Sodium in PDB 4wee: High-Resolution Structure of Synaptotagmin 1 C2A
Protein crystallography data
The structure of High-Resolution Structure of Synaptotagmin 1 C2A, PDB code: 4wee
was solved by
R.B.Sutton,
K.L.Fuson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
19.78 /
0.89
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
41.738,
38.547,
44.295,
90.00,
97.94,
90.00
|
|
R / Rfree (%)
|
14.9 /
16.4
|
Sodium Binding Sites:
The binding sites of Sodium atom in the High-Resolution Structure of Synaptotagmin 1 C2A
(pdb code 4wee). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the
High-Resolution Structure of Synaptotagmin 1 C2A, PDB code: 4wee:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
Sodium binding site 1 out
of 7 in 4wee
Go back to
Sodium Binding Sites List in 4wee
Sodium binding site 1 out
of 7 in the High-Resolution Structure of Synaptotagmin 1 C2A
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of High-Resolution Structure of Synaptotagmin 1 C2A within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na301
b:14.5
occ:1.00
|
NA
|
A:NA303
|
2.8
|
14.3
|
1.0
|
|
O
|
A:LEU135
|
2.8
|
10.2
|
1.0
|
|
O
|
A:MET138
|
2.8
|
8.5
|
1.0
|
|
O
|
A:HOH501
|
2.9
|
13.2
|
0.5
|
|
HB2
|
A:MET138
|
3.1
|
10.9
|
0.6
|
|
HA
|
A:ASP136
|
3.2
|
9.9
|
1.0
|
|
HG3
|
A:GLU140
|
3.3
|
0.6
|
0.0
|
|
O
|
A:ASP136
|
3.3
|
10.6
|
1.0
|
|
H
|
A:MET138
|
3.4
|
5.5
|
0.4
|
|
HG2
|
A:GLU140
|
3.4
|
0.4
|
0.0
|
|
H
|
A:MET138
|
3.4
|
36.2
|
0.6
|
|
HB2
|
A:MET138
|
3.5
|
87.0
|
0.4
|
|
O
|
A:HOH564
|
3.5
|
31.0
|
0.3
|
|
C
|
A:ASP136
|
3.6
|
9.0
|
1.0
|
|
C
|
A:MET138
|
3.6
|
7.5
|
1.0
|
|
N
|
A:MET138
|
3.7
|
8.1
|
1.0
|
|
CG
|
A:GLU140
|
3.8
|
10.2
|
1.0
|
|
CA
|
A:ASP136
|
3.8
|
9.7
|
1.0
|
|
CB
|
A:MET138
|
3.9
|
8.9
|
0.6
|
|
C
|
A:LEU135
|
3.9
|
10.1
|
1.0
|
|
O
|
A:HOH578
|
3.9
|
28.1
|
0.9
|
|
CA
|
A:MET138
|
3.9
|
8.3
|
0.6
|
|
CA
|
A:MET138
|
4.0
|
8.4
|
0.4
|
|
HA
|
A:GLU140
|
4.1
|
8.6
|
0.0
|
|
O
|
A:HOH401
|
4.1
|
11.6
|
0.5
|
|
CB
|
A:MET138
|
4.2
|
9.2
|
0.4
|
|
N
|
A:ASP136
|
4.4
|
10.1
|
1.0
|
|
N
|
A:SER137
|
4.4
