Calcium in PDB 4pkh: Complex of Adp-Actin with the N-Terminal Actin-Binding Domain of Tropomodulin
Protein crystallography data
The structure of Complex of Adp-Actin with the N-Terminal Actin-Binding Domain of Tropomodulin, PDB code: 4pkh
was solved by
J.N.Rao,
R.Dominguez,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
44.90 /
2.15
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
69.222,
135.136,
140.549,
90.00,
94.41,
90.00
|
|
R / Rfree (%)
|
27.4 /
32.6
|
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Calcium atom in the Complex of Adp-Actin with the N-Terminal Actin-Binding Domain of Tropomodulin
(pdb code 4pkh). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the
Complex of Adp-Actin with the N-Terminal Actin-Binding Domain of Tropomodulin, PDB code: 4pkh:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 12 in 4pkh
Go back to
Calcium Binding Sites List in 4pkh
Calcium binding site 1 out
of 12 in the Complex of Adp-Actin with the N-Terminal Actin-Binding Domain of Tropomodulin
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Complex of Adp-Actin with the N-Terminal Actin-Binding Domain of Tropomodulin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca402
b:63.4
occ:1.00
|
O1B
|
A:ADP401
|
2.3
|
30.6
|
1.0
|
|
O
|
A:HOH588
|
2.5
|
24.8
|
1.0
|
|
O
|
A:HOH516
|
2.6
|
35.8
|
1.0
|
|
O
|
A:HOH514
|
3.1
|
37.2
|
1.0
|
|
PB
|
A:ADP401
|
3.4
|
22.4
|
1.0
|
|
HZ2
|
A:LYS18
|
3.5
|
37.5
|
1.0
|
|
O3B
|
A:ADP401
|
3.6
|
18.8
|
1.0
|
|
HA3
|
A:GLY156
|
3.7
|
41.1
|
1.0
|
|
HA3
|
A:GLY13
|
3.7
|
37.2
|
1.0
|
|
HA2
|
A:GLY13
|
3.9
|
37.2
|
1.0
|
|
OD2
|
A:ASP154
|
3.9
|
37.9
|
1.0
|
|
O1A
|
A:ADP401
|
4.0
|
31.1
|
1.0
|
|
O
|
A:HOH511
|
4.0
|
29.8
|
1.0
|
|
O3A
|
A:ADP401
|
4.3
|
33.8
|
1.0
|
|
CA
|
A:GLY13
|
4.3
|
31.0
|
1.0
|
|
NZ
|
A:LYS18
|
4.3
|
31.3
|
1.0
|
|
HA2
|
A:GLY156
|
4.3
|
41.1
|
1.0
|
|
HZ3
|
A:LYS18
|
4.4
|
37.5
|
1.0
|
|
CA
|
A:GLY156
|
4.4
|
34.3
|
1.0
|
|
HG21
|
A:VAL339
|
4.6
|
26.8
|
1.0
|
|
O2B
|
A:ADP401
|
4.6
|
31.8
|
1.0
|
|
OD1
|
A:ASP154
|
4.6
|
42.8
|
1.0
|
|
H
|
A:SER14
|
4.7
|
43.8
|
1.0
|
|
CG
|
A:ASP154
|
4.7
|
37.2
|
1.0
|
|
PA
|
A:ADP401
|
4.7
|
29.4
|
1.0
|
|
OE1
|
A:GLN137
|
4.7
|
27.5
|
1.0
|
|
HZ1
|
A:LYS18
|
4.7
|
37.5
|
1.0
|
|
CD
|
A:GLN137
|
4.9
|
24.0
|
1.0
|
|
HG2
|
A:GLN137
|
4.9
|
22.4
|
1.0
|
|
OD1
|
A:ASP11
|
4.9
|
19.8
|
1.0
|
|
HA2
|
A:GLY301
|
5.0
|
35.2
|
1.0
|
|
Calcium binding site 2 out
of 12 in 4pkh
Go back to
Calcium Binding Sites List in 4pkh
Calcium binding site 2 out
of 12 in the Complex of Adp-Actin with the N-Terminal Actin-Binding Domain of Tropomodulin
