Calcium in PDB 2wyf: Crystal Structure of Pa-Il Lectin Complexed with AGAL12BGAL- O-Met at 2.4 A Resolution
Protein crystallography data
The structure of Crystal Structure of Pa-Il Lectin Complexed with AGAL12BGAL- O-Met at 2.4 A Resolution, PDB code: 2wyf
was solved by
A.Nurisso,
B.Blanchard,
A.Varrot,
A.Imberty,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
89.80 /
2.40
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
49.885,
99.788,
91.318,
90.00,
100.77,
90.00
|
|
R / Rfree (%)
|
16.574 /
25.891
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Pa-Il Lectin Complexed with AGAL12BGAL- O-Met at 2.4 A Resolution
(pdb code 2wyf). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the
Crystal Structure of Pa-Il Lectin Complexed with AGAL12BGAL- O-Met at 2.4 A Resolution, PDB code: 2wyf:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Calcium binding site 1 out
of 8 in 2wyf
Go back to
Calcium Binding Sites List in 2wyf
Calcium binding site 1 out
of 8 in the Crystal Structure of Pa-Il Lectin Complexed with AGAL12BGAL- O-Met at 2.4 A Resolution
 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 Pa-Il Lectin Complexed with AGAL12BGAL- O-Met at 2.4 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca200
b:21.9
occ:1.00
|
O
|
A:THR104
|
2.3
|
12.3
|
1.0
|
|
OD1
|
A:ASN108
|
2.3
|
13.2
|
1.0
|
|
O
|
A:TYR36
|
2.4
|
14.3
|
1.0
|
|
OD1
|
A:ASN107
|
2.4
|
11.2
|
1.0
|
|
O3
|
A:GLA201
|
2.5
|
26.5
|
1.0
|
|
O4
|
A:GLA201
|
2.6
|
23.2
|
1.0
|
|
OD2
|
A:ASP100
|
2.8
|
10.9
|
1.0
|
|
C
|
A:TYR36
|
3.2
|
15.2
|
1.0
|
|
C3
|
A:GLA201
|
3.4
|
24.3
|
1.0
|
|
CG
|
A:ASN108
|
3.4
|
10.5
|
1.0
|
|
C
|
A:THR104
|
3.5
|
11.7
|
1.0
|
|
C4
|
A:GLA201
|
3.5
|
22.9
|
1.0
|
|
CG
|
A:ASN107
|
3.5
|
12.3
|
1.0
|
|
CG
|
A:ASP100
|
3.7
|
11.6
|
1.0
|
|
CA
|
A:TYR36
|
3.8
|
15.3
|
1.0
|
|
OD1
|
A:ASP100
|
3.9
|
7.2
|
1.0
|
|
C2
|
A:GLA201
|
3.9
|
24.9
|
1.0
|
|
ND2
|
A:ASN108
|
3.9
|
10.8
|
1.0
|
|
ND2
|
A:ASN107
|
4.1
|
12.8
|
1.0
|
|
CB
|