|
8.2
|
1.0
|
|
HB3
|
A:MET138
|
4.4
|
11.0
|
0.6
|
|
N
|
A:GLU140
|
4.5
|
7.6
|
1.0
|
|
C
|
A:SER137
|
4.5
|
8.0
|
1.0
|
|
O
|
A:HOH488
|
4.5
|
35.5
|
0.8
|
|
HB3
|
A:MET138
|
4.6
|
7.4
|
0.4
|
|
C
|
A:VAL139
|
4.6
|
7.2
|
1.0
|
|
CA
|
A:GLU140
|
4.6
|
7.4
|
1.0
|
|
H
|
A:GLU140
|
4.7
|
0.0
|
0.0
|
|
N
|
A:VAL139
|
4.7
|
7.0
|
1.0
|
|
OD1
|
A:ASP136
|
4.7
|
10.3
|
1.0
|
|
CD
|
A:GLU140
|
4.8
|
10.0
|
1.0
|
|
OE2
|
A:GLU140
|
4.8
|
9.7
|
1.0
|
|
HG2
|
A:MET138
|
4.8
|
0.9
|
0.6
|
|
CB
|
A:GLU140
|
4.8
|
8.2
|
1.0
|
|
O
|
A:VAL139
|
4.9
|
8.2
|
1.0
|
|
H
|
A:SER137
|
4.9
|
6.7
|
0.9
|
|
HA
|
A:MET138
|
4.9
|
0.5
|
0.6
|
|
CG
|
A:MET138
|
4.9
|
12.0
|
0.6
|
|
HA
|
A:MET138
|
5.0
|
0.5
|
0.4
|
|
CA
|
A:SER137
|
5.0
|
8.5
|
1.0
|
|
Sodium binding site 2 out
of 7 in 4wee
Go back to
Sodium Binding Sites List in 4wee
Sodium binding site 2 out
of 7 in the High-Resolution Structure of Synaptotagmin 1 C2A
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of High-Resolution Structure of Synaptotagmin 1 C2A within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na302
b:30.0
occ:1.00
|
O
|
A:HOH476
|
2.5
|
17.2
|
0.7
|
|
OE1
|
A:GLN164
|
2.7
|
10.8
|
1.0
|
|
O
|
A:ALA165
|
2.7
|
6.5
|
1.0
|
|
HB2
|
A:GLN164
|
3.0
|
5.0
|
0.8
|
|
HB3
|
A:ASN203
|
3.2
|
8.1
|
1.0
|
|
HB3
|
A:ALA166
|
3.4
|
11.5
|
1.0
|
|
CD
|
A:GLN164
|
3.6
|
7.9
|
1.0
|
|
HH2
|
A:TRP259
|
3.6
|
11.0
|
0.9
|
|
C
|
A:ALA165
|
3.6
|
6.0
|
1.0
|
|
HG3
|
A:GLN164
|
3.7
|
9.5
|
0.9
|
|
HA
|
A:ALA166
|
3.8
|
7.9
|
0.8
|
|
CB
|
A:GLN164
|
3.9
|
6.2
|
1.0
|
|
O
|
A:ASN203
|
3.9
|
8.2
|
1.0
|
|
HA
|
A:ASN203
|
3.9
|
3.4
|
0.6
|
|
CG
|
A:GLN164
|
3.9
|
7.0
|
1.0
|
|
HG21
|
A:VAL205
|
4.0
|
32.7
|
0.8
|
|
O
|
A:PRO204
|
4.0
|
7.0
|
1.0
|
|
C
|
A:ASN203
|
4.1
|
7.1
|
1.0
|
|
CB
|
A:ASN203
|
4.1
|
7.8
|
1.0
|
|
H
|
A:ALA165
|
4.1
|
6.5
|
0.8
|
|
HG23
|
A:VAL205
|
4.1
|
53.5
|
1.0
|
|
CB
|
A:ALA166
|
4.2
|
10.0
|
1.0
|
|
CA
|
A:ASN203
|
4.3
|
7.1
|
1.0
|
|
CA
|
A:ALA166
|
4.3
|
7.2
|
1.0
|
|
N
|
A:ALA165
|
4.3
|
5.9
|
1.0
|
|
N
|
A:ALA166
|
4.3
|
6.4
|
1.0
|
|
HB3
|
A:GLN164
|
4.4
|
11.9
