Calcium in PDB 7p74: The Pdz Domain of SYNJ2BP Complexed with the Phosphorylated Pdz- Binding Motif of RSK1
Enzymatic activity of The Pdz Domain of SYNJ2BP Complexed with the Phosphorylated Pdz- Binding Motif of RSK1
All present enzymatic activity of The Pdz Domain of SYNJ2BP Complexed with the Phosphorylated Pdz- Binding Motif of RSK1:
2.7.11.1;
Protein crystallography data
The structure of The Pdz Domain of SYNJ2BP Complexed with the Phosphorylated Pdz- Binding Motif of RSK1, PDB code: 7p74
was solved by
G.Gogl,
A.Cousido-Siah,
G.Trave,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.71 /
1.90
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
59.62,
75.15,
108.46,
90,
90,
90
|
R / Rfree (%)
|
18.1 /
21.1
|
Calcium Binding Sites:
The binding sites of Calcium atom in the The Pdz Domain of SYNJ2BP Complexed with the Phosphorylated Pdz- Binding Motif of RSK1
(pdb code 7p74). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
The Pdz Domain of SYNJ2BP Complexed with the Phosphorylated Pdz- Binding Motif of RSK1, PDB code: 7p74:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 7p74
Go back to
Calcium Binding Sites List in 7p74
Calcium binding site 1 out
of 4 in the The Pdz Domain of SYNJ2BP Complexed with the Phosphorylated Pdz- Binding Motif of RSK1
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of The Pdz Domain of SYNJ2BP Complexed with the Phosphorylated Pdz- Binding Motif of RSK1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca501
b:43.9
occ:1.00
|
O
|
A:VAL134
|
2.4
|
40.6
|
1.0
|
O
|
A:HOH733
|
2.4
|
62.5
|
1.0
|
O
|
A:GLY133
|
2.4
|
50.3
|
1.0
|
O
|
A:HOH780
|
2.4
|
43.5
|
1.0
|
OE1
|
A:GLU136
|
2.4
|
52.0
|
1.0
|
O
|
A:HOH794
|
2.6
|
53.2
|
1.0
|
OE2
|
A:GLU136
|
2.7
|
49.2
|
1.0
|
CD
|
A:GLU136
|
2.9
|
48.9
|
1.0
|
C
|
A:GLY133
|
3.4
|
49.5
|
1.0
|
C
|
A:VAL134
|
3.5
|
43.0
|
1.0
|
O
|
A:HOH792
|
4.1
|
52.1
|
1.0
|
N
|
A:VAL134
|
4.1
|
41.3
|
1.0
|
CA
|
A:VAL134
|
4.1
|
41.1
|
1.0
|
CB
|
A:VAL134
|
4.2
|
38.3
|
1.0
|
CG
|
A:GLU136
|
4.4
|
40.0
|
1.0
|
CA
|
A:GLY133
|
4.4
|
58.7
|
1.0
|
O
|
A:HOH727
|
4.5
|
53.9
|
1.0
|
N
|
A:GLU136
|
4.6
|
31.1
|
1.0
|
N
|
A:ASP135
|
4.6
|
32.3
|
1.0
|
O
|
A:HOH767
|
4.8
|
46.9
|
1.0
|
CG1
|
A:VAL134
|
4.9
|
38.6
|
1.0
|
CA
|
A:ASP135
|
4.9
|
33.0
|
1.0
|
|
