Calcium in PDB 6ygq: Ecla N-Terminal Domain; Plla-Like Lectin
Protein crystallography data
The structure of Ecla N-Terminal Domain; Plla-Like Lectin, PDB code: 6ygq
was solved by
J.Koehnke,
A.Sikandar,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
40.87 /
1.90
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
65.793,
50.461,
73.859,
90,
109.36,
90
|
|
R / Rfree (%)
|
18.1 /
22.4
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Ecla N-Terminal Domain; Plla-Like Lectin
(pdb code 6ygq). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Ecla N-Terminal Domain; Plla-Like Lectin, PDB code: 6ygq:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 6ygq
Go back to
Calcium Binding Sites List in 6ygq
Calcium binding site 1 out
of 4 in the Ecla N-Terminal Domain; Plla-Like Lectin
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Ecla N-Terminal Domain; Plla-Like Lectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca201
b:15.6
occ:1.00
|
O
|
A:GLN118
|
2.3
|
19.3
|
1.0
|
|
OD1
|
A:ASN122
|
2.4
|
16.6
|
1.0
|
|
O
|
A:ASN54
|
2.4
|
22.6
|
1.0
|
|
OD1
|
A:ASP121
|
2.4
|
17.2
|
1.0
|
|
O
|
A:HOH317
|
2.5
|
17.6
|
1.0
|
|
OD2
|
A:ASP114
|
2.5
|
18.6
|
1.0
|
|
O
|
A:HOH309
|
2.5
|
20.9
|
1.0
|
|
HB3
|
A:GLN118
|
3.3
|
39.8
|
1.0
|
|
C
|
A:ASN54
|
3.4
|
20.8
|
1.0
|
|
CG
|
A:ASN122
|
3.4
|
15.7
|
1.0
|
|
HD21
|
A:ASN122
|
3.5
|
20.9
|
1.0
|
|
CG
|
A:ASP121
|
3.5
|
18.6
|
1.0
|
|
C
|
A:GLN118
|
3.5
|
22.6
|
1.0
|
|
CG
|
A:ASP114
|
3.5
|
18.5
|
1.0
|
|
HB2
|
A:ASN54
|
3.7
|
24.1
|
1.0
|
|
OD2
|
A:ASP121
|
3.8
|
19.8
|
1.0
|
|
HA
|
A:ASN54
|
3.8
|
22.7
|
1.0
|
|
ND2
|
A:ASN122
|
3.8
|
17.4
|
1.0
|
|
HA
|
A:TYR119
|
3.8
|
24.6
|
1.0
|
|
OD1
|
A:ASP114
|
3.9
|
21.0
|
1.0
|
|
HA2
|
A:GLY55
|
4.0
|
23.4
|
1.0
|
|
CA
|
A:ASN54
|
4.1
|
18.9
|
1.0
|
|
CB
|
A:GLN118
|
4.1
|
33.2
|
1.0
|
|
H
|
A:ASP121
|
4.1
|
20.8
|
1.0
|
|
HB2
|
A:GLN118
|
4.2
|
39.8
|
1.0
|
|
N
|
A:GLY55
|
4.3
|
17.4
|
1.0
|
|
CA
|
A:GLN118
|
4.3
|
26.3
|
1.0
|
|
CB
|
A:ASN54
|
4.4
|
20.1
|
1.0
|
|
N
|
A:TYR119
|
4.4
|
23.7
|
1.0
|
|
CA
|
A:TYR119
|
4.4
|
20.5
|
1.0
|
|
CA
|
A:GLY55
|
4.5
|
19.4
|
1.0
|
|
N
|
A:ASN122
|
4.5
|
14.3
|
1.0
|
|
O
|
A:HOH371
|
4.6
|
39.0
|
1.0
|
|
HA
|
A:GLN118
|
4.6
|
31.6
|
1.0
|
|
H
|
A:ASN122
|
4.6
|
17.2
|
1.0
|
|
HA
|
