Calcium in PDB 7p73: The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1
Protein crystallography data
The structure of The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1, PDB code: 7p73
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)
|
46.68 /
1.85
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.45,
63.99,
146.95,
90,
90,
90
|
R / Rfree (%)
|
16.8 /
19.2
|
Calcium Binding Sites:
The binding sites of Calcium atom in the The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1
(pdb code 7p73). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the
The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1, PDB code: 7p73:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
Calcium binding site 1 out
of 7 in 7p73
Go back to
Calcium Binding Sites List in 7p73
Calcium binding site 1 out
of 7 in the The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1
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 Pdz-Binding Motif of HTLV1-TAX1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca501
b:37.6
occ:1.00
|
O
|
A:GLY133
|
2.3
|
33.9
|
1.0
|
O
|
A:HOH855
|
2.3
|
44.8
|
1.0
|
O
|
A:VAL134
|
2.3
|
34.8
|
1.0
|
O
|
A:HOH782
|
2.4
|
40.5
|
1.0
|
OE1
|
A:GLU136
|
2.4
|
33.2
|
1.0
|
O
|
A:HOH802
|
2.4
|
51.4
|
1.0
|
OE2
|
A:GLU136
|
2.6
|
36.8
|
1.0
|
CD
|
A:GLU136
|
2.8
|
41.1
|
1.0
|
C
|
A:GLY133
|
3.3
|
37.2
|
1.0
|
C
|
A:VAL134
|
3.5
|
33.8
|
1.0
|
N
|
A:VAL134
|
4.0
|
34.7
|
1.0
|
CA
|
A:VAL134
|
4.1
|
28.9
|
1.0
|
CB
|
A:VAL134
|
4.2
|
27.5
|
1.0
|
CA
|
A:GLY133
|
4.3
|
42.0
|
1.0
|
CG
|
A:GLU136
|
4.3
|
35.5
|
1.0
|
O
|
A:HOH642
|
4.4
|
46.3
|
1.0
|
O
|
A:HOH932
|
4.6
|
47.3
|
1.0
|
N
|
A:ASP135
|
4.6
|
33.9
|
1.0
|
N
|
A:GLU136
|
4.6
|
32.8
|
1.0
|
O
|
A:HOH659
|
4.9
|
41.9
|
1.0
|
CG1
|
A:VAL134
|
4.9
|
30.9
|
1.0
|
CA
|
A:ASP135
|
5.0
|
32.7
|
1.0
|
|
Calcium binding site 2 out
of 7 in 7p73
Go back to
Calcium Binding Sites List in 7p73
Calcium binding site 2 out
of 7 in the The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1
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 Pdz-Binding Motif of HTLV1-TAX1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca502
b:26.8
occ:1.00
|
O
|
A:LYS171
|
2.3
|
24.9
|
1.0
|
OE1
|
A:GLU179
|
2.4
|
34.6
|
1.0
|
O
|
A:LEU174
|
2.4
|
27.6
|
1.0
|
O
|
A:HOH660
|
2.4
|
44.5
|
1.0
|
CD
|
A:GLU179
|
3.3
|
34.1
|
