Calcium in PDB 7w52: Crystal Structure of Fragmin Domain-1 (15-160) in Complex with Actin
Protein crystallography data
The structure of Crystal Structure of Fragmin Domain-1 (15-160) in Complex with Actin, PDB code: 7w52
was solved by
S.Takeda,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
46.67 /
2.00
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
56.987,
96.26,
426.923,
90,
90,
90
|
|
R / Rfree (%)
|
21 /
24.6
|
Other elements in 7w52:
The structure of Crystal Structure of Fragmin Domain-1 (15-160) in Complex with Actin also contains other interesting chemical elements:
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Calcium atom in the Crystal Structure of Fragmin Domain-1 (15-160) in Complex with Actin
(pdb code 7w52). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the
Crystal Structure of Fragmin Domain-1 (15-160) in Complex with Actin, PDB code: 7w52:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 12 in 7w52
Go back to
Calcium Binding Sites List in 7w52
Calcium binding site 1 out
of 12 in the Crystal Structure of Fragmin Domain-1 (15-160) in Complex with Actin
 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 Fragmin Domain-1 (15-160) in Complex with Actin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca402
b:29.4
occ:1.00
|
O2B
|
A:ATP401
|
2.1
|
31.2
|
1.0
|
|
O
|
A:HOH594
|
2.3
|
29.3
|
1.0
|
|
O3G
|
A:ATP401
|
2.4
|
33.5
|
1.0
|
|
O
|
A:HOH648
|
2.4
|
26.6
|
1.0
|
|
O
|
A:HOH549
|
2.6
|
22.1
|
1.0
|
|
O
|
A:HOH616
|
2.6
|
30.6
|
1.0
|
|
O
|
A:HOH547
|
2.6
|
20.6
|
1.0
|
|
PB
|
A:ATP401
|
3.5
|
32.6
|
1.0
|
|
PG
|
A:ATP401
|
3.5
|
35.1
|
1.0
|
|
O1G
|
A:ATP401
|
3.8
|
34.1
|
1.0
|
|
O3B
|
A:ATP401
|
3.9
|
36.2
|
1.0
|
|
O3A
|
A:ATP401
|
4.1
|
24.2
|
1.0
|
|
CA
|
A:GLY13
|
4.2
|
36.5
|
1.0
|
|
O
|
A:HOH620
|
4.3
|
32.6
|
1.0
|
|
O1A
|
A:ATP401
|
4.4
|
28.3
|
1.0
|
|
OE1
|
A:GLN137
|
4.4
|
30.3
|
1.0
|
|
NZ
|
A:LYS18
|
4.4
|
30.4
|
1.0
|
|
O
|
A:HOH524
|
4.5
|
28.9
|
1.0
|
|
CD
|
A:GLN137
|
4.7
|
36.5
|
1.0
|
|
OD2
|
A:ASP154
|
4.7
|
30.7
|
1.0
|
|
PA
|
A:ATP401
|
4.7
|
27.0
|
1.0
|
|
O1B
|
A:ATP401
|
4.7
|
28.0
|
1.0
