3
|
1.0
|
|
CB
|
A:VAL240
|
4.8
|
9.4
|
1.0
|
|
N
|
A:ASN242
|
4.9
|
8.8
|
1.0
|
|
CA
|
A:ALA248
|
4.9
|
7.3
|
1.0
|
|
O
|
A:ASP163
|
5.0
|
9.6
|
1.0
|
|
Calcium binding site 2 out
of 6 in 7w2a
Go back to
Calcium Binding Sites List in 7w2a
Calcium binding site 2 out
of 6 in the Gliadinase BGA1903
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Gliadinase BGA1903 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca502
b:7.3
occ:1.00
|
OD2
|
A:ASP188
|
2.3
|
7.9
|
1.0
|
|
OD1
|
A:ASN185
|
2.3
|
9.4
|
1.0
|
|
O
|
A:GLY186
|
2.3
|
7.8
|
1.0
|
|
O
|
A:HOH761
|
2.4
|
7.4
|
1.0
|
|
O
|
A:ASN185
|
2.4
|
7.9
|
1.0
|
|
OD2
|
A:ASP183
|
2.5
|
9.2
|
1.0
|
|
OD1
|
A:ASP183
|
2.5
|
9.0
|
1.0
|
|
CG
|
A:ASP183
|
2.8
|
9.1
|
1.0
|
|
C
|
A:ASN185
|
3.2
|
8.2
|
1.0
|
|
C
|
A:GLY186
|
3.4
|
7.2
|
1.0
|
|
CG
|
A:ASP188
|
3.4
|
8.0
|
1.0
|
|
CG
|
A:ASN185
|
3.5
|
9.9
|
1.0
|
|
CB
|
A:ALA181
|
3.9
|
7.8
|
1.0
|
|
N
|
A:GLY186
|
3.9
|
8.4
|
1.0
|
|
CA
|
A:CA503
|
3.9
|
7.9
|
1.0
|
|
CA
|
A:GLY186
|
4.0
|
7.5
|
1.0
|
|
CA
|
A:ASN185
|
4.0
|
8.1
|
1.0
|
|
N
|
A:ASN185
|
4.1
|
9.8
|
1.0
|
|
OD2
|
A:ASP173
|
4.1
|
7.1
|
1.0
|
|
CB
|
A:ASP188
|
4.1
|
8.2
|
1.0
|
|
CB
|
A:ASN185
|
4.2
|
9.0
|
1.0
|
|
CB
|
A:ASP183
|
4.3
|
9.5
|
1.0
|
|
OD1
|
A:ASP188
|
4.4
|
8.8
|
1.0
|
|
CG
|
A:ASP173
|
4.4
|
6.2
|
1.0
|
|
N
|
A:ARG187
|
4.5
|
7.2
|
1.0
|
|
ND2
|
A:ASN185
|
4.5
|
12.0
|
1.0
|
|
O
|
A:ILE175
|
4.6
|
8.5
|
1.0
|
|
C
|
A:ARG187
|
4.6
|
7.4
|
1.0
|
|
N
|
A:ASP188
|
4.7
|
7.2
|
1.0
|
|
OD1
|
A:ASP173
|
4.7
|
7.3
|
1.0
|
|
O
|
A:HOH936
|
4.7
|
10.2
|
1.0
|
|
CA
|
A:ARG187
|
4.7
|
6.8
|
1.0
|
|
O
|
A:ARG187
|
4.9
|
8.4
|
1.0
|
|
C
|
A:ASP183
|
5.0
|
9.4
|
1.0
|
|
Calcium binding site 3 out
of 6 in 7w2a
Go back to
Calcium Binding Sites List in 7w2a
Calcium binding site 3 out
of 6 in the Gliadinase BGA1903
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Gliadinase BGA1903 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca503
