Calcium in PDB 7f9g: Thrombocorticin in Complex with CA2+ and Fucose
Protein crystallography data
The structure of Thrombocorticin in Complex with CA2+ and Fucose, PDB code: 7f9g
was solved by
H.Kageyama,
K.Onodera,
R.Sakai,
Y.Tanaka,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
30.43 /
1.33
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
41.52,
44.72,
108.58,
90,
90,
90
|
|
R / Rfree (%)
|
15.5 /
16.8
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Thrombocorticin in Complex with CA2+ and Fucose
(pdb code 7f9g). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Thrombocorticin in Complex with CA2+ and Fucose, PDB code: 7f9g:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 7f9g
Go back to
Calcium Binding Sites List in 7f9g
Calcium binding site 1 out
of 4 in the Thrombocorticin in Complex with CA2+ and Fucose
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Thrombocorticin in Complex with CA2+ and Fucose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca202
b:5.9
occ:1.00
|
OD1
|
A:ASP121
|
2.3
|
5.7
|
1.0
|
|
OD1
|
A:ASN120
|
2.4
|
6.2
|
1.0
|
|
O
|
A:GLN26
|
2.4
|
6.7
|
1.0
|
|
OD2
|
A:ASP118
|
2.4
|
6.9
|
1.0
|
|
OXT
|
B:GLY132
|
2.4
|
6.2
|
1.0
|
|
O4
|
A:FUC201
|
2.5
|
6.7
|
1.0
|
|
O3
|
A:FUC201
|
2.5
|
6.5
|
1.0
|
|
CG
|
A:ASP118
|
3.1
|
6.1
|
1.0
|
|
OD1
|
A:ASP118
|
3.2
|
7.5
|
1.0
|
|
CG
|
A:ASN120
|
3.4
|
5.5
|
1.0
|
|
C3
|
A:FUC201
|
3.4
|
8.2
|
1.0
|
|
C
|
B:GLY132
|
3.4
|
7.8
|
1.0
|
|
C4
|
A:FUC201
|
3.4
|
7.2
|
1.0
|
|
CG
|
A:ASP121
|
3.5
|
4.8
|
1.0
|
|
C
|
A:GLN26
|
3.6
|
6.6
|
1.0
|
|
O
|
B:GLY132
|
3.6
|
8.8
|
1.0
|
|
C2
|
A:FUC201
|
3.8
|
6.8
|
1.0
|
|
ND2
|
A:ASN120
|
3.8
|
5.8
|
1.0
|
|
CA
|
A:CA203
|
3.9
|
6.6
|
1.0
|
|
CB
|
A:GLN26
|
4.2
|
8.0
|
1.0
|
|
CA
|
A:ASP121
|
4.2
|
5.9
|
1.0
|
|
N
|
A:ASP121
|
4.3
|
5.4
|
1.0
|
|
OD2
|
A:ASP121
|
4.3
|
6.3
|
1.0
|
|
OD2
|
A:ASP116
|
4.4
|
8.8
|
1.0
|
|
O2
|
A:FUC201
|
4.4
|
7.7
|
1.0
|
|
N
|
A:SER27
|
4.5
|
6.7
|
1.0
|
|
CB
|
A:ASP121
|
4.5
|
6.3
|
1.0
|
|
O
|
A:HOH342
|
4.5
|
8.0
|
1.0
|
|
CA
|
A:SER27
|
