Calcium in PDB 8vsd: AVB8/L-Tgf-B1/Garp
Other elements in 8vsd:
The structure of AVB8/L-Tgf-B1/Garp also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the AVB8/L-Tgf-B1/Garp
(pdb code 8vsd). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the
AVB8/L-Tgf-B1/Garp, PDB code: 8vsd:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
Calcium binding site 1 out
of 5 in 8vsd
Go back to
Calcium Binding Sites List in 8vsd
Calcium binding site 1 out
of 5 in the AVB8/L-Tgf-B1/Garp
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of AVB8/L-Tgf-B1/Garp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca602
b:21.6
occ:1.00
|
OD1
|
A:ASP292
|
2.3
|
20.4
|
1.0
|
|
O
|
A:TYR290
|
2.3
|
27.3
|
1.0
|
|
OD1
|
A:ASP288
|
2.3
|
31.7
|
1.0
|
|
OD1
|
A:ASN286
|
2.3
|
26.5
|
1.0
|
|
OD2
|
A:ASP292
|
2.7
|
20.4
|
1.0
|
|
CG
|
A:ASP292
|
2.8
|
20.4
|
1.0
|
|
CG
|
A:ASP288
|
3.1
|
31.7
|
1.0
|
|
CG
|
A:ASN286
|
3.2
|
26.5
|
1.0
|
|
OD2
|
A:ASP288
|
3.3
|
31.7
|
1.0
|
|
C
|
A:TYR290
|
3.4
|
27.3
|
1.0
|
|
ND2
|
A:ASN286
|
3.5
|
26.5
|
1.0
|
|
OD1
|
A:ASP284
|
3.5
|
23.7
|
1.0
|
|
CB
|
A:TYR290
|
3.8
|
27.3
|
1.0
|
|
CA
|
A:TYR290
|
3.9
|
27.3
|
1.0
|
|
N
|
A:TYR290
|
4.0
|
27.3
|
1.0
|
|
O
|
A:GLN320
|
4.2
|
21.1
|
1.0
|
|
CB
|
A:ASP292
|
4.3
|
20.4
|
1.0
|
|
N
|
A:ALA291
|
4.5
|
20.7
|
1.0
|
|
CG
|
A:ASP284
|
4.5
|
23.7
|
1.0
|
|
CB
|
A:ASP288
|
4.5
|
31.7
|
1.0
|
|
C
|
A:ALA291
|
4.6
|
20.7
|
1.0
|
|
N
|
A:ASP288
|
4.6
|
31.7
|
1.0
|
|
CB
|
A:ASN286
|
4.6
|
26.5
|
1.0
|
|
N
|
A:ASN286
|
4.6
|
26.5
|
1.0
|
|
N
|
A:ASP292
|
4.7
|
20.4
|
1.0
|
|
N
|
A:GLN320
|
4.7
|
21.1
|
1.0
|
|
O
|
A:ALA291
|
4.8
|
20.7
|
1.0
|
|
CA
|
A:ALA291
|
4.8
|
20.7
|
1.0
|
|
N
|
A:ILE285
|
4.8
|
22.2
|
1.0
|
|
CD2
|
A:LEU319
|
4.9
|
19.5
|
1.0
|
|
CA
|
A:ASP284
|
4.9
|
23.7
|
1.0
|
|
CA
|
A:ASP288
|
5.0
|
31.7
|
1.0
|
|
CA
|
A:ASP292
|
5.0
|
20.4
|
1.0
|
|
Calcium binding site 2 out
of 5 in 8vsd
Go back to
Calcium Binding Sites List in 8vsd
Calcium binding site 2 out
of 5 in the AVB8/L-Tgf-B1/Garp
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of AVB8/L-Tgf-B1/Garp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca603
