Sodium in PDB 7a2n: Crystal Structure of the Fyn SH3 Domain A95S-D99T Mutant in Space Group P21
Enzymatic activity of Crystal Structure of the Fyn SH3 Domain A95S-D99T Mutant in Space Group P21
All present enzymatic activity of Crystal Structure of the Fyn SH3 Domain A95S-D99T Mutant in Space Group P21:
2.7.10.2;
Protein crystallography data
The structure of Crystal Structure of the Fyn SH3 Domain A95S-D99T Mutant in Space Group P21, PDB code: 7a2n
was solved by
A.Camara-Artigas,
M.Plaza-Garrido,
M.C.Salinas-Garcia,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
19.94 /
1.40
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
42.176,
47.795,
73.089,
90,
98.35,
90
|
|
R / Rfree (%)
|
17 /
20.4
|
Sodium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Sodium atom in the Crystal Structure of the Fyn SH3 Domain A95S-D99T Mutant in Space Group P21
(pdb code 7a2n). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the
Crystal Structure of the Fyn SH3 Domain A95S-D99T Mutant in Space Group P21, PDB code: 7a2n:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 12 in 7a2n
Go back to
Sodium Binding Sites List in 7a2n
Sodium binding site 1 out
of 12 in the Crystal Structure of the Fyn SH3 Domain A95S-D99T Mutant in Space Group P21
 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 Fyn SH3 Domain A95S-D99T Mutant in Space Group P21 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na202
b:34.5
occ:1.00
|
O
|
A:HOH325
|
2.2
|
28.2
|
1.0
|
|
O
|
A:SER102
|
2.3
|
12.2
|
1.0
|
|
O
|
A:HOH307
|
2.3
|
13.8
|
1.0
|
|
O
|
A:HOH321
|
2.3
|
15.5
|
1.0
|
|
OE1
|
A:GLU129
|
2.6
|
26.9
|
1.0
|
|
HD11
|
A:LEU101
|
2.9
|
18.3
|
1.0
|
|
HG1
|
A:THR127
|
3.1
|
14.2
|
1.0
|
|
HA
|
A:PHE103
|
3.3
|
11.3
|
1.0
|
|
C
|
A:SER102
|
3.4
|
10.3
|
1.0
|
|
HG21
|
A:THR127
|
3.5
|
16.1
|
1.0
|
|
HD12
|
A:LEU101
|
3.6
|
18.3
|
1.0
|
|
CD
|
A:GLU129
|
3.6
|
25.6
|
1.0
|
|
CD1
|
A:LEU101
|
3.6
|
15.2
|
1.0
|
|
HG
|
A:LEU101
|
3.7
|
16.2
|
1.0
|
|
HB2
|
A:GLU129
|
3.9
|
17.4
|
1.0
|
|
HB3
|
A:PHE103
|
4.0
|
11.7
|
1.0
|
|
OG1
|
A:THR127
|
4.0
|
11.8
|
1.0
|
|
O
|
A:HOH345
|
4.0
|
19.1
|
1.0
|
|
HB2
|
A:SER102
|
4.0
|
15.6
|
1.0
|
|
CA
|
A:PHE103
|
4.1
|
9.4
|
1.0
|
|
OE2
|
A:GLU129
|
4.1
|
29.6
|
1.0
|
|
N
|
A:PHE103
|
4.2
|
10.2
|
1.0
|
|
CG
|
A:LEU101
|
4.2
|
13.5
|
1.0
|
|
HD21
|
A:LEU101
|
4.3
|
16.3
|
1.0
|
|
CG2