A:ASN122
|
4.6
|
17.5
|
1.0
|
|
HD22
|
A:ASN122
|
4.7
|
20.9
|
1.0
|
|
C
|
A:TYR119
|
4.7
|
18.8
|
1.0
|
|
C
|
A:ASP121
|
4.7
|
14.3
|
1.0
|
|
CB
|
A:ASN122
|
4.7
|
13.9
|
1.0
|
|
HA3
|
A:GLY55
|
4.7
|
23.4
|
1.0
|
|
CB
|
A:ASP121
|
4.8
|
18.0
|
1.0
|
|
O
|
A:TYR119
|
4.8
|
16.9
|
1.0
|
|
N
|
A:ASP121
|
4.8
|
17.3
|
1.0
|
|
CB
|
A:ASP114
|
4.9
|
15.6
|
1.0
|
|
CA
|
A:ASN122
|
4.9
|
14.6
|
1.0
|
|
HB3
|
A:ASP114
|
5.0
|
18.8
|
1.0
|
|
HB3
|
A:ASN54
|
5.0
|
24.1
|
1.0
|
|
Calcium binding site 2 out
of 4 in 6ygq
Go back to
Calcium Binding Sites List in 6ygq
Calcium binding site 2 out
of 4 in the Ecla N-Terminal Domain; Plla-Like Lectin
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Ecla N-Terminal Domain; Plla-Like Lectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca201
b:18.4
occ:1.00
|
O
|
B:GLN118
|
2.3
|
17.5
|
1.0
|
|
OD1
|
B:ASN122
|
2.4
|
14.8
|
1.0
|
|
O
|
B:ASN54
|
2.4
|
25.1
|
1.0
|
|
OD2
|
B:ASP114
|
2.4
|
17.7
|
1.0
|
|
O
|
B:HOH313
|
2.4
|
16.7
|
1.0
|
|
OD1
|
B:ASP121
|
2.5
|
21.7
|
1.0
|
|
O
|
B:HOH302
|
2.6
|
19.4
|
1.0
|
|
HB3
|
B:GLN118
|
3.1
|
26.5
|
1.0
|
|
C
|
B:ASN54
|
3.3
|
31.5
|
1.0
|
|
HD21
|
B:ASN122
|
3.4
|
17.8
|
1.0
|
|
CG
|
B:ASN122
|
3.4
|
14.2
|
1.0
|
|
CG
|
B:ASP114
|
3.4
|
17.9
|
1.0
|
|
C
|
B:GLN118
|
3.5
|
19.5
|
1.0
|
|
CG
|
B:ASP121
|
3.5
|
22.4
|
1.0
|
|
HB2
|
B:ASN54
|
3.7
|
36.0
|
1.0
|
|
HA
|
B:ASN54
|
3.7
|
42.3
|
1.0
|
|
OD1
|
B:ASP114
|
3.7
|
18.8
|
1.0
|
|
OD2
|
B:ASP121
|
3.8
|
23.2
|
1.0
|
|
O
|
B:HOH366
|
3.8
|
37.5
|
1.0
|
|
ND2
|
B:ASN122
|
3.8
|
14.8
|
1.0
|
|
HA
|
B:TYR119
|
3.8
|
22.5
|
1.0
|
|
CB
|
B:GLN118
|
3.9
|
22.1
|
1.0
|
|
HB2
|
B:GLN118
|
3.9
|
26.5
|
1.0
|
|
HA2
|
B:GLY55
|
4.0
|
30.8
|
1.0
|
|
CA
|
B:ASN54
|
4.0
|
35.2
|
1.0
|
|
CA
|
B:GLN118
|
4.2
|
21.0
|
1.0
|
|
H
|
B:ASP121
|
4.3
|
25.2
|
1.0
|
|
N
|
B:GLY55
|
4.3
|
22.4
|
1.0
|
|
CB
|
B:ASN54
|
4.3
|
30.0
|
1.0
|
|
N
|
B:TYR119
|
4.4
|
19.8
|
1.0
|
|
CA
|
B:TYR119
|
4.5
|
18.7
|
1.0
|
|
CA
|
B:GLY55
|
4.5
|
25.8
|
1.0
|
|
HA
|
B:GLN118
|
4.5
|
25.2
|
1.0
|
|
N
|
B:ASN122
|
4.6
|
15.2
|
1.0
|
|
HD22
|
B:ASN122
|
4.6
|
17.8
|
1.0
|
|
H
|
B:ASN122
|
4.7
|
18.3
|
1.0
|
|
HA3
|
B:GLY55
|
4.7
|
30.8
|
1.0
|
|
HA
|
B:ASN122
|
4.7
|
16.7
|
1.0
|
|
CB
|
B:ASN122
|
4.7
|
13.3
|
1.0
|
|
CB
|
B:ASP114