A:TYR36
|
4.2
|
15.3
|
1.0
|
|
N
|
A:GLY37
|
4.2
|
15.0
|
1.0
|
|
OG1
|
A:THR104
|
4.2
|
11.4
|
1.0
|
|
CB
|
A:THR104
|
4.2
|
11.7
|
1.0
|
|
N
|
A:ASN108
|
4.3
|
11.5
|
1.0
|
|
CA
|
A:TYR105
|
4.3
|
11.1
|
1.0
|
|
N
|
A:TYR105
|
4.3
|
11.4
|
1.0
|
|
CA
|
A:THR104
|
4.4
|
11.7
|
1.0
|
|
CA
|
A:GLY37
|
4.5
|
15.2
|
1.0
|
|
O2
|
A:GLA201
|
4.5
|
23.4
|
1.0
|
|
C
|
A:ASN107
|
4.7
|
11.4
|
1.0
|
|
N
|
A:ASN107
|
4.7
|
11.9
|
1.0
|
|
C
|
A:TYR105
|
4.7
|
12.2
|
1.0
|
|
CB
|
A:ASN108
|
4.7
|
10.7
|
1.0
|
|
CA
|
A:ASN108
|
4.8
|
11.4
|
1.0
|
|
CB
|
A:ASN107
|
4.8
|
11.8
|
1.0
|
|
CA
|
A:ASN107
|
4.9
|
11.9
|
1.0
|
|
O
|
A:HOH2086
|
4.9
|
18.4
|
1.0
|
|
C5
|
A:GLA201
|
4.9
|
22.8
|
1.0
|
|
O
|
A:TYR105
|
4.9
|
12.1
|
1.0
|
|
O
|
A:HOH2075
|
5.0
|
28.9
|
1.0
|
|
Calcium binding site 2 out
of 8 in 2wyf
Go back to
Calcium Binding Sites List in 2wyf
Calcium binding site 2 out
of 8 in the Crystal Structure of Pa-Il Lectin Complexed with AGAL12BGAL- O-Met at 2.4 A Resolution
 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 Pa-Il Lectin Complexed with AGAL12BGAL- O-Met at 2.4 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca200
b:32.5
occ:1.00
|
OD1
|
B:ASN108
|
2.4
|
8.1
|
1.0
|
|
O
|
B:THR104
|
2.4
|
21.0
|
1.0
|
|
O
|
B:TYR36
|
2.4
|
14.3
|
1.0
|
|
OD1
|
B:ASN107
|
2.5
|
15.1
|
1.0
|
|
OD2
|
B:ASP100
|
2.5
|
21.5
|
1.0
|
|
O3
|
B:GLA201
|
2.6
|
29.3
|
1.0
|
|
O4
|
B:GLA201
|
2.8
|
29.1
|
1.0
|
|
C
|
B:TYR36
|
3.4
|
14.3
|
1.0
|
|
CG
|
B:ASN108
|
3.5
|
9.6
|
1.0
|
|
CG
|
B:ASN107
|
3.5
|
13.7
|
1.0
|
|
C3
|
B:GLA201
|
3.6
|
29.6
|
1.0
|
|
C
|
B:THR104
|
3.6
|
20.8
|
1.0
|
|
OG1
|
B:THR104
|
3.6
|
19.3
|
1.0
|
|
CG
|
B:ASP100
|
3.6
|
19.5
|
1.0
|
|
C4
|
B:GLA201
|
3.7
|
29.8
|
1.0
|
|
ND2
|
B:ASN107
|
4.0
|
9.5
|
1.0
|
|
CA
|
B:TYR36
|
4.0
|
14.2
|
1.0
|
|
ND2
|
B:ASN108
|
4.0
|
9.3
|
1.0
|
|
C2
|
B:GLA201
|
4.1
|
28.9
|
1.0
|
|
OD1
|
B:ASP100
|
4.1
|
15.4
|
1.0
|
|
CB
|
B:THR104
|
4.1
|
20.4
|
1.0
|
|
CB
|
B:TYR36
|
4.2
|
14.4
|
1.0
|
|
N
|