|
1.0
|
|
HB2
|
A:ALA166
|
4.4
|
22.1
|
0.0
|
|
OD1
|
A:ASN203
|
4.5
|
9.3
|
1.0
|
|
CG2
|
A:VAL205
|
4.5
|
9.4
|
1.0
|
|
CH2
|
A:TRP259
|
4.6
|
9.3
|
1.0
|
|
CA
|
A:ALA165
|
4.6
|
6.0
|
1.0
|
|
C
|
A:PRO204
|
4.6
|
6.7
|
1.0
|
|
N
|
A:PRO204
|
4.7
|
6.7
|
1.0
|
|
NE2
|
A:GLN164
|
4.7
|
7.7
|
1.0
|
|
HB2
|
A:ASN203
|
4.7
|
0.0
|
0.3
|
|
C
|
A:GLN164
|
4.8
|
5.5
|
1.0
|
|
CG
|
A:ASN203
|
4.8
|
7.9
|
1.0
|
|
HG2
|
A:GLN164
|
4.9
|
6.0
|
1.0
|
|
CA
|
A:GLN164
|
4.9
|
5.6
|
1.0
|
|
HB1
|
A:ALA166
|
5.0
|
0.0
|
0.6
|
|
HE22
|
A:GLN164
|
5.0
|
2.6
|
0.3
|
|
HZ3
|
A:TRP259
|
5.0
|
10.0
|
1.0
|
|
HA
|
A:ALA165
|
5.0
|
4.7
|
0.8
|
|
Sodium binding site 3 out
of 7 in 4wee
Go back to
Sodium Binding Sites List in 4wee
Sodium binding site 3 out
of 7 in the High-Resolution Structure of Synaptotagmin 1 C2A
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of High-Resolution Structure of Synaptotagmin 1 C2A within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na303
b:14.3
occ:1.00
|
O
|
A:HOH401
|
2.0
|
11.6
|
0.5
|
|
OD1
|
A:ASP136
|
2.7
|
10.3
|
1.0
|
|
NA
|
A:NA301
|
2.8
|
14.5
|
1.0
|
|
HA
|
A:ASP136
|
3.0
|
9.9
|
1.0
|
|
O
|
A:HOH488
|
3.1
|
35.5
|
0.8
|
|
OE2
|
A:GLU140
|
3.2
|
9.7
|
1.0
|
|
O
|
A:ASP136
|
3.3
|
10.6
|
1.0
|
|
HG2
|
A:GLU140
|
3.4
|
0.4
|
0.0
|
|
HG3
|
A:GLU140
|
3.7
|
0.6
|
0.0
|
|
CG
|
A:ASP136
|
3.8
|
10.3
|
1.0
|
|
CA
|
A:ASP136
|
3.8
|
9.7
|
1.0
|
|
CG
|
A:GLU140
|
3.8
|
10.2
|
1.0
|
|
NA
|
A:NA304
|
3.9
|
15.1
|
1.0
|
|
CD
|
A:GLU140
|
3.9
|
10.0
|
1.0
|
|
C
|
A:ASP136
|
4.0
|
9.0
|
1.0
|
|
O
|
A:HOH450
|
4.0
|
16.8
|
0.4
|
|
O
|
A:HOH578
|
4.2
|
28.1
|
0.9
|
|
CB
|
A:ASP136
|
4.4
|
10.5
|
1.0
|
|
O
|
A:LEU135
|
4.6
|
10.2
|
1.0
|
|
OD2
|
A:ASP136
|
4.8
|
12.6
|
1.0
|
|
O
|
A:HOH501
|
4.8
|
13.2
|
0.5
|
|
HB2
|
A:ASP136
|
4.9
|
12.4
|
1.0
|
|
O
|
A:MET138
|
4.9
|
8.5
|
1.0
|
|
N
|
A:ASP136
|
5.0
|
10.1
|
1.0
|
|
OE1
|
A:GLU140
|
5.0
|
12.8
|
1.0
|
|
Sodium binding site 4 out
of 7 in 4wee
Go back to
Sodium Binding Sites List in 4wee
Sodium binding site 4 out
of 7 in the High-Resolution Structure of Synaptotagmin 1 C2A