|
A:THR127
|
4.3
|
13.4
|
1.0
|
|
OE2
|
A:GLU107
|
4.3
|
13.2
|
1.0
|
|
HD13
|
A:LEU101
|
4.4
|
18.3
|
1.0
|
|
OE1
|
A:GLU107
|
4.4
|
13.1
|
1.0
|
|
CA
|
A:SER102
|
4.4
|
11.2
|
1.0
|
|
O
|
D:HOH346
|
4.5
|
23.6
|
1.0
|
|
HB
|
A:THR127
|
4.5
|
14.3
|
1.0
|
|
CB
|
A:PHE103
|
4.5
|
9.7
|
1.0
|
|
CB
|
A:THR127
|
4.5
|
11.9
|
1.0
|
|
H
|
A:SER102
|
4.5
|
13.4
|
1.0
|
|
HG23
|
A:THR127
|
4.6
|
16.1
|
1.0
|
|
N
|
A:SER102
|
4.6
|
11.1
|
1.0
|
|
CB
|
A:GLU129
|
4.6
|
14.5
|
1.0
|
|
CB
|
A:SER102
|
4.6
|
13.0
|
1.0
|
|
CG
|
A:GLU129
|
4.7
|
18.7
|
1.0
|
|
HB3
|
A:GLU129
|
4.8
|
17.4
|
1.0
|
|
CD2
|
A:LEU101
|
4.8
|
13.6
|
1.0
|
|
CD
|
A:GLU107
|
4.8
|
11.8
|
1.0
|
|
HB3
|
A:SER102
|
4.9
|
15.6
|
1.0
|
|
HB2
|
A:PHE103
|
4.9
|
11.7
|
1.0
|
|
HG3
|
A:GLU129
|
4.9
|
22.5
|
1.0
|
|
Sodium binding site 2 out
of 12 in 7a2n
Go back to
Sodium Binding Sites List in 7a2n
Sodium binding site 2 out
of 12 in the Crystal Structure of the Fyn SH3 Domain A95S-D99T Mutant in Space Group P21
 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 Fyn SH3 Domain A95S-D99T Mutant in Space Group P21 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na203
b:16.6
occ:1.00
|
O
|
A:VAL138
|
2.2
|
11.9
|
1.0
|
|
O
|
A:SER135
|
2.4
|
12.3
|
1.0
|
|
HA
|
A:ASN136
|
3.1
|
15.9
|
1.0
|
|
C
|
A:VAL138
|
3.4
|
10.2
|
1.0
|
|
H
|
A:VAL138
|
3.4
|
12.3
|
1.0
|
|
C
|
A:SER135
|
3.6
|
11.5
|
1.0
|
|
HA
|
A:ALA139
|
3.7
|
13.2
|
1.0
|
|
CA
|
A:ASN136
|
3.9
|
13.2
|
1.0
|
|
HG23
|
A:VAL138
|
4.1
|
14.6
|
1.0
|
|
N
|
A:VAL138
|
4.1
|
10.2
|
1.0
|
|
HG22
|
A:VAL138
|
4.2
|
14.6
|
1.0
|
|
N
|
A:ASN136
|
4.2
|
12.1
|
1.0
|
|
C
|
A:ASN136
|
4.2
|
12.7
|
1.0
|
|
N
|
A:ALA139
|
4.3
|
10.9
|
1.0
|
|
CA
|
A:VAL138
|
4.3
|
10.6
|
1.0
|
|
HD11
|
A:LEU90
|
4.3
|
18.9
|
1.0
|
|
HB2
|
A:SER135
|
4.3
|
17.0
|
1.0
|
|
CA
|
A:ALA139
|
4.4
|
11.0
|
1.0
|
|
O
|
A:ASN136
|
4.5
|
15.0
|
1.0
|
|
CG2
|
A:VAL138
|
4.5
|
12.2
|
1.0
|
|
HB2
|
A:ALA139
|
4.7
|
15.0
|
1.0
|
|
CA
|
A:SER135
|
4.7
|
11.4
|
1.0
|
|
N
|
A:TYR137
|
4.7
|
10.1
|
1.0
|
|
HA
|
A:SER135
|
4.7
|
13.8
|
1.0
|
|
HD3
|
A:PRO140
|
4.8
|
15.7
|
1.0
|
|
H
|
A:TYR137
|
4.9
|
12.1
|
1.0
|
|
CB
|
A:SER135
|
4.9
|
14.2
|
1.0
|
|
HD12
|
A:LEU90
|
5.0
|
18.9
|
1.0
|
|
Sodium binding site 3 out
of 12 in 7a2n
Go back to
Sodium Binding Sites List in 7a2n
Sodium binding site 3 out