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Complex of Adp-Actin with the N-Terminal Actin-Binding Domain of Tropomodulin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca403
b:40.0
occ:1.00
|
O
|
B:ALA143
|
2.3
|
29.0
|
1.0
|
|
O
|
B:HOH1331
|
2.4
|
23.1
|
1.0
|
|
OD2
|
B:ASP136
|
2.4
|
20.1
|
1.0
|
|
O
|
B:GLY141
|
2.7
|
24.2
|
1.0
|
|
OE1
|
A:GLU167
|
2.8
|
31.6
|
1.0
|
|
OD1
|
B:ASP136
|
2.8
|
21.4
|
1.0
|
|
CG
|
B:ASP136
|
2.9
|
25.9
|
1.0
|
|
C
|
B:GLY141
|
3.4
|
27.4
|
1.0
|
|
C
|
B:ALA143
|
3.4
|
22.4
|
1.0
|
|
H
|
B:ALA143
|
3.4
|
28.2
|
1.0
|
|
N
|
B:ALA143
|
3.5
|
23.5
|
1.0
|
|
HA2
|
B:GLY141
|
3.6
|
29.7
|
1.0
|
|
O
|
B:HOH1374
|
3.6
|
46.8
|
1.0
|
|
CD
|
A:GLU167
|
3.7
|
39.5
|
1.0
|
|
HB3
|
B:ALA143
|
3.9
|
27.1
|
1.0
|
|
C
|
B:ARG142
|
3.9
|
25.1
|
1.0
|
|
CA
|
B:ALA143
|
4.0
|
23.7
|
1.0
|
|
OE2
|
A:GLU167
|
4.0
|
39.7
|
1.0
|
|
CA
|
B:GLY141
|
4.0
|
24.7
|
1.0
|
|
HA
|
B:VAL144
|
4.0
|
31.8
|
1.0
|
|
HG3
|
B:GLN145
|
4.0
|
29.4
|
1.0
|
|
HE21
|
B:GLN145
|
4.1
|
20.9
|
1.0
|
|
N
|
B:ARG142
|
4.2
|
24.4
|
1.0
|
|
HA3
|
B:GLY141
|
4.3
|
29.7
|
1.0
|
|
O
|
B:HOH1321
|
4.3
|
37.6
|
1.0
|
|
HA
|
B:ARG142
|
4.3
|
32.3
|
1.0
|
|
CA
|
B:ARG142
|
4.4
|
26.9
|
1.0
|
|
CB
|
B:ASP136
|
4.4
|
28.0
|
1.0
|
|
N
|
B:VAL144
|
4.5
|
32.1
|
1.0
|
|
CB
|
B:ALA143
|
4.5
|
22.5
|
1.0
|
|
HB2
|
B:ASP136
|
4.6
|
33.6
|
1.0
|
|
HB3
|
A:GLU167
|
4.6
|
40.5
|
1.0
|
|
O
|
B:ARG142
|
4.6
|
25.2
|
1.0
|
|
CA
|
B:VAL144
|
4.7
|
26.5
|
1.0
|
|
NE2
|
B:GLN145
|
4.8
|
17.4
|
1.0
|
|
HB3
|
B:ASP136
|
4.8
|
33.6
|
1.0
|
|
H
|
B:ARG142
|
4.8
|
29.2
|
1.0
|
|
HA
|
B:ALA143
|
4.8
|
28.5
|
1.0
|
|
H
|
B:GLN145
|
4.9
|
26.1
|
1.0
|
|
CG
|
A:GLU167
|
5.0
|
37.8
|
1.0
|
|
CG
|
B:GLN145
|
5.0
|
24.5
|
1.0
|
|
Calcium binding site 3 out
of 12 in 4pkh
Go back to
Calcium Binding Sites List in 4pkh
Calcium binding site 3 out
of 12 in the Complex of Adp-Actin with the N-Terminal Actin-Binding Domain of Tropomodulin
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Complex of Adp-Actin with the N-Terminal Actin-Binding Domain of Tropomodulin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca1201
b:26.6
occ:1.00
|
O
|
B:GLY92
|
2.2
|
27.6
|
1.0
|
|
O
|
B:HOH1315
|
2.2
|
23.0
|
1.0
|
|
O
|
B:VAL172
|
2.2
|
40.5
|
1.0
|
|
OD1
|
B:ASP93
|
2.3
|
27.2
|
1.0
|
|
OE1
|
B:GLU124
|
2.5
|
29.6
|
1.0
|
|
O
|
B:HOH1345
|
2.5
|
25.1
|
1.0
|
|
OE2
|
B:GLU124
|
2.6
|
30.9
|
1.0
|
|
CD
|
B:GLU124
|
2.9
|
29.3
|
1.0
|
|
HA
|
B:ASP93
|
3.3
|
32.4
|
1.0
|
|
C
|
B:GLY92
|
3.3
|
37.5
|
1.0
|
|
C
|
B:VAL172
|
3.4
|
42.3
|
1.0
|
|
H
|
B:VAL172
|
3.5
|
53.8
|
