Calcium in PDB 1tcf: Crystal Structure of Calcium-Saturated Rabbit Skeletal Troponin C
Protein crystallography data
The structure of Crystal Structure of Calcium-Saturated Rabbit Skeletal Troponin C, PDB code: 1tcf
was solved by
J.Soman,
G.N.Phillips Jr.,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
1.90
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
32.100,
59.600,
48.000,
90.00,
101.10,
90.00
|
R / Rfree (%)
|
27.8 /
35.8
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Calcium-Saturated Rabbit Skeletal Troponin C
(pdb code 1tcf). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the
Crystal Structure of Calcium-Saturated Rabbit Skeletal Troponin C, PDB code: 1tcf:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
Calcium binding site 1 out
of 5 in 1tcf
Go back to
Calcium Binding Sites List in 1tcf
Calcium binding site 1 out
of 5 in the Crystal Structure of Calcium-Saturated Rabbit Skeletal Troponin C
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 Calcium-Saturated Rabbit Skeletal Troponin C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca160
b:8.0
occ:1.00
|
OD1
|
A:ASP29
|
2.3
|
7.8
|
1.0
|
OD1
|
A:ASP27
|
2.3
|
5.2
|
1.0
|
O
|
A:ASP33
|
2.5
|
14.4
|
1.0
|
O
|
A:HOH215
|
2.5
|
27.5
|
1.0
|
OE2
|
A:GLU38
|
2.5
|
8.2
|
1.0
|
OE1
|
A:GLU38
|
2.5
|
9.3
|
1.0
|
O
|
A:HOH182
|
2.7
|
13.8
|
1.0
|
CD
|
A:GLU38
|
2.9
|
2.4
|
1.0
|
CG
|
A:ASP29
|
3.3
|
9.8
|
1.0
|
CG
|
A:ASP27
|
3.5
|
12.4
|
1.0
|
C
|
A:ASP33
|
3.7
|
8.8
|
1.0
|
OD2
|
A:ASP29
|
3.9
|
12.9
|
1.0
|
O
|
A:HOH327
|
4.1
|
68.5
|
1.0
|
N
|
A:GLY31
|
4.1
|
10.4
|
1.0
|
O
|
A:HOH205
|
4.2
|
20.0
|
1.0
|
N
|
A:ASP29
|
4.2
|
13.2
|
1.0
|
OD1
|
A:ASP33
|
4.3
|
12.8
|
1.0
|
CA
|
A:ASP27
|
4.3
|
12.1
|
1.0
|
N
|
A:ASP33
|
4.3
|
10.7
|
1.0
|
OD2
|
A:ASP27
|
4.3
|
7.1
|
1.0
|
C
|
A:ASP27
|
4.3
|
13.7
|
1.0
|
CG
|
A:GLU38
|
4.4
|
2.4
|
1.0
|
CB
|
A:ASP27
|
4.4
|
8.6
|
1.0
|
CB
|
A:ASP29
|
4.5
|
8.9
|
1.0
|
CA
|
A:GLY31
|
4.5
|
5.3
|
1.0
|
CA
|
A:ILE34
|
4.6
|
4.6
|
1.0
|
N
|
A:ILE34
|
4.6
|
5.1
|
1.0
|
O
|
A:ASP27
|
4.6
|
16.4
|
1.0
|
N
|
A:ALA28
|
4.6
|
11.6
|
1.0
|
CA
|
A:ASP33
|
4.6
|
9.2
|
1.0
|
N
|
A:GLY30
|
4.6
|
11.0
|