4.5
|
6.1
|
1.0
|
|
CB
|
A:ASP118
|
4.5
|
7.7
|
1.0
|
|
C
|
A:ASN120
|
4.5
|
5.8
|
1.0
|
|
CA
|
A:GLN26
|
4.5
|
5.3
|
1.0
|
|
CB
|
A:SER27
|
4.7
|
7.4
|
1.0
|
|
C5
|
A:FUC201
|
4.7
|
8.7
|
1.0
|
|
CB
|
A:ASN120
|
4.7
|
5.3
|
1.0
|
|
CA
|
B:GLY132
|
4.7
|
9.0
|
1.0
|
|
O
|
A:ASN120
|
4.8
|
6.0
|
1.0
|
|
OD1
|
A:ASP116
|
4.9
|
8.7
|
1.0
|
|
N
|
A:ASN120
|
5.0
|
5.6
|
1.0
|
|
CA
|
A:ASN120
|
5.0
|
5.0
|
1.0
|
|
O5
|
A:FUC201
|
5.0
|
9.3
|
1.0
|
|
Calcium binding site 2 out
of 4 in 7f9g
Go back to
Calcium Binding Sites List in 7f9g
Calcium binding site 2 out
of 4 in the Thrombocorticin in Complex with CA2+ and Fucose
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Thrombocorticin in Complex with CA2+ and Fucose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca203
b:6.6
occ:1.00
|
OD1
|
A:ASP118
|
2.4
|
7.5
|
1.0
|
|
OD2
|
A:ASP121
|
2.4
|
6.3
|
1.0
|
|
O
|
A:HOH374
|
2.4
|
8.0
|
1.0
|
|
OD1
|
A:ASP116
|
2.4
|
8.7
|
1.0
|
|
O3
|
A:FUC201
|
2.5
|
6.5
|
1.0
|
|
OD1
|
A:ASN108
|
2.5
|
6.0
|
1.0
|
|
O2
|
A:FUC201
|
2.6
|
7.7
|
1.0
|
|
OD1
|
A:ASP121
|
2.9
|
5.7
|
1.0
|
|
CG
|
A:ASP121
|
3.0
|
4.8
|
1.0
|
|
CG
|
A:ASP118
|
3.4
|
6.1
|
1.0
|
|
C3
|
A:FUC201
|
3.4
|
8.2
|
1.0
|
|
CG
|
A:ASP116
|
3.4
|
7.0
|
1.0
|
|
C2
|
A:FUC201
|
3.4
|
6.8
|
1.0
|
|
CG
|
A:ASN108
|
3.6
|
6.4
|
1.0
|
|
OD2
|
A:ASP116
|
3.7
|
8.8
|
1.0
|
|
OD2
|
A:ASP118
|
3.8
|
6.9
|
1.0
|
|
CA
|
A:CA202
|
3.9
|
5.9
|
1.0
|
|
N
|
A:ASP118
|
4.2
|
8.2
|
1.0
|
|
ND2
|
A:ASN108
|
4.2
|
6.7
|
1.0
|
|
N
|
A:ASP109
|
4.2
|
5.7
|
1.0
|
|
O
|
A:HOH430
|
4.3
|
25.1
|
1.0
|
|
CB
|
A:ASP121
|
4.5
|
6.3
|
1.0
|
|
CA
|
A:ASN108
|
4.5
|
5.8
|
1.0
|
|
OD2
|
A:ASP109
|
4.5
|
7.0
|
1.0
|
|
CB
|
A:ASP118
|
4.6
|
7.7
|
1.0
|
|
CB
|
A:ASN108
|
4.6
|
6.0
|
1.0
|
|
N
|
A:ARG117
|
4.7
|
7.4
|
1.0
|
|
CB
|
A:ASP109
|
4.7
|
7.0
|
1.0
|
|
N
|
A:PHE119
|
4.7
|
6.2
|
1.0
|
|
C4
|
A:FUC201
|
4.8
|
7.2
|
1.0
|
|
C
|
A:ASN108
|
4.8
|
6.0
|
1.0
|
|
O
|
A:HOH435
|
4.8
|
16.1
|
1.0
|
|
CA
|
A:ASP118
|
4.8
|
6.5
|
1.0
|
|
CB
|
A:ASP116
|
4.8
|
8.7
|
1.0
|
|
O
|
A:ASP109
|
4.9
|