B:ASN108
|
4.4
|
14.1
|
1.0
|
|
CA
|
B:TYR105
|
4.4
|
19.6
|
1.0
|
|
O
|
B:HOH2075
|
4.4
|
14.0
|
1.0
|
|
N
|
B:GLY37
|
4.5
|
14.5
|
1.0
|
|
N
|
B:TYR105
|
4.5
|
20.4
|
1.0
|
|
CA
|
B:THR104
|
4.6
|
20.7
|
1.0
|
|
C
|
B:ASN107
|
4.6
|
15.0
|
1.0
|
|
O2
|
B:GLA201
|
4.6
|
28.4
|
1.0
|
|
C
|
B:TYR105
|
4.6
|
19.5
|
1.0
|
|
CB
|
B:ASN108
|
4.7
|
12.2
|
1.0
|
|
N
|
B:ASN107
|
4.7
|
16.6
|
1.0
|
|
CA
|
B:GLY37
|
4.7
|
15.7
|
1.0
|
|
O
|
B:TYR105
|
4.8
|
19.1
|
1.0
|
|
CB
|
B:ASN107
|
4.8
|
14.9
|
1.0
|
|
CA
|
B:ASN108
|
4.8
|
13.0
|
1.0
|
|
CB
|
B:ASP100
|
4.9
|
19.2
|
1.0
|
|
CD1
|
B:TYR36
|
4.9
|
15.3
|
1.0
|
|
CA
|
B:ASN107
|
4.9
|
15.2
|
1.0
|
|
Calcium binding site 3 out
of 8 in 2wyf
Go back to
Calcium Binding Sites List in 2wyf
Calcium binding site 3 out
of 8 in the Crystal Structure of Pa-Il Lectin Complexed with AGAL12BGAL- O-Met at 2.4 A Resolution
 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 Pa-Il Lectin Complexed with AGAL12BGAL- O-Met at 2.4 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca200
b:15.6
occ:1.00
|
O
|
C:THR104
|
2.2
|
9.8
|
1.0
|
|
O
|
C:TYR36
|
2.4
|
11.7
|
1.0
|
|
OD1
|
C:ASN108
|
2.5
|
11.5
|
1.0
|
|
O3
|
C:GLA201
|
2.5
|
26.2
|
1.0
|
|
OD1
|
C:ASN107
|
2.5
|
12.4
|
1.0
|
|
OD2
|
C:ASP100
|
2.6
|
11.8
|
1.0
|
|
O4
|
C:GLA201
|
2.8
|
26.4
|
1.0
|
|
C
|
C:THR104
|
3.4
|
9.8
|
1.0
|
|
C
|
C:TYR36
|
3.5
|
11.2
|
1.0
|
|
C3
|
C:GLA201
|
3.5
|
26.3
|
1.0
|
|
CG
|
C:ASP100
|
3.6
|
10.5
|
1.0
|
|
CG
|
C:ASN107
|
3.6
|
10.1
|
1.0
|
|
CG
|
C:ASN108
|
3.6
|
10.4
|
1.0
|
|
C4
|
C:GLA201
|
3.6
|
25.7
|
1.0
|
|
OG1
|
C:THR104
|
3.7
|
10.9
|
1.0
|
|
OD1
|
C:ASP100
|
3.8
|
11.0
|
1.0
|
|
C2
|
C:GLA201
|
4.0
|
27.2
|
1.0
|
|
CA
|
C:TYR36
|
4.1
|
11.2
|
1.0
|
|
ND2
|
C:ASN107
|
4.1
|
6.9
|
1.0
|
|
CB
|
C:THR104
|
4.1
|
10.6
|
1.0
|
|
ND2
|
C:ASN108
|
4.2
|
9.3
|
1.0
|
|
N
|
C:TYR105
|
4.3
|
9.4
|
1.0
|
|
CB
|
C:TYR36
|
4.3
|
10.9
|
1.0
|
|
CA
|
C:TYR105
|
4.3
|
8.8
|
1.0
|
|
N
|
C:ASN108
|
4.4
|
10.7
|
1.0
|
|
CA
|