b:7.9
occ:1.00
|
O
|
A:HOH660
|
2.4
|
9.7
|
1.0
|
|
OD2
|
A:ASP183
|
2.4
|
9.2
|
1.0
|
|
OD2
|
A:ASP173
|
2.4
|
7.1
|
1.0
|
|
O
|
A:HOH936
|
2.4
|
10.2
|
1.0
|
|
O
|
A:ASN190
|
2.4
|
7.7
|
1.0
|
|
OD1
|
A:ASP188
|
2.5
|
8.8
|
1.0
|
|
OD2
|
A:ASP188
|
2.5
|
7.9
|
1.0
|
|
CG
|
A:ASP188
|
2.8
|
8.0
|
1.0
|
|
CG
|
A:ASP173
|
3.3
|
6.2
|
1.0
|
|
CG
|
A:ASP183
|
3.5
|
9.1
|
1.0
|
|
CB
|
A:ASP173
|
3.6
|
7.0
|
1.0
|
|
C
|
A:ASN190
|
3.6
|
6.8
|
1.0
|
|
CA
|
A:CA502
|
3.9
|
7.3
|
1.0
|
|
CB
|
A:ASN190
|
4.1
|
9.5
|
1.0
|
|
CB
|
A:ASP183
|
4.1
|
9.5
|
1.0
|
|
CA
|
A:ASN190
|
4.2
|
9.8
|
1.0
|
|
NH1
|
A:ARG260
|
4.2
|
8.3
|
1.0
|
|
CB
|
A:ASP188
|
4.4
|
8.2
|
1.0
|
|
N
|
A:ASN190
|
4.4
|
7.8
|
1.0
|
|
OD1
|
A:ASP173
|
4.4
|
7.3
|
1.0
|
|
OD1
|
A:ASP183
|
4.5
|
9.0
|
1.0
|
|
O
|
A:HOH761
|
4.5
|
7.4
|
1.0
|
|
O
|
A:ALA192
|
4.6
|
9.1
|
1.0
|
|
CG
|
A:ASN190
|
4.6
|
12.1
|
1.0
|
|
N
|
A:ALA191
|
4.7
|
7.4
|
1.0
|
|
O
|
A:HOH946
|
4.7
|
40.3
|
1.0
|
|
O
|
A:HOH937
|
4.7
|
15.7
|
1.0
|
|
O
|
A:HOH1088
|
4.7
|
17.1
|
1.0
|
|
OD1
|
A:ASN185
|
4.8
|
9.4
|
1.0
|
|
CA
|
A:ALA191
|
5.0
|
7.9
|
1.0
|
|
Calcium binding site 4 out
of 6 in 7w2a
Go back to
Calcium Binding Sites List in 7w2a
Calcium binding site 4 out
of 6 in the Gliadinase BGA1903
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Gliadinase BGA1903 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca501
b:8.2
occ:1.00
|
OD2
|
B:ASP118
|
2.3
|
8.5
|
1.0
|
|
O
|
B:VAL240
|
2.4
|
8.7
|
1.0
|
|
O
|
B:THR245
|
2.4
|
9.8
|
1.0
|
|
OD1
|
B:ASN243
|
2.4
|
9.8
|
1.0
|
|
O
|
B:VAL247
|
2.4
|
8.9
|
1.0
|
|
OD1
|
B:ASP163
|
2.5
|
8.8
|
1.0
|
|
OD2
|
B:ASP163
|
2.5
|
8.1
|
1.0
|
|
CG
|
B:ASP163
|
2.8
|
8.5
|
1.0
|
|
CG
|
B:ASP118
|
3.4
|
8.7
|
1.0
|
|
CG
|
B:ASN243
|
3.4
|
10.8
|
1.0
|
|
C
|
B:VAL240
|
3.6
|
8.7
|
1.0
|
|
C
|
B:VAL247
|
3.6
|
8.4
|
1.0
|
|
C
|
B:THR245
|
3.6
|
11.0
|
1.0
|
|
N
|
B:VAL247