1.0
|
C
|
A:LEU174
|
3.5
|
30.7
|
1.0
|
C
|
A:LYS171
|
3.6
|
29.4
|
1.0
|
OE2
|
A:GLU179
|
3.7
|
41.3
|
1.0
|
CA
|
A:SER175
|
4.2
|
27.8
|
1.0
|
N
|
A:SER175
|
4.3
|
28.9
|
1.0
|
O
|
A:SER172
|
4.4
|
33.9
|
1.0
|
CB
|
A:SER175
|
4.4
|
30.7
|
1.0
|
C
|
A:SER172
|
4.5
|
31.3
|
1.0
|
CA
|
A:SER172
|
4.5
|
28.2
|
1.0
|
N
|
A:SER172
|
4.5
|
24.4
|
1.0
|
CA
|
A:LYS171
|
4.5
|
30.9
|
1.0
|
N
|
A:LEU174
|
4.5
|
26.0
|
1.0
|
CG
|
A:GLU179
|
4.6
|
27.8
|
1.0
|
CA
|
A:LEU174
|
4.6
|
25.4
|
1.0
|
O
|
A:HOH957
|
4.7
|
47.0
|
1.0
|
CG
|
A:LYS171
|
4.8
|
38.5
|
1.0
|
|
Calcium binding site 3 out
of 7 in 7p73
Go back to
Calcium Binding Sites List in 7p73
Calcium binding site 3 out
of 7 in the The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1
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 Pdz-Binding Motif of HTLV1-TAX1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca503
b:27.8
occ:1.00
|
O
|
A:MET201
|
2.3
|
31.0
|
1.0
|
O
|
A:GLY203
|
2.4
|
33.7
|
1.0
|
O
|
A:GLY205
|
2.4
|
31.0
|
1.0
|
OD1
|
A:ASP245
|
2.4
|
29.0
|
1.0
|
O
|
A:HOH928
|
2.4
|
32.5
|
1.0
|
OD2
|
A:ASP245
|
2.6
|
29.4
|
1.0
|
CG
|
A:ASP245
|
2.8
|
30.7
|
1.0
|
C
|
A:MET201
|
3.4
|
28.2
|
1.0
|
C
|
A:GLY205
|
3.6
|
35.6
|
1.0
|
C
|
A:GLY203
|
3.6
|
35.3
|
1.0
|
N
|
A:GLY205
|
3.9
|
36.5
|
1.0
|
CA
|
A:MET201
|
4.1
|
21.6
|
1.0
|
C
|
A:LEU204
|
4.2
|
34.8
|
1.0
|
N
|
A:GLY203
|
4.2
|
37.1
|
1.0
|
CB
|
A:ASP245
|
4.3
|
24.0
|
1.0
|
CA
|
A:GLY205
|
4.3
|
38.6
|
1.0
|
OG1
|
A:THR206
|
4.3
|
34.9
|
1.0
|
C
|
A:LYS202
|
4.4
|
34.0
|
1.0
|
O1
|
A:GOL509
|
4.4
|
45.0
|
1.0
|
O
|
A:HOH830
|
4.4
|
38.3
|
1.0
|
CA
|
A:LEU204
|
4.5
|
31.7
|
1.0
|
N
|
A:LEU204
|
4.5
|
35.5
|
1.0
|
N
|
A:LYS202
|
4.5
|
31.4
|
1.0
|
CA
|
A:GLY203
|
4.5
|
37.9
|
1.0
|
N
|
A:THR206
|
4.6
|
27.8
|
1.0
|
CB
|
A:MET201
|
4.6
|
25.1
|
1.0
|
O
|
A:HOH720
|
4.7
|
60.0
|
1.0
|
O
|
A:HOH863
|
4.7
|
46.9
|
1.0
|
O
|
A:LEU204
|
4.7
|
40.4
|
1.0
|
CA
|
A:LYS202
|
4.7
|
33.2
|
1.0
|
CA
|
A:THR206
|
4.8
|
23.7
|
1.0
|
O
|
A:LYS202
|
4.9
|
37.8
|
1.0
|
C1
|
A:GOL509
|
4.9
|
56.8
|
1.0
|
CA
|
A:ASP245
|
4.9
|
29.7
|
1.0
|
|
Calcium binding site 4 out
of 7 in 7p73
Go back to
Calcium Binding Sites List in 7p73
Calcium binding site 4 out
of 7 in the The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1