|
|
OD2
|
A:ASP11
|
4.8
|
31.2
|
1.0
|
|
OD1
|
A:ASP11
|
4.8
|
24.2
|
1.0
|
|
O2G
|
A:ATP401
|
4.8
|
37.7
|
1.0
|
|
NE2
|
A:GLN137
|
4.9
|
33.3
|
1.0
|
|
OD1
|
A:ASP154
|
4.9
|
36.5
|
1.0
|
|
O
|
A:ASN12
|
4.9
|
32.5
|
1.0
|
|
N
|
A:GLY13
|
5.0
|
30.7
|
1.0
|
|
Calcium binding site 2 out
of 12 in 7w52
Go back to
Calcium Binding Sites List in 7w52
Calcium binding site 2 out
of 12 in the Crystal Structure of Fragmin Domain-1 (15-160) in Complex with Actin
 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 Fragmin Domain-1 (15-160) in Complex with Actin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca201
b:33.6
occ:1.00
|
O
|
B:PRO122
|
2.3
|
38.6
|
1.0
|
|
OD2
|
B:ASP115
|
2.4
|
29.8
|
1.0
|
|
O
|
B:HOH409
|
2.4
|
45.0
|
1.0
|
|
OE1
|
A:GLU167
|
2.5
|
37.4
|
1.0
|
|
O
|
B:GLY120
|
2.5
|
39.8
|
1.0
|
|
OD1
|
B:ASP115
|
2.6
|
28.0
|
1.0
|
|
O
|
B:HOH406
|
2.7
|
32.3
|
1.0
|
|
CG
|
B:ASP115
|
2.8
|
33.5
|
1.0
|
|
C
|
B:GLY120
|
3.5
|
41.5
|
1.0
|
|
C
|
B:PRO122
|
3.5
|
34.9
|
1.0
|
|
CD
|
A:GLU167
|
3.6
|
36.8
|
1.0
|
|
O
|
A:HOH643
|
3.8
|
45.5
|
1.0
|
|
CA
|
B:GLY120
|
3.9
|
38.2
|
1.0
|
|
OE2
|
A:GLU167
|
4.0
|
31.2
|
1.0
|
|
O
|
B:HOH373
|
4.1
|
41.8
|
1.0
|
|
N
|
B:PRO122
|
4.2
|
42.8
|
1.0
|
|
C
|
B:LEU121
|
4.3
|
41.9
|
1.0
|
|
CB
|
B:ASP115
|
4.3
|
31.6
|
1.0
|
|
CA
|
B:PRO122
|
4.4
|
36.4
|
1.0
|
|
N
|
B:VAL123
|
4.5
|
31.9
|
1.0
|
|
O
|
A:HOH591
|
4.5
|
43.2
|
1.0
|
|
O
|
B:LEU121
|
4.5
|
36.5
|
1.0
|
|
N
|
B:LEU121
|
4.6
|
39.0
|
1.0
|
|
NE2
|
B:GLN124
|
4.6
|
27.5
|
1.0
|
|
CA
|
B:VAL123
|
4.7
|
28.9
|
1.0
|
|
CD
|
B:PRO122
|
4.7
|
33.4
|
1.0
|
|
O
|
B:HOH313
|
4.8
|
38.1
|
1.0
|
|
CG
|
B:GLN124
|
4.8
|
32.9
|
1.0
|
|
CG
|
A:GLU167
|
4.9
|
31.7
|
1.0
|
|
CB
|
B:PRO122
|
4.9
|
33.7
|
1.0
|
|
CA
|
B:LEU121
|
4.9
|
40.9
|
1.0
|
|
Calcium binding site 3 out
of 12 in 7w52
Go back to
Calcium Binding Sites List in 7w52
Calcium binding site 3 out
of 12 in the Crystal Structure of Fragmin Domain-1 (15-160) in Complex with Actin
 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 Fragmin Domain-1 (15-160) in Complex with Actin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca202
