Calcium in PDB 4gkx: Crystal Structure of A Carbohydrate-Binding Domain
Protein crystallography data
The structure of Crystal Structure of A Carbohydrate-Binding Domain, PDB code: 4gkx
was solved by
R.C.Page,
C.Zheng,
J.C.Nix,
S.Misra,
B.Zhang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
37.19 /
2.70
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
39.283,
111.498,
111.388,
60.09,
89.21,
86.25
|
|
R / Rfree (%)
|
24.6 /
28.6
|
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 A Carbohydrate-Binding Domain
(pdb code 4gkx). 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 A Carbohydrate-Binding Domain, PDB code: 4gkx:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 12 in 4gkx
Go back to
Calcium Binding Sites List in 4gkx
Calcium binding site 1 out
of 12 in the Crystal Structure of A Carbohydrate-Binding Domain
 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 A Carbohydrate-Binding Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca301
b:43.9
occ:1.00
|
O
|
A:HOH448
|
2.5
|
33.3
|
1.0
|
|
OD1
|
A:ASP152
|
2.5
|
33.5
|
1.0
|
|
OD2
|
A:ASP152
|
2.5
|
44.0
|
1.0
|
|
OD1
|
A:ASP181
|
2.7
|
48.1
|
1.0
|
|
O
|
A:PHE154
|
2.8
|
35.8
|
1.0
|
|
CG
|
A:ASP152
|
2.8
|
34.1
|
1.0
|
|
OD1
|
A:ASN156
|
2.9
|
46.1
|
1.0
|
|
CG
|
A:ASP181
|
3.6
|
46.4
|
1.0
|
|
CG
|
A:ASN156
|
3.8
|
50.1
|
1.0
|
|
C
|
A:PHE154
|
3.9
|
31.6
|
1.0
|
|
CB
|
A:ASP181
|
4.2
|
33.3
|
1.0
|
|
CA
|
A:ASP181
|
4.3
|
37.2
|
1.0
|
|
N
|
A:ASN156
|
4.3
|
41.3
|
1.0
|
|
CB
|
A:ASP152
|
4.3
|
31.4
|
1.0
|
|
CB
|
A:ASN156
|
4.4
|
47.9
|
1.0
|
|
OD2
|
A:ASP181
|
4.4
|
48.5
|
1.0
|
|
N
|
A:PHE154
|
4.4
|
35.1
|
1.0
|
|
CB
|
A:PHE154
|
4.4
|
42.4
|
1.0
|
|
CA
|
A:PHE154
|
4.5
|
34.2
|
1.0
|
|
NE2
|
A:HIS178
|
4.5
|
49.9
|
1.0
|
|
CE1
|
A:HIS178
|
4.5
|
48.7
|
1.0
|
|
ND2
|
A:ASN162
|
4.6
|
36.5
|
1.0
|
|
O
|
A:HIS178
|
4.6
|
52.9
|
1.0
|
|
O
|
A:HOH435
|
4.7
|
36.8
|
1.0
|
|
ND2
|
A:ASN156
|
4.7
|
57.7
|
1.0
|
|
OH
|
A:TYR176
|
4.7
|
42.8
|
1.0
|
|
OD1
|
A:ASP121
|
4.8
|
42.5
|
1.0
|
|
N
|
A:ASP181
|
4.8
|
38.3
|
1.0
|
|
HO7
|