1.0
|
|
HG13
|
B:VAL172
|
3.5
|
52.7
|
1.0
|
|
CG
|
B:ASP93
|
3.5
|
28.6
|
1.0
|
|
HG
|
B:SER121
|
3.6
|
41.7
|
1.0
|
|
H
|
B:SER121
|
3.7
|
36.0
|
1.0
|
|
HA
|
B:CYS120
|
3.8
|
34.4
|
1.0
|
|
N
|
B:VAL172
|
3.8
|
44.9
|
1.0
|
|
HG12
|
B:VAL172
|
3.8
|
52.7
|
1.0
|
|
CA
|
B:ASP93
|
4.0
|
27.0
|
1.0
|
|
CG1
|
B:VAL172
|
4.1
|
43.9
|
1.0
|
|
N
|
B:ASP93
|
4.1
|
30.9
|
1.0
|
|
CA
|
B:VAL172
|
4.2
|
42.4
|
1.0
|
|
HA3
|
B:GLY92
|
4.2
|
37.9
|
1.0
|
|
HA3
|
B:GLY171
|
4.2
|
53.3
|
1.0
|
|
HA
|
B:ALA173
|
4.2
|
51.7
|
1.0
|
|
OG
|
B:SER121
|
4.4
|
34.8
|
1.0
|
|
CB
|
B:ASP93
|
4.4
|
28.3
|
1.0
|
|
OD2
|
B:ASP93
|
4.4
|
29.1
|
1.0
|
|
CA
|
B:GLY92
|
4.4
|
31.6
|
1.0
|
|
N
|
B:ALA173
|
4.5
|
41.2
|
1.0
|
|
O
|
B:HOH1366
|
4.5
|
42.6
|
1.0
|
|
C
|
B:GLY171
|
4.5
|
48.5
|
1.0
|
|
O
|
B:HOH1329
|
4.5
|
33.2
|
1.0
|
|
CG
|
B:GLU124
|
4.5
|
27.1
|
1.0
|
|
N
|
B:SER121
|
4.5
|
30.0
|
1.0
|
|
HB2
|
B:CYS120
|
4.6
|
39.8
|
1.0
|
|
CA
|
B:CYS120
|
4.7
|
28.7
|
1.0
|
|
CA
|
B:ALA173
|
4.7
|
43.1
|
1.0
|
|
C
|
B:ALA173
|
4.7
|
45.1
|
1.0
|
|
HA2
|
B:GLY92
|
4.8
|
37.9
|
1.0
|
|
CB
|
B:VAL172
|
4.8
|
46.6
|
1.0
|
|
CA
|
B:GLY171
|
4.9
|
44.5
|
1.0
|
|
N
|
B:SER174
|
4.9
|
44.8
|
1.0
|
|
HG11
|
B:VAL172
|
4.9
|
52.7
|
1.0
|
|
HG3
|
B:GLU124
|
4.9
|
32.5
|
1.0
|
|
HG2
|
B:GLU124
|
4.9
|
32.5
|
1.0
|
|
O
|
B:HOH1333
|
4.9
|
28.2
|
1.0
|
|
H
|
B:ASP93
|
4.9
|
37.1
|
1.0
|
|
HB2
|
B:GLU124
|
5.0
|
33.1
|
1.0
|
|
HB3
|
B:ASP93
|
5.0
|
34.0
|
1.0
|
|
H
|
B:SER174
|
5.0
|
53.8
|
1.0
|
|
Calcium binding site 4 out
of 12 in 4pkh
Go back to
Calcium Binding Sites List in 4pkh
Calcium binding site 4 out
of 12 in the Complex of Adp-Actin with the N-Terminal Actin-Binding Domain of Tropomodulin
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Complex of Adp-Actin with the N-Terminal Actin-Binding Domain of Tropomodulin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca402
b:64.7
occ:1.00
|
O1B
|
D:ADP401
|
2.4
|
24.9
|
1.0
|
|
O
|
D:HOH541
|
2.4
|
20.1
|
1.0
|
|
O
|
D:HOH511
|
2.6
|
19.7
|
1.0
|
|
O
|
D:HOH510
|
2.9
|
24.0
|
1.0
|
|
HA2
|
D:GLY13
|
3.3
|
35.5
|
1.0
|
|
HZ3
|
D:LYS18
|
3.3
|
36.2
|
1.0
|
|
PB
|
D:ADP401
|
3.5
|
23.0
|
1.0
|
|
O
|
D:HOH527
|
3.5
|
25.0
|
1.0
|
|
HA3
|
D:GLY13
|
3.7
|
35.5
|
1.0
|
|
O3B
|
D:ADP401
|
3.8
|
23.0
|
1.0
|
|
CA
|
D:GLY13
|
3.9
|
29.6
|
1.0
|
|
OE1
|
D:GLN137
|
4.0
|
22.9
|
1.0
|
|
NZ
|
D:LYS18
|
4.1
|
30.2
|
1.0
|
|
OD2
|
D:ASP11
|
4.3
|
28.3
|
1.0
|
|
HZ2
|
D:LYS18
|
4.3
|
36.2
|
1.0
|
|
H
|
D:SER14
|
4.3
|
29.2
|
1.0
|
|
OD1
|
D:ASP11
|
4.4
|
26.7
|
1.0
|
|
CD
|
D:GLN137
|
4.4
|
20.5
|
1.0
|
|
HZ1
|
D:LYS18
|
4.4
|
