Calcium in PDB 5zc0: Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions
Protein crystallography data
The structure of Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions, PDB code: 5zc0
was solved by
K.Wangkanont,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
34.19 /
2.75
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
124.300,
111.410,
124.360,
90.00,
119.94,
90.00
|
|
R / Rfree (%)
|
19.6 /
23.8
|
Other elements in 5zc0:
The structure of Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions also contains other interesting chemical elements:
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 Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions
(pdb code 5zc0). 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 Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions, PDB code: 5zc0:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 12 in 5zc0
Go back to
Calcium Binding Sites List in 5zc0
Calcium binding site 1 out
of 12 in the Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions
 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 Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca401
b:7.4
occ:1.00
|
O
|
A:GLY121
|
2.3
|
13.5
|
1.0
|
|
O
|
A:HOH525
|
2.3
|
7.9
|
1.0
|
|
OE2
|
A:GLU116
|
2.3
|
13.5
|
1.0
|
|
O
|
A:HOH508
|
2.4
|
8.0
|
1.0
|
|
OD1
|
A:ASP127
|
2.5
|
11.0
|
1.0
|
|
O
|
A:ASN118
|
2.5
|
18.8
|
1.0
|
|
OD2
|
A:ASP127
|
2.6
|
10.4
|
1.0
|
|
CG
|
A:ASP127
|
2.9
|
12.8
|
1.0
|
|
CD
|
A:GLU116
|
3.3
|
15.6
|
1.0
|
|
C
|
A:GLY121
|
3.4
|
15.7
|
1.0
|
|
C
|
A:ASN118
|
3.5
|
11.0
|
1.0
|
|
OE1
|
A:GLU116
|
3.8
|
11.7
|
1.0
|
|
CA
|
A:GLY121
|
4.1
|
11.4
|
1.0
|
|
OD1
|
A:ASN117
|
4.1
|
14.3
|
1.0
|
|
N
|
A:ASN118
|
4.1
|
14.9
|
1.0
|
|
N
|
A:GLY121
|
4.2
|
27.2
|
1.0
|
|
CA
|
A:ASN118
|
4.3
|
12.7
|
1.0
|
|
OG1
|
A:THR124
|
4.3
|
6.4
|
1.0
|
|
O
|
A:HOH501
|
4.4
|
10.1
|
1.0
|
|
N
|
A:MET119
|
4.4
|
9.6
|
1.0
|
|
CB
|
A:ASP127
|
4.5
|
11.2
|
1.0
|
|
CB
|
A:ASN118
|
4.5
|
14.2
|
1.0
|
|
N
|
A:LYS122
|
4.5
|
9.3
|
1.0
|
|
CG
|
A:GLU116
|
4.5
|
10.1
|
1.0
|
|
N
|
A:CYS123
|
4.6
|
13.1
|
1.0
|
|
CA
|
A:MET119
|
4.6
|
11.4
|
1.0
|
|
CA
|
A:GLY310
|
4.6
|
8.5
|
1.0
|
|
C
|
A:MET119
|
4.7
|
13.9
|
1.0
|
|
N
|
A:ASP311
|
4.7
|
7.2
|
1.0
|
|
CA
|
A:LYS122
|
4.8
|
11.2
|
1.0
|
|
O
|
A:MET119
|
4.9
|
14.5
|
1.0
|
|
N
|
A:THR124
|
4.9
|
16.3