C:THR104
|
4.4
|
10.8
|
1.0
|
|
N
|
C:GLY37
|
4.6
|
10.6
|
1.0
|
|
O2
|
C:GLA201
|
4.6
|
26.8
|
1.0
|
|
C
|
C:TYR105
|
4.6
|
9.2
|
1.0
|
|
C
|
C:ASN107
|
4.6
|
10.5
|
1.0
|
|
N
|
C:ASN107
|
4.8
|
10.0
|
1.0
|
|
CB
|
C:ASN108
|
4.8
|
11.3
|
1.0
|
|
CA
|
C:ASN108
|
4.8
|
11.2
|
1.0
|
|
CB
|
C:ASN107
|
4.9
|
10.2
|
1.0
|
|
CA
|
C:GLY37
|
4.9
|
9.8
|
1.0
|
|
CB
|
C:ASP100
|
4.9
|
9.2
|
1.0
|
|
CA
|
C:ASN107
|
5.0
|
10.5
|
1.0
|
|
O
|
C:TYR105
|
5.0
|
8.0
|
1.0
|
|
Calcium binding site 4 out
of 8 in 2wyf
Go back to
Calcium Binding Sites List in 2wyf
Calcium binding site 4 out
of 8 in the Crystal Structure of Pa-Il Lectin Complexed with AGAL12BGAL- O-Met at 2.4 A Resolution
 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 Pa-Il Lectin Complexed with AGAL12BGAL- O-Met at 2.4 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca200
b:23.2
occ:1.00
|
O
|
D:THR104
|
2.3
|
9.1
|
1.0
|
|
OD1
|
D:ASN107
|
2.4
|
10.6
|
1.0
|
|
OD1
|
D:ASN108
|
2.5
|
7.6
|
1.0
|
|
O
|
D:TYR36
|
2.5
|
12.0
|
1.0
|
|
O3
|
D:GLA201
|
2.5
|
18.1
|
1.0
|
|
O4
|
D:GLA201
|
2.6
|
19.6
|
1.0
|
|
OD2
|
D:ASP100
|
2.6
|
9.7
|
1.0
|
|
C3
|
D:GLA201
|
3.4
|
19.7
|
1.0
|
|
C
|
D:TYR36
|
3.4
|
12.3
|
1.0
|
|
CG
|
D:ASN107
|
3.4
|
8.9
|
1.0
|
|
C4
|
D:GLA201
|
3.5
|
20.5
|
1.0
|
|
C
|
D:THR104
|
3.5
|
8.8
|
1.0
|
|
CG
|
D:ASN108
|
3.6
|
6.5
|
1.0
|
|
CG
|
D:ASP100
|
3.6
|
9.3
|
1.0
|
|
ND2
|
D:ASN107
|
3.9
|
8.0
|
1.0
|
|
OD1
|
D:ASP100
|
3.9
|
7.8
|
1.0
|
|
OG1
|
D:THR104
|
3.9
|
8.8
|
1.0
|
|
C2
|
D:GLA201
|
3.9
|
21.0
|
1.0
|
|
CA
|
D:TYR36
|
4.0
|
12.2
|
1.0
|
|
CB
|
D:THR104
|
4.0
|
8.6
|
1.0
|
|
CB
|
D:TYR36
|
4.1
|
11.8
|
1.0
|
|
ND2
|
D:ASN108
|
4.1
|
4.3
|
1.0
|
|
N
|
D:TYR105
|
4.4
|
8.7
|
1.0
|
|
CA
|
D:THR104
|
4.4
|
8.3
|
1.0
|
|
CA
|
D:TYR105
|
4.4
|
8.5
|
1.0
|
|
N
|
D:ASN108
|
4.4
|
8.1
|
1.0
|
|
N
|
D:GLY37
|
4.4
|
12.8
|
1.0
|
|
C
|
D:ASN107
|
4.6
|
8.9
|
1.0
|
|
O2
|
D:GLA201
|
4.6
|
17.9
|
1.0
|
|
N
|
D:ASN107
|
4.6
|
9.2
|
1.0
|
|
CB
|
D:ASN107
|
4.7
|
8.6