1.0
|
N
|
A:GLY32
|
4.7
|
5.9
|
1.0
|
NZ
|
A:LYS37
|
4.7
|
8.1
|
1.0
|
CA
|
A:ASP29
|
4.7
|
13.5
|
1.0
|
N
|
A:SER35
|
4.7
|
6.6
|
1.0
|
C
|
A:GLY31
|
4.8
|
8.9
|
1.0
|
C
|
A:ASP29
|
4.9
|
10.2
|
1.0
|
|
Calcium binding site 2 out
of 5 in 1tcf
Go back to
Calcium Binding Sites List in 1tcf
Calcium binding site 2 out
of 5 in the Crystal Structure of Calcium-Saturated Rabbit Skeletal Troponin C
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 Calcium-Saturated Rabbit Skeletal Troponin C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca161
b:4.1
occ:1.00
|
O
|
A:HOH175
|
2.2
|
22.2
|
1.0
|
OG
|
A:SER67
|
2.2
|
7.5
|
1.0
|
OD1
|
A:ASP63
|
2.4
|
12.4
|
1.0
|
OD1
|
A:ASP65
|
2.4
|
15.2
|
1.0
|
O
|
A:THR69
|
2.5
|
2.4
|
1.0
|
OE2
|
A:GLU74
|
2.5
|
11.0
|
1.0
|
OE1
|
A:GLU74
|
2.7
|
11.8
|
1.0
|
CD
|
A:GLU74
|
3.0
|
8.3
|
1.0
|
CG
|
A:ASP65
|
3.4
|
10.8
|
1.0
|
CG
|
A:ASP63
|
3.6
|
11.8
|
1.0
|
C
|
A:THR69
|
3.6
|
4.0
|
1.0
|
CB
|
A:SER67
|
3.6
|
8.5
|
1.0
|
OD2
|
A:ASP65
|
3.7
|
10.4
|
1.0
|
N
|
A:SER67
|
3.9
|
2.4
|
1.0
|
OG1
|
A:THR69
|
4.2
|
3.7
|
1.0
|
OD2
|
A:ASP63
|
4.3
|
2.4
|
1.0
|
N
|
A:THR69
|
4.3
|
2.4
|
1.0
|
CA
|
A:SER67
|
4.3
|
3.6
|
1.0
|
N
|
A:ILE70
|
4.4
|
3.2
|
1.0
|
CA
|
A:ASP63
|
4.4
|
11.8
|
1.0
|
CA
|
A:ILE70
|
4.4
|
3.6
|
1.0
|
CG
|
A:GLU74
|
4.4
|
11.0
|
1.0
|
N
|
A:ASP65
|
4.5
|
14.6
|
1.0
|
N
|
A:ASP71
|
4.5
|
7.3
|
1.0
|
CA
|
A:THR69
|
4.5
|
7.5
|
1.0
|
CB
|
A:ASP63
|
4.5
|
12.2
|
1.0
|
N
|
A:GLY68
|
4.6
|
2.4
|
1.0
|
CB
|
A:ASP65
|
4.6
|
10.1
|
1.0
|
N
|
A:GLY66
|
4.6
|
11.2
|
1.0
|
C
|
A:ASP63
|
4.8
|
12.9
|
1.0
|
C
|
A:SER67
|
4.8
|
3.4
|
1.0
|
O
|
A:HOH207
|
4.9
|
19.0
|
1.0
|
CA
|
A:ASP65
|
4.9
|
11.8
|
1.0
|
N
|
A:GLU64
|
4.9
|
15.7
|
1.0
|
C
|
A:ASP65
|
4.9
|
14.0
|
1.0
|
C
|
A:ILE70
|
4.9
|
4.4
|
1.0
|
|
Calcium binding site 3 out
of 5 in 1tcf
Go back to
Calcium Binding Sites List in 1tcf
Calcium binding site 3 out
of 5 in the Crystal Structure of Calcium-Saturated Rabbit Skeletal Troponin C
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 Calcium-Saturated Rabbit Skeletal Troponin C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca162
b:17.7
occ:1.00
|
O
|
A:TYR109