|
1.0
|
|
O
|
A:HOH513
|
4.9
|
17.5
|
1.0
|
|
Calcium binding site 2 out
of 12 in 5zc0
Go back to
Calcium Binding Sites List in 5zc0
Calcium binding site 2 out
of 12 in the Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions
 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 Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca402
b:8.3
occ:1.00
|
OD2
|
A:ASP311
|
2.3
|
8.4
|
1.0
|
|
OD1
|
A:ASP162
|
2.3
|
15.9
|
1.0
|
|
O
|
A:HIS115
|
2.4
|
16.2
|
1.0
|
|
O
|
A:GLY126
|
2.4
|
13.0
|
1.0
|
|
O
|
A:HOH530
|
2.4
|
7.3
|
1.0
|
|
OD2
|
A:ASP162
|
2.5
|
8.0
|
1.0
|
|
O
|
A:HOH501
|
2.6
|
10.1
|
1.0
|
|
CG
|
A:ASP162
|
2.7
|
10.0
|
1.0
|
|
CG
|
A:ASP311
|
3.4
|
11.1
|
1.0
|
|
C
|
A:HIS115
|
3.6
|
11.6
|
1.0
|
|
C
|
A:GLY126
|
3.6
|
12.5
|
1.0
|
|
N
|
A:ARG128
|
4.1
|
10.3
|
1.0
|
|
CB
|
A:ASP311
|
4.1
|
6.1
|
1.0
|
|
CA
|
A:ASP127
|
4.2
|
13.3
|
1.0
|
|
CB
|
A:ASP162
|
4.2
|
9.3
|
1.0
|
|
N
|
A:HIS115
|
4.3
|
9.4
|
1.0
|
|
N
|
A:ASP127
|
4.3
|
9.0
|
1.0
|
|
OD1
|
A:ASN117
|
4.3
|
14.3
|
1.0
|
|
OD1
|
A:ASP311
|
4.4
|
7.7
|
1.0
|
|
CA
|
A:HIS115
|
4.4
|
8.8
|
1.0
|
|
N
|
A:GLU116
|
4.5
|
7.4
|
1.0
|
|
CA
|
A:GLU116
|
4.5
|
7.4
|
1.0
|
|
CD1
|
A:TRP129
|
4.6
|
6.7
|
1.0
|
|
CA
|
A:GLY126
|
4.6
|
5.6
|
1.0
|
|
C
|
A:ASP127
|
4.6
|
12.5
|
1.0
|
|
N
|
A:ASN117
|
4.6
|
14.7
|
1.0
|
|
N
|
A:ASP162
|
4.7
|
8.3
|
1.0
|
|
CB
|
A:HIS115
|
4.7
|
9.1
|
1.0
|
|
ND1
|
A:HIS115
|
4.8
|
7.8
|
1.0
|
|
CA
|
A:ASP162
|
4.8
|
12.4
|
1.0
|
|
OD1
|
A:ASP127
|
4.9
|
11.0
|
1.0
|
|
Calcium binding site 3 out
of 12 in 5zc0
Go back to
Calcium Binding Sites List in 5zc0
Calcium binding site 3 out
of 12 in the Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions
 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 Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca401
b:18.7
occ:1.00
|
O
|
B:HOH518
|
2.2
|
10.9
|
1.0
|
|
O
|
B:HOH508
|
2.2
|
23.2
|
1.0
|
|
O
|
B:GLY121
|
2.4
|
17.1
|
1.0
|
|
OD1
|
B:ASP127
|
2.4
|
16.0
|
1.0
|
|
OD2
|
B:ASP127
|
2.5
|
18.7
|
1.0
|
|
OE2
|
B:GLU116
|
2.6
|
23.3
|
1.0
|
|
O
|
B:ASN118
|
2.6
|
16.8
|
1.0
|
|
CG
|
B:ASP127
|
2.8
|
12.9
|
1.0
|
|
CD
|
B:GLU116
|
3.4
|
17.9
|
1.0
|
|
OE1
|
B:GLU116
|
3.4
|
19.0
|
1.0
|
|
C
|
B:GLY121
|
3.6
|
15.2
|
1.0
|
|
C
|
B:ASN118
|
3.6
|
16.1
|
1.0
|
|
O
|
B:HOH509
|
4.2
|
8.1
|
1.0
|
|
OD1
|
B:ASN117
|
4.3
|
19.0
|
1.0
|
|
N
|
B:ASN118