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of High-Resolution Structure of Synaptotagmin 1 C2A within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na304
b:15.1
occ:1.00
|
OD1
|
A:ASP136
|
2.7
|
10.3
|
1.0
|
|
O
|
A:HOH417
|
3.3
|
18.9
|
0.9
|
|
CG
|
A:ASP136
|
3.6
|
10.3
|
1.0
|
|
OD2
|
A:ASP136
|
3.8
|
12.6
|
1.0
|
|
NA
|
A:NA303
|
3.9
|
14.3
|
1.0
|
|
O
|
A:HOH401
|
4.1
|
11.6
|
0.5
|
|
O
|
A:HOH450
|
4.5
|
16.8
|
0.4
|
|
CB
|
A:ASP136
|
4.9
|
10.5
|
1.0
|
|
O
|
A:HOH488
|
4.9
|
35.5
|
0.8
|
|
Sodium binding site 5 out
of 7 in 4wee
Go back to
Sodium Binding Sites List in 4wee
Sodium binding site 5 out
of 7 in the High-Resolution Structure of Synaptotagmin 1 C2A
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of High-Resolution Structure of Synaptotagmin 1 C2A within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na305
b:12.8
occ:1.00
|
HA
|
A:GLN263
|
2.6
|
0.8
|
0.3
|
|
O
|
A:HOH575
|
2.7
|
32.4
|
1.0
|
|
O
|
A:GLU140
|
2.8
|
7.5
|
1.0
|
|
HG2
|
A:GLN263
|
2.8
|
62.4
|
0.3
|
|
O
|
A:LEU262
|
2.8
|
10.2
|
1.0
|
|
HG13
|
A:VAL139
|
2.8
|
0.9
|
0.5
|
|
HD13
|
A:LEU142
|
2.8
|
20.2
|
1.0
|
|
H
|
A:GLU140
|
3.0
|
0.0
|
0.0
|
|
HB2
|
A:GLU140
|
3.0
|
6.2
|
0.8
|
|
HA
|
A:GLN263
|
3.0
|
0.2
|
0.7
|
|
HG
|
A:LEU142
|
3.1
|
11.4
|
1.0
|
|
HG12
|
A:VAL139
|
3.3
|
56.4
|
1.0
|
|
N
|
A:GLU140
|
3.4
|
7.6
|
1.0
|
|
HB2
|
A:LEU142
|
3.5
|
9.0
|
1.0
|
|
CG1
|
A:VAL139
|
3.5
|
9.1
|
1.0
|
|
CD1
|
A:LEU142
|
3.5
|
12.8
|
1.0
|
|
CA
|
A:GLN263
|
3.5
|
11.5
|
0.3
|
|
H
|
A:SER264
|
3.5
|
71.5
|
1.0
|
|
C
|
A:GLU140
|
3.6
|
7.2
|
1.0
|
|
CG
|
A:GLN263
|
3.6
|
13.2
|
0.3
|
|
CG
|
A:LEU142
|
3.7
|
11.6
|
1.0
|
|
NA
|
A:NA306
|
3.7
|
11.1
|
1.0
|
|
HD12
|
A:LEU142
|
3.7
|
15.5
|
1.0
|
|
CA
|
A:GLU140
|
3.8
|
7.4
|
1.0
|
|
CB
|
A:GLU140
|
3.8
|
8.2
|
1.0
|
|
C
|
A:LEU262
|
3.8
|
8.8
|
1.0
|
|
CA
|
A:GLN263
|
3.8
|
11.3
|
0.7
|
|
H
|
A:LEU142
|
3.9
|
8.5
|
0.9
|
|
N
|
A:SER264
|
3.9
|
15.1
|
1.0
|
|
HB3
|
A:GLN263
|
3.9
|
25.5
|
0.3
|
|
CB
|
A:GLN263
|
4.0
|
11.2
|
0.3
|
|
HG11
|
A:VAL139
|
4.0
|
1.6
|
0.5
|
|
HG3
|