b:26.8
occ:1.00
|
O
|
B:VAL152
|
2.3
|
25.6
|
1.0
|
|
OD1
|
B:ASP70
|
2.3
|
28.1
|
1.0
|
|
OE1
|
B:GLU103
|
2.3
|
24.1
|
1.0
|
|
O
|
B:HOH357
|
2.3
|
23.2
|
1.0
|
|
O
|
B:GLY69
|
2.4
|
29.8
|
1.0
|
|
OE2
|
B:GLU103
|
2.5
|
23.5
|
1.0
|
|
O
|
B:HOH399
|
2.6
|
30.2
|
1.0
|
|
CD
|
B:GLU103
|
2.7
|
26.8
|
1.0
|
|
C
|
B:GLY69
|
3.4
|
30.4
|
1.0
|
|
C
|
B:VAL152
|
3.5
|
28.3
|
1.0
|
|
CG
|
B:ASP70
|
3.5
|
27.9
|
1.0
|
|
N
|
B:VAL152
|
3.9
|
25.8
|
1.0
|
|
CA
|
B:ASP70
|
4.0
|
23.0
|
1.0
|
|
CG1
|
B:VAL152
|
4.1
|
25.2
|
1.0
|
|
N
|
B:ASP70
|
4.1
|
24.5
|
1.0
|
|
C
|
B:GLY151
|
4.2
|
28.7
|
1.0
|
|
CA
|
B:VAL152
|
4.2
|
26.5
|
1.0
|
|
O
|
B:HOH332
|
4.2
|
21.2
|
1.0
|
|
CG
|
B:GLU103
|
4.2
|
19.8
|
1.0
|
|
O
|
B:HOH344
|
4.3
|
29.9
|
1.0
|
|
CB
|
B:ASP70
|
4.3
|
23.7
|
1.0
|
|
CA
|
B:GLY69
|
4.4
|
27.8
|
1.0
|
|
OD2
|
B:ASP70
|
4.4
|
26.9
|
1.0
|
|
OG1
|
B:THR100
|
4.5
|
27.6
|
1.0
|
|
N
|
B:GLU153
|
4.5
|
27.5
|
1.0
|
|
C
|
B:GLU153
|
4.5
|
28.4
|
1.0
|
|
CA
|
B:GLY151
|
4.6
|
26.3
|
1.0
|
|
O
|
B:HOH322
|
4.6
|
28.2
|
1.0
|
|
CA
|
B:GLU153
|
4.6
|
29.7
|
1.0
|
|
N
|
B:THR154
|
4.7
|
25.4
|
1.0
|
|
OG1
|
B:THR99
|
4.7
|
29.0
|
1.0
|
|
O
|
B:GLY151
|
4.8
|
27.3
|
1.0
|
|
O
|
B:GLU153
|
4.8
|
24.2
|
1.0
|
|
CB
|
B:VAL152
|
4.8
|
29.2
|
1.0
|
|
N
|
B:THR100
|
4.8
|
31.6
|
1.0
|
|
CA
|
B:THR99
|
4.9
|
26.0
|
1.0
|
|
Calcium binding site 4 out
of 12 in 7w52
Go back to
Calcium Binding Sites List in 7w52
Calcium binding site 4 out
of 12 in the Crystal Structure of Fragmin Domain-1 (15-160) in Complex with Actin
 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 Fragmin Domain-1 (15-160) in Complex with Actin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca402
b:28.9
occ:1.00
|
O2B
|
C:ATP401
|
2.3
|
26.4
|
1.0
|
|
O
|
C:HOH583
|
2.3
|
31.0
|
1.0
|
|
O
|
C:HOH548
|
2.4
|
26.8
|
1.0
|
|
O3G
|
C:ATP401
|
2.4
|
33.0
|
1.0
|
|
O
|
C:HOH544
|
2.6
|
25.6
|
1.0
|
|
O
|
C:HOH629
|
2.6
|
26.0
|
1.0
|
|
O
|
C:HOH638
|
2.7
|
30.2
|
1.0
|
|
PG
|
C:ATP401
|
3.6
|
29.6
|
1.0
|
|
PB
|
C:ATP401
|
3.6
|
30.0
|
1.0
|
|
O1G
|
C:ATP401
|
4.0
|
29.1
|
1.0
|
|
O3B