A:2M4303
|
4.8
|
51.2
|
0.7
|
|
N
|
A:ASP155
|
4.9
|
40.3
|
1.0
|
|
O
|
A:ASP121
|
4.9
|
31.2
|
1.0
|
|
CD2
|
A:HIS178
|
5.0
|
40.5
|
1.0
|
|
ND1
|
A:HIS178
|
5.0
|
57.0
|
1.0
|
|
Calcium binding site 2 out
of 12 in 4gkx
Go back to
Calcium Binding Sites List in 4gkx
Calcium binding site 2 out
of 12 in the Crystal Structure of A Carbohydrate-Binding Domain
 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 A Carbohydrate-Binding Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca302
b:46.2
occ:1.00
|
OD2
|
A:ASP181
|
2.1
|
48.5
|
1.0
|
|
OD1
|
A:ASN162
|
2.2
|
37.9
|
1.0
|
|
OD1
|
A:ASN161
|
2.3
|
39.9
|
1.0
|
|
OD1
|
A:ASP157
|
2.3
|
47.5
|
1.0
|
|
OD1
|
A:ASP155
|
2.6
|
44.0
|
1.0
|
|
O
|
A:HOH446
|
2.9
|
38.7
|
1.0
|
|
CG
|
A:ASN161
|
2.9
|
36.6
|
1.0
|
|
ND2
|
A:ASN161
|
3.0
|
36.1
|
1.0
|
|
CG
|
A:ASP157
|
3.3
|
47.9
|
1.0
|
|
CG
|
A:ASP181
|
3.4
|
46.4
|
1.0
|
|
CG
|
A:ASN162
|
3.4
|
39.2
|
1.0
|
|
OD2
|
A:ASP157
|
3.6
|
48.6
|
1.0
|
|
CG
|
A:ASP155
|
3.7
|
42.4
|
1.0
|
|
CB
|
A:ASP181
|
4.1
|
33.3
|
1.0
|
|
ND2
|
A:ASN162
|
4.1
|
36.5
|
1.0
|
|
O
|
A:ASN161
|
4.1
|
35.5
|
1.0
|
|
CB
|
A:ASN161
|
4.2
|
33.2
|
1.0
|
|
CA
|
A:ASP155
|
4.2
|
43.6
|
1.0
|
|
C
|
A:ASN161
|
4.3
|
38.0
|
1.0
|
|
N
|
A:ASN161
|
4.3
|
41.1
|
1.0
|
|
CB
|
A:LYS159
|
4.3
|
41.7
|
1.0
|
|
OD1
|
A:ASP181
|
4.3
|
48.1
|
1.0
|
|
CB
|
A:ASP155
|
4.4
|
41.9
|
1.0
|
|
CA
|
A:ASN161
|
4.5
|
35.6
|
1.0
|
|
N
|
A:ASP157
|
4.5
|
44.3
|
1.0
|
|
N
|
A:LYS159
|
4.5
|
40.8
|
1.0
|
|
CB
|
A:ASN162
|
4.6
|
35.1
|
1.0
|
|
C
|
A:ASP155
|
4.6
|
42.7
|
1.0
|
|
CG
|
A:LYS159
|
4.6
|
44.1
|
1.0
|
|
OD2
|
A:ASP155
|
4.6
|
42.0
|
1.0
|
|
CB
|
A:ASP157
|
4.7
|
47.0
|
1.0
|
|
N
|
A:ASN156
|
4.7
|
41.3
|
1.0
|
|
N
|
A:ASN162
|
4.8
|
35.0
|
1.0
|
|
N
|
A:GLY158
|
4.8
|
50.8
|
1.0
|
|
CA
|
A:LYS159
|
4.9
|
44.9
|
1.0
|
|
CA
|
A:ASP157
|
5.0
|
44.8
|
1.0
|
|
Calcium binding site 3 out
of 12 in 4gkx
Go back to
Calcium Binding Sites List in 4gkx
Calcium binding site 3 out
of 12 in the Crystal Structure of A Carbohydrate-Binding Domain
