Calcium in PDB 8fn9: Crystal Structure of the C-Terminal Fg Domain of Tnr with the Single Fn Domain of Ptprz
Enzymatic activity of Crystal Structure of the C-Terminal Fg Domain of Tnr with the Single Fn Domain of Ptprz
All present enzymatic activity of Crystal Structure of the C-Terminal Fg Domain of Tnr with the Single Fn Domain of Ptprz:
3.1.3.48;
Protein crystallography data
The structure of Crystal Structure of the C-Terminal Fg Domain of Tnr with the Single Fn Domain of Ptprz, PDB code: 8fn9
was solved by
S.Bouyain,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
42.96 /
1.80
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
48.325,
75.656,
88.322,
104.41,
92.4,
91.81
|
R / Rfree (%)
|
17.4 /
21
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of the C-Terminal Fg Domain of Tnr with the Single Fn Domain of Ptprz
(pdb code 8fn9). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Crystal Structure of the C-Terminal Fg Domain of Tnr with the Single Fn Domain of Ptprz, PDB code: 8fn9:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 8fn9
Go back to
Calcium Binding Sites List in 8fn9
Calcium binding site 1 out
of 4 in the Crystal Structure of the C-Terminal Fg Domain of Tnr with the Single Fn Domain of Ptprz
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 the C-Terminal Fg Domain of Tnr with the Single Fn Domain of Ptprz within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1401
b:24.5
occ:1.00
|
OD1
|
A:ASP1284
|
2.3
|
22.4
|
1.0
|
O
|
A:HOH1565
|
2.3
|
32.0
|
1.0
|
O
|
A:ALA1286
|
2.4
|
22.6
|
1.0
|
OD2
|
A:ASP1282
|
2.4
|
27.1
|
1.0
|
O
|
A:THR1288
|
2.5
|
25.9
|
1.0
|
OD1
|
A:ASP1282
|
2.7
|
31.1
|
1.0
|
CG
|
A:ASP1282
|
2.9
|
33.1
|
1.0
|
CG
|
A:ASP1284
|
3.1
|
25.7
|
1.0
|
OD2
|
A:ASP1284
|
3.2
|
26.9
|
1.0
|
C
|
A:ALA1286
|
3.5
|
25.3
|
1.0
|
C
|
A:THR1288
|
3.6
|
32.1
|
1.0
|
O
|
A:VAL1287
|
4.0
|
30.7
|
1.0
|
N
|
A:ALA1286
|
4.0
|
20.6
|
1.0
|
C
|
A:VAL1287
|
4.1
|
24.2
|
1.0
|
CA
|
A:ALA1286
|
4.2
|
25.6
|
1.0
|
O
|
A:ASP1284
|
4.3
|
26.2
|
1.0
|
O
|
A:HOH1506
|
4.3
|
34.7
|
1.0
|
CA
|
A:ASN1289
|
4.4
|
30.2
|
1.0
|
N
|
A:ASN1289
|
4.4
|
28.6
|
1.0
|
N
|
A:THR1288
|
4.4
|
24.7
|
1.0
|
N
|
A:VAL1287
|
4.4
|
27.8
|
1.0
|
CB
|
A:ASP1282
|
4.5
|
24.5
|
1.0
|
C
|
A:ASP1284
|
4.5
|
22.3
|
1.0
|
CB
|
A:ASP1284
|
4.5
|
22.6
|
1.0
|
CB
|
A:ALA1286
|
4.5
|
27.2
|
1.0
|
CA
|
A:VAL1287
|
4.6
|
25.9
|
1.0
|
CA
|
A:THR1288
|
4.6
|
30.9
|
1.0
|
N
|
A:ASP1284
|
4.8
|
26.2
|
1.0
|
CA
|
A:ASP1284
|
4.8
|
23.9
|
1.0
|
N
|
A:CYS1290
|
5.0
|
21.9
|
1.0
|
N
|
A:VAL1285
|
5.0
|
19.2
|
1.0
|
C
