Calcium in PDB 1wrl: Crystal Structure of the N-Terminal Domain of Human Cardiac Troponin C in Complex with Trifluoperazine (Monoclinic Crystal Form)
Protein crystallography data
The structure of Crystal Structure of the N-Terminal Domain of Human Cardiac Troponin C in Complex with Trifluoperazine (Monoclinic Crystal Form), PDB code: 1wrl
was solved by
S.Takeda,
T.Igarashi,
Y.Oishi,
H.Mori,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
2.60
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
48.930,
67.460,
90.280,
90.00,
96.75,
90.00
|
R / Rfree (%)
|
24 /
27.3
|
Other elements in 1wrl:
The structure of Crystal Structure of the N-Terminal Domain of Human Cardiac Troponin C in Complex with Trifluoperazine (Monoclinic Crystal Form) also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of the N-Terminal Domain of Human Cardiac Troponin C in Complex with Trifluoperazine (Monoclinic Crystal Form)
(pdb code 1wrl). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
Crystal Structure of the N-Terminal Domain of Human Cardiac Troponin C in Complex with Trifluoperazine (Monoclinic Crystal Form), PDB code: 1wrl:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 1wrl
Go back to
Calcium Binding Sites List in 1wrl
Calcium binding site 1 out
of 6 in the Crystal Structure of the N-Terminal Domain of Human Cardiac Troponin C in Complex with Trifluoperazine (Monoclinic Crystal Form)
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 the N-Terminal Domain of Human Cardiac Troponin C in Complex with Trifluoperazine (Monoclinic Crystal Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca101
b:30.2
occ:1.00
|
OD1
|
A:ASP67
|
2.2
|
30.7
|
1.0
|
OD2
|
A:ASP65
|
2.3
|
32.0
|
1.0
|
O
|
A:THR71
|
2.4
|
27.7
|
1.0
|
O
|
A:HOH206
|
2.4
|
32.5
|
1.0
|
OG
|
A:SER69
|
2.4
|
34.0
|
1.0
|
OE2
|
A:GLU76
|
2.5
|
25.1
|
1.0
|
OE1
|
A:GLU76
|
2.5
|
31.6
|
1.0
|
CD
|
A:GLU76
|
2.8
|
29.0
|
1.0
|
CG
|
A:ASP67
|
3.1
|
31.2
|
1.0
|
OD2
|
A:ASP67
|
3.3
|
31.6
|
1.0
|
CG
|
A:ASP65
|
3.5
|
31.5
|
1.0
|
C
|
A:THR71
|
3.5
|
25.6
|
1.0
|
CB
|
A:SER69
|
3.6
|
29.9
|
1.0
|
N
|
A:SER69
|
4.0
|
29.1
|
1.0
|
OG1
|
A:THR71
|
4.2
|
24.8
|
1.0
|
N
|
A:THR71
|
4.2
|
23.4
|
1.0
|
OD1
|
A:ASP65
|
4.3
|
27.8
|
1.0
|
CA
|
A:ASP65
|
4.3
|
29.8
|
1.0
|
CG
|
A:GLU76
|
4.3
|
27.1
|
1.0
|
CA
|
A:SER69