|
1.0
|
|
C
|
D:TYR105
|
4.7
|
8.4
|
1.0
|
|
CA
|
D:GLY37
|
4.8
|
13.8
|
1.0
|
|
CB
|
D:ASN108
|
4.8
|
7.7
|
1.0
|
|
O
|
D:HOH2087
|
4.8
|
16.6
|
1.0
|
|
CA
|
D:ASN107
|
4.8
|
9.1
|
1.0
|
|
C5
|
D:GLA201
|
4.9
|
21.9
|
1.0
|
|
CA
|
D:ASN108
|
4.9
|
7.7
|
1.0
|
|
CD1
|
D:TYR36
|
4.9
|
11.6
|
1.0
|
|
CB
|
D:ASP100
|
5.0
|
7.5
|
1.0
|
|
O
|
D:ASN107
|
5.0
|
10.0
|
1.0
|
|
Calcium binding site 5 out
of 8 in 2wyf
Go back to
Calcium Binding Sites List in 2wyf
Calcium binding site 5 out
of 8 in the Crystal Structure of Pa-Il Lectin Complexed with AGAL12BGAL- O-Met at 2.4 A Resolution
 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 Pa-Il Lectin Complexed with AGAL12BGAL- O-Met at 2.4 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca200
b:22.5
occ:1.00
|
OD1
|
E:ASN107
|
2.3
|
12.7
|
1.0
|
|
O
|
E:THR104
|
2.4
|
15.7
|
1.0
|
|
OD1
|
E:ASN108
|
2.4
|
11.4
|
1.0
|
|
O
|
E:TYR36
|
2.4
|
15.6
|
1.0
|
|
O3
|
E:GLA201
|
2.5
|
37.1
|
1.0
|
|
OD2
|
E:ASP100
|
2.7
|
11.8
|
1.0
|
|
O4
|
E:GLA201
|
2.7
|
34.1
|
1.0
|
|
C
|
E:TYR36
|
3.4
|
15.1
|
1.0
|
|
CG
|
E:ASN107
|
3.4
|
11.7
|
1.0
|
|
CG
|
E:ASN108
|
3.4
|
9.7
|
1.0
|
|
C
|
E:THR104
|
3.5
|
15.4
|
1.0
|
|
C4
|
E:GLA201
|
3.5
|
35.7
|
1.0
|
|
C3
|
E:GLA201
|
3.5
|
37.3
|
1.0
|
|
CG
|
E:ASP100
|
3.7
|
12.7
|
1.0
|
|
OD1
|
E:ASP100
|
3.9
|
12.3
|
1.0
|
|
CA
|
E:TYR36
|
3.9
|
14.0
|
1.0
|
|
ND2
|
E:ASN108
|
3.9
|
8.0
|
1.0
|
|
ND2
|
E:ASN107
|
4.0
|
11.1
|
1.0
|
|
OG1
|
E:THR104
|
4.0
|
16.0
|
1.0
|
|
CB
|
E:THR104
|
4.1
|
15.7
|
1.0
|
|
CB
|
E:TYR36
|
4.1
|
13.6
|
1.0
|
|
CA
|
E:TYR105
|
4.3
|
13.9
|
1.0
|
|
N
|
E:TYR105
|
4.3
|
14.6
|
1.0
|
|
C2
|
E:GLA201
|
4.4
|
37.6
|
1.0
|
|
N
|
E:GLY37
|
4.4
|
16.2
|
1.0
|
|
CA
|
E:THR104
|
4.4
|
15.5
|
1.0
|
|
N
|
E:ASN108
|
4.5
|
11.7
|
1.0
|
|
N
|
E:ASN107
|
4.6
|
11.5
|
1.0
|
|
C
|
E:ASN107
|
4.6
|
11.5
|
1.0
|
|
CB
|
E:ASN107
|
4.7
|
10.7
|
1.0
|
|
C
|
E:TYR105
|
4.7
|
13.9
|
1.0
|
|
CB
|
E:ASN108
|
4.7
|
11.2
|
1.0
|
|
CA
|
E:GLY37
|
4.8
|
16.4
|