|
2.2
|
15.6
|
1.0
|
OE1
|
A:GLU114
|
2.4
|
9.3
|
1.0
|
OD1
|
A:ASN105
|
2.4
|
30.4
|
1.0
|
OD1
|
A:ASP107
|
2.4
|
27.8
|
1.0
|
OD1
|
A:ASP103
|
2.5
|
27.9
|
1.0
|
OE2
|
A:GLU114
|
2.5
|
10.7
|
1.0
|
CD
|
A:GLU114
|
2.8
|
13.3
|
1.0
|
CG
|
A:ASN105
|
3.2
|
30.0
|
1.0
|
CG
|
A:ASP107
|
3.4
|
24.4
|
1.0
|
ND2
|
A:ASN105
|
3.4
|
36.8
|
1.0
|
CG
|
A:ASP103
|
3.4
|
29.5
|
1.0
|
C
|
A:TYR109
|
3.5
|
13.2
|
1.0
|
OD2
|
A:ASP107
|
3.8
|
22.1
|
1.0
|
CA
|
A:ASP103
|
4.0
|
29.3
|
1.0
|
N
|
A:ASP107
|
4.1
|
18.6
|
1.0
|
N
|
A:TYR109
|
4.1
|
12.3
|
1.0
|
CB
|
A:ASP103
|
4.2
|
29.7
|
1.0
|
OD2
|
A:ASP103
|
4.2
|
24.9
|
1.0
|
CG
|
A:GLU114
|
4.3
|
10.1
|
1.0
|
CA
|
A:TYR109
|
4.3
|
14.4
|
1.0
|
N
|
A:ALA106
|
4.3
|
27.0
|
1.0
|
N
|
A:ASN105
|
4.4
|
30.6
|
1.0
|
C
|
A:ASP103
|
4.4
|
31.6
|
1.0
|
N
|
A:ILE110
|
4.4
|
14.3
|
1.0
|
CA
|
A:ILE110
|
4.4
|
13.8
|
1.0
|
CB
|
A:ASN105
|
4.5
|
29.6
|
1.0
|
CB
|
A:ASP107
|
4.5
|
20.6
|
1.0
|
O
|
A:HOH285
|
4.6
|
33.3
|
1.0
|
C
|
A:ASN105
|
4.6
|
30.6
|
1.0
|
CA
|
A:ASN105
|
4.7
|
28.8
|
1.0
|
N
|
A:ASP111
|
4.7
|
15.3
|
1.0
|
O
|
A:ASP103
|
4.8
|
30.2
|
1.0
|
CA
|
A:ALA106
|
4.8
|
22.5
|
1.0
|
CB
|
A:TYR109
|
4.8
|
19.2
|
1.0
|
N
|
A:ARG104
|
4.8
|
33.0
|
1.0
|
N
|
A:GLY108
|
4.8
|
15.5
|
1.0
|
CA
|
A:ASP107
|
4.9
|
19.2
|
1.0
|
OD2
|
A:ASP111
|
4.9
|
10.4
|
1.0
|
C
|
A:ALA106
|
5.0
|
21.9
|
1.0
|
|
Calcium binding site 4 out
of 5 in 1tcf
Go back to
Calcium Binding Sites List in 1tcf
Calcium binding site 4 out
of 5 in the Crystal Structure of Calcium-Saturated Rabbit Skeletal Troponin C
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 Calcium-Saturated Rabbit Skeletal Troponin C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca163
b:27.9
occ:1.00
|
OE2
|
A:GLU150
|
2.3
|
10.7
|
1.0
|
OD1
|
A:ASP143
|
2.4
|
28.4
|
1.0
|
OD1
|
A:ASN141
|
2.4
|
32.3
|
1.0
|
O
|
A:HOH229
|
2.4
|
27.6
|
1.0
|
OE1
|
A:GLU150
|
2.6
|
14.5
|
1.0
|
OD1
|
A:ASP139
|
2.6
|
27.1
|
1.0
|
O
|
A:ARG145
|
2.6
|
31.0
|
1.0
|
CD
|
A:GLU150
|
2.8
|
12.0
|
1.0
|
CG
|
A:ASP143
|
3.3
|
25.8
|
1.0
|
CG
|
A:ASN141
|
3.4
|
26.9
|
1.0
|
OD2
|
A:ASP143
|
3.5
|
26.7
|
1.0
|
C
|
A:ARG145
|
3.7
|
27.6
|
1.0
|
CG
|
