Calcium in PDB 8q2a: TTX122B - A Domain of Unknown Function From the Teredinibacter Turnerae Protein TERTU_2913
Protein crystallography data
The structure of TTX122B - A Domain of Unknown Function From the Teredinibacter Turnerae Protein TERTU_2913, PDB code: 8q2a
was solved by
B.S.Rajagopal,
G.R.Hemsworth,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
46.69 /
2.20
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
69.141,
75.324,
116.863,
90,
90,
90
|
|
R / Rfree (%)
|
20.9 /
25.9
|
Calcium Binding Sites:
The binding sites of Calcium atom in the TTX122B - A Domain of Unknown Function From the Teredinibacter Turnerae Protein TERTU_2913
(pdb code 8q2a). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the
TTX122B - A Domain of Unknown Function From the Teredinibacter Turnerae Protein TERTU_2913, PDB code: 8q2a:
Jump to Calcium binding site number:
1;
2;
3;
Calcium binding site 1 out
of 3 in 8q2a
Go back to
Calcium Binding Sites List in 8q2a
Calcium binding site 1 out
of 3 in the TTX122B - A Domain of Unknown Function From the Teredinibacter Turnerae Protein TERTU_2913
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of TTX122B - A Domain of Unknown Function From the Teredinibacter Turnerae Protein TERTU_2913 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca301
b:7.6
occ:1.00
|
O
|
A:GLN55
|
2.2
|
9.2
|
1.0
|
|
O
|
A:SER52
|
2.3
|
12.0
|
1.0
|
|
OE2
|
A:GLU11
|
2.3
|
14.9
|
1.0
|
|
HG
|
A:SER52
|
2.3
|
24.4
|
0.0
|
|
OD1
|
A:ASP224
|
2.4
|
4.5
|
1.0
|
|
O
|
A:ASP9
|
2.4
|
13.7
|
1.0
|
|
OG
|
A:SER52
|
2.4
|
24.4
|
1.0
|
|
OD2
|
A:ASP224
|
2.4
|
5.2
|
1.0
|
|
CG
|
A:ASP224
|
2.7
|
5.3
|
1.0
|
|
H
|
A:SER52
|
3.2
|
19.3
|
1.0
|
|
C
|
A:SER52
|
3.3
|
15.7
|
1.0
|
|
C
|
A:GLN55
|
3.4
|
8.0
|
1.0
|
|
H
|
A:GLN55
|
3.4
|
9.9
|
1.0
|
|
CD
|
A:GLU11
|
3.5
|
18.5
|
1.0
|
|
HB1
|
A:ALA50
|
3.5
|
13.6
|
1.0
|
|
C
|
A:ASP9
|
3.6
|
12.3
|
1.0
|
|
HG2
|
A:GLU11
|
3.6
|
17.0
|
1.0
|
|
HB2
|
A:ASP9
|
3.6
|
17.9
|
1.0
|
|
CB
|
A:SER52
|
3.6
|
24.4
|
1.0
|
|
CA
|
A:SER52
|
3.8
|
20.6
|
1.0
|
|
N
|
A:SER52
|
3.8
|
18.8
|
1.0
|
|
HB2
|
A:PHE10
|
3.8
|
9.9
|
1.0
|
|
HA
|
A:SER56
|
4.0
|
7.1
|
1.0
|
|
N
|
A:GLN55
|
4.1
|
9.3
|
1.0
|
|
HA
|
A:ASP9
|
4.1
|
14.9
|
1.0
|
|
CG
|
A:GLU11
|
4.1
|
16.3
|
1.0
|
|
HB2
|
A:SER52
|
4.2
|
23.5
|
1.0
|
|
HB3
|
A:SER52
|
4.2
|
23.6
|
1.0
|
|
OD1
|
A:ASP225
|
4.2
|
33.5
|
1.0
|