 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 A Carbohydrate-Binding Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca301
b:45.8
occ:1.00
|
OD1
|
B:ASP152
|
2.5
|
43.3
|
1.0
|
|
O
|
B:PHE154
|
2.5
|
42.0
|
1.0
|
|
O
|
B:HOH435
|
2.5
|
40.4
|
1.0
|
|
OD2
|
B:ASP152
|
2.5
|
35.2
|
1.0
|
|
OD1
|
B:ASN156
|
2.5
|
49.4
|
1.0
|
|
OD1
|
B:ASP181
|
2.5
|
39.5
|
1.0
|
|
CG
|
B:ASP152
|
2.8
|
35.0
|
1.0
|
|
CG
|
B:ASP181
|
3.4
|
43.4
|
1.0
|
|
CG
|
B:ASN156
|
3.6
|
48.7
|
1.0
|
|
C
|
B:PHE154
|
3.7
|
44.4
|
1.0
|
|
CB
|
B:ASN156
|
4.1
|
50.3
|
1.0
|
|
N
|
B:ASN156
|
4.1
|
52.8
|
1.0
|
|
CB
|
B:ASP181
|
4.1
|
43.7
|
1.0
|
|
CA
|
B:ASP181
|
4.2
|
45.9
|
1.0
|
|
OD2
|
B:ASP181
|
4.2
|
44.0
|
1.0
|
|
O
|
B:HIS178
|
4.3
|
50.6
|
1.0
|
|
CB
|
B:ASP152
|
4.3
|
31.0
|
1.0
|
|
N
|
B:PHE154
|
4.4
|
32.3
|
1.0
|
|
CA
|
B:PHE154
|
4.4
|
36.2
|
1.0
|
|
ND2
|
B:ASN162
|
4.6
|
40.5
|
1.0
|
|
CB
|
B:PHE154
|
4.6
|
37.9
|
1.0
|
|
OH
|
B:TYR176
|
4.6
|
39.7
|
1.0
|
|
ND2
|
B:ASN156
|
4.7
|
49.6
|
1.0
|
|
N
|
B:ASP155
|
4.7
|
45.9
|
1.0
|
|
N
|
B:ASP181
|
4.8
|
52.4
|
1.0
|
|
CA
|
B:ASN156
|
4.8
|
49.4
|
1.0
|
|
CE1
|
B:HIS178
|
4.8
|
50.6
|
1.0
|
|
HO7
|
B:2M4303
|
4.9
|
51.3
|
0.7
|
|
O
|
B:ASP121
|
4.9
|
34.8
|
1.0
|
|
CD2
|
B:PHE154
|
5.0
|
45.2
|
1.0
|
|
CZ
|
B:PHE138
|
5.0
|
33.0
|
1.0
|
|
OD1
|
B:ASP121
|
5.0
|
36.6
|
1.0
|
|
CA
|
B:ASP155
|
5.0
|
49.7
|
1.0
|
|
Calcium binding site 4 out
of 12 in 4gkx
Go back to
Calcium Binding Sites List in 4gkx
Calcium binding site 4 out
of 12 in the Crystal Structure of A Carbohydrate-Binding Domain
 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 A Carbohydrate-Binding Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca302
b:54.1
occ:1.00
|
OD2
|
B:ASP181
|
2.2
|
44.0
|
1.0
|
|
OD1
|
B:ASN161
|
2.3
|
46.0
|
1.0
|
|
OD1
|
B:ASP157
|
2.3
|
52.0
|
1.0
|
|
OD1
|
B:ASN162
|
2.5
|
51.6
|
1.0
|
|
ND2
|
B:ASN161
|
2.7
|
52.4
|
1.0
|
|
CG
|
B:ASN161
|
2.8
|
48.2
|
1.0
|
|
OD1
|
B:ASP155
|
3.0
|
50.3
|
1.0
|
|
CG
|
B:ASP157
|
3.2
|
47.2
|
1.0
|
|
CG
|
B:ASP181
|
3.3
|
43.4
|
1.0
|
|
OD2
|
B:ASP157
|
3.4