1.0
|
|
CA
|
E:ASN107
|
4.8
|
11.5
|
1.0
|
|
CA
|
E:ASN108
|
4.9
|
11.4
|
1.0
|
|
C5
|
E:GLA201
|
5.0
|
35.8
|
1.0
|
|
Calcium binding site 6 out
of 8 in 2wyf
Go back to
Calcium Binding Sites List in 2wyf
Calcium binding site 6 out
of 8 in the Crystal Structure of Pa-Il Lectin Complexed with AGAL12BGAL- O-Met at 2.4 A Resolution
 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 Pa-Il Lectin Complexed with AGAL12BGAL- O-Met at 2.4 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca200
b:18.4
occ:1.00
|
O3
|
F:GLA201
|
2.2
|
33.4
|
1.0
|
|
O
|
F:THR104
|
2.3
|
15.3
|
1.0
|
|
O
|
F:TYR36
|
2.4
|
13.5
|
1.0
|
|
OD1
|
F:ASN107
|
2.5
|
16.2
|
1.0
|
|
OD1
|
F:ASN108
|
2.5
|
12.0
|
1.0
|
|
OD2
|
F:ASP100
|
2.6
|
5.0
|
1.0
|
|
O4
|
F:GLA201
|
2.6
|
29.1
|
1.0
|
|
C3
|
F:GLA201
|
3.3
|
31.4
|
1.0
|
|
C4
|
F:GLA201
|
3.3
|
30.4
|
1.0
|
|
C
|
F:TYR36
|
3.4
|
13.3
|
1.0
|
|
C
|
F:THR104
|
3.5
|
14.4
|
1.0
|
|
OG1
|
F:THR104
|
3.5
|
11.3
|
1.0
|
|
CG
|
F:ASN107
|
3.6
|
14.2
|
1.0
|
|
CG
|
F:ASP100
|
3.6
|
6.7
|
1.0
|
|
CG
|
F:ASN108
|
3.6
|
11.1
|
1.0
|
|
OD1
|
F:ASP100
|
3.8
|
4.2
|
1.0
|
|
C2
|
F:GLA201
|
3.9
|
32.7
|
1.0
|
|
CA
|
F:TYR36
|
3.9
|
12.5
|
1.0
|
|
CB
|
F:THR104
|
3.9
|
13.1
|
1.0
|
|
ND2
|
F:ASN107
|
4.0
|
14.6
|
1.0
|
|
ND2
|
F:ASN108
|
4.1
|
9.3
|
1.0
|
|
CB
|
F:TYR36
|
4.2
|
11.8
|
1.0
|
|
CA
|
F:THR104
|
4.4
|
13.3
|
1.0
|
|
N
|
F:TYR105
|
4.4
|
14.1
|
1.0
|
|
CA
|
F:TYR105
|
4.5
|
13.9
|
1.0
|
|
N
|
F:GLY37
|
4.5
|
14.3
|
1.0
|
|
O2
|
F:GLA201
|
4.5
|
32.4
|
1.0
|
|
N
|
F:ASN108
|
4.6
|
12.6
|
1.0
|
|
N
|
F:ASN107
|
4.7
|
13.0
|
1.0
|
|
C5
|
F:GLA201
|
4.8
|
30.4
|
1.0
|
|
C
|
F:TYR105
|
4.8
|
14.3
|
1.0
|
|
C
|
F:ASN107
|
4.8
|
13.3
|
1.0
|
|
CB
|
F:ASN107
|
4.9
|
13.2
|
1.0
|
|
CB
|
F:ASP100
|
4.9
|
7.3
|
1.0
|
|
CA
|
F:GLY37
|
4.9
|
15.9
|
1.0
|
|
CB
|
F:ASN108
|
4.9
|
11.7
|
1.0
|
|
Calcium binding site 7 out
of 8 in 2wyf
Go back to
Calcium Binding Sites List in 2wyf
Calcium binding site 7 out