|
4.8
|
16.1
|
1.0
|
|
C
|
B:ASP121
|
4.8
|
18.1
|
1.0
|
|
C
|
B:TYR119
|
4.8
|
19.0
|
1.0
|
|
CB
|
B:ASP121
|
4.8
|
22.5
|
1.0
|
|
HB3
|
B:ASN54
|
4.9
|
36.0
|
1.0
|
|
CA
|
B:ASN122
|
4.9
|
13.9
|
1.0
|
|
HB2
|
B:ASP114
|
4.9
|
19.4
|
1.0
|
|
N
|
B:ASP121
|
5.0
|
20.9
|
1.0
|
|
HB3
|
B:ASP114
|
5.0
|
19.4
|
1.0
|
|
OE1
|
B:GLN118
|
5.0
|
32.2
|
1.0
|
|
Calcium binding site 3 out
of 4 in 6ygq
Go back to
Calcium Binding Sites List in 6ygq
Calcium binding site 3 out
of 4 in the Ecla N-Terminal Domain; Plla-Like Lectin
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Ecla N-Terminal Domain; Plla-Like Lectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca201
b:35.5
occ:1.00
|
O
|
C:GLN118
|
2.3
|
22.8
|
1.0
|
|
O
|
C:ASN54
|
2.4
|
29.4
|
1.0
|
|
O
|
C:HOH311
|
2.4
|
19.4
|
1.0
|
|
OD2
|
C:ASP114
|
2.4
|
19.6
|
1.0
|
|
OD1
|
C:ASP121
|
2.4
|
23.1
|
1.0
|
|
OD1
|
C:ASN122
|
2.5
|
17.9
|
1.0
|
|
O
|
C:HOH320
|
2.7
|
20.0
|
1.0
|
|
HB3
|
C:GLN118
|
3.3
|
33.1
|
1.0
|
|
C
|
C:ASN54
|
3.4
|
30.3
|
1.0
|
|
CG
|
C:ASP121
|
3.4
|
23.9
|
1.0
|
|
HD21
|
C:ASN122
|
3.4
|
23.1
|
1.0
|
|
CG
|
C:ASP114
|
3.5
|
20.1
|
1.0
|
|
CG
|
C:ASN122
|
3.5
|
18.3
|
1.0
|
|
C
|
C:GLN118
|
3.5
|
24.1
|
1.0
|
|
HB2
|
C:ASN54
|
3.5
|
33.0
|
1.0
|
|
OD2
|
C:ASP121
|
3.6
|
25.6
|
1.0
|
|
HA
|
C:ASN54
|
3.7
|
34.6
|
1.0
|
|
OD1
|
C:ASP114
|
3.8
|
21.4
|
1.0
|
|
HA
|
C:TYR119
|
3.8
|
24.8
|
1.0
|
|
ND2
|
C:ASN122
|
3.9
|
19.2
|
1.0
|
|
CA
|
C:ASN54
|
4.0
|
28.8
|
1.0
|
|
HA2
|
C:GLY55
|
4.0
|
39.9
|
1.0
|
|
CB
|
C:GLN118
|
4.1
|
27.6
|
1.0
|
|
HB2
|
C:GLN118
|
4.2
|
33.1
|
1.0
|
|
H
|
C:ASP121
|
4.2
|
29.3
|
1.0
|
|
CB
|
C:ASN54
|
4.2
|
27.5
|
1.0
|
|
CA
|
C:GLN118
|
4.3
|
27.1
|
1.0
|
|
N
|
C:GLY55
|
4.4
|
29.4
|
1.0
|
|
N
|
C:TYR119
|
4.5
|
22.1
|
1.0
|
|
CA
|
C:TYR119
|
4.5
|
20.6
|
1.0
|
|
HA
|
C:GLN118
|
4.6
|
32.5
|
1.0
|
|
CA
|
C:GLY55
|
4.6
|
33.2
|
1.0
|
|
N
|
C:ASN122
|
4.7
|
19.6
|
1.0
|
|
HD22
|
C:ASN122
|
4.7
|
23.1
|
1.0
|
|
CB
|
C:ASP121
|
4.8
|
23.5
|
1.0
|
|
C
|
C:ASP121
|
4.8
|
22.2
|
1.0
|
|
CB
|
C:ASP114
|
4.8
|
18.9
|
1.0
|
|
HA
|
C:ASN122
|
4.8
|
21.4
|
1.0
|
|
H
|
C:ASN122
|
4.8
|
23.5
|
1.0
|
|
CB
|
C:ASN122
|
4.8
|
17.4
|
1.0
|
|
C
|
C:TYR119
|
4.8
|
21.1
|
1.0
|
|
HB3
|
C:ASP114
|
4.9
|
22.7
|
1.0
|
|
HA3
|
C:GLY55
|