|
CA
|
A:ASP9
|
4.2
|
15.1
|
1.0
|
|
CB
|
A:ASP224
|
4.2
|
6.2
|
1.0
|
|
HA3
|
A:GLY53
|
4.2
|
14.6
|
1.0
|
|
CA
|
A:GLN55
|
4.3
|
9.2
|
1.0
|
|
H
|
A:TYR51
|
4.3
|
14.5
|
1.0
|
|
CB
|
A:ASP9
|
4.3
|
17.7
|
1.0
|
|
H
|
A:ASP225
|
4.4
|
9.3
|
1.0
|
|
N
|
A:GLY53
|
4.4
|
14.9
|
1.0
|
|
N
|
A:SER56
|
4.4
|
7.3
|
1.0
|
|
CB
|
A:ALA50
|
4.5
|
13.6
|
1.0
|
|
HB2
|
A:GLN55
|
4.5
|
9.8
|
1.0
|
|
HD2
|
A:PHE10
|
4.5
|
9.8
|
1.0
|
|
OE1
|
A:GLU11
|
4.5
|
21.2
|
1.0
|
|
HB2
|
A:ASP224
|
4.5
|
6.1
|
1.0
|
|
HG3
|
A:GLU11
|
4.5
|
17.0
|
1.0
|
|
HB2
|
A:ALA50
|
4.6
|
13.6
|
1.0
|
|
N
|
A:PHE10
|
4.6
|
12.0
|
1.0
|
|
HB3
|
A:SER56
|
4.6
|
7.0
|
1.0
|
|
CA
|
A:SER56
|
4.7
|
7.0
|
1.0
|
|
HB3
|
A:ASP224
|
4.7
|
6.1
|
1.0
|
|
CA
|
A:GLY53
|
4.7
|
14.4
|
1.0
|
|
CB
|
A:PHE10
|
4.7
|
9.7
|
1.0
|
|
HA
|
A:SER52
|
4.7
|
19.8
|
1.0
|
|
H
|
A:SER54
|
4.8
|
14.7
|
1.0
|
|
N
|
A:GLU11
|
4.9
|
14.9
|
1.0
|
|
C
|
A:GLY53
|
4.9
|
14.6
|
1.0
|
|
C
|
A:PHE10
|
4.9
|
12.4
|
1.0
|
|
HA
|
A:ASP224
|
4.9
|
6.7
|
1.0
|
|
N
|
A:SER54
|
4.9
|
14.7
|
1.0
|
|
H
|
A:GLU11
|
4.9
|
14.8
|
1.0
|
|
N
|
A:TYR51
|
4.9
|
14.9
|
1.0
|
|
CA
|
A:PHE10
|
4.9
|
11.2
|
1.0
|
|
CB
|
A:GLN55
|
4.9
|
9.9
|
1.0
|
|
HB3
|
A:ALA50
|
5.0
|
13.6
|
1.0
|
|
Calcium binding site 2 out
of 3 in 8q2a
Go back to
Calcium Binding Sites List in 8q2a
Calcium binding site 2 out
of 3 in the TTX122B - A Domain of Unknown Function From the Teredinibacter Turnerae Protein TERTU_2913
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of TTX122B - A Domain of Unknown Function From the Teredinibacter Turnerae Protein TERTU_2913 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca301
b:12.2
occ:1.00
|
O
|
B:GLN55
|
2.1
|
10.1
|
1.0
|
|
O
|
B:ASP9
|
2.3
|
8.7
|
1.0
|
|
HG
|
B:SER52
|
2.3
|
16.7
|
0.0
|
|
OE2
|
B:GLU11
|
2.3
|
20.1
|
1.0
|
|
OG
|
B:SER52
|
2.4
|
16.6
|
1.0
|
|
O
|
B:SER52
|
2.5
|
12.8
|
1.0
|
|
OD1
|
B:ASP224
|
2.5
|
6.3
|
1.0
|
|
OD2
|
B:ASP224
|
2.5
|
6.7
|
1.0
|
|
CG
|
B:ASP224
|
2.8
|
6.8
|
1.0
|
|
C
|
B:GLN55
|
3.3
|
14.2
|
1.0
|
|
H
|
B:SER52
|
3.4
|
15.1
|
1.0
|
|
H
|
B:GLN55
|
3.4
|
17.3
|
1.0
|
|
C
|
B:ASP9
|
3.4
|
10.1
|
1.0
|
|
C
|
B:SER52
|
3.5
|
13.4
|
1.0
|
|
HB2
|
B:ASP9
|
3.5
|
13.2
|
1.0
|
|
CD
|
B:GLU11
|
3.5
|
27.0
|
1.0
|
|
HG2
|
B:GLU11
|
3.7
|
24.6
|
1.0
|
|
CB
|
B:SER52
|
3.7
|
17.2
|
1.0
|
|
HB2
|
B:PHE10
|
3.7
|
11.4
|
1.0
|
|
HB1
|
B:ALA50
|
3.7