of 8 in the Crystal Structure of Pa-Il Lectin Complexed with AGAL12BGAL- O-Met at 2.4 A Resolution
 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 Pa-Il Lectin Complexed with AGAL12BGAL- O-Met at 2.4 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Ca200
b:18.8
occ:1.00
|
O
|
G:THR104
|
2.2
|
14.4
|
1.0
|
|
O
|
G:TYR36
|
2.4
|
11.6
|
1.0
|
|
OD1
|
G:ASN108
|
2.5
|
12.2
|
1.0
|
|
OD1
|
G:ASP100
|
2.5
|
16.1
|
1.0
|
|
OD1
|
G:ASN107
|
2.6
|
13.7
|
1.0
|
|
O4
|
G:GLA201
|
2.6
|
23.5
|
1.0
|
|
O3
|
G:GLA201
|
2.7
|
24.6
|
1.0
|
|
C
|
G:TYR36
|
3.3
|
12.4
|
1.0
|
|
C
|
G:THR104
|
3.4
|
14.3
|
1.0
|
|
C3
|
G:GLA201
|
3.5
|
24.1
|
1.0
|
|
CG
|
G:ASP100
|
3.5
|
13.8
|
1.0
|
|
C4
|
G:GLA201
|
3.5
|
24.6
|
1.0
|
|
CG
|
G:ASN108
|
3.5
|
9.7
|
1.0
|
|
CG
|
G:ASN107
|
3.6
|
12.9
|
1.0
|
|
CA
|
G:TYR36
|
3.9
|
11.7
|
1.0
|
|
OD2
|
G:ASP100
|
3.9
|
14.0
|
1.0
|
|
C2
|
G:GLA201
|
3.9
|
24.5
|
1.0
|
|
OG1
|
G:THR104
|
3.9
|
13.8
|
1.0
|
|
CB
|
G:TYR36
|
3.9
|
11.2
|
1.0
|
|
ND2
|
G:ASN108
|
4.0
|
8.3
|
1.0
|
|
ND2
|
G:ASN107
|
4.0
|
13.4
|
1.0
|
|
CB
|
G:THR104
|
4.0
|
14.9
|
1.0
|
|
CA
|
G:TYR105
|
4.3
|
13.0
|
1.0
|
|
N
|
G:TYR105
|
4.3
|
13.4
|
1.0
|
|
CA
|
G:THR104
|
4.4
|
14.8
|
1.0
|
|
N
|
G:GLY37
|
4.4
|
13.0
|
1.0
|
|
N
|
G:ASN108
|
4.5
|
10.8
|
1.0
|
|
O2
|
G:GLA201
|
4.7
|
23.7
|
1.0
|
|
C
|
G:TYR105
|
4.7
|
12.9
|
1.0
|
|
C
|
G:ASN107
|
4.8
|
11.1
|
1.0
|
|
CB
|
G:ASN108
|
4.8
|
10.5
|
1.0
|
|
C5
|
G:GLA201
|
4.8
|
24.4
|
1.0
|
|
CB
|
G:ASP100
|
4.8
|
12.2
|
1.0
|
|
O
|
G:HOH2085
|
4.8
|
17.7
|
1.0
|
|
N
|
G:ASN107
|
4.8
|
11.6
|
1.0
|
|
O
|
G:TYR105
|
4.8
|
12.9
|
1.0
|
|
CB
|
G:ASN107
|
4.9
|
11.3
|
1.0
|
|
CA
|
G:GLY37
|
4.9
|
14.4
|
1.0
|
|
CA
|
G:ASN108
|
4.9
|
10.6
|
1.0
|
|
CD2
|
G:TYR36
|
4.9
|
12.0
|
1.0
|
|
CG
|
G:TYR36
|
5.0
|
11.7
|
1.0
|
|
O5
|
G:GLA201
|
5.0
|
24.8
|
1.0
|
|
Calcium binding site 8 out
of 8 in 2wyf
Go back to
Calcium Binding Sites List in 2wyf
Calcium binding site 8 out
of 8 in the Crystal Structure of Pa-Il Lectin Complexed with AGAL12BGAL- O-Met at 2.4 A Resolution