4.9
|
39.9
|
1.0
|
|
N
|
C:ASP121
|
4.9
|
24.4
|
1.0
|
|
HB3
|
C:ASN54
|
5.0
|
33.0
|
1.0
|
|
Calcium binding site 4 out
of 4 in 6ygq
Go back to
Calcium Binding Sites List in 6ygq
Calcium binding site 4 out
of 4 in the Ecla N-Terminal Domain; Plla-Like Lectin
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Ecla N-Terminal Domain; Plla-Like Lectin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca201
b:28.2
occ:1.00
|
O
|
D:GLN118
|
2.2
|
46.9
|
1.0
|
|
OD2
|
D:ASP114
|
2.4
|
24.9
|
1.0
|
|
OD1
|
D:ASN122
|
2.4
|
24.0
|
1.0
|
|
O
|
D:ASN54
|
2.4
|
41.7
|
1.0
|
|
O
|
D:HOH441
|
2.5
|
27.4
|
1.0
|
|
OD1
|
D:ASP121
|
2.6
|
34.0
|
1.0
|
|
O
|
D:HOH415
|
2.8
|
25.1
|
1.0
|
|
HB3
|
D:GLN118
|
3.3
|
80.2
|
1.0
|
|
C
|
D:ASN54
|
3.4
|
38.8
|
1.0
|
|
C
|
D:GLN118
|
3.4
|
58.3
|
1.0
|
|
CG
|
D:ASP114
|
3.5
|
24.5
|
1.0
|
|
CG
|
D:ASN122
|
3.5
|
25.2
|
1.0
|
|
HD21
|
D:ASN122
|
3.5
|
30.8
|
1.0
|
|
HB2
|
D:ASN54
|
3.5
|
33.6
|
1.0
|
|
CG
|
D:ASP121
|
3.6
|
35.2
|
1.0
|
|
HA
|
D:TYR119
|
3.7
|
57.0
|
1.0
|
|
HA
|
D:ASN54
|
3.7
|
39.0
|
1.0
|
|
OD1
|
D:ASP114
|
3.8
|
24.8
|
1.0
|
|
ND2
|
D:ASN122
|
3.9
|
25.6
|
1.0
|
|
HB2
|
D:GLN118
|
3.9
|
80.2
|
1.0
|
|
OD2
|
D:ASP121
|
3.9
|
35.0
|
1.0
|
|
CB
|
D:GLN118
|
3.9
|
66.8
|
1.0
|
|
CA
|
D:ASN54
|
4.0
|
32.5
|
1.0
|
|
HA2
|
D:GLY55
|
4.1
|
42.3
|
1.0
|
|
CB
|
D:ASN54
|
4.2
|
28.0
|
1.0
|
|
H
|
D:ASP121
|
4.2
|
45.8
|
1.0
|
|
CA
|
D:GLN118
|
4.2
|
69.7
|
1.0
|
|
N
|
D:TYR119
|
4.3
|
55.7
|
1.0
|
|
N
|
D:GLY55
|
4.4
|
32.9
|
1.0
|
|
CA
|
D:TYR119
|
4.4
|
47.5
|
1.0
|
|
HA
|
D:GLN118
|
4.5
|
83.6
|
1.0
|
|
CA
|
D:GLY55
|
4.7
|
35.2
|
1.0
|
|
N
|
D:ASN122
|
4.7
|
26.6
|
1.0
|
|
HD22
|
D:ASN122
|
4.7
|
30.8
|
1.0
|
|
H
|
D:ASN122
|
4.7
|
31.9
|
1.0
|
|
C
|
D:TYR119
|
4.8
|
40.4
|
1.0
|
|
HA
|
D:ASN122
|
4.8
|
30.3
|
1.0
|
|
CB
|
D:ASP114
|
4.8
|
23.4
|
1.0
|
|
CB
|
D:ASN122
|
4.8
|
25.7
|
1.0
|
|
C
|
D:ASP121
|
4.8
|
32.4
|
1.0
|
|
HB3
|
D:ASN54
|
4.8
|
33.6
|
1.0
|
|
HA3
|
D:GLY55
|
4.8
|
42.3
|
1.0
|
|
HB3
|
D:ASP114
|
4.9
|
28.1
|
1.0
|
|
N
|
D:ASP121
|
4.9
|
38.2
|
1.0
|
|
CB
|
D:ASP121
|
4.9
|
37.5
|
1.0
|
|
HB2
|
D:ASP114
|
5.0
|
28.1
|
1.0
|
|
Reference:
J.Koehnke,
A.Sikandar.
Ecla N-Terminal Domain; Plla-Like Lectin To Be Published.
Page generated: Wed Jul 9 20:22:08 2025
|
