Calcium in PDB 1pz8: Modulation of Agrin Function By Alternative Splicing and CA2+ Binding
Protein crystallography data
The structure of Modulation of Agrin Function By Alternative Splicing and CA2+ Binding, PDB code: 1pz8
was solved by
J.Stetefeld,
A.T.Alexandrescu,
M.W.Maciejewski,
M.Jenny,
K.Rathgeb-Szabo,
T.Schulthess,
R.Landwehr,
S.Frank,
M.A.Ruegg,
R.A.Kammerer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.35
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
76.847,
56.556,
84.586,
90.00,
99.75,
90.00
|
R / Rfree (%)
|
21.8 /
26
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Modulation of Agrin Function By Alternative Splicing and CA2+ Binding
(pdb code 1pz8). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Modulation of Agrin Function By Alternative Splicing and CA2+ Binding, PDB code: 1pz8:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 1pz8
Go back to
Calcium Binding Sites List in 1pz8
Calcium binding site 1 out
of 4 in the Modulation of Agrin Function By Alternative Splicing and CA2+ Binding
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Modulation of Agrin Function By Alternative Splicing and CA2+ Binding within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca701
b:30.1
occ:1.00
|
O
|
A:LEU90
|
2.5
|
9.2
|
1.0
|
O
|
A:GLN140
|
2.5
|
15.0
|
1.0
|
OD1
|
A:ASP73
|
2.6
|
15.1
|
1.0
|
OD1
|
A:ASP142
|
3.1
|
24.3
|
1.0
|
CG
|
A:ASP142
|
3.4
|
20.1
|
1.0
|
CG
|
A:ASP73
|
3.5
|
11.6
|
1.0
|
C
|
A:LEU90
|
3.6
|
10.2
|
1.0
|
OD2
|
A:ASP142
|
3.7
|
23.7
|
1.0
|
C
|
A:GLN140
|
3.7
|
15.1
|
1.0
|
OD2
|
A:ASP73
|
3.9
|
10.3
|
1.0
|
N
|
A:ASP142
|
4.1
|
15.4
|
1.0
|
CB
|
A:ALA138
|
4.3
|
17.3
|
1.0
|
CA
|
A:LEU90
|
4.3
|
9.5
|
1.0
|
CB
|
A:ASP142
|
4.3
|
16.7
|
1.0
|
N
|
A:GLY91
|
4.5
|
11.1
|
1.0
|
CB
|
A:LEU90
|
4.5
|
9.8
|
1.0
|
CA
|
A:LEU141
|
4.5
|
15.4
|
1.0
|
N
|
A:LEU141
|
4.5
|
14.7
|
1.0
|
CA
|
A:GLN140
|
4.6
|
15.8
|
1.0
|
CB
|
A:GLN140
|
4.7
|
15.9
|
1.0
|
CA
|
A:GLY91
|
4.7
|
11.8
|
1.0
|
C
|
A:LEU141
|
4.7
|
15.2
|
1.0
|
CB
|
A:ASP73
|
4.7
|
10.0
|
1.0
|
N
|
A:GLN140
|
4.8
|
15.3
|
1.0
|
O
|
A:HOH849
|
4.8
|
34.6
|
1.0
|
CA
|
A:ASP142
|
4.8
|
16.7
|
1.0
|
|
Calcium binding site 2 out
of 4 in 1pz8
Go back to
Calcium Binding Sites List in 1pz8
Calcium binding site 2 out
of 4 in the Modulation of Agrin Function By Alternative Splicing and CA2+ Binding
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Modulation of Agrin Function By Alternative Splicing and CA2+ Binding within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca702
b:37.8
occ:1.00
|
O
|
B:LEU90
|
2.5
|
5.2
|
1.0
|
OD1
|
B:ASP73
|
2.6
|
11.5
|
1.0
|
O
|
B:GLN140
|
2.6
|
16.1
|
1.0
|
OD2
|
B:ASP142
|
3.0
|
31.8
|
1.0
|
O
|
B:HOH710
|
3.1
|
25.7
|
1.0
|
CG
|
B:ASP73
|
3.6
|
6.0
|
1.0
|
CG
|
B:GLN140
|
3.6
|
16.2
|
1.0
|
C
|
B:LEU90
|
3.6
|
4.6
|
1.0
|
C
|
B:GLN140
|
3.7
|
16.0
|
1.0
|
OD2
|
B:ASP73
|
3.9
|
7.4
|
1.0
|
CG
|
B:ASP142
|
4.0
|
28.0
|
1.0
|
N
|
B:ASP142
|
4.3
|
22.4
|
1.0
|
CA
|
B:LEU90
|
4.4
|
4.3
|
1.0
|
CA
|
B:GLN140
|
4.5
|
15.1
|
1.0
|
CB
|
B:ASP142
|
4.5
|
24.5
|
1.0
|
CB
|
B:GLN140
|
4.6
|
15.0
|
1.0
|
CB
|
B:LEU90
|
4.6
|
4.7
|
1.0
|
N
|
B:GLY91
|
4.6
|
5.9
|
1.0
|
N
|
B:GLN140
|
4.7
|
13.3
|
1.0
|
N
|
B:LEU141
|
4.7
|
17.6
|
1.0
|
CD
|
B:GLN140
|
4.7
|