of 12 in the Crystal Structure of the Fyn SH3 Domain A95S-D99T Mutant in Space Group P21
 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 Fyn SH3 Domain A95S-D99T Mutant in Space Group P21 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na204
b:16.4
occ:1.00
|
O
|
A:ASP100
|
2.3
|
13.1
|
1.0
|
|
O
|
A:THR97
|
2.3
|
14.9
|
1.0
|
|
O
|
A:HOH336
|
2.4
|
24.6
|
1.0
|
|
OG
|
A:SER95
|
2.4
|
14.0
|
1.0
|
|
O
|
A:HOH343
|
2.5
|
37.3
|
1.0
|
|
O
|
A:HOH327
|
2.9
|
20.3
|
1.0
|
|
HB2
|
A:SER95
|
3.1
|
17.2
|
1.0
|
|
HA
|
A:GLU98
|
3.2
|
22.0
|
1.0
|
|
CB
|
A:SER95
|
3.2
|
14.3
|
1.0
|
|
C
|
A:THR97
|
3.5
|
14.9
|
1.0
|
|
C
|
A:ASP100
|
3.5
|
12.2
|
1.0
|
|
HA
|
A:LEU101
|
3.5
|
13.3
|
1.0
|
|
HB3
|
A:SER95
|
3.6
|
17.2
|
1.0
|
|
H
|
A:SER102
|
3.8
|
13.4
|
1.0
|
|
HG
|
A:SER102
|
3.8
|
16.8
|
1.0
|
|
CA
|
A:GLU98
|
3.9
|
18.3
|
1.0
|
|
O
|
A:HOH330
|
4.0
|
42.1
|
1.0
|
|
N
|
A:GLU98
|
4.1
|
15.8
|
1.0
|
|
C
|
A:GLU98
|
4.2
|
16.6
|
1.0
|
|
CA
|
A:LEU101
|
4.3
|
11.0
|
1.0
|
|
N
|
A:LEU101
|
4.3
|
10.7
|
1.0
|
|
H
|
A:THR97
|
4.3
|
19.2
|
1.0
|
|
H
|
A:ASP100
|
4.4
|
13.3
|
1.0
|
|
N
|
A:SER102
|
4.4
|
11.1
|
1.0
|
|
O
|
A:GLU98
|
4.4
|
17.6
|
1.0
|
|
OD1
|
A:ASP100
|
4.5
|
12.4
|
1.0
|
|
N
|
A:ASP100
|
4.5
|
11.0
|
1.0
|
|
CA
|
A:ASP100
|
4.6
|
11.1
|
1.0
|
|
CA
|
A:SER95
|
4.6
|
13.7
|
1.0
|
|
N
|
A:THR97
|
4.6
|
16.0
|
1.0
|
|
OG
|
A:SER102
|
4.6
|
14.0
|
1.0
|
|
CA
|
A:THR97
|
4.6
|
14.7
|
1.0
|
|
C
|
A:LEU101
|
4.7
|
10.8
|
1.0
|
|
N
|
A:THR99
|
4.8
|
13.9
|
1.0
|
|
C
|
A:SER95
|
4.8
|
13.5
|
1.0
|
|
CG
|
A:ASP100
|
4.9
|
12.3
|
1.0
|
|
H
|
A:SER95
|
5.0
|
16.7
|
1.0
|
|
H
|
A:GLU98
|
5.0
|
19.0
|
1.0
|
|
Sodium binding site 4 out
of 12 in 7a2n
Go back to
Sodium Binding Sites List in 7a2n
Sodium binding site 4 out
of 12 in the Crystal Structure of the Fyn SH3 Domain A95S-D99T Mutant in Space Group P21
 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 Fyn SH3 Domain A95S-D99T Mutant in Space Group P21 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na205
b:16.5
occ:0.61
|
O
|
A:HOH347
|
2.1
|
34.4
|
1.0
|
|
O
|
A:SER114
|
2.2
|
20.4
|
1.0
|
|
O
|
A:HOH329
|
2.4
|
20.0
|
1.0
|
|
O
|
A:HOH334
|
2.5
|
41.9
|
1.0
|
|
O
|
A:GLY117
|
2.5
|
14.2
|
1.0
|
|
HE1
|
A:TRP120
|
2.9
|
13.8
|
1.0
|
|
H
|
A:GLY117
|
3.1
|
18.7
|
1.0
|
|
C
|
A:GLY117
|
3.3
|
13.4
|
1.0
|
|
C
|
A:SER114
|
3.4
|
18.1
|
1.0
|
|
O
|
A:HOH306
|
3.5
|