|
54.1
|
1.0
|
|
CG
|
B:ASN162
|
3.7
|
43.7
|
1.0
|
|
CB
|
B:ASP181
|
3.9
|
43.7
|
1.0
|
|
CG
|
B:ASP155
|
4.1
|
53.2
|
1.0
|
|
CB
|
B:ASN161
|
4.1
|
36.0
|
1.0
|
|
O
|
B:ASN161
|
4.2
|
44.0
|
1.0
|
|
ND2
|
B:ASN162
|
4.2
|
40.5
|
1.0
|
|
C
|
B:ASN161
|
4.3
|
48.9
|
1.0
|
|
OD1
|
B:ASP181
|
4.4
|
39.5
|
1.0
|
|
N
|
B:ASN161
|
4.5
|
52.0
|
1.0
|
|
CA
|
B:ASN161
|
4.6
|
45.2
|
1.0
|
|
CA
|
B:ASP155
|
4.6
|
49.7
|
1.0
|
|
CB
|
B:ASP157
|
4.6
|
51.1
|
1.0
|
|
CB
|
B:LYS159
|
4.7
|
51.6
|
1.0
|
|
N
|
B:ASP157
|
4.7
|
50.0
|
1.0
|
|
N
|
B:LYS159
|
4.8
|
52.8
|
1.0
|
|
CB
|
B:ASP155
|
4.8
|
52.4
|
1.0
|
|
CB
|
B:ASN162
|
4.9
|
35.5
|
1.0
|
|
N
|
B:ASN162
|
4.9
|
42.5
|
1.0
|
|
N
|
B:ASN156
|
5.0
|
52.8
|
1.0
|
|
C
|
B:ASP155
|
5.0
|
52.4
|
1.0
|
|
Calcium binding site 5 out
of 12 in 4gkx
Go back to
Calcium Binding Sites List in 4gkx
Calcium binding site 5 out
of 12 in the Crystal Structure of A Carbohydrate-Binding Domain
 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 A Carbohydrate-Binding Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca301
b:56.0
occ:1.00
|
OD1
|
C:ASN156
|
2.2
|
49.6
|
1.0
|
|
OD2
|
C:ASP152
|
2.4
|
46.5
|
1.0
|
|
OD1
|
C:ASP152
|
2.4
|
47.1
|
1.0
|
|
O
|
C:HOH435
|
2.5
|
44.7
|
1.0
|
|
O
|
C:PHE154
|
2.7
|
48.4
|
1.0
|
|
CG
|
C:ASP152
|
2.7
|
44.1
|
1.0
|
|
OD1
|
C:ASP181
|
2.8
|
55.5
|
1.0
|
|
CG
|
C:ASN156
|
3.4
|
49.0
|
1.0
|
|
CG
|
C:ASP181
|
3.6
|
51.7
|
1.0
|
|
C
|
C:PHE154
|
3.9
|
50.2
|
1.0
|
|
CB
|
C:ASP152
|
4.2
|
49.1
|
1.0
|
|
CB
|
C:ASP181
|
4.2
|
46.6
|
1.0
|
|
CB
|
C:ASN156
|
4.3
|
53.0
|
1.0
|
|
CA
|
C:ASP181
|
4.3
|
50.4
|
1.0
|
|
ND2
|
C:ASN156
|
4.3
|
44.0
|
1.0
|
|
O
|
C:HIS178
|
4.3
|
59.3
|
1.0
|
|
N
|
C:ASN156
|
4.3
|
40.7
|
1.0
|
|
OH
|
C:TYR176
|
4.4
|
56.0
|
1.0
|
|
OD2
|
C:ASP181
|
4.4
|
50.9
|
1.0
|
|
CE1
|
C:HIS178
|
4.5
|
55.1
|
1.0
|
|
N
|
C:PHE154
|
4.5
|
43.8
|
1.0
|
|
CA
|
C:PHE154
|
4.6
|
47.9
|
1.0
|
|
CZ
|
C:PHE138
|
4.7
|
39.0
|
1.0
|
|
CB
|
C:PHE154
|
4.7
|
49.5
|
1.0
|
|
ND2
|
C:ASN162
|
4.7
|
46.3
|
1.0
|
|
ND1
|
C:HIS178
|
4.8
|
52.7
|
1.0
