Sodium in PDB 8ot5: Crystal Structure of the Titin Domain FN3-85
Enzymatic activity of Crystal Structure of the Titin Domain FN3-85
All present enzymatic activity of Crystal Structure of the Titin Domain FN3-85:
2.7.11.1;
Protein crystallography data
The structure of Crystal Structure of the Titin Domain FN3-85, PDB code: 8ot5
was solved by
R.Nikoopour,
M.Rees,
M.Gautel,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
57.19 /
1.56
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
59.358,
99.829,
62.239,
90,
105.55,
90
|
|
R / Rfree (%)
|
16.3 /
19.1
|
Other elements in 8ot5:
The structure of Crystal Structure of the Titin Domain FN3-85 also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of the Titin Domain FN3-85
(pdb code 8ot5). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
Crystal Structure of the Titin Domain FN3-85, PDB code: 8ot5:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 8ot5
Go back to
Sodium Binding Sites List in 8ot5
Sodium binding site 1 out
of 4 in the Crystal Structure of the Titin Domain FN3-85
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystal Structure of the Titin Domain FN3-85 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na201
b:20.6
occ:1.00
|
H
|
A:ALA82
|
2.0
|
14.5
|
1.0
|
|
HD3
|
A:PRO9
|
2.7
|
16.7
|
1.0
|
|
O
|
A:LYS90
|
2.7
|
14.5
|
1.0
|
|
O
|
A:GLY7
|
2.8
|
15.6
|
1.0
|
|
HB3
|
A:ALA82
|
2.8
|
17.9
|
1.0
|
|
N
|
A:ALA82
|
2.9
|
12.1
|
1.0
|
|
HA3
|
A:GLY89
|
3.0
|
16.8
|
1.0
|
|
HA
|
A:PRO8
|
3.0
|
15.8
|
1.0
|
|
H
|
A:GLY89
|
3.2
|
15.5
|
1.0
|
|
C
|
A:GLY89
|
3.2
|
16.6
|
1.0
|
|
HG2
|
A:PRO6
|
3.2
|
19.8
|
1.0
|
|
HA
|
A:SER81
|
3.3
|
12.4
|
1.0
|
|
N
|
A:LYS90
|
3.4
|
14.1
|
1.0
|
|
CA
|
A:GLY89
|
3.4
|
14.0
|
1.0
|
|
HB3
|
A:SER81
|
3.5
|
17.3
|
1.0
|
|
O
|
A:ALA82
|
3.5
|
14.1
|
1.0
|
|
H
|
A:LYS90
|
3.5
|
17.0
|
1.0
|
|
CB
|
A:ALA82
|
3.5
|
14.9
|
1.0
|
|
C
|
A:GLY7
|
3.6
|
14.0
|
1.0
|
|
O
|
A:GLY89
|
3.6
|
14.4
|
1.0
|
|
CA
|
A:ALA82
|
3.6
|
13.1
|
1.0
|
|
CD
|
A:PRO9
|
3.6
|
13.9
|
1.0
|
|
N
|
A:GLY89
|
3.7
|
12.9
|
1.0
|
|
C
|
A:LYS90
|
3.7
|
14.9
|
1.0
|
|
HB2
|
A:ALA82
|
3.8
|
17.9
|
1.0
|
|
C
|
A:SER81
|
3.8
|
11.7
|
1.0
|
|
CA
|
A:PRO8
|
3.9
|
13.2
|