Calcium binding site 2 out
of 4 in 7p74
Go back to
Calcium Binding Sites List in 7p74
Calcium binding site 2 out
of 4 in the The Pdz Domain of SYNJ2BP Complexed with the Phosphorylated Pdz- Binding Motif of RSK1
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of The Pdz Domain of SYNJ2BP Complexed with the Phosphorylated Pdz- Binding Motif of RSK1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca502
b:32.4
occ:1.00
|
O
|
A:LYS171
|
2.3
|
37.7
|
1.0
|
O
|
A:LEU174
|
2.3
|
31.7
|
1.0
|
OE1
|
A:GLU179
|
2.4
|
43.8
|
1.0
|
O
|
A:HOH615
|
2.5
|
39.6
|
1.0
|
CD
|
A:GLU179
|
3.4
|
45.5
|
1.0
|
C
|
A:LYS171
|
3.5
|
40.7
|
1.0
|
C
|
A:LEU174
|
3.5
|
33.6
|
1.0
|
OE2
|
A:GLU179
|
3.8
|
44.3
|
1.0
|
CA
|
A:SER175
|
4.0
|
32.3
|
1.0
|
N
|
A:SER175
|
4.2
|
32.4
|
1.0
|
CB
|
A:SER175
|
4.2
|
34.0
|
1.0
|
CA
|
A:LYS171
|
4.3
|
39.2
|
1.0
|
N
|
A:SER172
|
4.5
|
36.8
|
0.4
|
N
|
A:SER172
|
4.5
|
36.4
|
0.6
|
O
|
A:HOH818
|
4.5
|
48.0
|
1.0
|
CA
|
A:SER172
|
4.6
|
38.6
|
0.4
|
N
|
A:LEU174
|
4.6
|
30.1
|
1.0
|
CA
|
A:SER172
|
4.6
|
38.7
|
0.6
|
CA
|
A:LEU174
|
4.7
|
29.8
|
1.0
|
CG
|
A:GLU179
|
4.7
|
33.7
|
1.0
|
C
|
A:SER172
|
4.8
|
38.2
|
0.6
|
C
|
A:SER172
|
4.8
|
38.3
|
0.4
|
O
|
A:SER172
|
4.8
|
43.3
|
0.6
|
O
|
A:SER172
|
4.9
|
42.7
|
0.4
|
CB
|
A:LYS171
|
4.9
|
39.5
|
1.0
|
O
|
A:LEU170
|
5.0
|
39.1
|
1.0
|
|
Calcium binding site 3 out
of 4 in 7p74
Go back to
Calcium Binding Sites List in 7p74
Calcium binding site 3 out
of 4 in the The Pdz Domain of SYNJ2BP Complexed with the Phosphorylated Pdz- Binding Motif of RSK1
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of The Pdz Domain of SYNJ2BP Complexed with the Phosphorylated Pdz- Binding Motif of RSK1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca503
b:46.6
occ:1.00
|
O
|
A:GLY285
|
2.3
|
44.0
|
1.0
|
O
|
A:ARG288
|
2.3
|
49.4
|
1.0
|
O
|
A:GLY290
|
2.4
|
44.0
|
1.0
|
O
|
A:HOH772
|
2.4
|
46.1
|
1.0
|
O
|
A:HOH730
|
2.4
|
61.3
|
1.0
|
OE1
|
A:GLU330
|
2.5
|
51.0
|
1.0
|
OE2
|
A:GLU330
|
2.7
|
52.3
|
1.0
|
CD
|
A:GLU330
|
2.9
|
46.4
|
1.0
|
C
|
A:GLY285
|
3.2
|
42.6
|
1.0
|
C
|
A:GLY290
|
3.4
|
53.0
|
1.0
|
C
|
A:ARG288
|
3.5
|
49.5
|
1.0
|
N
|
A:GLY290
|
3.7
|
51.0
|
1.0
|
N
|
A:VAL286
|
4.0
|
40.9
|
1.0
|
CA
|
A:GLY285
|
4.1
|
41.8
|
1.0
|
CA
|
A:VAL286
|
4.1
|
43.9
|
1.0
|
CA
|