b:18.0
occ:1.00
|
OD1
|
A:ASP357
|
2.5
|
19.0
|
1.0
|
|
OD1
|
A:ASP351
|
2.5
|
24.9
|
1.0
|
|
OD1
|
A:ASP349
|
2.6
|
23.2
|
1.0
|
|
O
|
A:PHE355
|
2.6
|
28.1
|
1.0
|
|
OD2
|
A:ASP357
|
2.8
|
19.0
|
1.0
|
|
CG
|
A:ASP357
|
3.0
|
19.0
|
1.0
|
|
CG
|
A:ASP351
|
3.6
|
24.9
|
1.0
|
|
CG
|
A:ASP349
|
3.8
|
23.2
|
1.0
|
|
C
|
A:PHE355
|
3.8
|
28.1
|
1.0
|
|
OD2
|
A:ASP351
|
4.0
|
24.9
|
1.0
|
|
CB
|
A:ASP353
|
4.3
|
28.1
|
1.0
|
|
N
|
A:ASP351
|
4.5
|
24.9
|
1.0
|
|
CB
|
A:ASP357
|
4.5
|
19.0
|
1.0
|
|
N
|
A:ASP353
|
4.5
|
28.1
|
1.0
|
|
OD2
|
A:ASP349
|
4.5
|
23.2
|
1.0
|
|
N
|
A:PHE355
|
4.5
|
28.1
|
1.0
|
|
N
|
A:LEU350
|
4.5
|
22.1
|
1.0
|
|
CA
|
A:ASP349
|
4.5
|
23.2
|
1.0
|
|
C
|
A:ASN356
|
4.6
|
22.3
|
1.0
|
|
CA
|
A:PHE355
|
4.6
|
28.1
|
1.0
|
|
O
|
A:ASN356
|
4.7
|
22.3
|
1.0
|
|
CG
|
A:ASP353
|
4.7
|
28.1
|
1.0
|
|
C
|
A:ASP349
|
4.8
|
23.2
|
1.0
|
|
N
|
A:GLY378
|
4.8
|
22.3
|
1.0
|
|
N
|
A:GLN352
|
4.8
|
27.5
|
1.0
|
|
CB
|
A:ASP349
|
4.8
|
23.2
|
1.0
|
|
ND2
|
A:ASN377
|
4.8
|
18.1
|
1.0
|
|
CB
|
A:PHE355
|
4.8
|
28.1
|
1.0
|
|
N
|
A:ASN356
|
4.8
|
22.3
|
1.0
|
|
N
|
A:ASP357
|
4.8
|
19.0
|
1.0
|
|
CA
|
A:ASN356
|
4.8
|
22.3
|
1.0
|
|
CB
|
A:ASP351
|
4.9
|
24.9
|
1.0
|
|
CA
|
A:ASP353
|
5.0
|
28.1
|
1.0
|
|
Calcium binding site 3 out
of 5 in 8vsd
Go back to
Calcium Binding Sites List in 8vsd
Calcium binding site 3 out
of 5 in the AVB8/L-Tgf-B1/Garp
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of AVB8/L-Tgf-B1/Garp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca604
b:23.9
occ:1.00
|
OD1
|
A:ASN417
|
2.4
|
33.3
|
1.0
|
|
ND2
|
A:ASN417
|
2.7
|
33.3
|
1.0
|
|
OD1
|
A:ASP421
|
2.8
|
22.0
|
1.0
|
|
CG
|
A:ASN417
|
2.8
|
33.3
|
1.0
|
|
OD2
|
A:ASP421
|
3.0
|
22.0
|
1.0
|
|
O
|
A:TYR419
|
3.0
|
31.8
|
1.0
|
|
CG
|
A:ASP421
|
3.2
|
22.0
|
1.0
|
|
OD1
|
A:ASP415
|
3.4
|
31.5
|
1.0
|
|
O
|
A:ALA437
|
3.7
|
24.5
|
1.0
|
|
CB
|
A:ASP415
|
3.7
|
31.5
|
1.0
|
|
N
|
A:ALA437
|
3.9
|
24.5
|
1.0
|
|
CG
|
A:ASP415
|
4.0
|
31.5
|
1.0
|
|
C
|
A:TYR419
|
4.1
|
31.8
|
1.0
|
|
CB
|
A:ASN417
|
4.3
|
33.3
|
1.0
|
|
N
|
A:ASP415
|
4.3
|
31.5
|
1.0
|
|
O
|