|
11.1
|
1.0
|
|
CA
|
B:SER52
|
3.9
|
15.8
|
1.0
|
|
HA
|
B:ASP9
|
4.0
|
11.8
|
1.0
|
|
HA
|
B:SER56
|
4.0
|
10.5
|
1.0
|
|
N
|
B:SER52
|
4.0
|
15.6
|
1.0
|
|
N
|
B:GLN55
|
4.0
|
17.1
|
1.0
|
|
CA
|
B:ASP9
|
4.1
|
11.3
|
1.0
|
|
CG
|
B:GLU11
|
4.2
|
24.3
|
1.0
|
|
CA
|
B:GLN55
|
4.2
|
16.2
|
1.0
|
|
CB
|
B:ASP9
|
4.3
|
13.2
|
1.0
|
|
HB2
|
B:SER52
|
4.3
|
16.8
|
1.0
|
|
CB
|
B:ASP224
|
4.3
|
7.6
|
1.0
|
|
OD1
|
B:ASP225
|
4.3
|
35.3
|
1.0
|
|
HB3
|
B:SER52
|
4.3
|
16.9
|
1.0
|
|
HB2
|
B:GLN55
|
4.3
|
17.8
|
1.0
|
|
HD2
|
B:PHE10
|
4.3
|
13.4
|
1.0
|
|
HA3
|
B:GLY53
|
4.4
|
14.2
|
1.0
|
|
N
|
B:SER56
|
4.4
|
12.8
|
1.0
|
|
H
|
B:ASP225
|
4.4
|
11.0
|
1.0
|
|
HB3
|
B:SER56
|
4.4
|
10.1
|
1.0
|
|
H
|
B:TYR51
|
4.4
|
11.2
|
1.0
|
|
N
|
B:PHE10
|
4.5
|
9.4
|
1.0
|
|
N
|
B:GLY53
|
4.5
|
15.1
|
1.0
|
|
OE1
|
B:GLU11
|
4.6
|
29.8
|
1.0
|
|
HB2
|
B:ASP224
|
4.6
|
7.3
|
1.0
|
|
CA
|
B:SER56
|
4.6
|
10.3
|
1.0
|
|
CB
|
B:PHE10
|
4.6
|
10.9
|
1.0
|
|
CB
|
B:ALA50
|
4.6
|
11.0
|
1.0
|
|
HG3
|
B:GLU11
|
4.7
|
24.6
|
1.0
|
|
HB2
|
B:ALA50
|
4.7
|
11.1
|
1.0
|
|
HB3
|
B:ASP224
|
4.7
|
7.4
|
1.0
|
|
C
|
B:PHE10
|
4.8
|
12.8
|
1.0
|
|
N
|
B:GLU11
|
4.8
|
17.5
|
1.0
|
|
CA
|
B:PHE10
|
4.8
|
11.5
|
1.0
|
|
CA
|
B:GLY53
|
4.8
|
13.1
|
1.0
|
|
H
|
B:GLU11
|
4.8
|
17.0
|
1.0
|
|
H
|
B:SER54
|
4.8
|
17.7
|
1.0
|
|
CB
|
B:GLN55
|
4.8
|
17.8
|
1.0
|
|
HA
|
B:SER52
|
4.9
|
15.5
|
1.0
|
|
C
|
B:GLY53
|
4.9
|
15.4
|
1.0
|
|
HB3
|
B:ASP9
|
5.0
|
13.2
|
1.0
|
|
HA
|
B:ASP224
|
5.0
|
7.5
|
1.0
|
|
N
|
B:SER54
|
5.0
|
17.8
|
1.0
|
|
CB
|
B:SER56
|
5.0
|
9.6
|
1.0
|
|
Calcium binding site 3 out
of 3 in 8q2a
Go back to
Calcium Binding Sites List in 8q2a
Calcium binding site 3 out
of 3 in the TTX122B - A Domain of Unknown Function From the Teredinibacter Turnerae Protein TERTU_2913
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of TTX122B - A Domain of Unknown Function From the Teredinibacter Turnerae Protein TERTU_2913 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca301
b:12.1
occ:1.00
|
HG
|
C:SER52
|
2.2
|
26.0
|
0.0
|
|
O
|
C:ASP9
|
2.2
|
10.6
|
1.0
|
|
O
|
C:GLN55
|
2.3
|
14.2
|
1.0
|
|
OG
|
C:SER52
|
2.3
|
26.1
|
1.0
|
|
O
|
C:SER52
|
2.3
|
14.2
|
1.0
|
|
OE2
|
C:GLU11
|
2.3
|
22.5
|
1.0
|
|
OD1
|
C:ASP224
|
2.6
|
13.9
|
1.0
|
|
OD2
|
C:ASP224
|
2.6
|
13.5
|
1.0
|
|
CG
|
C:ASP224
|
2.9
|
15.5
|
1.0
|
|
C
|
C:SER52
|
3.3
|
18.1
|