7.8
|
1.0
|
|
C1
|
A:FUC201
|
4.9
|
11.1
|
1.0
|
|
CG
|
A:ASP109
|
4.9
|
6.8
|
1.0
|
|
N
|
A:ASP116
|
4.9
|
8.3
|
1.0
|
|
OD1
|
A:ASN120
|
4.9
|
6.2
|
1.0
|
|
O4
|
A:FUC201
|
5.0
|
6.7
|
1.0
|
|
Calcium binding site 3 out
of 4 in 7f9g
Go back to
Calcium Binding Sites List in 7f9g
Calcium binding site 3 out
of 4 in the Thrombocorticin in Complex with CA2+ and Fucose
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Thrombocorticin in Complex with CA2+ and Fucose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca202
b:11.2
occ:1.00
|
OD1
|
B:ASP121
|
2.3
|
11.3
|
1.0
|
|
OD1
|
B:ASN120
|
2.4
|
9.9
|
1.0
|
|
OXT
|
A:GLY132
|
2.4
|
13.9
|
1.0
|
|
O
|
B:GLN26
|
2.4
|
11.0
|
1.0
|
|
OD2
|
B:ASP118
|
2.5
|
12.9
|
0.5
|
|
O4
|
B:FUC201
|
2.5
|
15.4
|
1.0
|
|
O3
|
B:FUC201
|
2.7
|
23.5
|
1.0
|
|
C
|
A:GLY132
|
3.4
|
19.7
|
1.0
|
|
CG
|
B:ASP118
|
3.4
|
8.9
|
0.5
|
|
CG
|
B:ASN120
|
3.4
|
8.1
|
1.0
|
|
C3
|
B:FUC201
|
3.5
|
22.8
|
1.0
|
|
CG
|
B:ASP121
|
3.5
|
7.7
|
1.0
|
|
C4
|
B:FUC201
|
3.5
|
28.5
|
1.0
|
|
O
|
A:GLY132
|
3.6
|
19.8
|
1.0
|
|
C
|
B:GLN26
|
3.6
|
9.3
|
1.0
|
|
OD1
|
B:ASP118
|
3.7
|
12.2
|
0.5
|
|
ND2
|
B:ASN120
|
3.8
|
9.6
|
1.0
|
|
C2
|
B:FUC201
|
3.8
|
16.3
|
1.0
|
|
CA
|
B:CA203
|
4.1
|
17.0
|
1.0
|
|
CB
|
B:GLN26
|
4.1
|
8.2
|
1.0
|
|
CA
|
B:ASP121
|
4.1
|
6.8
|
1.0
|
|
N
|
B:ASP121
|
4.2
|
6.5
|
1.0
|
|
OD2
|
B:ASP121
|
4.3
|
9.5
|
1.0
|
|
C
|
B:ASN120
|
4.4
|
6.4
|
1.0
|
|
CB
|
B:ASP121
|
4.4
|
7.2
|
1.0
|
|
O2
|
B:FUC201
|
4.5
|
17.5
|
1.0
|
|
CA
|
B:GLN26
|
4.5
|
7.2
|
1.0
|
|
OD1
|
B:ASP116
|
4.6
|
21.8
|
1.0
|
|
N
|
B:SER27
|
4.6
|
9.3
|
1.0
|
|
O
|
B:ASN120
|
4.6
|
7.4
|
1.0
|
|
CB
|
B:ASP118
|
4.6
|
11.1
|
0.5
|
|
CA
|
B:SER27
|
4.7
|
9.8
|
1.0
|
|
OD2
|
B:ASP118
|
4.7
|
13.7
|
0.5
|
|
CA
|
A:GLY132
|
4.7
|
22.8
|
1.0
|
|
CB
|
B:SER27
|
4.7
|
10.3
|
1.0
|
|
CB
|
B:ASN120
|
4.7
|
7.0
|
1.0
|
|
CB
|
B:ASP118
|
4.7
|
10.9
|
0.5
|
|
C5
|
B:FUC201
|
4.8
|
29.7
|
1.0
|
|
CA
|
B:ASN120
|
5.0
|
7.1
|
1.0
|
|
Calcium binding site 4 out
of 4 in 7f9g
Go back to
Calcium Binding Sites List in 7f9g