|
C:ATP401
|
4.1
|
26.1
|
1.0
|
|
CA
|
C:GLY13
|
4.2
|
30.6
|
1.0
|
|
O
|
C:HOH613
|
4.2
|
25.1
|
1.0
|
|
O3A
|
C:ATP401
|
4.4
|
31.2
|
1.0
|
|
OE1
|
C:GLN137
|
4.4
|
35.9
|
1.0
|
|
O1A
|
C:ATP401
|
4.4
|
29.0
|
1.0
|
|
NZ
|
C:LYS18
|
4.4
|
27.5
|
1.0
|
|
CD
|
C:GLN137
|
4.5
|
36.9
|
1.0
|
|
OD2
|
C:ASP154
|
4.6
|
31.7
|
1.0
|
|
O
|
C:HOH560
|
4.6
|
28.7
|
1.0
|
|
OD1
|
C:ASP11
|
4.6
|
24.2
|
1.0
|
|
NE2
|
C:GLN137
|
4.6
|
29.3
|
1.0
|
|
OD2
|
C:ASP11
|
4.7
|
29.7
|
1.0
|
|
O1B
|
C:ATP401
|
4.9
|
31.5
|
1.0
|
|
PA
|
C:ATP401
|
4.9
|
25.5
|
1.0
|
|
O
|
C:ASN12
|
4.9
|
32.4
|
1.0
|
|
O2G
|
C:ATP401
|
4.9
|
28.7
|
1.0
|
|
OD1
|
C:ASP154
|
4.9
|
34.4
|
1.0
|
|
N
|
C:GLY13
|
4.9
|
28.7
|
1.0
|
|
Calcium binding site 5 out
of 12 in 7w52
Go back to
Calcium Binding Sites List in 7w52
Calcium binding site 5 out
of 12 in the Crystal Structure of Fragmin Domain-1 (15-160) in Complex with Actin
 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 Fragmin Domain-1 (15-160) in Complex with Actin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca201
b:37.1
occ:1.00
|
O
|
D:PRO122
|
2.2
|
33.9
|
1.0
|
|
OD2
|
D:ASP115
|
2.4
|
35.1
|
1.0
|
|
O
|
C:HOH692
|
2.4
|
39.5
|
1.0
|
|
OE1
|
C:GLU167
|
2.4
|
31.5
|
1.0
|
|
O
|
D:HOH383
|
2.5
|
44.3
|
1.0
|
|
OD1
|
D:ASP115
|
2.6
|
33.1
|
1.0
|
|
O
|
D:GLY120
|
2.6
|
33.1
|
1.0
|
|
CG
|
D:ASP115
|
2.8
|
36.3
|
1.0
|
|
O
|
D:HOH303
|
3.3
|
48.8
|
1.0
|
|
C
|
D:PRO122
|
3.5
|
34.9
|
1.0
|
|
C
|
D:GLY120
|
3.5
|
35.3
|
1.0
|
|
CD
|
C:GLU167
|
3.5
|
37.0
|
1.0
|
|
O
|
D:HOH384
|
3.7
|
46.9
|
1.0
|
|
CA
|
D:GLY120
|
4.0
|
38.6
|
1.0
|
|
OE2
|
C:GLU167
|
4.0
|
31.1
|
1.0
|
|
N
|
D:PRO122
|
4.1
|
40.0
|
1.0
|
|
C
|
D:LEU121
|
4.2
|
44.0
|
1.0
|
|
CB
|
D:ASP115
|
4.3
|
30.3
|
1.0
|
|
CA
|
D:PRO122
|
4.3
|
36.9
|
1.0
|
|
N
|
D:VAL123
|
4.4
|
36.7
|
1.0
|
|
O
|
D:LEU121
|
4.5
|
36.1
|
1.0
|
|
N
|
D:LEU121
|
4.5
|
38.1
|
1.0
|
|
O
|
C:HOH656
|
4.5
|
43.2
|
1.0
|
|
CA
|
D:VAL123
|
4.6
|
38.8
|
1.0
|
|
NE2
|
D:GLN124
|
4.7
|
32.7
|
1.0
|
|
CD
|
D:PRO122
|
4.8
|
33.1
|
1.0
|
|
CG
|
C:GLU167
|
4.8
|
28.4
|
1.0
|
|
CA
|
D:LEU121
|
4.8
|
36.9
|
1.0
|