 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 Pa-Il Lectin Complexed with AGAL12BGAL- O-Met at 2.4 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Ca200
b:23.6
occ:1.00
|
O3
|
H:GLA201
|
2.4
|
26.9
|
1.0
|
|
OD1
|
H:ASN108
|
2.4
|
19.6
|
1.0
|
|
O
|
H:TYR36
|
2.5
|
16.1
|
1.0
|
|
O
|
H:THR104
|
2.5
|
20.3
|
1.0
|
|
OD1
|
H:ASP100
|
2.6
|
16.3
|
1.0
|
|
OD1
|
H:ASN107
|
2.6
|
19.7
|
1.0
|
|
O4
|
H:GLA201
|
2.7
|
24.3
|
1.0
|
|
C3
|
H:GLA201
|
3.3
|
26.7
|
1.0
|
|
C
|
H:TYR36
|
3.4
|
16.1
|
1.0
|
|
CG
|
H:ASN108
|
3.4
|
17.7
|
1.0
|
|
C4
|
H:GLA201
|
3.5
|
25.5
|
1.0
|
|
C
|
H:THR104
|
3.5
|
19.9
|
1.0
|
|
CG
|
H:ASN107
|
3.6
|
18.3
|
1.0
|
|
CG
|
H:ASP100
|
3.6
|
15.6
|
1.0
|
|
OG1
|
H:THR104
|
3.8
|
20.4
|
1.0
|
|
ND2
|
H:ASN108
|
3.8
|
17.0
|
1.0
|
|
ND2
|
H:ASN107
|
3.8
|
18.6
|
1.0
|
|
OD2
|
H:ASP100
|
3.9
|
15.1
|
1.0
|
|
CA
|
H:TYR36
|
3.9
|
16.0
|
1.0
|
|
C2
|
H:GLA201
|
3.9
|
27.8
|
1.0
|
|
CB
|
H:THR104
|
4.0
|
19.6
|
1.0
|
|
CB
|
H:TYR36
|
4.1
|
16.0
|
1.0
|
|
N
|
H:TYR105
|
4.4
|
19.6
|
1.0
|
|
CA
|
H:TYR105
|
4.4
|
19.1
|
1.0
|
|
CA
|
H:THR104
|
4.4
|
20.1
|
1.0
|
|
N
|
H:GLY37
|
4.4
|
15.9
|
1.0
|
|
O2
|
H:GLA201
|
4.6
|
27.6
|
1.0
|
|
N
|
H:ASN108
|
4.7
|
17.1
|
1.0
|
|
O
|
H:HOH2074
|
4.7
|
15.6
|
1.0
|
|
CB
|
H:ASN108
|
4.7
|
16.2
|
1.0
|
|
C
|
H:TYR105
|
4.8
|
19.8
|
1.0
|
|
CA
|
H:GLY37
|
4.8
|
15.4
|
1.0
|
|
C
|
H:ASN107
|
4.8
|
17.8
|
1.0
|
|
C5
|
H:GLA201
|
4.9
|
25.4
|
1.0
|
|
CB
|
H:ASN107
|
4.9
|
17.6
|
1.0
|
|
N
|
H:ASN107
|
4.9
|
17.6
|
1.0
|
|
CB
|
H:ASP100
|
5.0
|
15.4
|
1.0
|
|
CA
|
H:ASN108
|
5.0
|
16.6
|
1.0
|
|
Reference:
A.Nurisso,
B.Blanchard,
A.Audfray,
L.Rydner,
S.Oscarson,
A.Varrot,
A.Imberty.
Role of Water Molecules in Structure and Energetics of Pseudomonas Aeruginosa Lectin I Interacting with Disaccharides. J.Biol.Chem. V. 285 20316 2010.
ISSN: ISSN 0021-9258
PubMed: 20410292
DOI: 10.1074/JBC.M110.108340
Page generated: Fri Jul 12 18:55:17 2024
|
