Calcium in PDB 7p1v: Apo Structure of Kdnase From Trichophyton Rubrum
Protein crystallography data
The structure of Apo Structure of Kdnase From Trichophyton Rubrum, PDB code: 7p1v
was solved by
T.M.Gloster,
S.A.Mcmahon,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
47.36 /
1.47
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
49.03,
180.85,
98.34,
90,
103.77,
90
|
|
R / Rfree (%)
|
17.4 /
22.2
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Apo Structure of Kdnase From Trichophyton Rubrum
(pdb code 7p1v). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Apo Structure of Kdnase From Trichophyton Rubrum, PDB code: 7p1v:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 7p1v
Go back to
Calcium Binding Sites List in 7p1v
Calcium binding site 1 out
of 4 in the Apo Structure of Kdnase From Trichophyton Rubrum
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Apo Structure of Kdnase From Trichophyton Rubrum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca502
b:23.1
occ:1.00
|
OD1
|
A:ASP90
|
2.6
|
22.9
|
1.0
|
|
OD1
|
A:ASN92
|
2.7
|
22.4
|
1.0
|
|
O
|
A:HIS123
|
2.7
|
18.1
|
1.0
|
|
O
|
A:GLY121
|
2.9
|
21.2
|
1.0
|
|
O
|
A:GLY119
|
3.0
|
26.7
|
1.0
|
|
O
|
A:ILE91
|
3.4
|
15.8
|
1.0
|
|
C
|
A:GLY119
|
3.6
|
20.1
|
1.0
|
|
N
|
A:HIS123
|
3.7
|
20.2
|
1.0
|
|
O
|
A:THR120
|
3.7
|
21.1
|
1.0
|
|
CG
|
A:ASP90
|
3.7
|
20.9
|
1.0
|
|
N
|
A:ILE91
|
3.7
|
15.4
|
1.0
|
|
C
|
A:HIS123
|
3.8
|
17.1
|
1.0
|
|
O
|
A:HOH689
|
3.8
|
27.2
|
1.0
|
|
CD1
|
A:TRP125
|
3.8
|
20.2
|
1.0
|
|
C
|
A:GLY121
|
3.9
|
21.6
|
1.0
|
|
CG
|
A:ASN92
|
3.9
|
18.8
|
1.0
|
|
C
|
A:ILE91
|
3.9
|
16.3
|
1.0
|
|
C
|
A:PRO122
|
4.1
|
21.4
|
1.0
|
|
O
|
A:HOH638
|
4.1
|
79.1
|
1.0
|
|
CA
|
A:GLY119
|
4.1
|
16.9
|
1.0
|
|
NE1
|
A:TRP125
|
4.2
|
18.8
|
1.0
|
|
CA
|
A:ASP90
|
4.2
|
16.3
|
1.0
|
|
C
|
A:THR120
|
4.2
|
22.4
|
1.0
|
|
C
|
A:ASP90
|
4.2
|
17.2
|
1.0
|
|
CA
|
A:HIS123
|
4.3
|
19.6
|
1.0
|
|
CA
|
A:PRO122
|
4.4
|
22.9
|
1.0
|
|
N
|
A:THR120
|
4.5
|
21.3
|
1.0
|
|
CA
|
A:ILE91
|
4.5
|
15.1
|
1.0
|
|
OD2
|
A:ASP90
|
4.5
|
26.0
|
1.0
|
|
N
|
A:PRO122
|
4.5
|
20.9