1.0
|
|
CA
|
A:SER81
|
3.9
|
10.4
|
1.0
|
|
O
|
A:PRO6
|
3.9
|
15.6
|
1.0
|
|
C
|
A:ALA82
|
4.0
|
13.6
|
1.0
|
|
HB2
|
A:PRO6
|
4.1
|
22.2
|
1.0
|
|
N
|
A:PRO8
|
4.1
|
14.2
|
1.0
|
|
HD2
|
A:PRO9
|
4.1
|
16.7
|
1.0
|
|
CB
|
A:SER81
|
4.1
|
14.4
|
1.0
|
|
CA
|
A:LYS90
|
4.1
|
16.0
|
1.0
|
|
HG3
|
A:PRO9
|
4.1
|
15.8
|
1.0
|
|
CG
|
A:PRO6
|
4.2
|
16.5
|
1.0
|
|
C
|
A:PRO6
|
4.3
|
13.7
|
1.0
|
|
HA2
|
A:GLY89
|
4.4
|
16.8
|
1.0
|
|
HB1
|
A:ALA82
|
4.4
|
17.9
|
1.0
|
|
CG
|
A:PRO9
|
4.4
|
13.2
|
1.0
|
|
N
|
A:PRO9
|
4.5
|
14.2
|
1.0
|
|
HA
|
A:ALA82
|
4.5
|
15.7
|
1.0
|
|
CB
|
A:PRO6
|
4.6
|
18.5
|
1.0
|
|
C
|
A:PRO8
|
4.6
|
13.2
|
1.0
|
|
HG2
|
A:PRO9
|
4.6
|
15.8
|
1.0
|
|
HG3
|
A:PRO6
|
4.6
|
19.8
|
1.0
|
|
CA
|
A:GLY7
|
4.6
|
17.0
|
1.0
|
|
HA
|
A:PRO91
|
4.7
|
17.8
|
1.0
|
|
HG23
|
A:ILE88
|
4.7
|
16.8
|
1.0
|
|
HB2
|
A:LYS90
|
4.7
|
18.3
|
1.0
|
|
N
|
A:GLY7
|
4.7
|
15.3
|
1.0
|
|
HG3
|
A:PRO29
|
4.8
|
17.4
|
1.0
|
|
HA2
|
A:GLY7
|
4.8
|
20.4
|
1.0
|
|
N
|
A:PRO91
|
4.8
|
13.7
|
1.0
|
|
HA
|
A:LYS90
|
4.8
|
19.2
|
1.0
|
|
HB2
|
A:SER81
|
4.8
|
17.3
|
1.0
|
|
HB3
|
A:PRO8
|
4.8
|
19.0
|
1.0
|
|
O
|
A:HOH310
|
4.9
|
17.2
|
1.0
|
|
OG
|
A:SER81
|
4.9
|
16.6
|
1.0
|
|
HD2
|
A:PRO6
|
5.0
|
19.6
|
1.0
|
|
C
|
A:ILE88
|
5.0
|
14.6
|
1.0
|
|
Sodium binding site 2 out
of 4 in 8ot5
Go back to
Sodium Binding Sites List in 8ot5
Sodium binding site 2 out
of 4 in the Crystal Structure of the Titin Domain FN3-85
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystal Structure of the Titin Domain FN3-85 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na201
b:23.0
occ:0.77
|
HD23
|
C:LEU23
|
1.9
|
33.0
|
0.5
|
|
HB3
|
B:HIS27
|
2.4
|
20.7
|
1.0
|
|
HD21
|
C:LEU23
|
2.5
|
33.0
|
0.5
|
|
HD13
|
C:LEU23
|
2.5
|
30.1
|
0.5
|
|
OG1
|
C:THR15
|
2.6
|
16.5
|
1.0
|
|
CD2
|
C:LEU23
|
2.6
|
27.5
|
0.5
|
|
HG2
|
B:GLU28
|
2.7
|
35.7
|
1.0
|
|
O
|
B:GLU28
|
2.8
|
17.1
|
1.0
|
|
HB
|
C:THR15
|
3.1
|
19.0
|
1.0
|
|
O
|
B:HOH421
|
3.2
|
27.5
|
1.0
|
|
H
|
B:GLU28
|
3.2
|
20.2
|
1.0
|
|
HD22
|
C:LEU23
|
3.2
|
33.0
|
0.5
|
|
HD22
|
C:LEU23
|
3.3
|
19.1
|
0.5
|
|
HE21
|
C:GLN25
|
3.3
|
28.5
|
1.0
|
|
HB2
|
C:SER16
|
3.4
|
18.5
|
1.0
|
|
CB
|
C:THR15
|
3.4
|
15.8