Calcium binding site 4 out
of 4 in the Thrombocorticin in Complex with CA2+ and Fucose
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Thrombocorticin in Complex with CA2+ and Fucose within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca203
b:17.0
occ:1.00
|
OD2
|
B:ASP116
|
2.3
|
20.5
|
1.0
|
|
OD2
|
B:ASP121
|
2.3
|
9.5
|
1.0
|
|
O
|
B:HOH354
|
2.4
|
14.1
|
1.0
|
|
OD1
|
B:ASP118
|
2.4
|
12.2
|
0.5
|
|
O2
|
B:FUC201
|
2.6
|
17.5
|
1.0
|
|
O3
|
B:FUC201
|
2.7
|
23.5
|
1.0
|
|
OD1
|
B:ASN108
|
2.7
|
12.7
|
1.0
|
|
OD1
|
B:ASP121
|
2.9
|
11.3
|
1.0
|
|
CG
|
B:ASP121
|
3.0
|
7.7
|
1.0
|
|
CG
|
B:ASP118
|
3.3
|
8.9
|
0.5
|
|
CG
|
B:ASP116
|
3.4
|
19.8
|
1.0
|
|
C2
|
B:FUC201
|
3.4
|
16.3
|
1.0
|
|
C3
|
B:FUC201
|
3.5
|
22.8
|
1.0
|
|
OD2
|
B:ASP118
|
3.6
|
12.9
|
0.5
|
|
OD1
|
B:ASP116
|
3.8
|
21.8
|
1.0
|
|
CG
|
B:ASN108
|
3.8
|
9.1
|
1.0
|
|
CA
|
B:CA202
|
4.1
|
11.2
|
1.0
|
|
N
|
B:ASP109
|
4.2
|
7.0
|
1.0
|
|
N
|
B:ASP118
|
4.3
|
10.3
|
0.5
|
|
N
|
B:ARG117
|
4.4
|
12.4
|
0.5
|
|
N
|
B:ARG117
|
4.4
|
12.4
|
0.5
|
|
N
|
B:ASP116
|
4.4
|
25.3
|
1.0
|
|
N
|
B:ASP118
|
4.4
|
10.1
|
0.5
|
|
CB
|
B:ASP121
|
4.5
|
7.2
|
1.0
|
|
CB
|
B:ASP109
|
4.5
|
7.5
|
1.0
|
|
CA
|
B:ASN108
|
4.5
|
7.0
|
1.0
|
|
ND2
|
B:ASN108
|
4.6
|
11.4
|
1.0
|
|
CB
|
B:ASP116
|
4.7
|
22.9
|
1.0
|
|
CB
|
B:ASN108
|
4.7
|
8.2
|
1.0
|
|
CB
|
B:ASP118
|
4.7
|
11.1
|
0.5
|
|
O
|
B:HOH422
|
4.7
|
26.4
|
1.0
|
|
O
|
B:ASP109
|
4.7
|
8.9
|
1.0
|
|
C
|
B:ASN108
|
4.8
|
7.5
|
1.0
|
|
CB
|
B:ASP118
|
4.8
|
10.9
|
0.5
|
|
OD2
|
B:ASP109
|
4.8
|
12.3
|
1.0
|
|
CA
|
B:ASP116
|
4.8
|
21.4
|
1.0
|
|
C
|
B:ASP116
|
4.8
|
13.2
|
1.0
|
|
C4
|
B:FUC201
|
4.9
|
28.5
|
1.0
|
|
C1
|
B:FUC201
|
4.9
|
25.2
|
1.0
|
|
CG
|
B:ASP109
|
4.9
|
8.4
|
1.0
|
|
CA
|
B:ASP109
|
4.9
|
7.8
|
1.0
|
|
N
|
B:PHE119
|
4.9
|
8.0
|
1.0
|
|
OD1
|
B:ASN120
|
4.9
|
9.9
|
1.0
|
|
Reference:
H.Kageyama,
K.Onodera,
R.Sakai,
Y.Tanaka.
Crystal Structure of Thrombocorticin in Complex with CA2+ and Fucose To Be Published.
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