|
1.0
|
|
N
|
A:ASN92
|
4.6
|
16.3
|
1.0
|
|
CB
|
A:ASP90
|
4.6
|
18.9
|
1.0
|
|
ND2
|
A:ASN92
|
4.6
|
24.9
|
1.0
|
|
O
|
A:PRO122
|
4.7
|
20.6
|
1.0
|
|
N
|
A:GLY121
|
4.7
|
22.9
|
1.0
|
|
CA
|
A:ASN92
|
4.8
|
15.7
|
1.0
|
|
CA
|
A:GLY121
|
4.9
|
22.8
|
1.0
|
|
CB
|
A:HIS123
|
4.9
|
17.8
|
1.0
|
|
N
|
A:THR124
|
4.9
|
16.5
|
1.0
|
|
CA
|
A:THR120
|
5.0
|
25.2
|
1.0
|
|
CB
|
A:ASN92
|
5.0
|
18.8
|
1.0
|
|
Calcium binding site 2 out
of 4 in 7p1v
Go back to
Calcium Binding Sites List in 7p1v
Calcium binding site 2 out
of 4 in the Apo Structure of Kdnase From Trichophyton Rubrum
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Apo Structure of Kdnase From Trichophyton Rubrum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca502
b:20.3
occ:1.00
|
OD1
|
B:ASP90
|
2.6
|
20.5
|
1.0
|
|
OD1
|
B:ASN92
|
2.6
|
20.3
|
1.0
|
|
O
|
B:HIS123
|
2.7
|
16.4
|
1.0
|
|
O
|
B:GLY121
|
2.9
|
19.1
|
1.0
|
|
O
|
B:GLY119
|
3.0
|
22.8
|
1.0
|
|
O
|
B:ILE91
|
3.3
|
15.6
|
1.0
|
|
N
|
B:ILE91
|
3.7
|
14.6
|
1.0
|
|
C
|
B:GLY119
|
3.7
|
17.2
|
1.0
|
|
O
|
B:HOH703
|
3.7
|
35.2
|
1.0
|
|
O
|
B:THR120
|
3.7
|
19.4
|
0.5
|
|
CG
|
B:ASP90
|
3.7
|
18.7
|
1.0
|
|
N
|
B:HIS123
|
3.7
|
18.5
|
1.0
|
|
O
|
B:THR120
|
3.8
|
20.5
|
0.5
|
|
C
|
B:HIS123
|
3.8
|
15.0
|
1.0
|
|
C
|
B:ILE91
|
3.8
|
15.7
|
1.0
|
|
CG
|
B:ASN92
|
3.9
|
19.0
|
1.0
|
|
C
|
B:GLY121
|
3.9
|
19.2
|
1.0
|
|
CD1
|
B:TRP125
|
3.9
|
16.7
|
1.0
|
|
C
|
B:PRO122
|
4.1
|
19.1
|
1.0
|
|
CA
|
B:GLY119
|
4.2
|
16.4
|
1.0
|
|
C
|
B:ASP90
|
4.2
|
14.9
|
1.0
|
|
CA
|
B:ASP90
|
4.2
|
14.2
|
1.0
|
|
C
|
B:THR120
|
4.2
|
18.8
|
0.5
|
|
C
|
B:THR120
|
4.3
|
19.8
|
0.5
|
|
NE1
|
B:TRP125
|
4.3
|
16.0
|
1.0
|
|
CA
|
B:HIS123
|
4.3
|
16.3
|
1.0
|
|
O
|
B:HOH770
|
4.4
|
44.8
|
1.0
|
|
CA
|
B:PRO122
|
4.4
|
17.7
|
1.0
|
|
CA
|
B:ILE91
|
4.4
|
14.8
|
1.0
|
|
N
|
B:ASN92
|
4.5
|
14.1
|
1.0
|
|
N
|
B:THR120
|
4.5
|
19.3
|
0.5
|
|
N
|
B:PRO122
|
4.5
|
18.9
|
1.0
|
|
N
|
B:THR120
|
4.5
|
18.5
|
0.5
|
|
CB
|
B:ASP90
|
4.6
|
16.7
|
1.0
|
|
OD2
|
B:ASP90
|
4.6
|
23.5
|
1.0
|
|
ND2
|
B:ASN92
|
4.6
|
24.4
|
1.0
|
|
N
|
B:GLY121
|
4.7
|
18.6
|
1.0