|
1.0
|
|
CB
|
B:HIS27
|
3.4
|
17.2
|
1.0
|
|
HB3
|
C:LEU23
|
3.4
|
19.1
|
0.5
|
|
CD1
|
C:LEU23
|
3.4
|
25.1
|
0.5
|
|
N
|
B:GLU28
|
3.5
|
16.8
|
1.0
|
|
CG
|
B:GLU28
|
3.5
|
29.8
|
1.0
|
|
HG3
|
B:GLU28
|
3.5
|
35.7
|
1.0
|
|
HB3
|
C:LEU23
|
3.5
|
19.1
|
0.5
|
|
HB3
|
C:SER16
|
3.6
|
18.5
|
1.0
|
|
CG
|
C:LEU23
|
3.7
|
22.6
|
0.5
|
|
HG
|
C:LEU23
|
3.7
|
27.1
|
0.5
|
|
C
|
B:GLU28
|
3.7
|
16.1
|
1.0
|
|
HE22
|
C:GLN25
|
3.8
|
28.5
|
1.0
|
|
HB2
|
B:HIS27
|
3.8
|
20.7
|
1.0
|
|
NE2
|
C:GLN25
|
3.8
|
23.8
|
1.0
|
|
HD11
|
C:LEU23
|
3.9
|
30.1
|
0.5
|
|
CB
|
C:SER16
|
3.9
|
15.4
|
1.0
|
|
C
|
B:HIS27
|
3.9
|
13.9
|
1.0
|
|
HD12
|
C:LEU23
|
4.0
|
30.1
|
0.5
|
|
C
|
C:THR15
|
4.0
|
14.6
|
1.0
|
|
CG
|
C:LEU23
|
4.0
|
15.1
|
0.5
|
|
CD2
|
C:LEU23
|
4.0
|
15.9
|
0.5
|
|
CA
|
B:GLU28
|
4.0
|
18.1
|
1.0
|
|
CB
|
C:LEU23
|
4.0
|
15.9
|
0.5
|
|
CB
|
C:LEU23
|
4.1
|
15.9
|
0.5
|
|
CA
|
B:HIS27
|
4.1
|
16.0
|
1.0
|
|
O
|
C:THR15
|
4.1
|
18.0
|
1.0
|
|
HB2
|
C:LEU23
|
4.2
|
19.1
|
0.5
|
|
HA
|
B:HIS27
|
4.2
|
19.2
|
1.0
|
|
CG
|
B:HIS27
|
4.2
|
21.9
|
1.0
|
|
N
|
C:SER16
|
4.2
|
14.5
|
1.0
|
|
CA
|
C:THR15
|
4.3
|
14.2
|
1.0
|
|
HB2
|
C:LEU23
|
4.3
|
19.1
|
0.5
|
|
CB
|
B:GLU28
|
4.3
|
21.8
|
1.0
|
|
HD21
|
C:LEU23
|
4.3
|
19.1
|
0.5
|
|
H
|
C:SER16
|
4.5
|
17.4
|
1.0
|
|
HG21
|
C:THR15
|
4.5
|
21.9
|
1.0
|
|
HD2
|
B:HIS27
|
4.5
|
31.7
|
1.0
|
|
CG2
|
C:THR15
|
4.6
|
18.2
|
1.0
|
|
CD
|
B:GLU28
|
4.6
|
53.5
|
1.0
|
|
OE2
|
B:GLU28
|
4.6
|
44.1
|
1.0
|
|
CD2
|
B:HIS27
|
4.7
|
26.4
|
1.0
|
|
H
|
C:THR15
|
4.7
|
16.6
|
1.0
|
|
CA
|
C:SER16
|
4.7
|
14.2
|
1.0
|
|
HB3
|
B:GLU28
|
4.7
|
26.1
|
1.0
|
|
O
|
B:HIS27
|
4.7
|
15.2
|
1.0
|
|
HD23
|
C:LEU23
|
4.8
|
19.1
|
0.5
|
|
HA
|
B:GLU28
|
4.9
|
21.7
|
1.0
|
|
HG
|
C:LEU23
|
4.9
|
18.2
|
0.5
|
|
N
|
B:PRO29
|
5.0
|
15.5
|
1.0
|
|
Sodium binding site 3 out
of 4 in 8ot5
Go back to
Sodium Binding Sites List in 8ot5
Sodium binding site 3 out
of 4 in the Crystal Structure of the Titin Domain FN3-85
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Crystal Structure of the Titin Domain FN3-85 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na201
b:22.0
occ:0.98
|
H
|
C:ALA82
|
2.0
|
16.3
|
1.0
|
|
HD3
|