36.2
|
1.0
|
|
O2B
|
D:ADP401
|
4.5
|
16.3
|
1.0
|
|
O3A
|
D:ADP401
|
4.6
|
26.1
|
1.0
|
|
OD2
|
D:ASP154
|
4.6
|
34.9
|
1.0
|
|
HA3
|
D:GLY156
|
4.7
|
33.1
|
1.0
|
|
HE22
|
D:GLN137
|
4.7
|
22.2
|
1.0
|
|
O1A
|
D:ADP401
|
4.7
|
24.8
|
1.0
|
|
HG
|
D:SER14
|
4.7
|
46.8
|
1.0
|
|
NE2
|
D:GLN137
|
4.7
|
18.5
|
1.0
|
|
HG11
|
D:VAL339
|
4.8
|
32.4
|
1.0
|
|
HG21
|
D:VAL339
|
4.8
|
19.6
|
1.0
|
|
CG
|
D:ASP11
|
4.8
|
25.1
|
1.0
|
|
HG2
|
D:GLN137
|
4.8
|
25.1
|
1.0
|
|
N
|
D:GLY13
|
4.8
|
28.2
|
1.0
|
|
HB3
|
D:GLN137
|
4.9
|
21.6
|
1.0
|
|
O
|
D:ASN12
|
4.9
|
26.0
|
1.0
|
|
N
|
D:SER14
|
4.9
|
24.3
|
1.0
|
|
C
|
D:GLY13
|
5.0
|
30.6
|
1.0
|
|
Calcium binding site 5 out
of 12 in 4pkh
Go back to
Calcium Binding Sites List in 4pkh
Calcium binding site 5 out
of 12 in the Complex of Adp-Actin with the N-Terminal Actin-Binding Domain of Tropomodulin
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Complex of Adp-Actin with the N-Terminal Actin-Binding Domain of Tropomodulin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca403
b:63.2
occ:1.00
|
O
|
E:ALA143
|
2.3
|
38.5
|
1.0
|
|
OD2
|
E:ASP136
|
2.4
|
25.4
|
1.0
|
|
OD1
|
E:ASP136
|
2.6
|
27.6
|
1.0
|
|
O
|
E:GLY141
|
2.7
|
26.9
|
1.0
|
|
O
|
E:HOH1317
|
2.8
|
30.0
|
1.0
|
|
CG
|
E:ASP136
|
2.8
|
27.6
|
1.0
|
|
OE1
|
D:GLU167
|
3.0
|
34.1
|
1.0
|
|
O
|
D:HOH573
|
3.0
|
51.7
|
1.0
|
|
C
|
E:ALA143
|
3.3
|
34.8
|
1.0
|
|
C
|
E:GLY141
|
3.4
|
27.7
|
1.0
|
|
HA2
|
E:GLY141
|
3.4
|
30.8
|
1.0
|
|
H
|
E:ALA143
|
3.5
|
29.2
|
1.0
|
|
N
|
E:ALA143
|
3.6
|
24.3
|
1.0
|
|
HB3
|
E:ALA143
|
3.7
|
38.6
|
1.0
|
|
CD
|
D:GLU167
|
3.7
|
33.9
|
1.0
|
|
HG3
|
E:GLN145
|
3.9
|
27.8
|
1.0
|
|
CA
|
E:ALA143
|
3.9
|
32.2
|
1.0
|
|
CA
|
E:GLY141
|
3.9
|
25.6
|
1.0
|
|
OE2
|
D:GLU167
|
4.1
|
33.8
|
1.0
|
|
C
|
E:ARG142
|
4.1
|
34.6
|
1.0
|
|
HA
|
E:VAL144
|
4.2
|
34.9
|
1.0
|
|
CB
|
E:ASP136
|
4.2
|
21.3
|
1.0
|
|
CB
|
E:ALA143
|
4.3
|
32.2
|
1.0
|
|
N
|
E:ARG142
|
4.3
|
31.7
|
1.0
|
|
OE1
|
E:GLN145
|
4.4
|
21.4
|
1.0
|
|
HB3
|
D:GLU167
|
4.4
|
35.4
|
1.0
|
|
HA3
|
E:GLY141
|
4.4
|
30.8
|
1.0
|
|
HB2
|
E:ASP136
|
4.4
|
25.6
|
1.0
|
|
N
|
E:VAL144
|
4.5
|
25.4
|
1.0
|
|
HA
|
E:ARG142
|
4.6
|
53.0
|
1.0
|
|
CA
|
E:ARG142
|
4.6
|
44.1
|
1.0
|
|
HB3
|
E:ASP136
|
4.7
|
25.6
|
1.0
|
|
O
|
E:ARG142
|
4.7
|
33.7
|
1.0
|
|
CG
|
E:GLN145
|
4.8
|
23.2
|
1.0
|
|
CA
|
E:VAL144
|
4.8
|
29.1
|
1.0
|
|
HA
|
E:ALA143
|
4.8
|
38.7
|
1.0
|
|
HB1
|
E:ALA143
|
4.8
|
38.6
|
1.0
|
|
CG
|
D:GLU167
|
4.9
|
29.1
|
1.0
|
|
H
|
E:GLN145
|
4.9
|
22.8
|
1.0
|
|
CD
|
E:GLN145
|
4.9
|
26.1
|
1.0
|
|
HB2
|
D:GLU167
|
5.0
|
35.4
|
1.0
|
|