|
CG
|
D:GLN124
|
4.9
|
33.4
|
1.0
|
|
CB
|
D:PRO122
|
4.9
|
39.2
|
1.0
|
|
CB
|
C:GLU167
|
4.9
|
40.7
|
1.0
|
|
Calcium binding site 6 out
of 12 in 7w52
Go back to
Calcium Binding Sites List in 7w52
Calcium binding site 6 out
of 12 in the Crystal Structure of Fragmin Domain-1 (15-160) in Complex with Actin
 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 Fragmin Domain-1 (15-160) in Complex with Actin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca202
b:28.9
occ:1.00
|
O
|
D:GLY69
|
2.3
|
29.8
|
1.0
|
|
O
|
D:HOH357
|
2.3
|
30.4
|
1.0
|
|
OD1
|
D:ASP70
|
2.3
|
30.3
|
1.0
|
|
OE2
|
D:GLU103
|
2.4
|
30.0
|
1.0
|
|
O
|
D:VAL152
|
2.4
|
36.9
|
1.0
|
|
O
|
D:HOH377
|
2.5
|
26.1
|
1.0
|
|
OE1
|
D:GLU103
|
2.5
|
28.0
|
1.0
|
|
CD
|
D:GLU103
|
2.8
|
27.3
|
1.0
|
|
C
|
D:GLY69
|
3.3
|
25.8
|
1.0
|
|
CG
|
D:ASP70
|
3.5
|
31.1
|
1.0
|
|
C
|
D:VAL152
|
3.6
|
30.6
|
1.0
|
|
CA
|
D:ASP70
|
3.8
|
21.6
|
1.0
|
|
N
|
D:VAL152
|
3.9
|
37.0
|
1.0
|
|
N
|
D:ASP70
|
3.9
|
23.8
|
1.0
|
|
C
|
D:GLY151
|
4.1
|
33.7
|
1.0
|
|
CG1
|
D:VAL152
|
4.2
|
34.5
|
1.0
|
|
CB
|
D:ASP70
|
4.3
|
28.5
|
1.0
|
|
CG
|
D:GLU103
|
4.3
|
24.6
|
1.0
|
|
CA
|
D:GLY69
|
4.3
|
28.1
|
1.0
|
|
CA
|
D:VAL152
|
4.3
|
29.9
|
1.0
|
|
O
|
D:HOH341
|
4.3
|
31.7
|
1.0
|
|
O
|
D:HOH322
|
4.3
|
27.5
|
1.0
|
|
CA
|
D:GLY151
|
4.4
|
34.9
|
1.0
|
|
OD2
|
D:ASP70
|
4.4
|
33.0
|
1.0
|
|
OG1
|
D:THR100
|
4.6
|
28.9
|
1.0
|
|
C
|
D:GLU153
|
4.6
|
30.2
|
1.0
|
|
OG1
|
D:THR99
|
4.6
|
23.4
|
1.0
|
|
N
|
D:GLU153
|
4.7
|
30.4
|
1.0
|
|
O
|
D:HOH356
|
4.7
|
33.8
|
1.0
|
|
O
|
D:GLY151
|
4.7
|
34.0
|
1.0
|
|
O
|
D:HOH313
|
4.8
|
35.5
|
1.0
|
|
N
|
D:THR154
|
4.8
|
33.4
|
1.0
|
|
O
|
D:GLU153
|
4.8
|
29.3
|
1.0
|
|
CA
|
D:THR99
|
4.9
|
23.3
|
1.0
|
|
N
|
D:THR100
|
4.9
|
26.9
|
1.0
|
|
CA
|
D:GLU153
|
4.9
|
38.1
|
1.0
|
|
CB
|
D:VAL152
|
4.9
|
39.1
|
1.0
|
|
Calcium binding site 7 out
of 12 in 7w52
Go back to
Calcium Binding Sites List in 7w52
Calcium binding site 7 out
of 12 in the Crystal Structure of Fragmin Domain-1 (15-160) in Complex with Actin