A:PRO420
|
4.4
|
22.5
|
1.0
|
|
N
|
A:TYR419
|
4.5
|
31.8
|
1.0
|
|
C
|
A:ALA437
|
4.5
|
24.5
|
1.0
|
|
CA
|
A:ALA437
|
4.6
|
24.5
|
1.0
|
|
CA
|
A:ASP415
|
4.6
|
31.5
|
1.0
|
|
N
|
A:ASN417
|
4.6
|
33.3
|
1.0
|
|
CB
|
A:ALA437
|
4.6
|
24.5
|
1.0
|
|
CA
|
A:TYR419
|
4.7
|
31.8
|
1.0
|
|
CB
|
A:ASP421
|
4.7
|
22.0
|
1.0
|
|
CB
|
A:TYR419
|
4.7
|
31.8
|
1.0
|
|
CA
|
A:ARG436
|
4.7
|
25.0
|
1.0
|
|
CB
|
A:ARG436
|
4.7
|
25.0
|
1.0
|
|
CB
|
A:ASP413
|
4.7
|
30.2
|
1.0
|
|
C
|
A:PRO420
|
4.7
|
22.5
|
1.0
|
|
N
|
A:ILE414
|
4.7
|
29.8
|
1.0
|
|
C
|
A:ARG436
|
4.8
|
25.0
|
1.0
|
|
CA
|
A:ASP413
|
4.8
|
30.2
|
1.0
|
|
CD2
|
A:LEU574
|
5.0
|
49.6
|
1.0
|
|
CA
|
A:ASN417
|
5.0
|
33.3
|
1.0
|
|
CG
|
A:ARG436
|
5.0
|
25.0
|
1.0
|
|
Calcium binding site 4 out
of 5 in 8vsd
Go back to
Calcium Binding Sites List in 8vsd
Calcium binding site 4 out
of 5 in the AVB8/L-Tgf-B1/Garp
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of AVB8/L-Tgf-B1/Garp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca605
b:24.2
occ:1.00
|
OD1
|
A:ASP238
|
2.2
|
17.9
|
1.0
|
|
OD1
|
A:ASP234
|
2.3
|
21.5
|
1.0
|
|
OD1
|
A:ASN232
|
2.4
|
19.6
|
1.0
|
|
OD2
|
A:ASP234
|
2.5
|
21.5
|
1.0
|
|
OD2
|
A:ASP238
|
2.5
|
17.9
|
1.0
|
|
CG
|
A:ASP234
|
2.7
|
21.5
|
1.0
|
|
O
|
A:ILE236
|
2.7
|
20.1
|
1.0
|
|
CG
|
A:ASP238
|
2.7
|
17.9
|
1.0
|
|
OD1
|
A:ASP230
|
3.2
|
20.1
|
1.0
|
|
CG
|
A:ASN232
|
3.5
|
19.6
|
1.0
|
|
C
|
A:ILE236
|
3.8
|
20.1
|
1.0
|
|
CB
|
A:ASP234
|
4.1
|
21.5
|
1.0
|
|
N
|
A:ASN232
|
4.1
|
19.6
|
1.0
|
|
CB
|
A:ASP238
|
4.2
|
17.9
|
1.0
|
|
N
|
A:PHE231
|
4.2
|
17.5
|
1.0
|
|
OD1
|
A:ASP257
|
4.2
|
19.5
|
1.0
|
|
ND2
|
A:ASN232
|
4.3
|
19.6
|
1.0
|
|
CG
|
A:ASP230
|
4.3
|
20.1
|
1.0
|
|
N
|
A:ILE236
|
4.3
|
20.1
|
1.0
|
|
N
|
A:ASP234
|
4.4
|
21.5
|
1.0
|
|
CA
|
A:ILE236
|
4.5
|
20.1
|
1.0
|
|
CA
|
A:ASP230
|
4.5
|
20.1
|
1.0
|
|
CB
|
A:ASN232
|
4.6
|
19.6
|
1.0
|
|
C
|
A:ASP237
|
4.6
|
20.9
|
1.0
|
|
N
|
A:GLY235
|
4.6
|
21.3
|
1.0
|
|
N
|
A:GLY258
|
4.6
|
18.2
|
1.0
|
|
N
|
A:ASP238
|
4.6
|
17.9
|
1.0
|
|
CB
|
A:ILE236
|
4.7
|
20.1
|
1.0
|
|
CA
|
A:ASP234
|
4.7
|
21.5
|
1.0
|
|
CA
|
A:ASN232
|
4.8