CB
|
D:GLU167
|
5.0
|
29.5
|
1.0
|
|
Calcium binding site 6 out
of 12 in 4pkh
Go back to
Calcium Binding Sites List in 4pkh
Calcium binding site 6 out
of 12 in the Complex of Adp-Actin with the N-Terminal Actin-Binding Domain of Tropomodulin
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Complex of Adp-Actin with the N-Terminal Actin-Binding Domain of Tropomodulin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca1201
b:24.9
occ:1.00
|
OD1
|
E:ASP93
|
2.2
|
28.4
|
1.0
|
|
O
|
E:HOH1319
|
2.2
|
23.5
|
1.0
|
|
O
|
E:VAL172
|
2.3
|
30.7
|
1.0
|
|
O
|
E:GLY92
|
2.3
|
20.1
|
1.0
|
|
OE2
|
E:GLU124
|
2.5
|
19.7
|
1.0
|
|
OE1
|
E:GLU124
|
2.5
|
19.3
|
1.0
|
|
O
|
E:HOH1316
|
2.5
|
20.9
|
1.0
|
|
CD
|
E:GLU124
|
2.9
|
23.4
|
1.0
|
|
HA
|
E:ASP93
|
3.1
|
38.6
|
1.0
|
|
H
|
E:VAL172
|
3.2
|
43.9
|
1.0
|
|
C
|
E:GLY92
|
3.3
|
21.7
|
1.0
|
|
C
|
E:VAL172
|
3.4
|
27.4
|
1.0
|
|
CG
|
E:ASP93
|
3.4
|
28.9
|
1.0
|
|
N
|
E:VAL172
|
3.7
|
36.6
|
1.0
|
|
HA
|
E:CYS120
|
3.8
|
29.0
|
1.0
|
|
CA
|
E:ASP93
|
3.8
|
32.1
|
1.0
|
|
O
|
E:HOH1308
|
3.9
|
15.8
|
1.0
|
|
H
|
E:SER121
|
4.0
|
21.8
|
1.0
|
|
N
|
E:ASP93
|
4.0
|
23.8
|
1.0
|
|
O
|
E:HOH1327
|
4.0
|
26.6
|
1.0
|
|
CA
|
E:VAL172
|
4.1
|
35.9
|
1.0
|
|
HA3
|
E:GLY92
|
4.2
|
24.6
|
1.0
|
|
CB
|
E:ASP93
|
4.2
|
28.0
|
1.0
|
|
HA3
|
E:GLY171
|
4.2
|
43.7
|
1.0
|
|
HB
|
E:VAL172
|
4.3
|
44.4
|
1.0
|
|
OD2
|
E:ASP93
|
4.3
|
28.7
|
1.0
|
|
CA
|
E:GLY92
|
4.4
|
20.5
|
1.0
|
|
HA
|
E:ALA173
|
4.4
|
31.4
|
1.0
|
|
N
|
E:ALA173
|
4.5
|
26.1
|
1.0
|
|
CG
|
E:GLU124
|
4.5
|
18.7
|
1.0
|
|
C
|
E:GLY171
|
4.5
|
36.3
|
1.0
|
|
HB2
|
E:CYS120
|
4.6
|
25.4
|
1.0
|
|
C
|
E:ALA173
|
4.7
|
27.7
|
1.0
|
|
HB3
|
E:ASP93
|
4.7
|
33.6
|
1.0
|
|
CA
|
E:CYS120
|
4.7
|
24.1
|
1.0
|
|
N
|
E:SER121
|
4.8
|
18.2
|
1.0
|
|
CA
|
E:ALA173
|
4.8
|
26.2
|
1.0
|
|
CB
|
E:VAL172
|
4.8
|
37.0
|
1.0
|
|
OG
|
E:SER121
|
4.8
|
25.0
|
1.0
|
|
HA2
|
E:GLY92
|
4.8
|
24.6
|
1.0
|
|
HG
|
E:SER121
|
4.8
|
30.0
|
1.0
|
|
N
|
E:SER174
|
4.8
|
35.1
|
1.0
|
|
H
|
E:SER174
|
4.8
|
42.1
|
1.0
|
|
HG3
|
E:GLU124
|
4.8
|
22.5
|
1.0
|
|
HG2
|
E:GLU124
|
4.8
|
22.5
|
1.0
|
|
CA
|
E:GLY171
|
4.9
|
36.4
|
1.0
|
|
H
|
E:ASP93
|
4.9
|
28.6
|
1.0
|
|
HA
|
E:VAL172
|
4.9
|
43.1
|
1.0
|
|
HA
|
E:SER174
|
4.9
|
44.1
|
1.0
|
|
O
|
E:HOH1341
|
4.9
|
23.8
|
1.0
|
|
HB2
|
E:ASP93
|
4.9
|
33.6
|
1.0
|
|
O
|
E:ALA173
|
5.0
|
24.4
|
1.0
|
|
Calcium binding site 7 out
of 12 in 4pkh
Go back to
Calcium Binding Sites List in 4pkh
Calcium binding site 7 out
of 12 in the Complex of Adp-Actin with the N-Terminal Actin-Binding Domain of Tropomodulin