|
3.7
|
8.8
|
1.0
|
|
ND2
|
B:ASN243
|
3.8
|
10.9
|
1.0
|
|
CB
|
B:ASP118
|
4.0
|
7.5
|
1.0
|
|
C
|
B:GLY246
|
4.0
|
10.5
|
1.0
|
|
CA
|
B:VAL247
|
4.3
|
7.3
|
1.0
|
|
CA
|
B:SER241
|
4.3
|
8.0
|
1.0
|
|
CA
|
B:GLY246
|
4.3
|
8.2
|
1.0
|
|
N
|
B:SER241
|
4.4
|
7.6
|
1.0
|
|
CB
|
B:ASP163
|
4.4
|
8.2
|
1.0
|
|
OD1
|
B:ASP118
|
4.4
|
8.0
|
1.0
|
|
N
|
B:GLY246
|
4.4
|
8.9
|
1.0
|
|
CG2
|
B:THR245
|
4.5
|
15.4
|
1.0
|
|
N
|
B:THR245
|
4.5
|
11.4
|
1.0
|
|
O
|
B:GLY246
|
4.6
|
9.5
|
1.0
|
|
CA
|
B:VAL240
|
4.6
|
8.0
|
1.0
|
|
N
|
B:ALA248
|
4.6
|
7.3
|
1.0
|
|
CA
|
B:THR245
|
4.6
|
10.9
|
1.0
|
|
N
|
B:ASN243
|
4.7
|
9.3
|
1.0
|
|
CB
|
B:ASN243
|
4.7
|
10.0
|
1.0
|
|
N
|
B:VAL240
|
4.8
|
7.1
|
1.0
|
|
CB
|
B:VAL240
|
4.9
|
9.4
|
1.0
|
|
C
|
B:SER241
|
4.9
|
8.2
|
1.0
|
|
CA
|
B:ALA248
|
4.9
|
7.6
|
1.0
|
|
N
|
B:ASN242
|
4.9
|
8.3
|
1.0
|
|
O
|
B:ASP163
|
5.0
|
9.7
|
1.0
|
|
Calcium binding site 5 out
of 6 in 7w2a
Go back to
Calcium Binding Sites List in 7w2a
Calcium binding site 5 out
of 6 in the Gliadinase BGA1903
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Gliadinase BGA1903 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca502
b:7.3
occ:1.00
|
OD2
|
B:ASP188
|
2.3
|
8.7
|
1.0
|
|
OD1
|
B:ASN185
|
2.3
|
8.9
|
1.0
|
|
O
|
B:GLY186
|
2.3
|
8.2
|
1.0
|
|
O
|
B:HOH796
|
2.4
|
8.0
|
1.0
|
|
O
|
B:ASN185
|
2.5
|
8.2
|
1.0
|
|
OD1
|
B:ASP183
|
2.5
|
9.1
|
1.0
|
|
OD2
|
B:ASP183
|
2.5
|
9.0
|
1.0
|
|
CG
|
B:ASP183
|
2.8
|
8.9
|
1.0
|
|
C
|
B:ASN185
|
3.2
|
8.3
|
1.0
|
|
C
|
B:GLY186
|
3.4
|
7.4
|
1.0
|
|
CG
|
B:ASP188
|
3.4
|
8.9
|
1.0
|
|
CG
|
B:ASN185
|
3.5
|
9.7
|
1.0
|
|
N
|
B:GLY186
|
3.9
|
8.7
|
1.0
|
|
CB
|
B:ALA181
|
3.9
|
7.9
|
1.0
|
|
CA
|
B:CA503
|
3.9
|
8.2
|
1.0
|
|
CA
|
B:GLY186
|
4.0
|
8.1
|
1.0
|
|
CA
|
B:ASN185
|
4.0
|
8.5
|
1.0
|
|
OD2
|
B:ASP173
|
4.0
|
7.4
|
1.0
|
|
N
|
B:ASN185
|
4.1
|
10.2
|
1.0
|
|
CB
|
B:ASP188
|
4.1
|
8.4
|
1.0
|
|
CB
|
B:ASN185