|
4.3
|
12.0
|
1.0
|
|
CB
|
B:ASP127
|
4.3
|
8.8
|
1.0
|
|
CA
|
B:GLY121
|
4.3
|
8.0
|
1.0
|
|
CA
|
B:ASN118
|
4.4
|
12.9
|
1.0
|
|
CA
|
B:GLY310
|
4.4
|
11.5
|
1.0
|
|
N
|
B:GLY121
|
4.4
|
17.5
|
1.0
|
|
N
|
B:CYS123
|
4.5
|
12.1
|
1.0
|
|
N
|
B:ASP311
|
4.5
|
12.4
|
1.0
|
|
N
|
B:MET119
|
4.5
|
21.0
|
1.0
|
|
CA
|
B:MET119
|
4.6
|
16.6
|
1.0
|
|
N
|
B:LYS122
|
4.6
|
14.6
|
1.0
|
|
OG1
|
B:THR124
|
4.6
|
9.2
|
1.0
|
|
CB
|
B:ASN118
|
4.6
|
10.2
|
1.0
|
|
C
|
B:MET119
|
4.7
|
15.9
|
1.0
|
|
CG
|
B:GLU116
|
4.8
|
15.9
|
1.0
|
|
CA
|
B:LYS122
|
4.8
|
10.7
|
1.0
|
|
O
|
B:MET119
|
4.9
|
20.2
|
1.0
|
|
Calcium binding site 4 out
of 12 in 5zc0
Go back to
Calcium Binding Sites List in 5zc0
Calcium binding site 4 out
of 12 in the Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions
 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 Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca402
b:6.7
occ:1.00
|
O
|
B:HIS115
|
2.1
|
11.8
|
1.0
|
|
O
|
B:HOH520
|
2.3
|
19.3
|
1.0
|
|
OD2
|
B:ASP311
|
2.4
|
8.8
|
1.0
|
|
OD1
|
B:ASP162
|
2.4
|
8.1
|
1.0
|
|
O
|
B:HOH509
|
2.4
|
8.1
|
1.0
|
|
O
|
B:GLY126
|
2.5
|
20.2
|
1.0
|
|
OD2
|
B:ASP162
|
2.6
|
13.9
|
1.0
|
|
CG
|
B:ASP162
|
2.8
|
12.0
|
1.0
|
|
C
|
B:HIS115
|
3.4
|
9.9
|
1.0
|
|
CG
|
B:ASP311
|
3.5
|
13.3
|
1.0
|
|
C
|
B:GLY126
|
3.6
|
18.7
|
1.0
|
|
OD1
|
B:ASN117
|
4.2
|
19.0
|
1.0
|
|
CB
|
B:ASP311
|
4.2
|
13.1
|
1.0
|
|
CA
|
B:HIS115
|
4.2
|
7.2
|
1.0
|
|
N
|
B:HIS115
|
4.2
|
9.3
|
1.0
|
|
CB
|
B:ASP162
|
4.3
|
8.6
|
1.0
|
|
N
|
B:GLU116
|
4.3
|
9.0
|
1.0
|
|
CA
|
B:ASP127
|
4.3
|
9.4
|
1.0
|
|
N
|
B:ARG128
|
4.3
|
9.4
|
1.0
|
|
CA
|
B:GLU116
|
4.4
|
8.5
|
1.0
|
|
N
|
B:ASP127
|
4.4
|
14.4
|
1.0
|
|
CB
|
B:HIS115
|
4.4
|
4.3
|
1.0
|
|
N
|
B:ASN117
|
4.5
|
12.7
|
1.0
|
|
CD2
|
B:HIS115
|
4.5
|
7.8
|
1.0
|
|
OD1
|
B:ASP311
|
4.5
|
10.3
|
1.0
|
|
CA
|
B:GLY126
|
4.6
|
12.2
|
1.0
|
|
N
|
B:ASP162
|
4.7
|
9.6
|
1.0
|
|
CD1
|
B:TRP129
|
4.7
|
5.4
|
1.0
|
|
OD1
|
B:ASP127
|
4.8
|
16.0
|
1.0
|
|
CG
|
B:HIS115
|
4.8
|
9.4
|
1.0
|
|
C
|
B:ASP127
|
4.8
|
8.4
|
1.0
|
|
CA
|
B:ASP162
|
4.9
|
8.6
|
1.0
|
|
C
|
B:GLU116
|
4.9
|
14.8
|
1.0
|
|
CG
|
B:ASN117
|
4.9
|
13.1
|
1.0
|
|
OD2
|
B:ASP161
|
4.9
|
28.0
|
1.0
|
|
Calcium binding site 5 out
of 12 in 5zc0
Go back to
Calcium Binding Sites List in 5zc0
Calcium binding site 5 out