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Complex of Adp-Actin with the N-Terminal Actin-Binding Domain of Tropomodulin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca402
b:91.1
occ:1.00
|
OD2
|
F:ASP11
|
2.4
|
70.5
|
1.0
|
|
HG21
|
F:VAL339
|
2.7
|
69.9
|
1.0
|
|
OD1
|
F:ASP11
|
2.7
|
70.3
|
1.0
|
|
CG
|
F:ASP11
|
2.9
|
69.9
|
1.0
|
|
HZ1
|
F:LYS18
|
3.1
|
92.8
|
1.0
|
|
HG11
|
F:VAL339
|
3.2
|
70.2
|
1.0
|
|
O1B
|
F:ADP401
|
3.3
|
38.4
|
1.0
|
|
HB
|
F:VAL339
|
3.4
|
69.8
|
1.0
|
|
CG2
|
F:VAL339
|
3.5
|
58.2
|
1.0
|
|
CB
|
F:VAL339
|
3.8
|
58.2
|
1.0
|
|
HE2
|
F:LYS18
|
3.8
|
94.5
|
1.0
|
|
NZ
|
F:LYS18
|
3.9
|
77.3
|
1.0
|
|
HG23
|
F:VAL339
|
3.9
|
69.9
|
1.0
|
|
CG1
|
F:VAL339
|
3.9
|
58.5
|
1.0
|
|
HG2
|
F:GLN137
|
4.0
|
77.6
|
1.0
|
|
O
|
F:HOH512
|
4.1
|
19.2
|
1.0
|
|
HZ3
|
F:LYS18
|
4.1
|
92.8
|
1.0
|
|
O
|
F:HOH563
|
4.2
|
33.7
|
1.0
|
|
HB3
|
F:GLN137
|
4.2
|
76.9
|
1.0
|
|
HG22
|
F:VAL339
|
4.2
|
69.9
|
1.0
|
|
CE
|
F:LYS18
|
4.2
|
78.7
|
1.0
|
|
HE3
|
F:LYS18
|
4.3
|
94.5
|
1.0
|
|
CD
|
F:GLN137
|
4.3
|
65.5
|
1.0
|
|
NE2
|
F:GLN137
|
4.4
|
66.0
|
1.0
|
|
CB
|
F:ASP11
|
4.4
|
69.1
|
1.0
|
|
HE21
|
F:GLN137
|
4.4
|
79.2
|
1.0
|
|
HG12
|
F:VAL339
|
4.5
|
70.2
|
1.0
|
|
HA2
|
F:GLY13
|
4.5
|
80.8
|
1.0
|
|
HZ2
|
F:LYS18
|
4.5
|
92.8
|
1.0
|
|
HG13
|
F:VAL339
|
4.6
|
70.2
|
1.0
|
|
CG
|
F:GLN137
|
4.6
|
64.7
|
1.0
|
|
HE22
|
F:GLN137
|
4.6
|
79.2
|
1.0
|
|
HB3
|
F:ASP11
|
4.6
|
82.9
|
1.0
|
|
OD2
|
F:ASP154
|
4.6
|
79.5
|
1.0
|
|
OE1
|
F:GLN137
|
4.7
|
65.9
|
1.0
|
|
HG1
|
F:THR106
|
4.7
|
78.2
|
1.0
|
|
PB
|
F:ADP401
|
4.8
|
40.2
|
1.0
|
|
HB2
|
F:ASP11
|
4.8
|
82.9
|
1.0
|
|
CB
|
F:GLN137
|
4.9
|
64.1
|
1.0
|
|
HA3
|
F:GLY13
|
4.9
|
80.8
|
1.0
|
|
Calcium binding site 8 out
of 12 in 4pkh
Go back to
Calcium Binding Sites List in 4pkh
Calcium binding site 8 out
of 12 in the Complex of Adp-Actin with the N-Terminal Actin-Binding Domain of Tropomodulin
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Complex of Adp-Actin with the N-Terminal Actin-Binding Domain of Tropomodulin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca403
b:55.6
occ:1.00
|
OE1
|
F:GLU167
|
2.3
|
79.6
|
1.0
|
|
OD2
|
G:ASP136
|
2.5
|
66.7
|
1.0
|
|
O
|
G:ALA143
|
2.8
|
63.4
|
1.0
|
|
O
|
G:GLY141
|
2.8
|
66.3
|
1.0
|
|
CD
|
F:GLU167
|
3.0
|
77.8
|
1.0
|
|
OD1
|
G:ASP136
|
3.1
|
68.5
|
1.0
|
|
CG
|
G:ASP136
|
3.1
|
67.1
|
1.0
|
|
OE2
|
F:GLU167
|
3.3
|
77.8
|
1.0
|
|
H
|
G:ALA143
|
3.6
|
75.5
|
1.0
|
|
C
|
G:ALA143
|
3.6
|
62.0
|
1.0
|
|
O
|
G:HOH1336
|
3.6
|
41.7
|
1.0
|
|
C
|
G:GLY141
|
3.7
|
66.7
|
1.0
|
|
N
|
G:ALA143
|
3.7
|
62.9
|
1.0
|
|