A:GLY290
|
4.1
|
58.2
|
1.0
|
C
|
A:LYS289
|
4.1
|
51.7
|
1.0
|
OG1
|
A:THR291
|
4.2
|
56.6
|
1.0
|
CG
|
A:ARG288
|
4.2
|
57.2
|
1.0
|
N
|
A:ARG288
|
4.3
|
48.9
|
1.0
|
CA
|
A:LYS289
|
4.3
|
52.8
|
1.0
|
C
|
A:VAL286
|
4.3
|
43.3
|
1.0
|
N
|
A:LYS289
|
4.3
|
51.3
|
1.0
|
O
|
A:VAL286
|
4.4
|
48.0
|
1.0
|
CA
|
A:ARG288
|
4.4
|
53.2
|
1.0
|
CG
|
A:GLU330
|
4.4
|
41.2
|
1.0
|
O
|
A:HOH703
|
4.4
|
56.6
|
1.0
|
N
|
A:THR291
|
4.5
|
52.5
|
1.0
|
O
|
A:HOH790
|
4.8
|
67.1
|
1.0
|
CA
|
A:THR291
|
4.8
|
52.2
|
1.0
|
O
|
A:LYS289
|
4.8
|
64.9
|
1.0
|
CB
|
A:ARG288
|
4.9
|
53.3
|
1.0
|
N
|
A:LYS287
|
5.0
|
39.7
|
1.0
|
|
Calcium binding site 4 out
of 4 in 7p74
Go back to
Calcium Binding Sites List in 7p74
Calcium binding site 4 out
of 4 in the The Pdz Domain of SYNJ2BP Complexed with the Phosphorylated Pdz- Binding Motif of RSK1
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of The Pdz Domain of SYNJ2BP Complexed with the Phosphorylated Pdz- Binding Motif of RSK1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca504
b:28.7
occ:1.00
|
O
|
A:GLY365
|
2.4
|
30.4
|
1.0
|
O
|
A:MET361
|
2.4
|
30.1
|
1.0
|
O
|
A:GLY363
|
2.4
|
31.7
|
1.0
|
OD2
|
A:ASP405
|
2.5
|
26.0
|
1.0
|
OD1
|
A:ASP405
|
2.5
|
30.2
|
1.0
|
CG
|
A:ASP405
|
2.8
|
34.1
|
1.0
|
C
|
A:MET361
|
3.4
|
26.2
|
1.0
|
C
|
A:GLY365
|
3.5
|
31.8
|
1.0
|
C
|
A:GLY363
|
3.6
|
34.5
|
1.0
|
N
|
A:GLY365
|
3.9
|
31.3
|
1.0
|
CA
|
A:MET361
|
4.0
|
26.2
|
1.0
|
N
|
A:GLY363
|
4.1
|
33.8
|
1.0
|
CA
|
A:GLY365
|
4.2
|
33.3
|
1.0
|
C
|
A:LYS364
|
4.3
|
35.0
|
1.0
|
C
|
A:LYS362
|
4.3
|
32.6
|
1.0
|
CB
|
A:ASP405
|
4.3
|
27.9
|
1.0
|
OG1
|
A:THR366
|
4.4
|
34.7
|
1.0
|
CA
|
A:GLY363
|
4.4
|
31.9
|
1.0
|
N
|
A:LYS362
|
4.5
|
29.7
|
1.0
|
O
|
A:HOH674
|
4.5
|
38.9
|
1.0
|
O
|
A:LYS362
|
4.5
|
33.0
|
1.0
|
N
|
A:THR366
|
4.6
|
29.7
|
1.0
|
N
|
A:LYS364
|
4.6
|
32.7
|
1.0
|
CB
|
A:MET361
|
4.6
|
23.7
|
1.0
|
O
|
A:LYS364
|
4.7
|
31.5
|
1.0
|
O
|
A:HOH635
|
4.7
|
24.6
|
1.0
|
CA
|
A:LYS364
|
4.7
|
30.6
|
1.0
|
CA
|
A:THR366
|
4.8
|
30.0
|
1.0
|
CA
|
A:LYS362
|
4.9
|
29.2
|
1.0
|
O
|
A:HOH759
|
4.9
|
40.2
|
1.0
|
|
Reference:
G.Gogl,
A.Cousido-Siah,
G.Trave.
The Pdz Domain of SYNJ2BP Complexed with the Phosphorylated Pdz-Binding Motif of RSK1 To Be Published.
Page generated: Fri Jul 19 02:46:22 2024
|