|
4.4
|
29.5
|
1.0
|
OD1
|
A:ASP73
|
4.4
|
36.9
|
1.0
|
N
|
A:VAL72
|
4.4
|
27.8
|
1.0
|
CB
|
A:ASP65
|
4.4
|
27.9
|
1.0
|
N
|
A:ASP73
|
4.4
|
30.1
|
1.0
|
CA
|
A:VAL72
|
4.5
|
27.1
|
1.0
|
CA
|
A:THR71
|
4.5
|
24.6
|
1.0
|
CB
|
A:ASP67
|
4.5
|
31.3
|
1.0
|
O
|
A:HOH219
|
4.6
|
35.6
|
1.0
|
N
|
A:ASP67
|
4.6
|
33.0
|
1.0
|
C
|
A:ASP65
|
4.7
|
31.9
|
1.0
|
N
|
A:GLY70
|
4.7
|
26.3
|
1.0
|
N
|
A:GLY68
|
4.8
|
29.4
|
1.0
|
C
|
A:SER69
|
4.8
|
27.7
|
1.0
|
CG
|
A:ASP73
|
4.9
|
34.3
|
1.0
|
C
|
A:VAL72
|
4.9
|
28.9
|
1.0
|
CA
|
A:ASP67
|
5.0
|
31.3
|
1.0
|
CB
|
A:THR71
|
5.0
|
24.0
|
1.0
|
|
Calcium binding site 2 out
of 6 in 1wrl
Go back to
Calcium Binding Sites List in 1wrl
Calcium binding site 2 out
of 6 in the Crystal Structure of the N-Terminal Domain of Human Cardiac Troponin C in Complex with Trifluoperazine (Monoclinic Crystal Form)
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 the N-Terminal Domain of Human Cardiac Troponin C in Complex with Trifluoperazine (Monoclinic Crystal Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca102
b:24.6
occ:1.00
|
OD1
|
B:ASP67
|
2.1
|
31.1
|
1.0
|
OD2
|
B:ASP65
|
2.3
|
26.5
|
1.0
|
OE1
|
B:GLU76
|
2.3
|
28.0
|
1.0
|
O
|
B:THR71
|
2.3
|
29.2
|
1.0
|
O
|
B:HOH214
|
2.5
|
30.6
|
1.0
|
OE2
|
B:GLU76
|
2.5
|
26.9
|
1.0
|
OG
|
B:SER69
|
2.6
|
26.0
|
1.0
|
CD
|
B:GLU76
|
2.7
|
31.5
|
1.0
|
CG
|
B:ASP67
|
3.1
|
32.3
|
1.0
|
OD2
|
B:ASP67
|
3.4
|
30.5
|
1.0
|
C
|
B:THR71
|
3.5
|
27.8
|
1.0
|
CG
|
B:ASP65
|
3.6
|
29.2
|
1.0
|
CB
|
B:SER69
|
3.7
|
26.4
|
1.0
|
N
|
B:SER69
|
4.1
|
27.3
|
1.0
|
CA
|
B:ASP65
|
4.1
|
28.8
|
1.0
|
OG1
|
B:THR71
|
4.2
|
28.9
|
1.0
|
N
|
B:THR71
|
4.2
|
27.6
|
1.0
|
CG
|
B:GLU76
|
4.2
|
29.9
|
1.0
|
CB
|
B:ASP67
|
4.4
|
28.0
|
1.0
|
CA
|
B:SER69
|
4.4
|
28.2
|
1.0
|
N
|
B:ASP67
|
4.4
|
30.5
|
1.0
|
CB
|
B:ASP65
|
4.4
|
26.3
|
1.0
|
N
|
B:VAL72
|
4.4
|
25.9
|
1.0
|
CA
|
B:VAL72
|
4.4
|
26.3
|
1.0
|
OD1
|
B:ASP65
|
4.5
|
29.5
|
1.0
|
CA
|
B:THR71
|
4.5
|
27.0
|
1.0
|
C
|
B:ASP65
|
4.5
|
29.9
|
1.0
|
OD1
|
B:ASP73
|
4.6
|
36.6
|
1.0
|
N
|
B:ASP73
|
4.6
|
25.0
|
1.0
|
N
|
B:GLY70
|
4.7
|
29.1
|
1.0
|
N
|
B:GLU66
|
4.7
|
30.8
|
1.0
|
N
|
B:GLY68
|
4.8
|
25.8
|
1.0
|
C
|
B:SER69
|
4.8
|
28.0
|
1.0
|
CA
|
B:ASP67
|
4.8
|
28.2
|
1.0
|
C
|
B:ASP67
|
4.9
|
28.9
|
1.0
|
CG
|
B:ASP73
|
4.9
|
30.1
|
1.0