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Crystal Structure of Fragmin Domain-1 (15-160) in Complex with Actin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca402
b:26.8
occ:1.00
|
O2B
|
E:ATP401
|
2.2
|
24.5
|
1.0
|
|
O
|
E:HOH542
|
2.4
|
22.7
|
1.0
|
|
O
|
E:HOH531
|
2.4
|
26.7
|
1.0
|
|
O3G
|
E:ATP401
|
2.5
|
25.1
|
1.0
|
|
O
|
E:HOH588
|
2.5
|
27.0
|
1.0
|
|
O
|
E:HOH521
|
2.5
|
31.1
|
1.0
|
|
O
|
E:HOH591
|
2.8
|
33.3
|
1.0
|
|
PB
|
E:ATP401
|
3.5
|
29.9
|
1.0
|
|
PG
|
E:ATP401
|
3.6
|
27.6
|
1.0
|
|
O1G
|
E:ATP401
|
3.9
|
26.7
|
1.0
|
|
O3B
|
E:ATP401
|
4.0
|
24.9
|
1.0
|
|
O3A
|
E:ATP401
|
4.2
|
26.4
|
1.0
|
|
O1A
|
E:ATP401
|
4.3
|
30.8
|
1.0
|
|
CA
|
E:GLY13
|
4.3
|
35.9
|
1.0
|
|
O
|
E:HOH613
|
4.3
|
29.4
|
1.0
|
|
NZ
|
E:LYS18
|
4.3
|
22.6
|
1.0
|
|
O
|
E:HOH577
|
4.3
|
29.1
|
1.0
|
|
OE1
|
E:GLN137
|
4.5
|
32.3
|
1.0
|
|
OD2
|
E:ASP11
|
4.6
|
27.1
|
1.0
|
|
CD
|
E:GLN137
|
4.6
|
40.4
|
1.0
|
|
PA
|
E:ATP401
|
4.7
|
30.3
|
1.0
|
|
OD1
|
E:ASP11
|
4.7
|
23.2
|
1.0
|
|
OD2
|
E:ASP154
|
4.7
|
32.4
|
1.0
|
|
OD1
|
E:ASP154
|
4.7
|
32.7
|
1.0
|
|
O1B
|
E:ATP401
|
4.8
|
28.6
|
1.0
|
|
NE2
|
E:GLN137
|
4.9
|
29.4
|
1.0
|
|
O2G
|
E:ATP401
|
4.9
|
27.9
|
1.0
|
|
O2A
|
E:ATP401
|
4.9
|
36.3
|
1.0
|
|
Calcium binding site 8 out
of 12 in 7w52
Go back to
Calcium Binding Sites List in 7w52
Calcium binding site 8 out
of 12 in the Crystal Structure of Fragmin Domain-1 (15-160) in Complex with Actin
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Crystal Structure of Fragmin Domain-1 (15-160) in Complex with Actin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca400
b:36.3
occ:1.00
|
O
|
F:HOH557
|
2.2
|
40.1
|
1.0
|
|
O
|
F:PRO122
|
2.3
|
37.0
|
1.0
|
|
OD2
|
F:ASP115
|
2.3
|
38.1
|
1.0
|
|
OE1
|
E:GLU167
|
2.5
|
36.4
|
1.0
|
|
O
|
F:GLY120
|
2.5
|
41.0
|
1.0
|
|
OD1
|
F:ASP115
|
2.6
|
31.8
|
1.0
|
|
O
|
F:HOH566
|
2.6
|
32.8
|
1.0
|
|
CG
|
F:ASP115
|
2.8
|
39.6
|
1.0
|
|
C
|
F:GLY120
|
3.4
|
38.4
|
1.0
|
|
C
|
F:PRO122
|
3.6
|
34.9
|
1.0
|
|
CD
|
E:GLU167
|
3.6
|
35.4
|
1.0
|
|
O
|
E:HOH565
|
3.7
|
46.9
|
1.0
|
|
CA
|
F:GLY120
|
4.0
|
39.6
|
1.0
|
|
OE2
|
E:GLU167
|
4.0
|
35.1
|
1.0
|
|
N
|
F:PRO122
|
4.2
|
36.8
|