36.6
|
1.0
|
|
HB2
|
A:SER114
|
3.5
|
21.4
|
1.0
|
|
NE1
|
A:TRP120
|
3.6
|
11.4
|
1.0
|
|
N
|
A:GLY117
|
3.7
|
15.5
|
1.0
|
|
HA2
|
A:GLY117
|
3.8
|
17.8
|
1.0
|
|
CA
|
A:GLY117
|
3.9
|
14.8
|
1.0
|
|
HD1
|
A:TRP120
|
4.0
|
14.1
|
1.0
|
|
HA
|
A:SER115
|
4.0
|
24.1
|
1.0
|
|
HA
|
A:ASP118
|
4.1
|
13.8
|
1.0
|
|
CD1
|
A:TRP120
|
4.1
|
11.7
|
1.0
|
|
CB
|
A:SER114
|
4.2
|
17.8
|
1.0
|
|
CA
|
A:SER114
|
4.3
|
16.6
|
1.0
|
|
HA
|
A:SER114
|
4.3
|
19.9
|
1.0
|
|
N
|
A:ASP118
|
4.4
|
12.7
|
1.0
|
|
N
|
A:SER115
|
4.4
|
17.9
|
1.0
|
|
CA
|
A:SER115
|
4.5
|
20.1
|
1.0
|
|
H
|
A:GLU116
|
4.5
|
23.8
|
1.0
|
|
C
|
A:SER115
|
4.6
|
20.3
|
1.0
|
|
OG
|
A:SER114
|
4.6
|
20.6
|
1.0
|
|
CE2
|
A:TRP120
|
4.6
|
12.4
|
1.0
|
|
N
|
A:GLU116
|
4.6
|
19.8
|
1.0
|
|
OD1
|
A:ASP118
|
4.7
|
22.0
|
1.0
|
|
CA
|
A:ASP118
|
4.7
|
11.5
|
1.0
|
|
HZ2
|
A:TRP120
|
4.8
|
17.4
|
1.0
|
|
HA3
|
A:GLY117
|
4.8
|
17.8
|
1.0
|
|
HG
|
A:SER114
|
4.8
|
24.8
|
1.0
|
|
C
|
A:GLU116
|
4.9
|
17.7
|
1.0
|
|
Sodium binding site 5 out
of 12 in 7a2n
Go back to
Sodium Binding Sites List in 7a2n
Sodium binding site 5 out
of 12 in the Crystal Structure of the Fyn SH3 Domain A95S-D99T Mutant in Space Group P21
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Crystal Structure of the Fyn SH3 Domain A95S-D99T Mutant in Space Group P21 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na203
b:27.6
occ:1.00
|
O
|
B:HOH343
|
2.3
|
29.6
|
1.0
|
|
O
|
B:SER135
|
2.3
|
15.6
|
1.0
|
|
O
|
B:HOH338
|
2.5
|
30.3
|
1.0
|
|
O
|
B:VAL138
|
2.5
|
16.4
|
1.0
|
|
O
|
B:HOH344
|
2.6
|
45.3
|
1.0
|
|
HA
|
B:ASN136
|
3.2
|
17.4
|
1.0
|
|
C
|
B:SER135
|
3.5
|
14.9
|
1.0
|
|
H
|
B:VAL138
|
3.6
|
16.1
|
1.0
|
|
HH2
|
B:TRP120
|
3.6
|
18.8
|
1.0
|
|
HG23
|
B:VAL138
|
3.6
|
17.7
|
1.0
|
|
C
|
B:VAL138
|
3.7
|
15.5
|
1.0
|
|
HG22
|
B:VAL138
|
3.8
|
17.7
|
1.0
|
|
HA
|
B:ALA139
|
3.9
|
20.3
|
1.0
|
|
HZ3
|
B:TRP120
|
4.0
|
18.2
|
1.0
|
|
HB2
|
B:SER135
|
4.0
|
18.1
|
1.0
|
|
CA
|
B:ASN136
|
4.0
|
14.4
|
1.0
|
|
CH2
|
B:TRP120
|
4.1
|
15.6
|
1.0
|
|
CG2
|
B:VAL138
|
4.2
|
14.7
|
1.0
|
|
N
|
B:ASN136
|
4.2
|
14.6
|
1.0
|
|
CZ3
|
B:TRP120
|
4.3
|
15.1
|
1.0
|
|
N
|
B:VAL138
|
4.3
|
13.4
|
1.0
|
|
C
|
B:ASN136
|
4.4
|
14.7
|
1.0
|
|
CA
|
B:SER135
|
4.5
|
13.7
|
1.0
|
|
HA
|
B:SER135
|
4.5
|
16.5
|
1.0
|
|
CA
|
B:VAL138
|
4.5
|
14.0
|
1.0
|
|
N
|
B:ALA139
|
4.6
|
15.5
|