HB3
|
F:GLU167
|
3.8
|
91.3
|
1.0
|
|
HA2
|
G:GLY141
|
4.0
|
82.9
|
1.0
|
|
C
|
G:ARG142
|
4.0
|
66.2
|
1.0
|
|
HE21
|
G:GLN145
|
4.0
|
83.4
|
1.0
|
|
HA
|
G:VAL144
|
4.1
|
73.6
|
1.0
|
|
CG
|
F:GLU167
|
4.1
|
75.8
|
1.0
|
|
O
|
G:ARG142
|
4.3
|
65.6
|
1.0
|
|
CA
|
G:ALA143
|
4.3
|
62.3
|
1.0
|
|
CB
|
F:GLU167
|
4.3
|
76.1
|
1.0
|
|
HB2
|
F:GLU167
|
4.4
|
91.3
|
1.0
|
|
CA
|
G:GLY141
|
4.4
|
69.1
|
1.0
|
|
HG2
|
F:GLU167
|
4.4
|
91.0
|
1.0
|
|
HE1
|
F:TYR166
|
4.4
|
92.7
|
1.0
|
|
HG3
|
G:GLN145
|
4.5
|
80.2
|
1.0
|
|
N
|
G:VAL144
|
4.5
|
60.9
|
1.0
|
|
N
|
G:ARG142
|
4.5
|
65.5
|
1.0
|
|
CB
|
G:ASP136
|
4.6
|
65.0
|
1.0
|
|
NE2
|
G:GLN145
|
4.6
|
69.5
|
1.0
|
|
HA3
|
G:GLY141
|
4.7
|
82.9
|
1.0
|
|
CA
|
G:ARG142
|
4.8
|
65.8
|
1.0
|
|
CA
|
G:VAL144
|
4.8
|
61.3
|
1.0
|
|
HB2
|
G:ASP136
|
4.8
|
78.0
|
1.0
|
|
HB3
|
G:ALA143
|
4.9
|
74.7
|
1.0
|
|
HB3
|
G:ASP136
|
4.9
|
78.0
|
1.0
|
|
HA
|
G:ARG142
|
4.9
|
78.9
|
1.0
|
|
HG3
|
F:GLU167
|
4.9
|
91.0
|
1.0
|
|
H
|
G:GLN145
|
4.9
|
76.2
|
1.0
|
|
HE22
|
G:GLN145
|
4.9
|
83.4
|
1.0
|
|
HA
|
G:ALA143
|
5.0
|
74.8
|
1.0
|
|
Calcium binding site 9 out
of 12 in 4pkh
Go back to
Calcium Binding Sites List in 4pkh
Calcium binding site 9 out
of 12 in the Complex of Adp-Actin with the N-Terminal Actin-Binding Domain of Tropomodulin
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Complex of Adp-Actin with the N-Terminal Actin-Binding Domain of Tropomodulin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Ca1201
b:56.2
occ:1.00
|
O
|
G:HOH1331
|
2.3
|
25.3
|
1.0
|
|
O
|
G:GLY92
|
2.3
|
75.1
|
1.0
|
|
O
|
G:VAL172
|
2.4
|
90.7
|
1.0
|
|
OE1
|
G:GLU124
|
2.6
|
62.5
|
1.0
|
|
OD1
|
G:ASP93
|
2.7
|
65.8
|
1.0
|
|
O
|
G:HOH1338
|
2.7
|
52.7
|
1.0
|
|
OE2
|
G:GLU124
|
2.7
|
63.3
|
1.0
|
|
CD
|
G:GLU124
|
2.9
|
62.3
|
1.0
|
|
HA
|
G:ASP93
|
3.2
|
77.3
|
1.0
|
|
O
|
G:HOH1302
|
3.4
|
50.6
|
1.0
|
|
C
|
G:GLY92
|
3.5
|
74.5
|
1.0
|
|
C
|
G:VAL172
|
3.6
|
92.0
|
1.0
|
|
HA
|
G:ALA173
|
3.8
|
0.5
|
1.0
|
|
HA
|
G:CYS120
|
3.8
|
76.8
|
1.0
|
|
CG
|
G:ASP93
|
3.9
|
66.1
|
1.0
|
|
H
|
G:SER121
|
4.0
|
75.1
|
1.0
|
|
CA
|
G:ASP93
|
4.1
|
64.5
|
1.0
|
|
HA3
|
G:GLY171
|
4.1
|
0.6
|
1.0
|
|
N
|
G:ASP93
|
4.2
|
65.6
|
1.0
|
|
N
|
G:VAL172
|
4.3
|
89.4
|
1.0
|
|
H
|
G:VAL172
|
4.4
|
0.2
|
1.0
|
|
HA3
|
G:GLY92
|
4.4
|
87.7
|
1.0
|
|
CA
|
G:ALA173
|
4.4
|
96.3
|
1.0
|
|
HG23
|
G:VAL172
|
4.4
|
0.6
|
1.0
|
|
C
|
G:ALA173
|
4.4
|
95.7
|
1.0
|
|
CG
|
G:GLU124
|
4.4
|
61.1
|
1.0
|
|
N
|
G:ALA173
|
4.5
|
94.5
|
1.0
|
|
OG
|
G:SER121
|
4.5
|
62.5
|
1.0
|
|
HB2
|
G:CYS120
|
4.5
|
75.1
|
1.0
|
|
CA
|
G:GLY92
|
4.6
|