|
|
N
|
C:ASP181
|
4.8
|
53.3
|
1.0
|
|
O
|
C:ASP121
|
4.8
|
38.5
|
1.0
|
|
HO7
|
C:2M4303
|
4.9
|
61.3
|
0.6
|
|
NE2
|
C:HIS178
|
4.9
|
49.5
|
1.0
|
|
N
|
C:ASP155
|
4.9
|
50.8
|
1.0
|
|
CA
|
C:ASN156
|
5.0
|
54.1
|
1.0
|
|
OD1
|
C:ASP121
|
5.0
|
51.2
|
1.0
|
|
CA
|
C:ASP152
|
5.0
|
47.1
|
1.0
|
|
Calcium binding site 6 out
of 12 in 4gkx
Go back to
Calcium Binding Sites List in 4gkx
Calcium binding site 6 out
of 12 in the Crystal Structure of A Carbohydrate-Binding Domain
 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 A Carbohydrate-Binding Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca302
b:63.4
occ:1.00
|
OD1
|
C:ASN161
|
2.2
|
55.7
|
1.0
|
|
OD2
|
C:ASP181
|
2.2
|
50.9
|
1.0
|
|
OD1
|
C:ASN162
|
2.4
|
49.9
|
1.0
|
|
OD1
|
C:ASP157
|
2.4
|
57.7
|
1.0
|
|
CG
|
C:ASN161
|
2.7
|
57.7
|
1.0
|
|
ND2
|
C:ASN161
|
2.7
|
55.9
|
1.0
|
|
OD1
|
C:ASP155
|
3.0
|
53.3
|
1.0
|
|
CG
|
C:ASP157
|
3.3
|
55.0
|
1.0
|
|
CG
|
C:ASP181
|
3.4
|
51.7
|
1.0
|
|
OD2
|
C:ASP157
|
3.5
|
49.7
|
1.0
|
|
CG
|
C:ASN162
|
3.5
|
44.7
|
1.0
|
|
CB
|
C:ASP181
|
4.0
|
46.6
|
1.0
|
|
O
|
C:ASN161
|
4.0
|
56.0
|
1.0
|
|
CB
|
C:ASN161
|
4.0
|
44.5
|
1.0
|
|
CG
|
C:ASP155
|
4.1
|
53.0
|
1.0
|
|
ND2
|
C:ASN162
|
4.1
|
46.3
|
1.0
|
|
C
|
C:ASN161
|
4.2
|
50.4
|
1.0
|
|
N
|
C:ASN161
|
4.3
|
49.3
|
1.0
|
|
CA
|
C:ASN161
|
4.4
|
44.3
|
1.0
|
|
OD1
|
C:ASP181
|
4.4
|
55.5
|
1.0
|
|
CA
|
C:ASP155
|
4.6
|
51.5
|
1.0
|
|
CB
|
C:LYS159
|
4.6
|
55.6
|
1.0
|
|
CB
|
C:ASP157
|
4.7
|
55.5
|
1.0
|
|
N
|
C:ASP157
|
4.8
|
50.7
|
1.0
|
|
N
|
C:LYS159
|
4.8
|
56.0
|
1.0
|
|
CB
|
C:ASN162
|
4.8
|
47.1
|
1.0
|
|
CB
|
C:ASP155
|
4.8
|
51.1
|
1.0
|
|
N
|
C:ASN162
|
4.8
|
43.8
|
1.0
|
|
OD2
|
C:ASP155
|
5.0
|
57.7
|
1.0
|
|
C
|
C:ASP155
|
5.0
|
45.1
|
1.0
|
|
Calcium binding site 7 out
of 12 in 4gkx
Go back to
Calcium Binding Sites List in 4gkx
Calcium binding site 7 out
of 12 in the Crystal Structure of A Carbohydrate-Binding Domain
 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 A Carbohydrate-Binding Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca301