1.0
|
|
CB
|
B:SER135
|
4.6
|
15.1
|
1.0
|
|
CA
|
B:ALA139
|
4.7
|
16.9
|
1.0
|
|
HD3
|
B:PRO140
|
4.7
|
24.5
|
1.0
|
|
O
|
B:ASN136
|
4.7
|
16.4
|
1.0
|
|
HE2
|
B:PHE87
|
4.9
|
17.3
|
1.0
|
|
HG21
|
B:VAL138
|
4.9
|
17.7
|
1.0
|
|
N
|
B:TYR137
|
4.9
|
13.6
|
1.0
|
|
HD2
|
B:PHE87
|
5.0
|
17.2
|
1.0
|
|
CZ2
|
B:TRP120
|
5.0
|
15.0
|
1.0
|
|
H
|
B:ASN136
|
5.0
|
17.5
|
1.0
|
|
Sodium binding site 6 out
of 12 in 7a2n
Go back to
Sodium Binding Sites List in 7a2n
Sodium binding site 6 out
of 12 in the Crystal Structure of the Fyn SH3 Domain A95S-D99T Mutant in Space Group P21
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Crystal Structure of the Fyn SH3 Domain A95S-D99T Mutant in Space Group P21 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na204
b:24.3
occ:1.00
|
O
|
B:VAL84
|
2.3
|
20.9
|
1.0
|
|
OG
|
B:SER114
|
2.5
|
24.1
|
1.0
|
|
O
|
B:ILE111
|
2.6
|
12.7
|
1.0
|
|
O
|
B:LEU112
|
2.6
|
17.6
|
1.0
|
|
HA
|
B:THR85
|
3.0
|
20.8
|
1.0
|
|
HG22
|
B:THR85
|
3.1
|
23.1
|
1.0
|
|
HE1
|
B:PHE87
|
3.2
|
17.8
|
1.0
|
|
C
|
B:LEU112
|
3.3
|
14.7
|
1.0
|
|
H
|
B:SER114
|
3.3
|
21.9
|
1.0
|
|
HB3
|
B:SER114
|
3.4
|
27.4
|
1.0
|
|
C
|
B:VAL84
|
3.4
|
20.8
|
1.0
|
|
CB
|
B:SER114
|
3.5
|
22.8
|
1.0
|
|
HA
|
B:LEU112
|
3.5
|
15.5
|
1.0
|
|
C
|
B:ILE111
|
3.7
|
12.0
|
1.0
|
|
N
|
B:SER114
|
3.8
|
18.2
|
1.0
|
|
CA
|
B:THR85
|
3.8
|
17.3
|
1.0
|
|
CA
|
B:LEU112
|
3.9
|
12.9
|
1.0
|
|
CG2
|
B:THR85
|
3.9
|
19.2
|
1.0
|
|
HG23
|
B:THR85
|
4.0
|
23.1
|
1.0
|
|
CE1
|
B:PHE87
|
4.1
|
14.8
|
1.0
|
|
N
|
B:THR85
|
4.1
|
18.5
|
1.0
|
|
HZ
|
B:PHE87
|
4.1
|
17.6
|
1.0
|
|
N
|
B:ASN113
|
4.1
|
14.3
|
1.0
|
|
HA
|
B:ASN113
|
4.2
|
18.1
|
1.0
|
|
N
|
B:LEU112
|
4.2
|
12.3
|
1.0
|
|
HB2
|
B:SER114
|
4.2
|
27.4
|
1.0
|
|
CA
|
B:SER114
|
4.3
|
21.6
|
1.0
|
|
HB
|
B:ILE111
|
4.3
|
14.8
|
1.0
|
|
H
|
B:VAL84
|
4.4
|
33.3
|
1.0
|
|
HG22
|
B:ILE111
|
4.4
|
15.7
|
1.0
|
|
CB
|
B:THR85
|
4.4
|
19.0
|
1.0
|
|
C
|
B:ASN113
|
4.5
|
17.3
|
1.0
|
|
CZ
|
B:PHE87
|
4.5
|
14.6
|
1.0
|
|
CA
|
B:ASN113
|
4.5
|
15.1
|
1.0
|
|
N
|
B:VAL84
|
4.6
|
27.8
|
1.0
|
|
CA
|
B:VAL84
|
4.6
|
25.3
|
1.0
|
|
HG21
|
B:THR85
|
4.7
|
23.1
|
1.0
|
|
HB
|
B:THR85
|
4.7
|
22.9
|
1.0
|
|
HB
|
B:VAL84
|
4.7
|
33.5
|
1.0
|
|
H
|
B:ASN113
|
4.8
|
17.2
|
1.0
|
|
CA
|
B:ILE111
|
4.9
|
12.2
|
1.0
|
|
H
|
B:THR85
|
4.9
|
22.2
|
1.0
|
|
CB
|
B:ILE111
|
4.9
|
12.3