|
19.6
|
1.0
|
|
O
|
A:ASP237
|
4.8
|
20.9
|
1.0
|
|
CA
|
A:ASP238
|
4.8
|
17.9
|
1.0
|
|
CB
|
A:ASP230
|
4.8
|
20.1
|
1.0
|
|
N
|
A:ASP237
|
4.9
|
20.9
|
1.0
|
|
N
|
A:GLY233
|
4.9
|
19.7
|
1.0
|
|
C
|
A:ASP230
|
4.9
|
20.1
|
1.0
|
|
C
|
A:ASN232
|
5.0
|
19.6
|
1.0
|
|
C
|
A:PHE231
|
5.0
|
17.5
|
1.0
|
|
Calcium binding site 5 out
of 5 in 8vsd
Go back to
Calcium Binding Sites List in 8vsd
Calcium binding site 5 out
of 5 in the AVB8/L-Tgf-B1/Garp
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of AVB8/L-Tgf-B1/Garp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca503
b:16.3
occ:1.00
|
OD2
|
B:ASP151
|
2.2
|
15.8
|
1.0
|
|
O
|
B:PRO211
|
2.2
|
13.7
|
1.0
|
|
OD1
|
B:ASP209
|
2.3
|
16.2
|
1.0
|
|
ND2
|
B:ASN207
|
2.3
|
19.8
|
1.0
|
|
CG
|
B:GLU212
|
2.7
|
14.7
|
1.0
|
|
CA
|
B:GLU212
|
2.9
|
14.7
|
1.0
|
|
CG
|
B:ASP209
|
3.0
|
16.2
|
1.0
|
|
CG
|
B:ASP151
|
3.0
|
15.8
|
1.0
|
|
OD2
|
B:ASP209
|
3.1
|
16.2
|
1.0
|
|
C
|
B:PRO211
|
3.2
|
13.7
|
1.0
|
|
CB
|
B:GLU212
|
3.2
|
14.7
|
1.0
|
|
N
|
B:GLU212
|
3.4
|
14.7
|
1.0
|
|
CG
|
B:ASN207
|
3.5
|
19.8
|
1.0
|
|
CB
|
B:ASP151
|
3.6
|
15.8
|
1.0
|
|
OD1
|
B:ASP151
|
3.9
|
15.8
|
1.0
|
|
O
|
B:ASP209
|
4.0
|
16.2
|
1.0
|
|
OD1
|
B:ASN207
|
4.0
|
19.8
|
1.0
|
|
CD
|
B:GLU212
|
4.0
|
14.7
|
1.0
|
|
C
|
B:GLU212
|
4.0
|
14.7
|
1.0
|
|
O
|
B:VAL150
|
4.1
|
18.9
|
1.0
|
|
N
|
B:GLY213
|
4.2
|
15.0
|
1.0
|
|
OE2
|
B:GLU212
|
4.4
|
14.7
|
1.0
|
|
CB
|
B:ASP209
|
4.4
|
16.2
|
1.0
|
|
NE2
|
B:HIS247
|
4.6
|
14.9
|
1.0
|
|
CA
|
B:PRO211
|
4.6
|
13.7
|
1.0
|
|
C
|
B:ASP209
|
4.6
|
16.2
|
1.0
|
|
CD2
|
B:HIS247
|
4.6
|
14.9
|
1.0
|
|
CB
|
B:ASN207
|
4.6
|
19.8
|
1.0
|
|
CA
|
B:ASP151
|
4.8
|
15.8
|
1.0
|
|
N
|
B:PRO211
|
4.9
|
13.7
|
1.0
|
|
CA
|
B:ASP209
|
4.9
|
16.2
|
1.0
|
|
O
|
B:THR210
|
4.9
|
16.1
|
1.0
|
|
N
|
B:ASP209
|
5.0
|
16.2
|
1.0
|
|
C
|
B:VAL150
|
5.0
|
18.9
|
1.0
|
|
Reference:
M.Jin,
Y.Cheng,
S.L.Nishimura.
Dynamic Allostery Drives Autocrine and Paracrine Tgf-Beta Signaling Cell(Cambridge,Mass.) 2024.
ISSN: ISSN 0092-8674
Page generated: Sat Sep 28 09:15:32 2024
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