of 12 in the Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions
 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 Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca401
b:10.6
occ:1.00
|
O
|
C:GLY121
|
2.3
|
18.5
|
1.0
|
|
O
|
C:HOH507
|
2.4
|
9.5
|
1.0
|
|
O
|
C:HOH502
|
2.4
|
10.2
|
1.0
|
|
O
|
C:ASN118
|
2.5
|
10.4
|
1.0
|
|
OD2
|
C:ASP127
|
2.5
|
9.6
|
1.0
|
|
OE2
|
C:GLU116
|
2.5
|
13.9
|
1.0
|
|
OD1
|
C:ASP127
|
2.5
|
12.8
|
1.0
|
|
CG
|
C:ASP127
|
2.9
|
9.0
|
1.0
|
|
CD
|
C:GLU116
|
3.4
|
14.8
|
1.0
|
|
C
|
C:GLY121
|
3.4
|
19.1
|
1.0
|
|
C
|
C:ASN118
|
3.5
|
9.9
|
1.0
|
|
OE1
|
C:GLU116
|
3.5
|
8.8
|
1.0
|
|
CA
|
C:GLY121
|
4.0
|
15.6
|
1.0
|
|
N
|
C:ASN118
|
4.1
|
13.5
|
1.0
|
|
N
|
C:GLY121
|
4.2
|
19.4
|
1.0
|
|
CA
|
C:ASN118
|
4.2
|
14.4
|
1.0
|
|
OG1
|
C:THR124
|
4.2
|
12.6
|
1.0
|
|
OD1
|
C:ASN117
|
4.3
|
9.8
|
1.0
|
|
O
|
C:HOH503
|
4.3
|
3.8
|
1.0
|
|
N
|
C:MET119
|
4.4
|
14.2
|
1.0
|
|
CB
|
C:ASP127
|
4.4
|
8.5
|
1.0
|
|
CB
|
C:ASN118
|
4.4
|
9.8
|
1.0
|
|
N
|
C:LYS122
|
4.5
|
13.2
|
1.0
|
|
CA
|
C:MET119
|
4.6
|
12.6
|
1.0
|
|
CA
|
C:GLY310
|
4.6
|
6.8
|
1.0
|
|
N
|
C:CYS123
|
4.7
|
12.6
|
1.0
|
|
CG
|
C:GLU116
|
4.7
|
14.8
|
1.0
|
|
C
|
C:MET119
|
4.7
|
17.9
|
1.0
|
|
N
|
C:ASP311
|
4.8
|
6.5
|
1.0
|
|
O
|
C:MET119
|
4.8
|
25.3
|
1.0
|
|
CA
|
C:LYS122
|
4.9
|
11.6
|
1.0
|
|
O
|
C:HOH513
|
5.0
|
11.7
|
1.0
|
|
Calcium binding site 6 out
of 12 in 5zc0
Go back to
Calcium Binding Sites List in 5zc0
Calcium binding site 6 out
of 12 in the Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions
 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 Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca402
b:9.2
occ:1.00
|
OD1
|
C:ASP311
|
2.3
|
8.0
|
1.0
|
|
O
|
C:GLY126
|
2.3
|
12.6
|
1.0
|
|
O
|
C:HIS115
|
2.4
|
11.2
|
1.0
|
|
OD2
|
C:ASP162
|
2.4
|
8.2
|
1.0
|
|
O
|
C:HOH503
|
2.4
|
3.8
|
1.0
|
|
O
|
C:HOH525
|
2.5
|
11.8
|
1.0
|
|
OD1
|
C:ASP162
|
2.6
|
10.0
|
1.0
|
|
CG
|
C:ASP162
|
2.8
|
7.1
|
1.0
|
|
CG
|
C:ASP311
|
3.5
|
15.9
|
1.0
|
|
C
|
C:GLY126
|
3.5
|
13.9
|
1.0
|
|
C
|
C:HIS115
|
3.6
|
12.2
|
1.0
|
|
N
|
C:ARG128
|
4.1
|
15.6
|
1.0
|
|
CA
|
C:ASP127
|
4.2
|
7.8
|
1.0
|
|
CB
|
C:ASP311
|
4.2
|
9.5
|
1.0
|
|
OD1
|
C:ASN117
|
4.2
|
9.8
|
1.0
|
|
N
|
C:HIS115
|
4.2
|
10.0
|
1.0
|
|
N
|
C:ASP127
|
4.3
|
10.9
|
1.0
|
|
CB
|
C:ASP162
|
4.3
|
6.3
|
1.0
|
|
CA
|
C:HIS115