|
A:VAL1285
|
5.0
|
29.7
|
1.0
|
|
Calcium binding site 2 out
of 4 in 8fn9
Go back to
Calcium Binding Sites List in 8fn9
Calcium binding site 2 out
of 4 in the Crystal Structure of the C-Terminal Fg Domain of Tnr with the Single Fn Domain of Ptprz
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 the C-Terminal Fg Domain of Tnr with the Single Fn Domain of Ptprz within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca1401
b:34.4
occ:1.00
|
OD1
|
C:ASP1284
|
2.2
|
28.9
|
1.0
|
O
|
C:ALA1286
|
2.3
|
34.3
|
1.0
|
OD2
|
C:ASP1282
|
2.3
|
32.9
|
1.0
|
O
|
C:HOH1555
|
2.4
|
41.5
|
1.0
|
O
|
C:THR1288
|
2.4
|
33.1
|
1.0
|
O
|
C:HOH1539
|
2.4
|
33.0
|
1.0
|
OD1
|
C:ASP1282
|
2.8
|
36.3
|
1.0
|
CG
|
C:ASP1282
|
2.9
|
35.7
|
1.0
|
CG
|
C:ASP1284
|
3.1
|
31.7
|
1.0
|
OD2
|
C:ASP1284
|
3.3
|
31.4
|
1.0
|
C
|
C:ALA1286
|
3.4
|
32.4
|
1.0
|
C
|
C:THR1288
|
3.5
|
33.9
|
1.0
|
O
|
C:VAL1287
|
4.0
|
38.4
|
1.0
|
C
|
C:VAL1287
|
4.0
|
35.4
|
1.0
|
N
|
C:ALA1286
|
4.0
|
27.7
|
1.0
|
O
|
C:HOH1567
|
4.1
|
45.2
|
1.0
|
CA
|
C:ALA1286
|
4.2
|
32.6
|
1.0
|
N
|
C:THR1288
|
4.3
|
34.9
|
1.0
|
O
|
C:HOH1582
|
4.3
|
48.0
|
1.0
|
O
|
C:ASP1284
|
4.3
|
32.8
|
1.0
|
N
|
C:ASN1289
|
4.4
|
31.6
|
1.0
|
CA
|
C:ASN1289
|
4.4
|
32.5
|
1.0
|
N
|
C:VAL1287
|
4.4
|
35.0
|
1.0
|
CB
|
C:ALA1286
|
4.4
|
29.4
|
1.0
|
CB
|
C:ASP1282
|
4.4
|
30.3
|
1.0
|
CA
|
C:VAL1287
|
4.5
|
35.8
|
0.2
|
CB
|
C:ASP1284
|
4.5
|
31.8
|
1.0
|
CA
|
C:THR1288
|
4.5
|
38.6
|
1.0
|
CA
|
C:VAL1287
|
4.5
|
35.8
|
0.8
|
C
|
C:ASP1284
|
4.6
|
32.4
|
1.0
|
N
|
C:ASP1284
|
4.8
|
31.4
|
1.0
|
CA
|
C:ASP1284
|
4.9
|
33.7
|
1.0
|
N
|
C:CYS1290
|
5.0
|
30.3
|
1.0
|
|
Calcium binding site 3 out
of 4 in 8fn9
Go back to
Calcium Binding Sites List in 8fn9
Calcium binding site 3 out
of 4 in the Crystal Structure of the C-Terminal Fg Domain of Tnr with the Single Fn Domain of Ptprz
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 the C-Terminal Fg Domain of Tnr with the Single Fn Domain of Ptprz within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca1401
b:33.2
occ:1.00
|
OD1
|
E:ASP1284
|
2.2
|
28.3
|
1.0
|
OD2
|
E:ASP1282
|
2.3
|
32.7
|
1.0
|
O
|
E:HOH1583
|
2.4
|
35.5
|
1.0
|
O
|
E:THR1288
|
2.4
|
32.5
|
1.0
|
O
|
E:ALA1286
|
2.5
|
30.5
|
1.0
|
O
|
E:HOH1536
|
2.5
|
38.4
|
1.0
|
OD1
|
E:ASP1282
|
2.7
|
40.3
|
1.0
|
CG
|
E:ASP1282
|
2.9
|
42.3
|
1.0
|
CG
|
E:ASP1284
|
3.0
|
36.1
|
1.0
|
OD2
|
E:ASP1284
|
3.2
|
34.5
|
1.0
|
C
|
E:ALA1286
|
3.5
|
30.7
|
1.0
|
C
|
E:THR1288
|
3.5
|
36.1
|
1.0
|
O
|
E:VAL1287
|
4.0
|
36.4
|
1.0
|
O
|
E:HOH1502
|
4.1
|
38.4
|
1.0
|
N
|
E:ALA1286