A:GLN263
|
4.0
|
15.2
|
0.3
|
|
CB
|
A:LEU142
|
4.1
|
9.3
|
1.0
|
|
HA
|
A:VAL139
|
4.1
|
5.7
|
1.0
|
|
C
|
A:VAL139
|
4.2
|
7.2
|
1.0
|
|
C
|
A:GLN263
|
4.2
|
10.9
|
1.0
|
|
N
|
A:GLN263
|
4.2
|
10.9
|
1.0
|
|
HB3
|
A:SER264
|
4.3
|
23.3
|
0.0
|
|
HB3
|
A:GLU140
|
4.3
|
13.3
|
1.0
|
|
HD11
|
A:LEU142
|
4.4
|
24.2
|
0.9
|
|
N
|
A:LEU142
|
4.5
|
7.8
|
1.0
|
|
HB2
|
A:SER264
|
4.5
|
0.0
|
0.1
|
|
CA
|
A:VAL139
|
4.5
|
7.0
|
1.0
|
|
CB
|
A:VAL139
|
4.6
|
8.0
|
1.0
|
|
OE1
|
A:GLU140
|
4.6
|
12.8
|
1.0
|
|
CB
|
A:SER264
|
4.7
|
21.4
|
1.0
|
|
CA
|
A:SER264
|
4.7
|
17.5
|
1.0
|
|
CD
|
A:GLN263
|
4.7
|
16.6
|
0.3
|
|
HA
|
A:SER264
|
4.7
|
0.7
|
0.2
|
|
HA
|
A:GLU140
|
4.7
|
8.6
|
0.0
|
|
N
|
A:LYS141
|
4.8
|
7.9
|
1.0
|
|
HG3
|
A:GLU140
|
4.8
|
0.6
|
0.0
|
|
HB3
|
A:LEU142
|
4.8
|
13.2
|
1.0
|
|
CG
|
A:GLU140
|
4.8
|
10.2
|
1.0
|
|
HB2
|
A:GLN263
|
4.9
|
0.5
|
0.3
|
|
CA
|
A:LEU142
|
4.9
|
8.9
|
1.0
|
|
HB3
|
A:ASP261
|
5.0
|
6.8
|
0.7
|
|
Sodium binding site 6 out
of 7 in 4wee
Go back to
Sodium Binding Sites List in 4wee
Sodium binding site 6 out
of 7 in the High-Resolution Structure of Synaptotagmin 1 C2A
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of High-Resolution Structure of Synaptotagmin 1 C2A within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na306
b:11.1
occ:1.00
|
H
|
A:LEU142
|
2.2
|
8.5
|
0.9
|
|
NA
|
A:NA307
|
2.7
|
14.5
|
1.0
|
|
O
|
A:LEU262
|
2.8
|
10.2
|
1.0
|
|
O
|
A:GLY143
|
2.8
|
6.6
|
1.0
|
|
HB2
|
A:LEU142
|
2.9
|
9.0
|
1.0
|
|
N
|
A:LEU142
|
3.0
|
7.8
|
1.0
|
|
H
|
A:LEU262
|
3.1
|
6.9
|
0.8
|
|
HB3
|
A:ASP261
|
3.1
|
18.7
|
0.3
|
|
HB3
|
A:ASP261
|
3.1
|
6.8
|
0.7
|
|
H
|
A:GLY143
|
3.1
|
0.5
|
0.8
|
|
O
|
A:GLU140
|
3.1
|
7.5
|
1.0
|
|
N
|
A:GLY143
|
3.3
|
8.8
|
1.0
|
|
N
|
A:LEU262
|
3.4
|
6.5
|
1.0
|
|
C
|
A:LEU142
|
3.5
|
9.1
|
1.0
|
|
CA
|
A:LEU142
|
3.5
|
8.9
|
1.0
|
|
HB2
|
A:LEU262
|
3.5
|
9.0
|
1.0
|
|
O
|
A:HOH579
|
3.5
|
15.5
|
0.7
|
|
CB
|
A:LEU142
|
3.6
|
9.3
|
1.0
|
|
NA
|
A:NA305
|
3.7
|
12.8
|
1.0
|
|
HA
|
A:LYS141
|
3.7
|
0.7
|
0.0
|
|
C
|
A:LEU262
|
3.7
|
8.8
|
1.0
|
|
C
|
A:GLY143