C:PRO9
|
2.6
|
19.3
|
1.0
|
|
O
|
C:LYS90
|
2.6
|
16.9
|
1.0
|
|
O
|
C:GLY7
|
2.8
|
16.8
|
1.0
|
|
N
|
C:ALA82
|
2.9
|
13.7
|
1.0
|
|
HA3
|
C:GLY89
|
2.9
|
23.1
|
1.0
|
|
HB3
|
C:ALA82
|
3.0
|
16.5
|
1.0
|
|
HA
|
C:PRO8
|
3.1
|
19.9
|
1.0
|
|
C
|
C:GLY89
|
3.2
|
17.2
|
1.0
|
|
HA
|
C:SER81
|
3.3
|
16.2
|
1.0
|
|
H
|
C:GLY89
|
3.3
|
21.9
|
1.0
|
|
CA
|
C:GLY89
|
3.4
|
19.2
|
1.0
|
|
HG2
|
C:PRO6
|
3.4
|
35.5
|
1.0
|
|
N
|
C:LYS90
|
3.4
|
19.9
|
1.0
|
|
HB3
|
C:SER81
|
3.5
|
18.6
|
1.0
|
|
O
|
C:ALA82
|
3.5
|
17.7
|
1.0
|
|
CD
|
C:PRO9
|
3.6
|
16.1
|
1.0
|
|
H
|
C:LYS90
|
3.6
|
23.9
|
1.0
|
|
C
|
C:GLY7
|
3.6
|
17.2
|
1.0
|
|
O
|
C:GLY89
|
3.6
|
17.8
|
1.0
|
|
CB
|
C:ALA82
|
3.6
|
13.8
|
1.0
|
|
CA
|
C:ALA82
|
3.6
|
13.8
|
1.0
|
|
C
|
C:LYS90
|
3.7
|
16.6
|
1.0
|
|
HB2
|
C:PRO6
|
3.7
|
22.3
|
1.0
|
|
N
|
C:GLY89
|
3.8
|
18.3
|
1.0
|
|
C
|
C:SER81
|
3.8
|
14.7
|
1.0
|
|
O
|
C:PRO6
|
3.8
|
20.9
|
1.0
|
|
HB2
|
C:ALA82
|
3.9
|
16.5
|
1.0
|
|
CA
|
C:SER81
|
3.9
|
13.5
|
1.0
|
|
CA
|
C:PRO8
|
4.0
|
16.6
|
1.0
|
|
HD2
|
C:PRO9
|
4.0
|
19.3
|
1.0
|
|
HG3
|
C:PRO9
|
4.0
|
16.7
|
1.0
|
|
C
|
C:ALA82
|
4.0
|
15.9
|
1.0
|
|
CB
|
C:SER81
|
4.1
|
15.5
|
1.0
|
|
N
|
C:PRO8
|
4.1
|
17.3
|
1.0
|
|
CA
|
C:LYS90
|
4.2
|
22.0
|
1.0
|
|
C
|
C:PRO6
|
4.2
|
18.6
|
1.0
|
|
CG
|
C:PRO9
|
4.2
|
13.9
|
1.0
|
|
CG
|
C:PRO6
|
4.3
|
29.6
|
1.0
|
|
HA2
|
C:GLY89
|
4.3
|
23.1
|
1.0
|
|
CB
|
C:PRO6
|
4.4
|
18.6
|
1.0
|
|
N
|
C:PRO9
|
4.4
|
14.2
|
1.0
|
|
HG2
|
C:PRO9
|
4.5
|
16.7
|
1.0
|
|
HB1
|
C:ALA82
|
4.5
|
16.5
|
1.0
|
|
HA
|
C:PRO91
|
4.5
|
19.1
|
1.0
|
|
HA
|
C:ALA82
|
4.5
|
16.4
|
1.0
|
|
C
|
C:PRO8
|
4.6
|
15.2
|
1.0
|
|
CA
|
C:GLY7
|
4.6
|
19.4
|
1.0
|
|
N
|
C:GLY7
|
4.7
|
19.2
|
1.0
|
|
HB2
|
C:LYS90
|
4.7
|
28.4
|
1.0
|
|
HG3
|
C:PRO29
|
4.7
|
17.5
|
1.0
|
|
N
|
C:PRO91
|
4.7
|
17.6
|
1.0
|
|
HA2
|
C:GLY7
|
4.8
|
23.3
|
1.0
|
|
OG
|
C:SER81
|
4.8
|
19.8
|
1.0
|
|
HA
|
C:LYS90
|
4.9
|
26.4
|
1.0
|
|
HG3
|
C:PRO6
|
4.9
|
35.5
|
1.0
|
|
HB2
|
C:SER81
|
4.9
|
18.6
|
1.0
|
|
O
|
C:HOH322
|
4.9
|
25.0
|
1.0
|
|
HG23
|
C:ILE88
|
4.9
|
27.1
|
1.0
|
|
CA
|
C:PRO6
|
4.9
|
18.5
|
1.0
|
|
HD2
|
C:PRO6
|
5.0
|
28.6
|
1.0
|
|
Sodium binding site 4 out
of 4 in 8ot5
Go back to