b:72.9
occ:1.00
|
OD1
|
D:ASN156
|
2.3
|
67.0
|
1.0
|
|
OD1
|
D:ASP152
|
2.4
|
57.6
|
1.0
|
|
OD2
|
D:ASP152
|
2.4
|
57.6
|
1.0
|
|
O
|
D:HOH446
|
2.5
|
53.8
|
1.0
|
|
CG
|
D:ASP152
|
2.7
|
55.3
|
1.0
|
|
O
|
D:PHE154
|
2.8
|
60.7
|
1.0
|
|
OD1
|
D:ASP181
|
2.9
|
76.0
|
1.0
|
|
CG
|
D:ASN156
|
3.5
|
72.8
|
1.0
|
|
CG
|
D:ASP181
|
3.8
|
74.4
|
1.0
|
|
C
|
D:PHE154
|
4.0
|
63.5
|
1.0
|
|
CB
|
D:ASP152
|
4.2
|
51.2
|
1.0
|
|
CE1
|
D:HIS178
|
4.4
|
74.9
|
1.0
|
|
O
|
D:HIS178
|
4.4
|
85.0
|
1.0
|
|
ND2
|
D:ASN156
|
4.4
|
75.8
|
1.0
|
|
CA
|
D:ASP181
|
4.4
|
74.7
|
1.0
|
|
CB
|
D:ASP181
|
4.4
|
77.1
|
1.0
|
|
CB
|
D:ASN156
|
4.4
|
77.9
|
1.0
|
|
N
|
D:PHE154
|
4.4
|
51.5
|
1.0
|
|
OH
|
D:TYR176
|
4.4
|
77.9
|
1.0
|
|
CZ
|
D:PHE138
|
4.5
|
44.2
|
1.0
|
|
N
|
D:ASN156
|
4.5
|
72.6
|
1.0
|
|
CA
|
D:PHE154
|
4.6
|
59.3
|
1.0
|
|
O
|
D:ASP121
|
4.6
|
39.5
|
1.0
|
|
OD2
|
D:ASP181
|
4.6
|
77.9
|
1.0
|
|
ND1
|
D:HIS178
|
4.7
|
76.3
|
1.0
|
|
OD1
|
D:ASP121
|
4.8
|
56.1
|
1.0
|
|
ND2
|
D:ASN162
|
4.8
|
62.5
|
1.0
|
|
HO7
|
D:2M4303
|
4.9
|
74.3
|
0.6
|
|
NE2
|
D:HIS178
|
4.9
|
67.7
|
1.0
|
|
CE2
|
D:PHE138
|
4.9
|
43.5
|
1.0
|
|
CA
|
D:ASP152
|
4.9
|
44.6
|
1.0
|
|
CB
|
D:PHE154
|
4.9
|
60.8
|
1.0
|
|
N
|
D:ASP181
|
5.0
|
71.3
|
1.0
|
|
Calcium binding site 8 out
of 12 in 4gkx
Go back to
Calcium Binding Sites List in 4gkx
Calcium binding site 8 out
of 12 in the Crystal Structure of A Carbohydrate-Binding Domain
 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 A Carbohydrate-Binding Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca302
b:70.3
occ:1.00
|
OD2
|
D:ASP181
|
2.2
|
77.9
|
1.0
|
|
OD1
|
D:ASN161
|
2.3
|
79.7
|
1.0
|
|
OD1
|
D:ASN162
|
2.3
|
70.5
|
1.0
|
|
OD1
|
D:ASP157
|
2.5
|
86.7
|
1.0
|
|
CG
|
D:ASN161
|
2.7
|
73.3
|
1.0
|
|
ND2
|
D:ASN161
|
2.8
|
76.7
|
1.0
|
|
OD1
|
D:ASP155
|
2.9
|
80.3
|
1.0
|
|
CG
|
D:ASP181
|
3.3
|
74.4
|
1.0
|
|
CG
|
D:ASP157
|
3.4
|
85.5
|
1.0
|
|
CG
|
D:ASN162
|
3.4
|
62.2
|
1.0
|
|
OD2
|
D:ASP157
|
3.6
|
83.5
|
1.0
|
|
CB
|
D:ASP181
|
3.9
|
77.1
|
1.0
|
|
O
|