|
4.4
|
9.1
|
1.0
|
|
OD2
|
C:ASP311
|
4.5
|
12.1
|
1.0
|
|
CA
|
C:GLY126
|
4.5
|
8.9
|
1.0
|
|
N
|
C:GLU116
|
4.6
|
7.5
|
1.0
|
|
CB
|
C:HIS115
|
4.6
|
4.9
|
1.0
|
|
CD1
|
C:TRP129
|
4.6
|
7.8
|
1.0
|
|
CA
|
C:GLU116
|
4.6
|
7.7
|
1.0
|
|
C
|
C:ASP127
|
4.6
|
13.8
|
1.0
|
|
ND1
|
C:HIS115
|
4.7
|
10.2
|
1.0
|
|
N
|
C:ASN117
|
4.7
|
9.8
|
1.0
|
|
OD1
|
C:ASP127
|
4.8
|
12.8
|
1.0
|
|
N
|
C:ASP162
|
4.8
|
11.7
|
1.0
|
|
OD2
|
C:ASP161
|
4.9
|
27.3
|
1.0
|
|
Calcium binding site 7 out
of 12 in 5zc0
Go back to
Calcium Binding Sites List in 5zc0
Calcium binding site 7 out
of 12 in the Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions
 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 Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca401
b:7.8
occ:1.00
|
O
|
D:GLY121
|
2.2
|
14.0
|
1.0
|
|
OE2
|
D:GLU116
|
2.3
|
15.0
|
1.0
|
|
O
|
D:HOH517
|
2.4
|
13.5
|
1.0
|
|
O
|
D:HOH507
|
2.4
|
12.9
|
1.0
|
|
OD2
|
D:ASP127
|
2.5
|
9.9
|
1.0
|
|
O
|
D:ASN118
|
2.5
|
16.8
|
1.0
|
|
OD1
|
D:ASP127
|
2.7
|
11.3
|
1.0
|
|
CG
|
D:ASP127
|
2.9
|
10.0
|
1.0
|
|
CD
|
D:GLU116
|
3.2
|
14.2
|
1.0
|
|
C
|
D:GLY121
|
3.4
|
16.6
|
1.0
|
|
OE1
|
D:GLU116
|
3.4
|
14.2
|
1.0
|
|
C
|
D:ASN118
|
3.6
|
16.3
|
1.0
|
|
CA
|
D:GLY121
|
3.9
|
15.8
|
1.0
|
|
N
|
D:GLY121
|
4.1
|
19.5
|
1.0
|
|
CG2
|
D:THR124
|
4.2
|
10.1
|
1.0
|
|
O
|
D:HOH504
|
4.2
|
12.8
|
1.0
|
|
N
|
D:ASN118
|
4.3
|
12.6
|
1.0
|
|
CA
|
D:ASN118
|
4.3
|
12.6
|
1.0
|
|
CB
|
D:ASN118
|
4.4
|
9.5
|
1.0
|
|
CB
|
D:ASP127
|
4.4
|
13.8
|
1.0
|
|
N
|
D:LYS122
|
4.5
|
10.3
|
1.0
|
|
OD1
|
D:ASN117
|
4.5
|
20.3
|
1.0
|
|
N
|
D:MET119
|
4.5
|
13.1
|
1.0
|
|
CG
|
D:GLU116
|
4.6
|
12.4
|
1.0
|
|
CA
|
D:GLY310
|
4.6
|
9.9
|
1.0
|
|
N
|
D:CYS123
|
4.6
|
12.5
|
1.0
|
|
N
|
D:ASP311
|
4.7
|
14.1
|
1.0
|
|
CA
|
D:MET119
|
4.7
|
14.5
|
1.0
|
|
C
|
D:MET119
|
4.8
|
16.9
|
1.0
|
|
O
|
D:MET119
|
4.8
|
16.3
|
1.0
|
|
O
|
D:HOH513
|
4.8
|
12.8
|
1.0
|
|
CA
|
D:LYS122
|
4.8
|
12.6
|
1.0
|
|
N
|
D:THR124
|
4.9
|
12.8
|
1.0
|
|
Calcium binding site 8 out
of 12 in 5zc0
Go back to
Calcium Binding Sites List in 5zc0
Calcium binding site 8 out
of 12 in the Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions
 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 Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca402
b:12.3
occ:1.00
|
O
|
D:HIS115
|
2.2
|
14.1