|
C
|
B:VAL72
|
5.0
|
27.1
|
1.0
|
CB
|
B:THR71
|
5.0
|
27.2
|
1.0
|
|
Calcium binding site 3 out
of 6 in 1wrl
Go back to
Calcium Binding Sites List in 1wrl
Calcium binding site 3 out
of 6 in the Crystal Structure of the N-Terminal Domain of Human Cardiac Troponin C in Complex with Trifluoperazine (Monoclinic Crystal Form)
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 the N-Terminal Domain of Human Cardiac Troponin C in Complex with Trifluoperazine (Monoclinic Crystal Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca103
b:48.8
occ:1.00
|
OG
|
C:SER69
|
2.1
|
56.7
|
1.0
|
OD2
|
C:ASP65
|
2.2
|
58.0
|
1.0
|
OE2
|
C:GLU76
|
2.4
|
50.1
|
1.0
|
OE1
|
C:GLU76
|
2.4
|
50.0
|
1.0
|
O
|
C:THR71
|
2.5
|
47.2
|
1.0
|
OD1
|
C:ASP67
|
2.5
|
68.6
|
1.0
|
O
|
C:HOH218
|
2.5
|
34.4
|
1.0
|
CD
|
C:GLU76
|
2.8
|
47.5
|
1.0
|
CG
|
C:ASP65
|
3.3
|
58.4
|
1.0
|
CB
|
C:SER69
|
3.3
|
54.6
|
1.0
|
CG
|
C:ASP67
|
3.6
|
65.6
|
1.0
|
C
|
C:THR71
|
3.7
|
46.8
|
1.0
|
N
|
C:SER69
|
3.9
|
55.7
|
1.0
|
OD1
|
C:ASP65
|
4.0
|
58.7
|
1.0
|
CA
|
C:ASP65
|
4.1
|
58.5
|
1.0
|
CA
|
C:SER69
|
4.1
|
54.2
|
1.0
|
OD2
|
C:ASP67
|
4.2
|
64.9
|
1.0
|
CB
|
C:ASP65
|
4.2
|
57.6
|
1.0
|
CG
|
C:GLU76
|
4.3
|
44.8
|
1.0
|
N
|
C:THR71
|
4.3
|
49.3
|
1.0
|
N
|
C:ASP67
|
4.4
|
63.9
|
1.0
|
N
|
C:GLU66
|
4.4
|
63.4
|
1.0
|
N
|
C:GLY70
|
4.5
|
49.6
|
1.0
|
OG1
|
C:THR71
|
4.5
|
47.1
|
1.0
|
CA
|
C:THR71
|
4.6
|
47.8
|
1.0
|
N
|
C:VAL72
|
4.6
|
44.8
|
1.0
|
C
|
C:ASP65
|
4.6
|
61.4
|
1.0
|
CA
|
C:VAL72
|
4.6
|
42.6
|
1.0
|
C
|
C:SER69
|
4.6
|
52.8
|
1.0
|
N
|
C:ASP73
|
4.8
|
45.4
|
1.0
|
C
|
C:ASP67
|
4.8
|
61.7
|
1.0
|
CB
|
C:ASP67
|
4.9
|
64.3
|
1.0
|
CA
|
C:ASP67
|
4.9
|
62.9
|
1.0
|
N
|
C:GLY68
|
4.9
|
60.0
|
1.0
|
|
Calcium binding site 4 out
of 6 in 1wrl
Go back to
Calcium Binding Sites List in 1wrl
Calcium binding site 4 out
of 6 in the Crystal Structure of the N-Terminal Domain of Human Cardiac Troponin C in Complex with Trifluoperazine (Monoclinic Crystal Form)
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 the N-Terminal Domain of Human Cardiac Troponin C in Complex with Trifluoperazine (Monoclinic Crystal Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca104
b:52.6
occ:1.00
|
O
|
D:THR71
|
2.3
|
65.9
|
1.0
|
OE1
|
D:GLU76
|
2.3
|
45.5
|
1.0
|
OG
|
D:SER69
|
2.3
|
76.0
|
1.0
|
OD1