|
3.7
|
6.8
|
1.0
|
|
HA
|
A:ASP261
|
3.8
|
5.5
|
0.7
|
|
HA
|
A:ASP261
|
3.8
|
4.6
|
0.3
|
|
CB
|
A:ASP261
|
3.9
|
7.5
|
0.3
|
|
CB
|
A:ASP261
|
3.9
|
7.8
|
0.7
|
|
CA
|
A:LEU262
|
4.0
|
7.0
|
1.0
|
|
HG12
|
A:VAL139
|
4.0
|
56.4
|
1.0
|
|
C
|
A:ASP261
|
4.0
|
7.1
|
1.0
|
|
C
|
A:LYS141
|
4.1
|
8.9
|
1.0
|
|
CA
|
A:GLY143
|
4.1
|
9.0
|
1.0
|
|
CA
|
A:ASP261
|
4.1
|
7.0
|
0.7
|
|
CA
|
A:ASP261
|
4.1
|
6.7
|
0.3
|
|
HG
|
A:LEU142
|
4.1
|
11.4
|
1.0
|
|
CB
|
A:LEU262
|
4.2
|
7.0
|
1.0
|
|
O
|
A:LEU142
|
4.2
|
11.1
|
1.0
|
|
OD1
|
A:ASP261
|
4.3
|
10.2
|
0.3
|
|
C
|
A:GLU140
|
4.3
|
7.2
|
1.0
|
|
CA
|
A:LYS141
|
4.3
|
9.8
|
1.0
|
|
HB3
|
A:LEU142
|
4.3
|
13.2
|
1.0
|
|
OD2
|
A:ASP261
|
4.4
|
10.0
|
0.7
|
|
HA
|
A:LEU142
|
4.4
|
56.5
|
1.0
|
|
CG
|
A:LEU142
|
4.5
|
11.6
|
1.0
|
|
HG11
|
A:VAL139
|
4.5
|
1.6
|
0.5
|
|
CG1
|
A:VAL139
|
4.5
|
9.1
|
1.0
|
|
HG13
|
A:VAL139
|
4.6
|
0.9
|
0.5
|
|
HB2
|
A:ASP261
|
4.6
|
10.9
|
0.3
|
|
HB2
|
A:ASP261
|
4.6
|
9.8
|
0.7
|
|
HA2
|
A:GLY143
|
4.6
|
15.8
|
1.0
|
|
CG
|
A:ASP261
|
4.6
|
9.0
|
0.7
|
|
CG
|
A:ASP261
|
4.7
|
9.0
|
0.3
|
|
HG2
|
A:GLN263
|
4.7
|
62.4
|
0.3
|
|
HA
|
A:GLN263
|
4.7
|
0.8
|
0.3
|
|
HD13
|
A:LEU142
|
4.7
|
20.2
|
1.0
|
|
HG
|
A:LEU262
|
4.7
|
6.9
|
1.0
|
|
N
|
A:LYS141
|
4.8
|
7.9
|
1.0
|
|
HA3
|
A:GLY143
|
4.8
|
2.3
|
0.3
|
|
O
|
A:ASP261
|
4.8
|
8.7
|
1.0
|
|
HG3
|
A:LYS144
|
4.8
|
18.7
|
0.7
|
|
HB3
|
A:LEU262
|
4.8
|
8.6
|
1.0
|
|
HZ2
|
A:LYS144
|
4.9
|
0.0
|
0.7
|
|
HA
|
A:LEU262
|
4.9
|
6.0
|
1.0
|
|
HG2
|
A:LYS144
|
4.9
|
0.1
|
0.7
|
|
O
|
A:HOH455
|
4.9
|
16.3
|
0.9
|
|
HG3
|
A:GLN263
|
4.9
|
15.2
|
0.3
|
|
HA
|
A:LYS144
|
5.0
|
7.7
|
0.3
|
|
N
|
A:GLN263
|
5.0
|
10.9
|
1.0
|
|
N
|
A:LYS144
|
5.0
|
6.8
|
1.0
|
|
HA
|
A:LYS144
|
5.0
|
5.7
|
0.7
|
|
Sodium binding site 7 out
of 7 in 4wee
Go back to
Sodium Binding Sites List in 4wee
Sodium binding site 7 out
of 7 in the High-Resolution Structure of Synaptotagmin 1 C2A
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of High-Resolution Structure of Synaptotagmin 1 C2A within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na307