|
|
O
|
B:PRO122
|
4.7
|
18.4
|
1.0
|
|
CA
|
B:ASN92
|
4.7
|
15.0
|
1.0
|
|
CA
|
B:GLY121
|
4.8
|
18.7
|
1.0
|
|
CB
|
B:ASN92
|
4.9
|
17.4
|
1.0
|
|
N
|
B:THR124
|
4.9
|
15.4
|
1.0
|
|
CB
|
B:HIS123
|
5.0
|
14.8
|
1.0
|
|
CA
|
B:THR120
|
5.0
|
18.3
|
0.5
|
|
CA
|
B:THR120
|
5.0
|
19.9
|
0.5
|
|
Calcium binding site 3 out
of 4 in 7p1v
Go back to
Calcium Binding Sites List in 7p1v
Calcium binding site 3 out
of 4 in the Apo Structure of Kdnase From Trichophyton Rubrum
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Apo Structure of Kdnase From Trichophyton Rubrum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca503
b:22.5
occ:1.00
|
OD1
|
C:ASP90
|
2.6
|
21.1
|
1.0
|
|
OD1
|
C:ASN92
|
2.7
|
20.9
|
1.0
|
|
O
|
C:HIS123
|
2.7
|
17.8
|
1.0
|
|
O
|
C:GLY121
|
2.8
|
21.8
|
1.0
|
|
O
|
C:GLY119
|
2.9
|
24.9
|
1.0
|
|
O
|
C:ILE91
|
3.4
|
16.3
|
1.0
|
|
C
|
C:GLY119
|
3.6
|
22.4
|
1.0
|
|
N
|
C:HIS123
|
3.6
|
20.1
|
1.0
|
|
CG
|
C:ASP90
|
3.7
|
21.0
|
1.0
|
|
O
|
C:THR120
|
3.7
|
22.2
|
1.0
|
|
C
|
C:HIS123
|
3.8
|
16.5
|
1.0
|
|
N
|
C:ILE91
|
3.8
|
15.2
|
1.0
|
|
C
|
C:GLY121
|
3.8
|
21.7
|
1.0
|
|
O
|
C:HOH680
|
3.8
|
26.8
|
1.0
|
|
CD1
|
C:TRP125
|
3.9
|
18.1
|
1.0
|
|
CG
|
C:ASN92
|
3.9
|
15.7
|
1.0
|
|
C
|
C:ILE91
|
4.0
|
15.3
|
1.0
|
|
C
|
C:PRO122
|
4.0
|
20.4
|
1.0
|
|
CA
|
C:GLY119
|
4.2
|
20.8
|
1.0
|
|
O
|
C:HOH629
|
4.2
|
50.4
|
1.0
|
|
C
|
C:THR120
|
4.2
|
21.6
|
1.0
|
|
CA
|
C:ASP90
|
4.2
|
17.5
|
1.0
|
|
NE1
|
C:TRP125
|
4.2
|
20.3
|
1.0
|
|
CA
|
C:HIS123
|
4.2
|
16.8
|
1.0
|
|
C
|
C:ASP90
|
4.3
|
15.8
|
1.0
|
|
CA
|
C:PRO122
|
4.3
|
19.5
|
1.0
|
|
N
|
C:PRO122
|
4.5
|
20.1
|
1.0
|
|
N
|
C:THR120
|
4.5
|
21.4
|
1.0
|
|
OD2
|
C:ASP90
|
4.5
|
23.6
|
1.0
|
|
CB
|
C:ASP90
|
4.6
|
17.4
|
1.0
|
|
CA
|
C:ILE91
|
4.6
|
14.4
|
1.0
|
|
ND2
|
C:ASN92
|
4.6
|
23.8
|
1.0
|
|
O
|
C:PRO122
|
4.6
|
21.3
|
1.0
|
|
N
|
C:GLY121
|
4.7
|
23.2
|
1.0
|
|
N
|
C:ASN92
|
4.7
|
15.8
|
1.0
|
|
CA
|
C:GLY121
|
4.8
|
22.9
|
1.0
|
|
O
|
C:HOH626
|
4.9
|
35.4
|
1.0
|
|
CB
|
C:HIS123
|
4.9
|
16.2
|
1.0
|
|
CA
|
C:ASN92
|
4.9
|
15.4
|
1.0
|
|
N
|
C:THR124
|
4.9
|
15.6
|
1.0
|