|
1.0
|
|
OD2
|
D:ASP311
|
2.2
|
12.7
|
1.0
|
|
O
|
D:HOH511
|
2.4
|
20.6
|
1.0
|
|
O
|
D:GLY126
|
2.4
|
14.4
|
1.0
|
|
OD1
|
D:ASP162
|
2.4
|
16.8
|
1.0
|
|
OD2
|
D:ASP162
|
2.5
|
7.9
|
1.0
|
|
O
|
D:HOH504
|
2.6
|
12.8
|
1.0
|
|
CG
|
D:ASP162
|
2.8
|
11.0
|
1.0
|
|
CG
|
D:ASP311
|
3.4
|
15.5
|
1.0
|
|
C
|
D:HIS115
|
3.4
|
13.5
|
1.0
|
|
C
|
D:GLY126
|
3.6
|
18.5
|
1.0
|
|
CB
|
D:ASP311
|
4.1
|
9.0
|
1.0
|
|
N
|
D:ARG128
|
4.2
|
8.8
|
1.0
|
|
N
|
D:HIS115
|
4.2
|
16.8
|
1.0
|
|
CA
|
D:ASP127
|
4.2
|
15.5
|
1.0
|
|
CB
|
D:ASP162
|
4.3
|
6.9
|
1.0
|
|
CA
|
D:HIS115
|
4.3
|
12.4
|
1.0
|
|
OD1
|
D:ASN117
|
4.3
|
20.3
|
1.0
|
|
OD1
|
D:ASP311
|
4.4
|
12.2
|
1.0
|
|
N
|
D:ASP127
|
4.4
|
13.5
|
1.0
|
|
N
|
D:GLU116
|
4.4
|
10.2
|
1.0
|
|
CA
|
D:GLU116
|
4.4
|
11.3
|
1.0
|
|
CB
|
D:HIS115
|
4.6
|
7.4
|
1.0
|
|
N
|
D:ASN117
|
4.6
|
11.5
|
1.0
|
|
ND1
|
D:HIS115
|
4.6
|
13.7
|
1.0
|
|
CD1
|
D:TRP129
|
4.7
|
6.0
|
1.0
|
|
OD1
|
D:ASP127
|
4.7
|
11.3
|
1.0
|
|
CA
|
D:GLY126
|
4.7
|
9.4
|
1.0
|
|
C
|
D:ASP127
|
4.7
|
11.0
|
1.0
|
|
N
|
D:ASP162
|
4.8
|
8.8
|
1.0
|
|
NH1
|
D:ARG128
|
4.8
|
9.3
|
1.0
|
|
CA
|
D:ASP162
|
4.9
|
8.7
|
1.0
|
|
C
|
D:GLU116
|
5.0
|
11.7
|
1.0
|
|
Calcium binding site 9 out
of 12 in 5zc0
Go back to
Calcium Binding Sites List in 5zc0
Calcium binding site 9 out
of 12 in the Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions
 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 Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca401
b:7.1
occ:1.00
|
O
|
E:GLY121
|
2.3
|
12.2
|
1.0
|
|
OD1
|
E:ASP127
|
2.4
|
9.8
|
1.0
|
|
O
|
E:HOH517
|
2.5
|
6.6
|
1.0
|
|
O
|
E:HOH516
|
2.5
|
13.3
|
1.0
|
|
OD2
|
E:ASP127
|
2.5
|
8.0
|
1.0
|
|
OE2
|
E:GLU116
|
2.5
|
7.3
|
1.0
|
|
O
|
E:ASN118
|
2.6
|
13.7
|
1.0
|
|
CG
|
E:ASP127
|
2.8
|
11.3
|
1.0
|
|
CD
|
E:GLU116
|
3.3
|
11.6
|
1.0
|
|
C
|
E:GLY121
|
3.4
|
26.5
|
1.0
|
|
OE1
|
E:GLU116
|
3.5
|
11.5
|
1.0
|
|
C
|
E:ASN118
|
3.6
|
11.2
|
1.0
|
|
CA
|
E:GLY121
|
4.1
|
13.7
|
1.0
|
|
N
|
E:GLY121
|
4.2
|
19.6
|
1.0
|
|
N
|
E:ASN118
|
4.3
|
11.7
|
1.0
|
|
CB
|
E:ASP127
|
4.4
|
11.3
|
1.0
|
|
OD1
|
E:ASN117
|
4.4
|
15.6
|
1.0
|
|
CA
|
E:ASN118
|
4.4
|
13.6
|
1.0
|
|
O
|
E:HOH519
|
4.5
|
3.8
|
1.0
|
|
OG1
|
E:THR124
|
4.5
|
6.5
|
1.0
|
|
CA
|
E:GLY310
|
4.5
|
7.1
|
1.0
|
|
N
|
E:LYS122
|
4.5
|
15.8
|
1.0
|
|
N
|
E:CYS123
|
4.5
|
9.1
|
1.0