b:14.5
occ:1.00
|
O
|
A:HOH455
|
2.7
|
16.3
|
0.9
|
|
OD2
|
A:ASP261
|
2.7
|
10.0
|
0.7
|
|
O
|
A:HOH579
|
2.7
|
15.5
|
0.7
|
|
NA
|
A:NA306
|
2.7
|
11.1
|
1.0
|
|
OD1
|
A:ASP261
|
2.8
|
10.2
|
0.3
|
|
HA
|
A:LYS141
|
2.9
|
0.7
|
0.0
|
|
HB3
|
A:ASP261
|
3.1
|
18.7
|
0.3
|
|
HB3
|
A:ASP261
|
3.1
|
6.8
|
0.7
|
|
HZ2
|
A:LYS144
|
3.1
|
0.0
|
0.7
|
|
HG12
|
A:VAL139
|
3.3
|
56.4
|
1.0
|
|
O
|
A:GLU140
|
3.3
|
7.5
|
1.0
|
|
H
|
A:LEU142
|
3.5
|
8.5
|
0.9
|
|
CG
|
A:ASP261
|
3.6
|
9.0
|
0.3
|
|
CG
|
A:ASP261
|
3.6
|
9.0
|
0.7
|
|
CB
|
A:ASP261
|
3.8
|
7.5
|
0.3
|
|
CB
|
A:ASP261
|
3.8
|
7.8
|
0.7
|
|
CA
|
A:LYS141
|
3.9
|
9.8
|
1.0
|
|
O
|
A:HOH416
|
3.9
|
18.3
|
0.5
|
|
NZ
|
A:LYS144
|
3.9
|
17.9
|
0.7
|
|
HG2
|
A:LYS141
|
3.9
|
19.2
|
1.0
|
|
HG11
|
A:VAL139
|
4.0
|
1.6
|
0.5
|
|
HZ3
|
A:LYS144
|
4.0
|
43.6
|
0.7
|
|
H
|
A:GLY143
|
4.0
|
0.5
|
0.8
|
|
CG1
|
A:VAL139
|
4.1
|
9.1
|
1.0
|
|
N
|
A:LEU142
|
4.2
|
7.8
|
1.0
|
|
C
|
A:GLU140
|
4.2
|
7.2
|
1.0
|
|
HZ1
|
A:LYS144
|
4.2
|
0.5
|
0.7
|
|
O
|
A:GLY143
|
4.3
|
6.6
|
1.0
|
|
O
|
A:HOH403
|
4.3
|
49.2
|
0.8
|
|
HA
|
A:ASP261
|
4.4
|
5.5
|
0.7
|
|
N
|
A:LYS141
|
4.4
|
7.9
|
1.0
|
|
HA
|
A:ASP261
|
4.4
|
4.6
|
0.3
|
|
HB2
|
A:ASP261
|
4.5
|
10.9
|
0.3
|
|
HG2
|
A:LYS144
|
4.5
|
0.1
|
0.7
|
|
C
|
A:LYS141
|
4.5
|
8.9
|
1.0
|
|
HG3
|
A:LYS144
|
4.5
|
18.7
|
0.7
|
|
HB2
|
A:ASP261
|
4.6
|
9.8
|
0.7
|
|
HZ3
|
A:LYS141
|
4.6
|
0.3
|
0.5
|
|
HG13
|
A:VAL139
|
4.7
|
0.9
|
0.5
|
|
N
|
A:GLY143
|
4.7
|
8.8
|
1.0
|
|
CG
|
A:LYS141
|
4.7
|
17.5
|
1.0
|
|
CA
|
A:ASP261
|
4.7
|
7.0
|
0.7
|
|
CA
|
A:ASP261
|
4.7
|
6.7
|
0.3
|
|
CB
|
A:LYS141
|
4.7
|
14.5
|
1.0
|
|
OD2
|
A:ASP261
|
4.8
|
9.6
|
0.3
|
|
OD1
|
A:ASP261
|
4.8
|
9.2
|
0.7
|
|
HB3
|
A:LYS141
|
4.8
|
0.2
|
0.3
|
|
HB
|
A:VAL139
|
4.8
|
93.5
|
1.0
|
|
O
|
A:VAL139
|
4.9
|
8.2
|
1.0
|
|
O
|
A:HOH420
|
4.9
|
29.2
|
0.8
|
|
HG3
|
A:LYS141
|
4.9
|
18.9
|
1.0
|
|
HE3
|
A:LYS144
|
4.9
|
0.7
|
0.7
|
|
CG
|
A:LYS144
|
5.0
|
10.0
|
0.7
|
|
Reference:
R.B.Sutton,
R.B.Sutton,
K.L.Fuson.
N/A N/A.
Page generated: Sun Aug 17 22:05:36 2025
|