18.1
|
1.0
|
CA
|
B:GLY91
|
4.7
|
6.5
|
1.0
|
CB
|
B:ALA138
|
4.7
|
11.3
|
1.0
|
CB
|
B:ASP73
|
4.8
|
4.2
|
1.0
|
CA
|
B:LEU141
|
4.8
|
19.3
|
1.0
|
OD1
|
B:ASP142
|
4.8
|
30.8
|
1.0
|
NE2
|
B:GLN140
|
4.9
|
18.0
|
1.0
|
C
|
B:LEU141
|
5.0
|
20.6
|
1.0
|
|
Calcium binding site 3 out
of 4 in 1pz8
Go back to
Calcium Binding Sites List in 1pz8
Calcium binding site 3 out
of 4 in the Modulation of Agrin Function By Alternative Splicing and CA2+ Binding
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Modulation of Agrin Function By Alternative Splicing and CA2+ Binding within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca703
b:31.7
occ:1.00
|
O
|
C:GLN140
|
2.3
|
11.7
|
1.0
|
O
|
C:LEU90
|
2.5
|
6.3
|
1.0
|
OD1
|
C:ASP73
|
2.6
|
9.4
|
1.0
|
OD2
|
C:ASP142
|
2.7
|
10.8
|
1.0
|
CG
|
C:ASP142
|
3.3
|
11.4
|
1.0
|
O
|
C:HOH762
|
3.4
|
31.9
|
1.0
|
C
|
C:GLN140
|
3.5
|
12.0
|
1.0
|
C
|
C:LEU90
|
3.6
|
5.8
|
1.0
|
CG
|
C:ASP73
|
3.6
|
8.0
|
1.0
|
OD1
|
C:ASP142
|
3.8
|
13.3
|
1.0
|
N
|
C:ASP142
|
3.9
|
9.0
|
1.0
|
OD2
|
C:ASP73
|
4.0
|
9.3
|
1.0
|
CA
|
C:LEU90
|
4.2
|
6.0
|
1.0
|
CB
|
C:ASP142
|
4.3
|
9.4
|
1.0
|
N
|
C:LEU141
|
4.3
|
11.4
|
1.0
|
CA
|
C:LEU141
|
4.3
|
11.6
|
1.0
|
CB
|
C:ALA138
|
4.3
|
14.3
|
1.0
|
CB
|
C:LEU90
|
4.4
|
6.4
|
1.0
|
CA
|
C:GLN140
|
4.5
|
12.9
|
1.0
|
C
|
C:LEU141
|
4.6
|
10.4
|
1.0
|
N
|
C:GLY91
|
4.6
|
6.6
|
1.0
|
N
|
C:GLN140
|
4.6
|
12.6
|
1.0
|
CB
|
C:GLN140
|
4.6
|
12.8
|
1.0
|
O
|
C:HOH803
|
4.7
|
23.2
|
1.0
|
CA
|
C:ASP142
|
4.8
|
9.5
|
1.0
|
CB
|
C:ASP73
|
4.9
|
3.4
|
1.0
|
CA
|
C:GLY91
|
4.9
|
7.1
|
1.0
|
|
Calcium binding site 4 out
of 4 in 1pz8
Go back to
Calcium Binding Sites List in 1pz8
Calcium binding site 4 out
of 4 in the Modulation of Agrin Function By Alternative Splicing and CA2+ Binding
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Modulation of Agrin Function By Alternative Splicing and CA2+ Binding within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca704
b:33.1
occ:1.00
|
O
|
D:GLN140
|
2.3
|
11.6
|
1.0
|
O
|
D:LEU90
|
2.5
|
7.6
|
1.0
|
OD1
|
D:ASP73
|
2.6
|
9.9
|
1.0
|
OD2
|
D:ASP142
|
2.8
|
14.7
|
1.0
|
O
|
D:HOH764
|
3.0
|
33.4
|
1.0
|
CG
|
D:ASP142
|
3.5
|
16.0
|
1.0
|
C
|
D:GLN140
|
3.5
|
11.7
|
1.0
|
C
|
D:LEU90
|
3.6
|
7.3
|
1.0
|
CG
|
D:ASP73
|
3.6
|
7.5
|
1.0
|
OD2
|
D:ASP73
|
3.9
|
11.8
|
1.0
|
O
|
D:HOH792
|
3.9
|
33.6
|
1.0
|
OD1
|
D:ASP142
|
4.0
|
17.5
|
1.0
|
N
|
D:ASP142
|
4.0
|
13.0
|
1.0
|
CA
|
D:LEU90
|
4.3
|
7.4
|
1.0
|
CA
|
D:LEU141
|
4.3
|
12.3
|
1.0
|
N
|
D:LEU141
|
4.3
|
11.6
|
1.0
|
CB
|
D:ASP142
|
4.4
|
13.8
|
1.0
|
CA
|
D:GLN140
|
4.5
|
12.1
|
1.0
|
N
|
D:GLY91
|
4.5
|
7.8
|
1.0
|
CB
|
D:LEU90
|
4.5
|
8.1
|
1.0
|
C
|
D:LEU141
|
4.6
|
12.6
|
1.0
|
CB
|
D:ALA138
|
4.6
|
12.2
|
1.0
|
N
|
D:GLN140
|
4.7
|
11.6
|
1.0
|
CA
|
D:GLY91
|
4.7
|
7.5
|
1.0
|
CB
|
D:GLN140
|
4.7
|
12.1
|
1.0
|
CA
|
D:ASP142
|
4.9
|
13.7
|
1.0
|
CB
|
D:ASP73
|
4.9
|
3.9
|
1.0
|
|
Reference:
J.Stetefeld,
A.T.Alexandrescu,
M.W.Maciejewski,
M.Jenny,
K.Rathgeb-Szabo,
T.Schulthess,
R.Landwehr,
S.Frank,
M.A.Ruegg,
R.A.Kammerer.
Modulation of Agrin Function By Alternative Splicing and CA2+ Binding. Structure V. 12 503 2004.
ISSN: ISSN 0969-2126
PubMed: 15016366
DOI: 10.1016/J.STR.2004.02.001
Page generated: Thu Jul 11 13:57:51 2024
|