|
4.1
|
29.4
|
1.0
|
C
|
E:VAL1287
|
4.2
|
36.5
|
1.0
|
O
|
E:ASP1284
|
4.2
|
30.0
|
1.0
|
CA
|
E:ASN1289
|
4.2
|
30.7
|
1.0
|
CA
|
E:ALA1286
|
4.3
|
31.6
|
1.0
|
N
|
E:ASN1289
|
4.3
|
33.4
|
1.0
|
CB
|
E:ASP1282
|
4.4
|
37.0
|
1.0
|
N
|
E:THR1288
|
4.4
|
39.6
|
1.0
|
C
|
E:ASP1284
|
4.4
|
33.0
|
1.0
|
CB
|
E:ASP1284
|
4.4
|
34.5
|
1.0
|
CB
|
E:ALA1286
|
4.5
|
32.0
|
1.0
|
O
|
E:HOH1591
|
4.5
|
33.0
|
1.0
|
N
|
E:VAL1287
|
4.5
|
33.5
|
1.0
|
CA
|
E:THR1288
|
4.6
|
35.1
|
1.0
|
CA
|
E:VAL1287
|
4.7
|
36.6
|
1.0
|
N
|
E:ASP1284
|
4.7
|
27.5
|
1.0
|
CA
|
E:ASP1284
|
4.8
|
31.7
|
1.0
|
N
|
E:CYS1290
|
4.8
|
26.7
|
1.0
|
|
Calcium binding site 4 out
of 4 in 8fn9
Go back to
Calcium Binding Sites List in 8fn9
Calcium binding site 4 out
of 4 in the Crystal Structure of the C-Terminal Fg Domain of Tnr with the Single Fn Domain of Ptprz
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 the C-Terminal Fg Domain of Tnr with the Single Fn Domain of Ptprz within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Ca1401
b:34.7
occ:1.00
|
OD1
|
G:ASP1284
|
2.3
|
32.8
|
1.0
|
O
|
G:THR1288
|
2.3
|
30.0
|
1.0
|
O
|
G:ALA1286
|
2.4
|
33.1
|
1.0
|
O
|
G:HOH1583
|
2.4
|
38.1
|
1.0
|
O
|
G:HOH1562
|
2.5
|
36.2
|
1.0
|
OD2
|
G:ASP1282
|
2.5
|
33.6
|
1.0
|
OD1
|
G:ASP1282
|
2.8
|
39.4
|
1.0
|
CG
|
G:ASP1282
|
3.0
|
37.8
|
1.0
|
CG
|
G:ASP1284
|
3.2
|
39.4
|
1.0
|
OD2
|
G:ASP1284
|
3.4
|
31.9
|
1.0
|
C
|
G:ALA1286
|
3.4
|
30.7
|
1.0
|
C
|
G:THR1288
|
3.5
|
42.5
|
1.0
|
N
|
G:ALA1286
|
4.0
|
31.5
|
1.0
|
C
|
G:VAL1287
|
4.1
|
34.2
|
1.0
|
CA
|
G:ALA1286
|
4.2
|
33.4
|
1.0
|
N
|
G:THR1288
|
4.2
|
37.5
|
1.0
|
O
|
G:VAL1287
|
4.2
|
39.6
|
1.0
|
N
|
G:ASN1289
|
4.3
|
39.2
|
1.0
|
CA
|
G:ASN1289
|
4.3
|
28.7
|
1.0
|
O
|
G:ASP1284
|
4.3
|
35.1
|
1.0
|
CB
|
G:ALA1286
|
4.4
|
29.2
|
1.0
|
O
|
G:HOH1541
|
4.4
|
43.5
|
1.0
|
CA
|
G:THR1288
|
4.4
|
37.4
|
1.0
|
N
|
G:VAL1287
|
4.5
|
31.1
|
1.0
|
CB
|
G:ASP1282
|
4.5
|
38.6
|
1.0
|
C
|
G:ASP1284
|
4.5
|
33.5
|
1.0
|
O
|
G:HOH1515
|
4.6
|
37.7
|
1.0
|
CB
|
G:ASP1284
|
4.6
|
32.1
|
1.0
|
CA
|
G:VAL1287
|
4.6
|
32.5
|
1.0
|
N
|
G:ASP1284
|
4.9
|
31.3
|
1.0
|
CA
|
G:ASP1284
|
4.9
|
33.2
|
1.0
|
|
Reference:
A.Sinha,
J.Kawakami,
K.S.Cole,
A.Ladutska,
M.Y.Nguyen,
M.S.Zalmai,
B.L.Holder,
V.M.Broerman,
R.T.Matthews,
S.Bouyain.
Protein-Protein Interactions Between Tenascin-R and Rptp Zeta /Phosphacan Are Critical to Maintain the Architecture of Perineuronal Nets. J.Biol.Chem. 04952 2023.
ISSN: ESSN 1083-351X
PubMed: 37356715
DOI: 10.1016/J.JBC.2023.104952
Page generated: Fri Jul 19 09:01:35 2024
|