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 Pdz-Binding Motif of HTLV1-TAX1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca504
b:32.3
occ:1.00
|
O
|
A:GLY290
|
2.4
|
34.8
|
1.0
|
O
|
A:HOH912
|
2.4
|
34.1
|
1.0
|
O
|
A:GLY285
|
2.4
|
29.0
|
1.0
|
O
|
A:ARG288
|
2.4
|
35.0
|
1.0
|
O
|
A:HOH787
|
2.4
|
40.5
|
1.0
|
OE1
|
A:GLU330
|
2.5
|
31.7
|
1.0
|
OE2
|
A:GLU330
|
2.5
|
34.9
|
1.0
|
CD
|
A:GLU330
|
2.8
|
31.3
|
1.0
|
C
|
A:GLY285
|
3.3
|
26.2
|
1.0
|
C
|
A:GLY290
|
3.4
|
34.6
|
1.0
|
C
|
A:ARG288
|
3.5
|
41.3
|
1.0
|
N
|
A:GLY290
|
3.7
|
31.7
|
1.0
|
CA
|
A:GLY290
|
4.1
|
35.9
|
1.0
|
C
|
A:LYS289
|
4.1
|
37.8
|
1.0
|
CA
|
A:GLY285
|
4.1
|
29.7
|
1.0
|
N
|
A:VAL286
|
4.2
|
24.3
|
1.0
|
CA
|
A:VAL286
|
4.3
|
28.9
|
1.0
|
OG1
|
A:THR291
|
4.3
|
38.8
|
1.0
|
CA
|
A:LYS289
|
4.3
|
37.5
|
1.0
|
O
|
A:HOH643
|
4.3
|
40.3
|
1.0
|
N
|
A:ARG288
|
4.4
|
33.5
|
1.0
|
CG
|
A:GLU330
|
4.4
|
28.1
|
1.0
|
O
|
A:HOH705
|
4.4
|
45.5
|
1.0
|
N
|
A:LYS289
|
4.4
|
37.7
|
1.0
|
O
|
A:HOH870
|
4.4
|
52.8
|
1.0
|
C
|
A:VAL286
|
4.5
|
34.5
|
1.0
|
CG
|
A:ARG288
|
4.5
|
35.4
|
1.0
|
O
|
A:VAL286
|
4.5
|
37.3
|
1.0
|
CA
|
A:ARG288
|
4.5
|
37.0
|
1.0
|
N
|
A:THR291
|
4.5
|
32.0
|
1.0
|
O
|
A:LYS289
|
4.8
|
34.5
|
1.0
|
CA
|
A:THR291
|
4.9
|
31.3
|
1.0
|
|
Calcium binding site 5 out
of 7 in 7p73
Go back to
Calcium Binding Sites List in 7p73
Calcium binding site 5 out
of 7 in the The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca505
b:21.1
occ:1.00
|
O
|
A:GLY365
|
2.3
|
26.9
|
1.0
|
O
|
A:MET361
|
2.3
|
23.3
|
1.0
|
O
|
A:GLY363
|
2.4
|
22.9
|
1.0
|
OD1
|
A:ASP405
|
2.5
|
25.4
|
1.0
|
OD2
|
A:ASP405
|
2.5
|
23.6
|
1.0
|
CG
|
A:ASP405
|
2.8
|
27.1
|
1.0
|
C
|
A:MET361
|
3.4
|
19.8
|
1.0
|
C
|
A:GLY365
|
3.5
|
29.6
|
1.0
|
C
|
A:GLY363
|
3.6
|
27.2
|
1.0
|
N
|
A:GLY365
|
3.9
|
22.9
|
1.0
|
CA
|
A:MET361
|
4.0
|
22.0
|
1.0
|
N
|
A:GLY363
|
4.1
|
25.2
|
1.0
|
CA
|
A:GLY365
|
4.2
|
27.4
|
1.0
|
C
|
A:LYS364
|
4.2
|
26.6
|
1.0
|
C
|
A:LYS362
|
4.3
|
25.8
|
1.0
|
CB
|
A:ASP405
|
4.3
|
19.6
|
1.0
|
OG1
|
A:THR366
|
4.4
|
29.6
|
1.0
|
CA
|
A:GLY363
|
4.4
|
22.7
|
1.0
|
O
|
A:HOH768
|
4.5
|
37.2
|
1.0
|
N
|
A:LYS362
|
4.5
|
22.0
|
1.0
|
N
|
A:THR366
|
4.5
|
24.5
|
1.0
|
N
|
A:LYS364
|
4.6
|
25.0
|
1.0
|
O
|
A:LYS362
|
4.6
|
29.7
|
1.0
|
CB
|
A:MET361
|
4.6
|
22.7
|
1.0
|
O
|
A:LYS364
|
4.6
|
23.6
|
1.0
|
CA
|
A:LYS364
|
4.7
|
25.4
|
1.0
|
CA
|
A:THR366
|
4.8
|
28.2