|
|
N
|
E:MET119
|
4.5
|
13.2
|
1.0
|
|
N
|
E:ASP311
|
4.6
|
10.2
|
1.0
|
|
CA
|
E:MET119
|
4.6
|
17.8
|
1.0
|
|
O
|
E:MET119
|
4.6
|
23.8
|
1.0
|
|
CG
|
E:GLU116
|
4.6
|
10.2
|
1.0
|
|
CB
|
E:ASN118
|
4.7
|
10.1
|
1.0
|
|
C
|
E:MET119
|
4.7
|
16.8
|
1.0
|
|
CA
|
E:LYS122
|
4.8
|
9.8
|
1.0
|
|
O
|
E:HOH507
|
4.8
|
13.3
|
1.0
|
|
N
|
E:THR124
|
5.0
|
10.4
|
1.0
|
|
Calcium binding site 10 out
of 12 in 5zc0
Go back to
Calcium Binding Sites List in 5zc0
Calcium binding site 10 out
of 12 in the Crystal Structure of Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions
 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 Xenopus Embryonic Epidermal Lectin in Complex with Samarium Ions within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca402
b:8.1
occ:1.00
|
O
|
E:HIS115
|
2.2
|
12.6
|
1.0
|
|
OD1
|
E:ASP311
|
2.3
|
10.1
|
1.0
|
|
OD2
|
E:ASP162
|
2.3
|
10.7
|
1.0
|
|
O
|
E:HOH519
|
2.3
|
3.8
|
1.0
|
|
O
|
E:GLY126
|
2.4
|
22.7
|
1.0
|
|
OD1
|
E:ASP162
|
2.5
|
12.1
|
1.0
|
|
O
|
E:HOH520
|
2.6
|
10.9
|
1.0
|
|
CG
|
E:ASP162
|
2.8
|
7.4
|
1.0
|
|
C
|
E:HIS115
|
3.4
|
13.4
|
1.0
|
|
CG
|
E:ASP311
|
3.5
|
10.4
|
1.0
|
|
C
|
E:GLY126
|
3.6
|
18.0
|
1.0
|
|
N
|
E:HIS115
|
4.1
|
11.8
|
1.0
|
|
CB
|
E:ASP311
|
4.2
|
8.5
|
1.0
|
|
CB
|
E:ASP162
|
4.2
|
6.8
|
1.0
|
|
N
|
E:ARG128
|
4.2
|
7.2
|
1.0
|
|
CA
|
E:HIS115
|
4.2
|
10.8
|
1.0
|
|
CA
|
E:ASP127
|
4.2
|
9.8
|
1.0
|
|
N
|
E:ASP127
|
4.4
|
13.8
|
1.0
|
|
N
|
E:GLU116
|
4.4
|
7.3
|
1.0
|
|
CB
|
E:HIS115
|
4.5
|
5.0
|
1.0
|
|
OD2
|
E:ASP311
|
4.5
|
10.2
|
1.0
|
|
ND1
|
E:HIS115
|
4.5
|
14.1
|
1.0
|
|
CA
|
E:GLU116
|
4.5
|
6.8
|
1.0
|
|
OD1
|
E:ASN117
|
4.5
|
15.6
|
1.0
|
|
CA
|
E:GLY126
|
4.6
|
11.5
|
1.0
|
|
N
|
E:ASN117
|
4.6
|
11.9
|
1.0
|
|
CD1
|
E:TRP129
|
4.6
|
10.8
|
1.0
|
|
N
|
E:ASP162
|
4.6
|
9.3
|
1.0
|
|
C
|
E:ASP127
|
4.7
|
9.3
|
1.0
|
|
NH2
|
E:ARG128
|
4.7
|
12.6
|
1.0
|
|
OD2
|
E:ASP161
|
4.8
|
21.4
|
1.0
|
|
OD1
|
E:ASP127
|
4.8
|
9.8
|
1.0
|
|
CA
|
E:ASP162
|
4.8
|
7.9
|
1.0
|
|
CG
|
E:HIS115
|
5.0
|
13.8
|
1.0
|
|
Reference:
J.J.Kozak,
H.B.Gray,
R.A.Garza-Lopez,
K.Wangkanont.
Structural Stabilities of Calcium Proteins: Human Intelectin-1 and Frog Lectin Xeel J. Inorg. Biochem. V. 185 86 2018.
ISSN: ISSN 1873-3344
PubMed: 29807191
DOI: 10.1016/J.JINORGBIO.2018.04.021
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