D:ASN161
|
4.0
|
67.3
|
1.0
|
|
CG
|
D:ASP155
|
4.0
|
82.8
|
1.0
|
|
ND2
|
D:ASN162
|
4.0
|
62.5
|
1.0
|
|
CB
|
D:ASN161
|
4.1
|
71.8
|
1.0
|
|
C
|
D:ASN161
|
4.2
|
70.8
|
1.0
|
|
N
|
D:ASN161
|
4.4
|
77.2
|
1.0
|
|
OD1
|
D:ASP181
|
4.4
|
76.0
|
1.0
|
|
CA
|
D:ASN161
|
4.4
|
79.2
|
1.0
|
|
CA
|
D:ASP155
|
4.5
|
74.8
|
1.0
|
|
CB
|
D:ASP155
|
4.7
|
78.7
|
1.0
|
|
CB
|
D:ASN162
|
4.7
|
61.9
|
1.0
|
|
N
|
D:ASP157
|
4.7
|
85.1
|
1.0
|
|
CB
|
D:LYS159
|
4.7
|
71.3
|
1.0
|
|
N
|
D:ASN162
|
4.8
|
62.0
|
1.0
|
|
CB
|
D:ASP157
|
4.8
|
79.0
|
1.0
|
|
N
|
D:LYS159
|
4.8
|
84.2
|
1.0
|
|
OD2
|
D:ASP155
|
4.9
|
84.7
|
1.0
|
|
C
|
D:ASP155
|
4.9
|
72.2
|
1.0
|
|
N
|
D:ASN156
|
4.9
|
72.6
|
1.0
|
|
Calcium binding site 9 out
of 12 in 4gkx
Go back to
Calcium Binding Sites List in 4gkx
Calcium binding site 9 out
of 12 in the Crystal Structure of A Carbohydrate-Binding Domain
 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 A Carbohydrate-Binding Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca301
b:57.4
occ:1.00
|
OD1
|
E:ASN156
|
2.2
|
72.9
|
1.0
|
|
OD1
|
E:ASP152
|
2.4
|
53.2
|
1.0
|
|
O
|
E:HOH423
|
2.5
|
49.1
|
1.0
|
|
O
|
E:PHE154
|
2.6
|
61.2
|
1.0
|
|
OD2
|
E:ASP152
|
2.6
|
55.4
|
1.0
|
|
CG
|
E:ASP152
|
2.9
|
48.6
|
1.0
|
|
OD1
|
E:ASP181
|
2.9
|
72.4
|
1.0
|
|
CG
|
E:ASN156
|
3.4
|
68.9
|
1.0
|
|
C
|
E:PHE154
|
3.7
|
64.2
|
1.0
|
|
CG
|
E:ASP181
|
3.8
|
68.1
|
1.0
|
|
ND2
|
E:ASN156
|
4.3
|
55.5
|
1.0
|
|
N
|
E:PHE154
|
4.3
|
56.4
|
1.0
|
|
CB
|
E:ASN156
|
4.3
|
75.3
|
1.0
|
|
CA
|
E:PHE154
|
4.3
|
57.1
|
1.0
|
|
CB
|
E:ASP152
|
4.3
|
40.0
|
1.0
|
|
N
|
E:ASN156
|
4.3
|
68.4
|
1.0
|
|
CE1
|
E:HIS178
|
4.4
|
62.7
|
1.0
|
|
O
|
E:HIS178
|
4.5
|
72.4
|
1.0
|
|
CB
|
E:PHE154
|
4.5
|
58.6
|
1.0
|
|
CB
|
E:ASP181
|
4.5
|
62.4
|
1.0
|
|
OD1
|
E:ASP121
|
4.5
|
50.7
|
1.0
|
|
CA
|
E:ASP181
|
4.5
|
68.2
|
1.0
|
|
OD2
|
E:ASP181
|
4.6
|
74.2
|
1.0
|
|
O
|
E:ASP121
|
4.6
|
46.2
|
1.0
|
|
OH
|
E:TYR176
|
4.7
|
55.4
|
1.0
|
|
HO7
|
E:2M4303
|
4.7
|
74.9
|
0.7
|
|
ND2
|
E:ASN162
|
4.7
|
51.0
|
1.0
|
|
CZ
|
E:PHE138
|
4.8