|
D:ASP67
|
2.4
|
78.8
|
1.0
|
OD2
|
D:ASP65
|
2.6
|
64.5
|
1.0
|
OE2
|
D:GLU76
|
2.7
|
40.3
|
1.0
|
CD
|
D:GLU76
|
2.9
|
43.9
|
1.0
|
C
|
D:THR71
|
3.2
|
64.3
|
1.0
|
CG
|
D:ASP67
|
3.4
|
76.9
|
1.0
|
CG
|
D:ASP65
|
3.4
|
64.8
|
1.0
|
OG1
|
D:THR71
|
3.5
|
69.3
|
1.0
|
CB
|
D:SER69
|
3.7
|
74.3
|
1.0
|
OD2
|
D:ASP67
|
3.8
|
76.2
|
1.0
|
N
|
D:VAL72
|
3.9
|
59.6
|
1.0
|
OD1
|
D:ASP65
|
4.0
|
64.6
|
1.0
|
CA
|
D:VAL72
|
4.0
|
54.2
|
1.0
|
CA
|
D:THR71
|
4.1
|
67.1
|
1.0
|
N
|
D:THR71
|
4.2
|
68.2
|
1.0
|
N
|
D:ASP73
|
4.3
|
46.2
|
1.0
|
CG
|
D:GLU76
|
4.4
|
41.7
|
1.0
|
CB
|
D:ASP65
|
4.4
|
64.7
|
1.0
|
CB
|
D:THR71
|
4.4
|
68.2
|
1.0
|
N
|
D:SER69
|
4.5
|
74.6
|
1.0
|
CA
|
D:ASP65
|
4.5
|
66.5
|
1.0
|
C
|
D:VAL72
|
4.5
|
51.4
|
1.0
|
CA
|
D:SER69
|
4.6
|
73.8
|
1.0
|
O
|
D:HOH214
|
4.6
|
44.8
|
1.0
|
CB
|
D:ASP67
|
4.7
|
75.7
|
1.0
|
C
|
D:SER69
|
4.8
|
72.8
|
1.0
|
CG
|
D:ASP73
|
4.9
|
53.2
|
1.0
|
OD1
|
D:ASP73
|
5.0
|
55.2
|
1.0
|
|
Calcium binding site 5 out
of 6 in 1wrl
Go back to
Calcium Binding Sites List in 1wrl
Calcium binding site 5 out
of 6 in the Crystal Structure of the N-Terminal Domain of Human Cardiac Troponin C in Complex with Trifluoperazine (Monoclinic Crystal Form)
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 the N-Terminal Domain of Human Cardiac Troponin C in Complex with Trifluoperazine (Monoclinic Crystal Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca105
b:31.7
occ:1.00
|
OD1
|
E:ASP67
|
2.2
|
47.7
|
1.0
|
OE2
|
E:GLU76
|
2.3
|
37.1
|
1.0
|
O
|
E:THR71
|
2.3
|
27.4
|
1.0
|
OD2
|
E:ASP65
|
2.4
|
31.1
|
1.0
|
O
|
E:HOH215
|
2.5
|
32.3
|
1.0
|
OE1
|
E:GLU76
|
2.6
|
38.0
|
1.0
|
OG
|
E:SER69
|
2.6
|
31.4
|
1.0
|
CD
|
E:GLU76
|
2.8
|
36.9
|
1.0
|
CG
|
E:ASP67
|
3.3
|
40.7
|
1.0
|
C
|
E:THR71
|
3.5
|
25.8
|
1.0
|
OD2
|
E:ASP67
|
3.6
|
40.2
|
1.0
|
CG
|
E:ASP65
|
3.7
|
34.6
|
1.0
|
CB
|
E:SER69
|
3.7
|
32.5
|
1.0
|
N
|
E:SER69
|
4.1
|
34.8
|
1.0
|
OG1
|
E:THR71
|
4.2
|
29.5
|
1.0
|
N
|
E:THR71
|
4.2
|
26.4
|
1.0
|
CG
|
E:GLU76
|
4.3
|
35.3
|
1.0
|
CA
|
E:ASP65
|
4.3
|
33.0
|
1.0
|
N
|
E:VAL72
|
4.4
|
26.6
|
1.0
|
CA
|
E:THR71
|
4.4
|
26.8
|
1.0
|
CA
|
E:VAL72
|
4.4
|
27.9
|
1.0
|
CA
|
E:SER69
|
4.4
|
31.6
|
1.0
|
OD1
|
E:ASP65
|
4.5
|
31.2
|
1.0
|
N
|
E:ASP67
|
4.5
|
37.0
|
1.0
|
CB
|
E:ASP65
|
4.6
|
32.8
|
1.0
|
CB
|
E:ASP67