1.0
|
|
O
|
F:HOH560
|
4.2
|
52.5
|
1.0
|
|
C
|
F:LEU121
|
4.2
|
37.5
|
1.0
|
|
CB
|
F:ASP115
|
4.3
|
33.6
|
1.0
|
|
CA
|
F:PRO122
|
4.4
|
34.0
|
1.0
|
|
N
|
F:LEU121
|
4.4
|
41.6
|
1.0
|
|
O
|
E:HOH528
|
4.4
|
38.3
|
1.0
|
|
O
|
F:LEU121
|
4.5
|
37.7
|
1.0
|
|
N
|
F:VAL123
|
4.5
|
38.9
|
1.0
|
|
O
|
F:HOH520
|
4.6
|
34.8
|
1.0
|
|
NE2
|
F:GLN124
|
4.6
|
30.2
|
1.0
|
|
CA
|
F:VAL123
|
4.7
|
34.7
|
1.0
|
|
CD
|
F:PRO122
|
4.8
|
36.7
|
1.0
|
|
CA
|
F:LEU121
|
4.8
|
31.3
|
1.0
|
|
CG
|
E:GLU167
|
4.8
|
29.8
|
1.0
|
|
CG
|
F:GLN124
|
4.8
|
29.7
|
1.0
|
|
CB
|
E:GLU167
|
4.9
|
32.0
|
1.0
|
|
CB
|
F:PRO122
|
5.0
|
34.7
|
1.0
|
|
Calcium binding site 9 out
of 12 in 7w52
Go back to
Calcium Binding Sites List in 7w52
Calcium binding site 9 out
of 12 in the Crystal Structure of Fragmin Domain-1 (15-160) in Complex with Actin
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Crystal Structure of Fragmin Domain-1 (15-160) in Complex with Actin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca401
b:34.9
occ:1.00
|
O
|
F:GLY69
|
2.3
|
38.7
|
1.0
|
|
OD1
|
F:ASP70
|
2.3
|
35.3
|
1.0
|
|
OE2
|
F:GLU103
|
2.4
|
30.1
|
1.0
|
|
O
|
F:VAL152
|
2.4
|
35.3
|
1.0
|
|
O
|
F:HOH542
|
2.4
|
27.7
|
1.0
|
|
OE1
|
F:GLU103
|
2.5
|
30.4
|
1.0
|
|
O
|
F:HOH534
|
2.5
|
33.5
|
1.0
|
|
CD
|
F:GLU103
|
2.7
|
34.7
|
1.0
|
|
C
|
F:GLY69
|
3.4
|
36.1
|
1.0
|
|
CG
|
F:ASP70
|
3.6
|
41.2
|
1.0
|
|
C
|
F:VAL152
|
3.6
|
44.1
|
1.0
|
|
N
|
F:VAL152
|
3.9
|
32.0
|
1.0
|
|
CA
|
F:ASP70
|
3.9
|
36.9
|
1.0
|
|
N
|
F:ASP70
|
4.1
|
32.1
|
1.0
|
|
CG1
|
F:VAL152
|
4.1
|
38.5
|
1.0
|
|
C
|
F:GLY151
|
4.2
|
39.6
|
1.0
|
|
CG
|
F:GLU103
|
4.3
|
31.9
|
1.0
|
|
CA
|
F:VAL152
|
4.3
|
38.3
|
1.0
|
|
CB
|
F:ASP70
|
4.3
|
36.0
|
1.0
|
|
O
|
F:HOH528
|
4.4
|
36.6
|
1.0
|
|
CA
|
F:GLY69
|
4.4
|
44.6
|
1.0
|
|
OD2
|
F:ASP70
|
4.5
|
44.0
|
1.0
|
|
CA
|
F:GLY151
|
4.5
|
40.9
|
1.0
|
|
O
|
F:HOH508
|
4.5
|
31.7
|
1.0
|
|
OG1
|
F:THR100
|
4.6
|
30.4
|
1.0
|
|
C
|
F:GLU153
|
4.7
|
42.1
|
1.0
|
|
N
|
F:GLU153
|
4.7
|
38.5
|
1.0
|
|
OG1
|
F:THR99
|
4.7
|
31.3
|
1.0
|
|
O
|
F:HOH530
|
4.7
|
43.0
|
1.0
|
|
N
|
F:THR154
|
4.8
|