A:ASP139
|
3.7
|
30.7
|
1.0
|
O
|
A:HOH208
|
3.8
|
38.9
|
1.0
|
ND2
|
A:ASN141
|
3.9
|
26.0
|
1.0
|
CA
|
A:ASP139
|
4.3
|
31.6
|
1.0
|
N
|
A:ASN141
|
4.3
|
27.3
|
1.0
|
CG
|
A:GLU150
|
4.3
|
10.9
|
1.0
|
CA
|
A:ILE146
|
4.3
|
22.5
|
1.0
|
N
|
A:ASP143
|
4.4
|
23.6
|
1.0
|
N
|
A:ILE146
|
4.5
|
24.4
|
1.0
|
N
|
A:ARG145
|
4.5
|
25.7
|
1.0
|
OD2
|
A:ASP139
|
4.5
|
33.2
|
1.0
|
N
|
A:ASP147
|
4.5
|
22.4
|
1.0
|
CB
|
A:ASN141
|
4.6
|
28.6
|
1.0
|
N
|
A:LYS140
|
4.6
|
27.4
|
1.0
|
CB
|
A:ASP139
|
4.6
|
31.1
|
1.0
|
CB
|
A:ASP143
|
4.6
|
26.3
|
1.0
|
CG
|
A:ARG145
|
4.6
|
31.4
|
1.0
|
OD2
|
A:ASP147
|
4.7
|
20.2
|
1.0
|
CA
|
A:ARG145
|
4.7
|
26.7
|
1.0
|
C
|
A:ASP139
|
4.7
|
30.6
|
1.0
|
N
|
A:ASN142
|
4.7
|
26.9
|
1.0
|
CA
|
A:ASN141
|
4.8
|
25.5
|
1.0
|
O
|
A:GLY138
|
4.8
|
33.5
|
1.0
|
C
|
A:ASN141
|
4.9
|
27.4
|
1.0
|
C
|
A:ILE146
|
4.9
|
22.3
|
1.0
|
CG
|
A:ASP147
|
5.0
|
20.8
|
1.0
|
CA
|
A:ASP143
|
5.0
|
25.6
|
1.0
|
|
Calcium binding site 5 out
of 5 in 1tcf
Go back to
Calcium Binding Sites List in 1tcf
Calcium binding site 5 out
of 5 in the Crystal Structure of Calcium-Saturated Rabbit Skeletal Troponin C
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 Calcium-Saturated Rabbit Skeletal Troponin C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca164
b:7.2
occ:1.00
|
OE2
|
A:GLU14
|
2.4
|
2.4
|
1.0
|
O
|
A:HOH219
|
2.5
|
56.4
|
1.0
|
O
|
A:HOH176
|
2.5
|
2.4
|
1.0
|
OE1
|
A:GLU14
|
2.5
|
3.5
|
1.0
|
CD
|
A:GLU14
|
2.8
|
2.4
|
1.0
|
CB
|
A:GLU13
|
3.8
|
17.9
|
1.0
|
O
|
A:HOH170
|
4.3
|
17.6
|
1.0
|
CG
|
A:GLU14
|
4.3
|
2.4
|
1.0
|
N
|
A:GLU13
|
4.5
|
14.7
|
1.0
|
CD
|
A:GLU13
|
4.7
|
29.4
|
1.0
|
O
|
A:HOH177
|
4.7
|
24.4
|
1.0
|
CG
|
A:GLU13
|
4.7
|
18.5
|
1.0
|
N
|
A:GLU14
|
4.8
|
10.5
|
1.0
|
CA
|
A:GLU13
|
4.8
|
11.5
|
1.0
|
OE1
|
A:GLU13
|
4.8
|
30.9
|
1.0
|
CB
|
A:SER12
|
4.9
|
2.4
|
1.0
|
OE2
|
A:GLU13
|
4.9
|
27.0
|
1.0
|
|
Reference:
J.Soman,
T.Tao,
G.N.Phillips Jr.
Conformational Variation of Calcium-Bound Troponin C. Proteins V. 37 510 1999.
ISSN: ISSN 0887-3585
PubMed: 10651267
DOI: 10.1002/(SICI)1097-0134(19991201)37:4<510::AID-PROT2>3.3.CO;2-K
Page generated: Thu Jul 11 22:59:01 2024
|