73.1
|
1.0
|
|
C
|
G:GLY171
|
4.6
|
90.6
|
1.0
|
|
CA
|
G:VAL172
|
4.6
|
91.1
|
1.0
|
|
CB
|
G:ASP93
|
4.6
|
65.4
|
1.0
|
|
O
|
G:ALA173
|
4.6
|
93.9
|
1.0
|
|
HG22
|
G:VAL172
|
4.7
|
0.6
|
1.0
|
|
HG3
|
G:GLU124
|
4.7
|
73.3
|
1.0
|
|
O
|
G:HOH1310
|
4.7
|
36.6
|
1.0
|
|
N
|
G:SER121
|
4.7
|
62.5
|
1.0
|
|
CA
|
G:CYS120
|
4.7
|
64.0
|
1.0
|
|
OD2
|
G:ASP93
|
4.8
|
67.2
|
1.0
|
|
CA
|
G:GLY171
|
4.8
|
88.8
|
1.0
|
|
N
|
G:SER174
|
4.9
|
97.3
|
1.0
|
|
HA2
|
G:GLY92
|
4.9
|
87.7
|
1.0
|
|
HG2
|
G:GLU124
|
4.9
|
73.3
|
1.0
|
|
HG
|
G:SER121
|
4.9
|
75.0
|
1.0
|
|
H
|
G:ALA94
|
5.0
|
74.9
|
1.0
|
|
CG2
|
G:VAL172
|
5.0
|
88.0
|
1.0
|
|
HA
|
G:SER174
|
5.0
|
0.7
|
1.0
|
|
Calcium binding site 10 out
of 12 in 4pkh
Go back to
Calcium Binding Sites List in 4pkh
Calcium binding site 10 out
of 12 in the Complex of Adp-Actin with the N-Terminal Actin-Binding Domain of Tropomodulin
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Complex of Adp-Actin with the N-Terminal Actin-Binding Domain of Tropomodulin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Ca402
b:81.4
occ:1.00
|
O1B
|
I:ADP401
|
2.4
|
43.4
|
1.0
|
|
O
|
I:HOH513
|
2.7
|
34.3
|
1.0
|
|
O
|
I:HOH510
|
2.8
|
26.8
|
1.0
|
|
HE21
|
I:GLN137
|
3.0
|
86.8
|
1.0
|
|
PB
|
I:ADP401
|
3.3
|
45.7
|
1.0
|
|
NE2
|
I:GLN137
|
3.3
|
72.3
|
1.0
|
|
O3B
|
I:ADP401
|
3.3
|
40.1
|
1.0
|
|
HA2
|
I:GLY13
|
3.4
|
89.3
|
1.0
|
|
HE22
|
I:GLN137
|
3.4
|
86.8
|
1.0
|
|
HA3
|
I:GLY13
|
3.7
|
89.3
|
1.0
|
|
HZ2
|
I:LYS18
|
3.9
|
90.1
|
1.0
|
|
O
|
I:HOH514
|
3.9
|
44.3
|
1.0
|
|
O1A
|
I:ADP401
|
3.9
|
35.3
|
1.0
|
|
CA
|
I:GLY13
|
4.0
|
74.4
|
1.0
|
|
HZ1
|
I:LYS18
|
4.0
|
90.1
|
1.0
|
|
CD
|
I:GLN137
|
4.1
|
72.5
|
1.0
|
|
HG21
|
I:VAL339
|
4.2
|
71.6
|
1.0
|
|
O3A
|
I:ADP401
|
4.3
|
42.8
|
1.0
|
|
HA3
|
I:GLY156
|
4.3
|
99.6
|
1.0
|
|
NZ
|
I:LYS18
|
4.4
|
75.1
|
1.0
|
|
OD2
|
I:ASP11
|
4.4
|
71.3
|
1.0
|
|
O2B
|
I:ADP401
|
4.4
|
47.9
|
1.0
|
|
OD1
|
I:ASP11
|
4.5
|
70.4
|
1.0
|
|
OE1
|
I:GLN137
|
4.5
|
73.4
|
1.0
|
|
OD1
|
I:ASP154
|
4.6
|
0.6
|
1.0
|
|
H
|
I:SER14
|
4.6
|
93.7
|
1.0
|
|
PA
|
I:ADP401
|
4.7
|
35.9
|
1.0
|
|
N
|
I:GLY13
|
4.7
|
73.3
|
1.0
|
|
CG
|
I:ASP11
|
4.8
|
70.5
|
1.0
|
|
HZ3
|
I:LYS18
|
4.8
|
90.1
|
1.0
|
|
O
|
I:ASN12
|
4.9
|
72.5
|
1.0
|
|
HG2
|
I:GLN137
|
5.0
|
85.4
|
1.0
|
|
HB3
|
I:GLN137
|
5.0
|
86.3
|
1.0
|
|
Reference:
J.N.Rao,
Y.Madasu,
R.Dominguez.
Actin Cytoskeleton. Mechanism of Actin Filament Pointed-End Capping By Tropomodulin. Science V. 345 463 2014.
ISSN: ESSN 1095-9203
PubMed: 25061212
DOI: 10.1126/SCIENCE.1256159
Page generated: Sun Jul 14 12:06:51 2024
|