37.4
|
1.0
|
|
O
|
F:GLY151
|
4.8
|
42.0
|
1.0
|
|
CA
|
F:THR99
|
4.9
|
31.6
|
1.0
|
|
O
|
F:HOH502
|
4.9
|
49.7
|
1.0
|
|
CA
|
F:GLU153
|
4.9
|
43.1
|
1.0
|
|
N
|
F:THR100
|
4.9
|
29.7
|
1.0
|
|
CB
|
F:VAL152
|
4.9
|
40.3
|
1.0
|
|
O
|
F:GLU153
|
4.9
|
33.2
|
1.0
|
|
O
|
F:HOH524
|
4.9
|
36.4
|
1.0
|
|
Calcium binding site 10 out
of 12 in 7w52
Go back to
Calcium Binding Sites List in 7w52
Calcium binding site 10 out
of 12 in the Crystal Structure of Fragmin Domain-1 (15-160) in Complex with Actin
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Crystal Structure of Fragmin Domain-1 (15-160) in Complex with Actin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Ca402
b:34.8
occ:1.00
|
O2B
|
G:ATP401
|
2.2
|
35.5
|
1.0
|
|
O
|
G:HOH556
|
2.4
|
36.6
|
1.0
|
|
O
|
G:HOH520
|
2.4
|
34.7
|
1.0
|
|
O
|
G:HOH595
|
2.4
|
29.3
|
1.0
|
|
O3G
|
G:ATP401
|
2.4
|
31.2
|
1.0
|
|
O
|
G:HOH531
|
2.5
|
29.7
|
1.0
|
|
O
|
G:HOH540
|
2.6
|
27.8
|
1.0
|
|
PG
|
G:ATP401
|
3.5
|
39.5
|
1.0
|
|
PB
|
G:ATP401
|
3.6
|
34.8
|
1.0
|
|
O1G
|
G:ATP401
|
3.7
|
34.1
|
1.0
|
|
O3B
|
G:ATP401
|
4.0
|
39.9
|
1.0
|
|
O
|
G:HOH538
|
4.0
|
38.6
|
1.0
|
|
O1A
|
G:ATP401
|
4.2
|
33.3
|
1.0
|
|
O3A
|
G:ATP401
|
4.2
|
29.6
|
1.0
|
|
CA
|
G:GLY13
|
4.3
|
31.6
|
1.0
|
|
OE1
|
G:GLN137
|
4.3
|
37.9
|
1.0
|
|
NZ
|
G:LYS18
|
4.4
|
33.1
|
1.0
|
|
OD2
|
G:ASP154
|
4.6
|
37.0
|
1.0
|
|
CD
|
G:GLN137
|
4.6
|
41.1
|
1.0
|
|
O
|
G:HOH516
|
4.6
|
31.3
|
1.0
|
|
OD2
|
G:ASP11
|
4.7
|
32.0
|
1.0
|
|
PA
|
G:ATP401
|
4.7
|
35.3
|
1.0
|
|
OD1
|
G:ASP154
|
4.8
|
40.4
|
1.0
|
|
O1B
|
G:ATP401
|
4.8
|
33.2
|
1.0
|
|
OD1
|
G:ASP11
|
4.8
|
26.6
|
1.0
|
|
O2G
|
G:ATP401
|
4.8
|
38.2
|
1.0
|
|
NE2
|
G:GLN137
|
4.9
|
34.8
|
1.0
|
|
O
|
G:ASN12
|
5.0
|
30.5
|
1.0
|
|
Reference:
Y.Kanematsu,
A.Narita,
T.Oda,
R.Koike,
M.Ota,
Y.Takano,
K.Moritsugu,
I.Fujiwara,
K.Tanaka,
H.Komatsu,
T.Nagae,
N.Watanabe,
M.Iwasa,
Y.Maeda,
S.Takeda.
Structures and Mechanisms of Actin Atp Hydrolysis. Proc.Natl.Acad.Sci.Usa V. 119 41119 2022.
ISSN: ESSN 1091-6490
PubMed: 36252034
DOI: 10.1073/PNAS.2122641119
Page generated: Tue Apr 4 19:08:50 2023
|