|
41.7
|
1.0
|
|
ND1
|
E:HIS178
|
4.8
|
69.3
|
1.0
|
|
N
|
E:ASP155
|
4.8
|
64.9
|
1.0
|
|
NE2
|
E:HIS178
|
4.8
|
62.2
|
1.0
|
|
CD2
|
E:PHE154
|
4.8
|
63.3
|
1.0
|
|
CA
|
E:ASN156
|
5.0
|
72.9
|
1.0
|
|
Calcium binding site 10 out
of 12 in 4gkx
Go back to
Calcium Binding Sites List in 4gkx
Calcium binding site 10 out
of 12 in the Crystal Structure of A Carbohydrate-Binding Domain
 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 A Carbohydrate-Binding Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca302
b:63.7
occ:1.00
|
OD2
|
E:ASP181
|
2.2
|
74.2
|
1.0
|
|
OD1
|
E:ASP157
|
2.2
|
70.8
|
1.0
|
|
OD1
|
E:ASN161
|
2.3
|
66.0
|
1.0
|
|
OD1
|
E:ASN162
|
2.5
|
67.9
|
1.0
|
|
ND2
|
E:ASN161
|
2.8
|
80.1
|
1.0
|
|
CG
|
E:ASN161
|
2.8
|
69.7
|
1.0
|
|
OD1
|
E:ASP155
|
2.9
|
67.5
|
1.0
|
|
CG
|
E:ASP157
|
3.1
|
76.8
|
1.0
|
|
OD2
|
E:ASP157
|
3.3
|
73.1
|
1.0
|
|
CG
|
E:ASP181
|
3.3
|
68.1
|
1.0
|
|
CG
|
E:ASN162
|
3.7
|
57.8
|
1.0
|
|
CB
|
E:ASP181
|
3.9
|
62.4
|
1.0
|
|
CG
|
E:ASP155
|
4.1
|
69.6
|
1.0
|
|
CB
|
E:ASN161
|
4.1
|
69.5
|
1.0
|
|
O
|
E:ASN161
|
4.2
|
64.5
|
1.0
|
|
ND2
|
E:ASN162
|
4.2
|
51.0
|
1.0
|
|
C
|
E:ASN161
|
4.4
|
72.5
|
1.0
|
|
OD1
|
E:ASP181
|
4.4
|
72.4
|
1.0
|
|
N
|
E:ASN161
|
4.5
|
73.2
|
1.0
|
|
CB
|
E:ASP157
|
4.5
|
78.5
|
1.0
|
|
CA
|
E:ASP155
|
4.6
|
62.2
|
1.0
|
|
CA
|
E:ASN161
|
4.6
|
70.8
|
1.0
|
|
N
|
E:ASP157
|
4.6
|
75.3
|
1.0
|
|
CB
|
E:LYS159
|
4.6
|
69.0
|
1.0
|
|
N
|
E:LYS159
|
4.7
|
79.3
|
1.0
|
|
CB
|
E:ASP155
|
4.8
|
63.9
|
1.0
|
|
N
|
E:ASN156
|
4.9
|
68.4
|
1.0
|
|
CB
|
E:ASN162
|
4.9
|
56.7
|
1.0
|
|
C
|
E:ASP155
|
4.9
|
70.8
|
1.0
|
|
N
|
E:ASN162
|
4.9
|
71.2
|
1.0
|
|
OD2
|
E:ASP155
|
4.9
|
70.6
|
1.0
|
|
N
|
E:GLY158
|
5.0
|
80.0
|
1.0
|
|
CA
|
E:ASP157
|
5.0
|
79.9
|
1.0
|
|
CG
|
E:LYS159
|
5.0
|
72.5
|
1.0
|
|
Reference:
C.Zheng,
R.C.Page,
V.Das,
J.C.Nix,
E.Wigren,
S.Misra,
B.Zhang.
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ISSN: ISSN 0021-9258
PubMed: 23709226
DOI: 10.1074/JBC.M113.461434
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