|
1.0
|
|
C
|
B:THR85
|
5.0
|
16.6
|
1.0
|
|
Sodium binding site 7 out
of 12 in 7a2n
Go back to
Sodium Binding Sites List in 7a2n
Sodium binding site 7 out
of 12 in the Crystal Structure of the Fyn SH3 Domain A95S-D99T Mutant in Space Group P21
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Crystal Structure of the Fyn SH3 Domain A95S-D99T Mutant in Space Group P21 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na204
b:21.9
occ:1.00
|
O
|
C:VAL138
|
2.2
|
12.7
|
1.0
|
|
O
|
C:SER135
|
2.5
|
12.7
|
1.0
|
|
HA
|
C:ASN136
|
3.3
|
16.3
|
1.0
|
|
C
|
C:VAL138
|
3.4
|
11.6
|
1.0
|
|
H
|
C:VAL138
|
3.4
|
14.7
|
1.0
|
|
HA
|
C:ALA139
|
3.7
|
14.9
|
1.0
|
|
C
|
C:SER135
|
3.7
|
12.1
|
1.0
|
|
HG23
|
C:VAL138
|
3.9
|
15.9
|
1.0
|
|
CA
|
C:ASN136
|
4.1
|
13.6
|
1.0
|
|
N
|
C:VAL138
|
4.1
|
12.2
|
1.0
|
|
HG22
|
C:VAL138
|
4.3
|
15.9
|
1.0
|
|
N
|
C:ALA139
|
4.3
|
11.8
|
1.0
|
|
CA
|
C:VAL138
|
4.3
|
11.8
|
1.0
|
|
N
|
C:ASN136
|
4.4
|
12.7
|
1.0
|
|
C
|
C:ASN136
|
4.4
|
13.6
|
1.0
|
|
HD11
|
C:LEU90
|
4.4
|
21.0
|
1.0
|
|
CA
|
C:ALA139
|
4.4
|
12.3
|
1.0
|
|
HB2
|
C:SER135
|
4.4
|
17.4
|
1.0
|
|
CG2
|
C:VAL138
|
4.5
|
13.2
|
1.0
|
|
HE2
|
C:PHE87
|
4.5
|
19.4
|
1.0
|
|
O
|
C:ASN136
|
4.7
|
16.4
|
1.0
|
|
HB2
|
C:ALA139
|
4.7
|
17.4
|
1.0
|
|
HD2
|
C:PHE87
|
4.7
|
18.9
|
1.0
|
|
HD3
|
C:PRO140
|
4.7
|
17.4
|
1.0
|
|
CA
|
C:SER135
|
4.8
|
12.5
|
1.0
|
|
N
|
C:TYR137
|
4.8
|
11.8
|
1.0
|
|
HA
|
C:SER135
|
4.8
|
15.0
|
1.0
|
|
Sodium binding site 8 out
of 12 in 7a2n
Go back to
Sodium Binding Sites List in 7a2n
Sodium binding site 8 out
of 12 in the Crystal Structure of the Fyn SH3 Domain A95S-D99T Mutant in Space Group P21
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of Crystal Structure of the Fyn SH3 Domain A95S-D99T Mutant in Space Group P21 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na205
b:16.1
occ:1.00
|
O
|
C:HOH348
|
2.2
|
26.2
|
1.0
|
|
O
|
C:THR97
|
2.3
|
14.2
|
1.0
|
|
O
|
C:ASP100
|
2.3
|
13.9
|
1.0
|
|
O
|
C:HOH342
|
2.3
|
24.0
|
1.0
|
|
OG
|
C:SER95
|
2.5
|
15.7
|
1.0
|
|
HB2
|
C:SER95
|
3.0
|
16.9
|
1.0
|
|
HA
|
C:GLU98
|
3.0
|
20.3
|
1.0
|
|
CB
|
C:SER95
|
3.2
|
14.1
|
1.0
|
|
O
|
C:HOH334
|
3.3
|
25.4
|
1.0
|
|
C
|
C:THR97
|
3.4
|
14.1
|
1.0
|
|
C
|
C:ASP100
|
3.5
|
12.0
|
1.0
|
|
HB3
|
C:SER95
|
3.5
|
16.9
|
1.0
|
|
HA
|
C:LEU101
|
3.7
|
15.9
|
1.0
|
|
CA
|
C:GLU98