1.0
|
|
C
|
C:ASP9
|
3.3
|
12.9
|
1.0
|
|
HB2
|
C:ASP9
|
3.4
|
20.3
|
1.0
|
|
C
|
C:GLN55
|
3.4
|
19.0
|
1.0
|
|
H
|
C:SER52
|
3.4
|
25.3
|
1.0
|
|
H
|
C:GLN55
|
3.5
|
22.7
|
1.0
|
|
CD
|
C:GLU11
|
3.5
|
24.3
|
1.0
|
|
CB
|
C:SER52
|
3.6
|
27.6
|
1.0
|
|
HB1
|
C:ALA50
|
3.7
|
21.2
|
1.0
|
|
HG2
|
C:GLU11
|
3.7
|
27.9
|
1.0
|
|
HB2
|
C:PHE10
|
3.7
|
13.3
|
1.0
|
|
CA
|
C:SER52
|
3.8
|
25.1
|
1.0
|
|
HA
|
C:ASP9
|
3.9
|
17.3
|
1.0
|
|
N
|
C:SER52
|
3.9
|
24.8
|
1.0
|
|
CA
|
C:ASP9
|
4.0
|
17.6
|
1.0
|
|
HA
|
C:SER56
|
4.1
|
16.3
|
1.0
|
|
HA3
|
C:GLY53
|
4.1
|
19.0
|
1.0
|
|
HB2
|
C:SER52
|
4.1
|
26.7
|
1.0
|
|
N
|
C:GLN55
|
4.1
|
22.3
|
1.0
|
|
CB
|
C:ASP9
|
4.1
|
20.5
|
1.0
|
|
HB3
|
C:SER52
|
4.2
|
26.8
|
1.0
|
|
CG
|
C:GLU11
|
4.2
|
30.5
|
1.0
|
|
CA
|
C:GLN55
|
4.3
|
22.7
|
1.0
|
|
N
|
C:GLY53
|
4.4
|
18.7
|
1.0
|
|
H
|
C:TYR51
|
4.4
|
22.3
|
1.0
|
|
OD1
|
C:ASP225
|
4.4
|
31.6
|
1.0
|
|
HB2
|
C:GLN55
|
4.4
|
23.8
|
1.0
|
|
N
|
C:PHE10
|
4.4
|
12.8
|
1.0
|
|
HD2
|
C:PHE10
|
4.4
|
12.7
|
1.0
|
|
H
|
C:ASP225
|
4.5
|
13.2
|
1.0
|
|
N
|
C:SER56
|
4.5
|
17.0
|
1.0
|
|
CB
|
C:ASP224
|
4.5
|
14.3
|
1.0
|
|
OE1
|
C:GLU11
|
4.5
|
24.5
|
1.0
|
|
H
|
C:GLU11
|
4.6
|
20.0
|
1.0
|
|
HB3
|
C:SER56
|
4.6
|
16.6
|
1.0
|
|
CB
|
C:ALA50
|
4.6
|
21.2
|
1.0
|
|
CA
|
C:GLY53
|
4.6
|
18.9
|
1.0
|
|
CB
|
C:PHE10
|
4.6
|
12.9
|
1.0
|
|
CA
|
C:SER56
|
4.7
|
17.2
|
1.0
|
|
HB2
|
C:ALA50
|
4.7
|
21.2
|
1.0
|
|
N
|
C:GLU11
|
4.7
|
19.3
|
1.0
|
|
HG3
|
C:GLU11
|
4.8
|
27.9
|
1.0
|
|
C
|
C:PHE10
|
4.8
|
18.1
|
1.0
|
|
CA
|
C:PHE10
|
4.8
|
15.0
|
1.0
|
|
HA
|
C:SER52
|
4.8
|
24.0
|
1.0
|
|
HB3
|
C:ASP9
|
4.8
|
20.4
|
1.0
|
|
HB2
|
C:ASP224
|
4.9
|
14.1
|
1.0
|
|
H
|
C:SER54
|
4.9
|
22.8
|
1.0
|
|
C
|
C:GLY53
|
4.9
|
19.7
|
1.0
|
|
CB
|
C:GLN55
|
4.9
|
23.2
|
1.0
|
|
HB3
|
C:ASP224
|
4.9
|
14.1
|
1.0
|
|
N
|
C:SER54
|
4.9
|
22.2
|
1.0
|
|
HA
|
C:ASP224
|
5.0
|
12.5
|
1.0
|
|
CG
|
C:ASP9
|
5.0
|
23.3
|
1.0
|
|
Reference:
B.S.Rajagopal,
N.Yates,
J.Smith,
A.Paradisi,
C.Tetard-Jones,
W.G.T.Willats,
S.Marcus,
P.J.Knox,
M.Firdaus-Raih,
B.Henrissat,
G.J.Davies,
P.H.Walton,
A.Parkin,
G.R.Hemsworth.
Structural Dissection of Two Redox Proteins From the Shipworm Symbiont Teredinibacter Turnerae Iucrj 2024.
ISSN: ESSN 2052-2525
DOI: 10.1107/S2052252524001386
Page generated: Fri Jul 19 11:15:42 2024
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