|
1.0
|
O
|
A:HOH673
|
4.8
|
22.7
|
1.0
|
CA
|
A:LYS362
|
4.9
|
20.7
|
1.0
|
CA
|
A:ASP405
|
5.0
|
24.4
|
1.0
|
|
Calcium binding site 6 out
of 7 in 7p73
Go back to
Calcium Binding Sites List in 7p73
Calcium binding site 6 out
of 7 in the The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca510
b:30.2
occ:1.00
|
O
|
A:THR206
|
2.3
|
29.9
|
1.0
|
O
|
A:HOH880
|
2.4
|
36.3
|
1.0
|
O
|
A:HOH805
|
2.5
|
40.8
|
1.0
|
OE2
|
A:GLU208
|
2.5
|
37.2
|
1.0
|
O
|
A:HOH938
|
2.6
|
37.1
|
1.0
|
O
|
A:HOH1010
|
2.6
|
33.3
|
1.0
|
O
|
A:HOH887
|
2.6
|
34.5
|
1.0
|
OE1
|
A:GLU208
|
2.8
|
41.3
|
1.0
|
CD
|
A:GLU208
|
3.0
|
40.9
|
1.0
|
C
|
A:THR206
|
3.6
|
28.8
|
1.0
|
N
|
A:THR206
|
4.1
|
27.8
|
1.0
|
CA
|
A:THR206
|
4.4
|
23.7
|
1.0
|
CG
|
A:GLU208
|
4.5
|
30.6
|
1.0
|
N
|
A:ASP207
|
4.5
|
25.3
|
1.0
|
N
|
A:GLU208
|
4.6
|
26.5
|
1.0
|
O
|
A:HOH995
|
4.6
|
48.8
|
1.0
|
CA
|
A:ASP207
|
4.7
|
25.4
|
1.0
|
O
|
A:HOH801
|
4.7
|
35.7
|
1.0
|
O
|
A:HOH721
|
4.8
|
54.1
|
1.0
|
CB
|
A:THR206
|
4.8
|
33.6
|
1.0
|
O
|
A:HOH605
|
5.0
|
49.4
|
1.0
|
|
Calcium binding site 7 out
of 7 in 7p73
Go back to
Calcium Binding Sites List in 7p73
Calcium binding site 7 out
of 7 in the The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca511
b:40.2
occ:1.00
|
O
|
A:HOH803
|
2.3
|
57.5
|
1.0
|
O
|
A:ARG328
|
2.3
|
32.3
|
1.0
|
OE1
|
A:GLU336
|
2.5
|
51.6
|
1.0
|
O
|
A:HOH924
|
2.5
|
50.1
|
1.0
|
O
|
A:HOH925
|
2.5
|
44.8
|
1.0
|
O
|
A:VAL331
|
2.5
|
33.0
|
1.0
|
O
|
A:HOH838
|
2.6
|
36.1
|
1.0
|
CD
|
A:GLU336
|
3.4
|
40.0
|
1.0
|
C
|
A:ARG328
|
3.4
|
34.3
|
1.0
|
OE2
|
A:GLU336
|
3.7
|
42.7
|
1.0
|
C
|
A:VAL331
|
3.7
|
35.5
|
1.0
|
CA
|
A:ARG328
|
4.0
|
30.0
|
1.0
|
CA
|
A:LYS332
|
4.1
|
29.8
|
1.0
|
CB
|
A:LYS332
|
4.2
|
34.1
|
1.0
|
N
|
A:LYS332
|
4.4
|
29.1
|
1.0
|
N
|
A:LYS329
|
4.5
|
30.4
|
1.0
|
O
|
A:ILE327
|
4.6
|
27.8
|
1.0
|
CG
|
A:GLU336
|
4.6
|
26.0
|
1.0
|
N
|
A:VAL331
|
4.6
|
26.3
|
1.0
|
O
|
A:HOH918
|
4.7
|
45.9
|
1.0
|
CB
|
A:ARG328
|
4.8
|
24.8
|
1.0
|
C
|
A:LYS329
|
4.8
|
32.2
|
1.0
|
CA
|
A:VAL331
|
4.8
|
27.3
|
1.0
|
CA
|
A:LYS329
|
4.8
|
29.9
|
1.0
|
O
|
A:HOH900
|
5.0
|
50.0
|
1.0
|
|
Reference:
G.Gogl,
A.Cousido-Siah,
G.Trave.
The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1 To Be Published.
Page generated: Fri Jul 19 02:46:20 2024
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