|
CA
|
C:THR120
|
4.9
|
23.1
|
1.0
|
|
Calcium binding site 4 out
of 4 in 7p1v
Go back to
Calcium Binding Sites List in 7p1v
Calcium binding site 4 out
of 4 in the Apo Structure of Kdnase From Trichophyton Rubrum
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Apo Structure of Kdnase From Trichophyton Rubrum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca502
b:22.1
occ:1.00
|
OD1
|
D:ASP90
|
2.6
|
19.6
|
1.0
|
|
OD1
|
D:ASN92
|
2.7
|
20.2
|
1.0
|
|
O
|
D:HIS123
|
2.7
|
16.8
|
1.0
|
|
O
|
D:GLY121
|
2.8
|
21.2
|
1.0
|
|
O
|
D:GLY119
|
3.0
|
24.4
|
1.0
|
|
O
|
D:ILE91
|
3.3
|
16.2
|
1.0
|
|
N
|
D:ILE91
|
3.7
|
16.0
|
1.0
|
|
C
|
D:GLY119
|
3.7
|
21.3
|
1.0
|
|
N
|
D:HIS123
|
3.7
|
19.0
|
1.0
|
|
O
|
D:THR120
|
3.7
|
21.9
|
0.5
|
|
CG
|
D:ASP90
|
3.7
|
20.5
|
1.0
|
|
C
|
D:HIS123
|
3.8
|
17.3
|
1.0
|
|
O
|
D:THR120
|
3.8
|
21.7
|
0.5
|
|
C
|
D:GLY121
|
3.8
|
18.8
|
1.0
|
|
C
|
D:ILE91
|
3.9
|
15.8
|
1.0
|
|
CG
|
D:ASN92
|
3.9
|
15.8
|
1.0
|
|
CD1
|
D:TRP125
|
3.9
|
16.7
|
1.0
|
|
C
|
D:PRO122
|
4.1
|
18.9
|
1.0
|
|
CA
|
D:ASP90
|
4.2
|
17.5
|
1.0
|
|
C
|
D:ASP90
|
4.2
|
17.4
|
1.0
|
|
CA
|
D:GLY119
|
4.2
|
21.3
|
1.0
|
|
C
|
D:THR120
|
4.2
|
21.4
|
0.5
|
|
C
|
D:THR120
|
4.2
|
21.9
|
0.5
|
|
CA
|
D:HIS123
|
4.3
|
17.1
|
1.0
|
|
NE1
|
D:TRP125
|
4.3
|
17.8
|
1.0
|
|
CA
|
D:PRO122
|
4.4
|
20.8
|
1.0
|
|
CA
|
D:ILE91
|
4.5
|
15.2
|
1.0
|
|
N
|
D:PRO122
|
4.5
|
20.9
|
1.0
|
|
N
|
D:THR120
|
4.5
|
20.2
|
0.5
|
|
N
|
D:THR120
|
4.5
|
20.3
|
0.5
|
|
N
|
D:ASN92
|
4.5
|
14.8
|
1.0
|
|
CB
|
D:ASP90
|
4.6
|
18.2
|
1.0
|
|
OD2
|
D:ASP90
|
4.6
|
25.9
|
1.0
|
|
ND2
|
D:ASN92
|
4.6
|
23.1
|
1.0
|
|
N
|
D:GLY121
|
4.6
|
21.4
|
1.0
|
|
O
|
D:PRO122
|
4.7
|
18.9
|
1.0
|
|
CA
|
D:GLY121
|
4.8
|
20.2
|
1.0
|
|
CA
|
D:ASN92
|
4.8
|
13.5
|
1.0
|
|
CB
|
D:HIS123
|
4.9
|
19.0
|
1.0
|
|
N
|
D:THR124
|
4.9
|
16.0
|
1.0
|
|
CA
|
D:THR120
|
5.0
|
22.6
|
0.5
|
|
CB
|
D:ASN92
|
5.0
|
14.8
|
1.0
|
|
CA
|
D:THR120
|
5.0
|
23.0
|
0.5
|
|
Reference:
T.M.Gloster,
S.A.Mcmahon.
Apo Structure of Kdnase From Trichophyton Rubrum To Be Published.
Page generated: Wed Jul 9 23:59:21 2025
|