Sodium Binding Sites List in 8ot5
Sodium binding site 4 out
of 4 in the Crystal Structure of the Titin Domain FN3-85
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Crystal Structure of the Titin Domain FN3-85 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na201
b:30.6
occ:0.76
|
HG21
|
D:THR11
|
2.0
|
23.6
|
0.0
|
|
HG23
|
D:THR11
|
2.3
|
23.6
|
0.0
|
|
CG2
|
D:THR11
|
2.5
|
19.7
|
0.0
|
|
O
|
F:HOH305
|
2.5
|
33.7
|
1.0
|
|
O
|
D:HOH399
|
2.7
|
49.2
|
1.0
|
|
OG1
|
D:THR11
|
2.7
|
18.8
|
1.0
|
|
HD2
|
D:LYS93
|
3.0
|
33.8
|
1.0
|
|
HG21
|
D:THR11
|
3.1
|
26.3
|
1.0
|
|
HB
|
D:THR11
|
3.2
|
23.2
|
1.0
|
|
HG22
|
D:THR11
|
3.3
|
23.6
|
0.0
|
|
OG1
|
D:THR11
|
3.4
|
20.1
|
0.0
|
|
CB
|
D:THR11
|
3.4
|
19.3
|
1.0
|
|
HG1
|
D:THR11
|
3.4
|
22.5
|
1.0
|
|
CB
|
D:THR11
|
3.4
|
19.2
|
0.0
|
|
HB
|
D:THR11
|
3.6
|
23.0
|
0.0
|
|
HB2
|
D:LYS93
|
3.7
|
23.8
|
1.0
|
|
CG2
|
D:THR11
|
3.7
|
21.9
|
1.0
|
|
CD
|
D:LYS93
|
3.8
|
28.1
|
1.0
|
|
O
|
F:HOH303
|
3.8
|
52.6
|
1.0
|
|
HD3
|
D:LYS93
|
3.9
|
33.8
|
1.0
|
|
O
|
D:HOH409
|
4.0
|
44.8
|
1.0
|
|
HG1
|
D:THR11
|
4.0
|
24.2
|
0.0
|
|
O
|
D:HOH383
|
4.2
|
29.7
|
1.0
|
|
HZ1
|
D:LYS93
|
4.2
|
41.8
|
1.0
|
|
HG23
|
D:THR11
|
4.3
|
26.3
|
1.0
|
|
OE1
|
F:GLU96
|
4.3
|
33.4
|
0.5
|
|
HB3
|
D:LYS93
|
4.3
|
23.8
|
1.0
|
|
CB
|
D:LYS93
|
4.4
|
19.9
|
1.0
|
|
O
|
D:HOH429
|
4.4
|
25.9
|
1.0
|
|
O
|
D:HOH337
|
4.4
|
21.9
|
1.0
|
|
HG22
|
D:THR11
|
4.4
|
26.3
|
1.0
|
|
H
|
D:THR11
|
4.6
|
17.3
|
1.0
|
|
H
|
D:THR11
|
4.6
|
17.3
|
0.0
|
|
CG
|
D:LYS93
|
4.6
|
22.5
|
1.0
|
|
NZ
|
D:LYS93
|
4.8
|
34.8
|
1.0
|
|
CA
|
D:THR11
|
4.8
|
15.7
|
0.0
|
|
CA
|
D:THR11
|
4.8
|
15.6
|
1.0
|
|
HZ2
|
D:LYS93
|
4.8
|
41.8
|
1.0
|
|
CE
|
D:LYS93
|
4.8
|
29.2
|
1.0
|
|
HG3
|
D:LYS93
|
4.9
|
27.0
|
1.0
|
|
Reference:
M.Rees,
R.Nikoopour,
A.Alexandrovich,
M.Pfuhl,
L.R.Lopes,
M.M.Akhtar,
P.Syrris,
P.Elliott,
G.Carr-White,
M.Gautel.
Structure Determination and Analysis of Titin A-Band Fibronectin Type III Domains Provides Insights For Disease-Linked Variants and Protein Oligomerisation. J.Struct.Biol. 08009 2023.
ISSN: ESSN 1095-8657
PubMed: 37549721
DOI: 10.1016/J.JSB.2023.108009
Page generated: Wed Oct 9 12:46:58 2024
|