|
3.7
|
16.9
|
1.0
|
|
H
|
C:SER102
|
3.8
|
16.1
|
1.0
|
|
HG
|
C:SER102
|
3.8
|
18.1
|
1.0
|
|
O
|
C:HOH351
|
3.8
|
43.1
|
1.0
|
|
N
|
C:GLU98
|
4.0
|
15.4
|
1.0
|
|
C
|
C:GLU98
|
4.0
|
14.6
|
1.0
|
|
O
|
C:GLU98
|
4.2
|
15.7
|
1.0
|
|
H
|
C:THR97
|
4.3
|
17.9
|
1.0
|
|
H
|
C:ASP100
|
4.3
|
14.4
|
1.0
|
|
O
|
C:HOH332
|
4.3
|
30.0
|
1.0
|
|
N
|
C:LEU101
|
4.3
|
12.1
|
1.0
|
|
CA
|
C:LEU101
|
4.3
|
13.3
|
1.0
|
|
N
|
C:SER102
|
4.4
|
13.4
|
1.0
|
|
OD1
|
C:ASP100
|
4.4
|
12.5
|
1.0
|
|
N
|
C:ASP100
|
4.4
|
12.0
|
1.0
|
|
CA
|
C:ASP100
|
4.5
|
11.2
|
1.0
|
|
N
|
C:THR97
|
4.6
|
14.9
|
1.0
|
|
CA
|
C:SER95
|
4.6
|
13.7
|
1.0
|
|
CA
|
C:THR97
|
4.6
|
14.0
|
1.0
|
|
OG
|
C:SER102
|
4.6
|
15.1
|
1.0
|
|
N
|
C:THR99
|
4.6
|
13.5
|
1.0
|
|
C
|
C:LEU101
|
4.7
|
13.5
|
1.0
|
|
HG2
|
C:GLU98
|
4.8
|
33.6
|
1.0
|
|
C
|
C:SER95
|
4.8
|
13.7
|
1.0
|
|
CG
|
C:ASP100
|
4.8
|
13.0
|
1.0
|
|
H
|
C:GLU98
|
4.8
|
18.6
|
1.0
|
|
H
|
C:THR99
|
4.9
|
16.3
|
1.0
|
|
HA
|
C:THR97
|
5.0
|
16.8
|
1.0
|
|
Sodium binding site 9 out
of 12 in 7a2n
Go back to
Sodium Binding Sites List in 7a2n
Sodium binding site 9 out
of 12 in the Crystal Structure of the Fyn SH3 Domain A95S-D99T Mutant in Space Group P21
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 9 of Crystal Structure of the Fyn SH3 Domain A95S-D99T Mutant in Space Group P21 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na206
b:22.4
occ:0.87
|
O
|
C:HOH353
|
2.2
|
36.2
|
1.0
|
|
O
|
C:SER114
|
2.2
|
16.6
|
1.0
|
|
O
|
C:HOH339
|
2.4
|
20.5
|
1.0
|
|
O
|
C:GLY117
|
2.4
|
14.4
|
1.0
|
|
HE1
|
C:TRP120
|
2.9
|
15.5
|
1.0
|
|
H
|
C:GLY117
|
3.1
|
20.4
|
1.0
|
|
O
|
C:HOH306
|
3.3
|
44.2
|
1.0
|
|
C
|
C:GLY117
|
3.3
|
14.0
|
1.0
|
|
C
|
C:SER114
|
3.5
|
16.2
|
1.0
|
|
NE1
|
C:TRP120
|
3.6
|
12.9
|
1.0
|
|
HA
|
C:SER115
|
3.7
|
20.8
|
1.0
|
|
N
|
C:GLY117
|
3.7
|
17.0
|
1.0
|
|
HA2
|
C:GLY117
|
3.8
|
17.9
|
1.0
|
|
HB2
|
C:SER114
|
3.8
|
20.3
|
1.0
|
|
CA
|
C:GLY117
|
3.8
|
14.9
|
1.0
|
|
HA
|
C:ASP118
|
4.0
|
15.3
|
1.0
|
|
HD1
|
C:TRP120
|
4.1
|
15.9
|
1.0
|
|
O
|
C:HOH310
|
4.2
|
36.5
|
1.0
|
|
CD1
|
C:TRP120
|
4.2
|
13.2
|
1.0
|
|
CA
|
C:SER115
|
4.3
|
17.3
|
1.0
|
|
N
|
C:SER115
|
4.3
|
16.6
|
1.0
|
|
N
|
C:ASP118
|
4.3
|
13.2
|
1.0
|
|
CA
|
C:SER114
|
4.4
|
15.7
|
1.0
|
|
C
|
C:SER115
|
4.5
|
17.4
|
1.0
|
|
HA
|
C:SER114
|
4.5
|
18.9
|
1.0
|
|
CB
|
C:SER114