|
4.6
|
38.8
|
1.0
|
N
|
E:ASP73
|
4.6
|
32.8
|
1.0
|
N
|
E:GLY70
|
4.7
|
30.1
|
1.0
|
C
|
E:ASP65
|
4.8
|
33.4
|
1.0
|
OD1
|
E:ASP73
|
4.8
|
41.2
|
1.0
|
N
|
E:GLY68
|
4.8
|
37.7
|
1.0
|
N
|
E:GLU66
|
4.8
|
34.4
|
1.0
|
C
|
E:SER69
|
4.9
|
31.5
|
1.0
|
CB
|
E:THR71
|
4.9
|
27.2
|
1.0
|
CA
|
E:ASP67
|
4.9
|
36.8
|
1.0
|
C
|
E:ASP67
|
4.9
|
37.0
|
1.0
|
|
Calcium binding site 6 out
of 6 in 1wrl
Go back to
Calcium Binding Sites List in 1wrl
Calcium binding site 6 out
of 6 in the Crystal Structure of the N-Terminal Domain of Human Cardiac Troponin C in Complex with Trifluoperazine (Monoclinic Crystal Form)
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 the N-Terminal Domain of Human Cardiac Troponin C in Complex with Trifluoperazine (Monoclinic Crystal Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca106
b:57.7
occ:1.00
|
OD2
|
F:ASP67
|
2.3
|
89.4
|
1.0
|
OE1
|
F:GLU76
|
2.5
|
63.5
|
1.0
|
OE2
|
F:GLU76
|
2.5
|
63.9
|
1.0
|
O
|
F:THR71
|
2.6
|
73.0
|
1.0
|
OD2
|
F:ASP65
|
2.7
|
80.2
|
1.0
|
CD
|
F:GLU76
|
2.7
|
63.9
|
1.0
|
OG
|
F:SER69
|
2.9
|
73.9
|
1.0
|
CG
|
F:ASP67
|
3.0
|
87.9
|
1.0
|
OD1
|
F:ASP67
|
3.1
|
88.8
|
1.0
|
CG
|
F:ASP65
|
3.7
|
80.5
|
1.0
|
C
|
F:THR71
|
3.7
|
72.7
|
1.0
|
CB
|
F:SER69
|
4.0
|
77.4
|
1.0
|
CG
|
F:GLU76
|
4.2
|
60.7
|
1.0
|
CA
|
F:VAL72
|
4.2
|
69.0
|
1.0
|
CA
|
F:ASP65
|
4.3
|
78.9
|
1.0
|
N
|
F:ASP73
|
4.3
|
66.4
|
1.0
|
OD1
|
F:ASP65
|
4.4
|
78.1
|
1.0
|
N
|
F:VAL72
|
4.4
|
71.3
|
1.0
|
CB
|
F:ASP67
|
4.4
|
86.1
|
1.0
|
CB
|
F:ASP65
|
4.5
|
79.2
|
1.0
|
N
|
F:SER69
|
4.5
|
80.3
|
1.0
|
N
|
F:THR71
|
4.7
|
74.5
|
1.0
|
C
|
F:ASP65
|
4.7
|
80.8
|
1.0
|
C
|
F:VAL72
|
4.7
|
68.0
|
1.0
|
N
|
F:ASP67
|
4.7
|
83.6
|
1.0
|
N
|
F:GLY68
|
4.7
|
83.5
|
1.0
|
CG
|
F:ASP73
|
4.7
|
68.9
|
1.0
|
OG1
|
F:THR71
|
4.8
|
78.2
|
1.0
|
CA
|
F:THR71
|
4.8
|
74.0
|
1.0
|
OD1
|
F:ASP73
|
4.8
|
70.8
|
1.0
|
CA
|
F:SER69
|
4.8
|
78.8
|
1.0
|
C
|
F:ASP67
|
4.9
|
84.1
|
1.0
|
CA
|
F:ASP67
|
4.9
|
84.5
|
1.0
|
N
|
F:GLY70
|
4.9
|
78.1
|
1.0
|
OD2
|
F:ASP73
|
5.0
|
70.1
|
1.0
|
|
Reference:
S.Takeda,
T.Igarashi,
Y.Oishi,
H.Mori.
Crystal Structure of the N-Terminal Domain of Human Cardiac Troponin C in Complex with Trifluoperazine To Be Published.
Page generated: Fri Jul 12 07:16:51 2024
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