|
4.2
|
8.9
|
1.0
|
|
CB
|
B:ASP183
|
4.3
|
9.5
|
1.0
|
|
CG
|
B:ASP173
|
4.4
|
6.5
|
1.0
|
|
OD1
|
B:ASP188
|
4.4
|
8.6
|
1.0
|
|
N
|
B:ARG187
|
4.5
|
7.3
|
1.0
|
|
ND2
|
B:ASN185
|
4.5
|
11.8
|
1.0
|
|
O
|
B:ILE175
|
4.6
|
8.7
|
1.0
|
|
C
|
B:ARG187
|
4.6
|
7.8
|
1.0
|
|
OD1
|
B:ASP173
|
4.7
|
6.9
|
1.0
|
|
N
|
B:ASP188
|
4.7
|
7.3
|
1.0
|
|
O
|
B:HOH962
|
4.7
|
10.3
|
1.0
|
|
CA
|
B:ARG187
|
4.7
|
7.2
|
1.0
|
|
O
|
B:ARG187
|
4.9
|
8.4
|
1.0
|
|
C
|
B:ASP183
|
5.0
|
9.3
|
1.0
|
|
Calcium binding site 6 out
of 6 in 7w2a
Go back to
Calcium Binding Sites List in 7w2a
Calcium binding site 6 out
of 6 in the Gliadinase BGA1903
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Gliadinase BGA1903 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca503
b:8.2
occ:1.00
|
O
|
B:HOH653
|
2.3
|
9.4
|
1.0
|
|
OD2
|
B:ASP183
|
2.4
|
9.0
|
1.0
|
|
OD2
|
B:ASP173
|
2.4
|
7.4
|
1.0
|
|
O
|
B:HOH962
|
2.4
|
10.3
|
1.0
|
|
O
|
B:ASN190
|
2.4
|
7.7
|
1.0
|
|
OD1
|
B:ASP188
|
2.5
|
8.6
|
1.0
|
|
OD2
|
B:ASP188
|
2.6
|
8.7
|
1.0
|
|
CG
|
B:ASP188
|
2.9
|
8.9
|
1.0
|
|
CG
|
B:ASP173
|
3.3
|
6.5
|
1.0
|
|
CG
|
B:ASP183
|
3.5
|
8.9
|
1.0
|
|
C
|
B:ASN190
|
3.6
|
7.2
|
1.0
|
|
CB
|
B:ASP173
|
3.6
|
7.1
|
1.0
|
|
CA
|
B:CA502
|
3.9
|
7.3
|
1.0
|
|
CB
|
B:ASN190
|
4.0
|
10.6
|
1.0
|
|
CB
|
B:ASP183
|
4.1
|
9.5
|
1.0
|
|
CA
|
B:ASN190
|
4.2
|
10.1
|
1.0
|
|
NH1
|
B:ARG260
|
4.3
|
7.4
|
1.0
|
|
CB
|
B:ASP188
|
4.4
|
8.4
|
1.0
|
|
N
|
B:ASN190
|
4.4
|
7.1
|
1.0
|
|
OD1
|
B:ASP173
|
4.4
|
6.9
|
1.0
|
|
OD1
|
B:ASP183
|
4.5
|
9.1
|
1.0
|
|
O
|
B:HOH796
|
4.5
|
8.0
|
1.0
|
|
O
|
B:ALA192
|
4.6
|
9.7
|
1.0
|
|
CG
|
B:ASN190
|
4.6
|
12.3
|
1.0
|
|
O
|
B:HOH964
|
4.6
|
16.2
|
1.0
|
|
N
|
B:ALA191
|
4.6
|
7.9
|
1.0
|
|
O
|
B:HOH1095
|
4.7
|
19.1
|
1.0
|
|
OD1
|
B:ASN185
|
4.8
|
8.9
|
1.0
|
|
CA
|
B:ALA191
|
4.9
|
7.4
|
1.0
|
|
Reference:
M.Meng,
M.Meng.
N/A N/A.
Page generated: Tue Apr 4 19:05:16 2023
|