|
4.5
|
16.9
|
1.0
|
|
OD1
|
C:ASP118
|
4.6
|
22.6
|
1.0
|
|
H
|
C:GLU116
|
4.6
|
21.5
|
1.0
|
|
N
|
C:GLU116
|
4.6
|
17.9
|
1.0
|
|
CA
|
C:ASP118
|
4.7
|
12.8
|
1.0
|
|
CE2
|
C:TRP120
|
4.7
|
12.7
|
1.0
|
|
HA3
|
C:GLY117
|
4.8
|
17.9
|
1.0
|
|
O
|
C:HOH326
|
4.8
|
20.4
|
1.0
|
|
HZ2
|
C:TRP120
|
4.9
|
17.0
|
1.0
|
|
C
|
C:GLU116
|
4.9
|
17.9
|
1.0
|
|
O
|
C:SER115
|
4.9
|
18.5
|
1.0
|
|
Sodium binding site 10 out
of 12 in 7a2n
Go back to
Sodium Binding Sites List in 7a2n
Sodium binding site 10 out
of 12 in the Crystal Structure of the Fyn SH3 Domain A95S-D99T Mutant in Space Group P21
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 10 of Crystal Structure of the Fyn SH3 Domain A95S-D99T Mutant in Space Group P21 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na204
b:21.4
occ:1.00
|
O
|
D:HOH353
|
2.3
|
31.7
|
1.0
|
|
O
|
D:VAL138
|
2.3
|
13.7
|
1.0
|
|
O
|
D:SER135
|
2.3
|
13.3
|
1.0
|
|
O
|
D:HOH357
|
2.4
|
30.3
|
1.0
|
|
O
|
D:HOH358
|
2.4
|
25.8
|
1.0
|
|
HA
|
D:ASN136
|
3.4
|
12.9
|
1.0
|
|
H
|
D:VAL138
|
3.5
|
13.6
|
1.0
|
|
C
|
D:SER135
|
3.5
|
12.1
|
1.0
|
|
C
|
D:VAL138
|
3.5
|
12.2
|
1.0
|
|
HG23
|
D:VAL138
|
3.7
|
15.4
|
1.0
|
|
HA
|
D:ALA139
|
3.8
|
16.8
|
1.0
|
|
HG22
|
D:VAL138
|
3.8
|
15.4
|
1.0
|
|
HH2
|
D:TRP120
|
3.9
|
17.9
|
1.0
|
|
CA
|
D:ASN136
|
4.1
|
10.7
|
1.0
|
|
HB2
|
D:SER135
|
4.1
|
14.5
|
1.0
|
|
N
|
D:VAL138
|
4.1
|
11.3
|
1.0
|
|
HZ3
|
D:TRP120
|
4.2
|
18.9
|
1.0
|
|
N
|
D:ASN136
|
4.2
|
12.4
|
1.0
|
|
CG2
|
D:VAL138
|
4.2
|
12.8
|
1.0
|
|
C
|
D:ASN136
|
4.3
|
11.5
|
1.0
|
|
CA
|
D:VAL138
|
4.4
|
11.2
|
1.0
|
|
CH2
|
D:TRP120
|
4.4
|
14.9
|
1.0
|
|
N
|
D:ALA139
|
4.4
|
13.1
|
1.0
|
|
CZ3
|
D:TRP120
|
4.5
|
15.8
|
1.0
|
|
CA
|
D:ALA139
|
4.5
|
14.0
|
1.0
|
|
CA
|
D:SER135
|
4.5
|
11.4
|
1.0
|
|
HA
|
D:SER135
|
4.5
|
13.7
|
1.0
|
|
O
|
D:ASN136
|
4.6
|
12.6
|
1.0
|
|
HD3
|
D:PRO140
|
4.7
|
19.2
|
1.0
|
|
CB
|
D:SER135
|
4.8
|
12.1
|
1.0
|
|
N
|
D:TYR137
|
4.8
|
11.0
|
1.0
|
|
HB2
|
D:ALA139
|
4.9
|
18.9
|
1.0
|
|
CB
|
D:VAL138
|
5.0
|
11.6
|
1.0
|
|
H
|
D:TYR137
|
5.0
|
13.2
|
1.0
|
|
O
|
D:HOH376
|
5.0
|
40.1
|
1.0
|
|
HG21
|
D:VAL138
|
5.0
|
15.4
|
1.0
|
|
Reference:
A.Camara-Artigas,
M.Plaza-Garrido,
M.C.Salinas-Garcia.
Crystal Structure of the Fyn SH3 Domain A95S-D99T Mutant in Space Group P21 To Be Published.
Page generated: Tue Oct 8 15:46:41 2024
|
