Sodium in PDB 7cjs: Structure of Aquaporin
Protein crystallography data
The structure of Structure of Aquaporin, PDB code: 7cjs
was solved by
Y.Saitoh,
J.F.Ma,
M.Suga,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.84 /
1.80
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
89.568,
92.453,
166.126,
90,
102.14,
90
|
R / Rfree (%)
|
24.5 /
27.3
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Structure of Aquaporin
(pdb code 7cjs). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the
Structure of Aquaporin, PDB code: 7cjs:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Sodium binding site 1 out
of 8 in 7cjs
Go back to
Sodium Binding Sites List in 7cjs
Sodium binding site 1 out
of 8 in the Structure of Aquaporin
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Structure of Aquaporin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na301
b:48.7
occ:1.00
|
O
|
A:ALA190
|
2.3
|
23.9
|
1.0
|
O
|
A:THR188
|
2.4
|
31.4
|
1.0
|
O
|
A:HOH420
|
2.6
|
50.1
|
1.0
|
O
|
A:HOH498
|
2.6
|
50.0
|
1.0
|
O
|
A:HOH470
|
2.6
|
35.5
|
1.0
|
HO3
|
A:BOG302
|
3.3
|
112.2
|
1.0
|
C
|
A:THR188
|
3.4
|
31.1
|
1.0
|
C
|
A:ALA190
|
3.5
|
25.8
|
1.0
|
H
|
A:GLY192
|
3.5
|
30.0
|
1.0
|
O3
|
A:BOG302
|
3.7
|
93.5
|
1.0
|
HA
|
A:VAL191
|
3.7
|
30.6
|
1.0
|
HA
|
A:THR188
|
3.8
|
38.2
|
1.0
|
C
|
A:ARG189
|
4.1
|
29.8
|
1.0
|
N
|
A:ALA190
|
4.1
|
28.8
|
1.0
|
CA
|
A:THR188
|
4.1
|
31.9
|
1.0
|
HA
|
A:ARG189
|
4.2
|
36.8
|
1.0
|
HO2
|
A:BOG302
|
4.2
|
111.0
|
1.0
|
N
|
A:ARG189
|
4.3
|
29.4
|
1.0
|
H
|
A:ALA190
|
4.3
|
34.6
|
1.0
|
O2
|
A:BOG302
|
4.3
|
92.5
|
1.0
|
N
|
A:GLY192
|
4.4
|
25.0
|
1.0
|
O
|
A:ARG189
|
4.4
|
29.6
|
1.0
|
CA
|
A:ARG189
|
4.4
|
30.7
|
1.0
|
N
|
A:VAL191
|
4.4
|
25.8
|
1.0
|
CA
|
A:ALA190
|
4.4
|
27.3
|
1.0
|
CA
|
A:VAL191
|
4.5
|
25.5
|
1.0
|
HB
|
A:THR188
|
4.5
|
39.9
|
1.0
|
O
|
A:ASP187
|
4.6
|
27.2
|
1.0
|
O
|
A:HOH426
|
4.7
|
37.3
|
1.0
|
H2
|
A:BOG302
|
4.8
|
111.5
|
1.0
|
O
|
A:HOH424
|
4.8
|
50.5
|
1.0
|
C3
|
A:BOG302
|
4.9
|
93.3
|
1.0
|
CB
|
A:THR188
|
4.9
|
33.2
|
1.0
|
C2
|
A:BOG302
|
5.0
|
92.9
|
1.0
|
C
|
A:VAL191
|
5.0
|
25.6
|
1.0
|
|
Sodium binding site 2 out
of 8 in 7cjs
Go back to
Sodium Binding Sites List in 7cjs
Sodium binding site 2 out
of 8 in the Structure of Aquaporin
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Structure of Aquaporin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na301
b:41.3
occ:1.00
|
O
|
B:HOH478
|
2.2
|
47.6
|
1.0
|
O
|
B:ALA190
|
2.2
|
22.4
|
1.0
|
O
|
B:HOH493
|
2.5
|
47.0
|
1.0
|
O
|
B:HOH482
|
2.5
|
31.9
|
1.0
|
O
|
B:HOH414
|
2.6
|
47.3
|
1.0
|
O
|
B:THR188
|
2.6
|
28.6
|
1.0
|
H
|
B:GLY192
|
3.4
|
28.6
|
1.0
|
C
|
B:ALA190
|
3.5
|
23.6
|
1.0
|
C
|
B:THR188
|
3.5
|
28.0
|
1.0
|
HA
|
B:VAL191
|
3.7
|
28.8
|
1.0
|
HA
|
B:THR188
|
3.8
|
33.3
|
1.0
|
C
|
B:ARG189
|
4.1
|
24.4
|
1.0
|
N
|
B:ALA190
|
4.1
|
23.8
|
1.0
|
N
|
B:GLY192
|
4.2
|
23.9
|
1.0
|
CA
|
B:THR188
|
4.2
|
27.8
|
1.0
|
H
|
B:ALA190
|
4.3
|
28.6
|
1.0
|
O
|
B:HOH426
|
4.3
|
28.4
|
1.0
|
HA
|
B:ARG189
|
4.3
|
30.6
|
1.0
|
N
|
B:VAL191
|
4.4
|
24.1
|
1.0
|
O
|
B:ARG189
|
4.4
|
24.3
|
1.0
|
CA
|
B:VAL191
|
4.4
|
23.9
|
1.0
|
N
|
B:ARG189
|
4.4
|
26.2
|
1.0
|
CA
|
B:ALA190
|
4.4
|
23.8
|
1.0
|
O
|
B:ASP187
|
4.5
|
24.6
|
1.0
|
CA
|
B:ARG189
|
4.5
|
25.5
|
1.0
|
HB
|
B:THR188
|
4.7
|
34.1
|
1.0
|
C
|
B:VAL191
|
4.9
|
23.9
|
1.0
|
HA3
|
B:GLY192
|
4.9
|
29.6
|
1.0
|
OE2
|
B:GLU193
|
5.0
|
34.8
|
1.0
|
|
Sodium binding site 3 out
of 8 in 7cjs
Go back to
Sodium Binding Sites List in 7cjs
Sodium binding site 3 out
of 8 in the Structure of Aquaporin
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Structure of Aquaporin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na301
b:45.9
occ:1.00
|
O
|
C:HOH487
|
2.0
|
49.1
|
1.0
|
O
|
C:ALA190
|
2.3
|
24.0
|
1.0
|
O
|
C:THR188
|
2.4
|
32.9
|
1.0
|
O
|
C:HOH444
|
2.5
|
45.0
|
1.0
|
O
|
C:HOH528
|
2.6
|
60.0
|
1.0
|
O
|
C:HOH499
|
2.6
|
38.3
|
1.0
|
C
|
C:THR188
|
3.4
|
32.3
|
1.0
|
H
|
C:GLY192
|
3.5
|
26.9
|
1.0
|
C
|
C:ALA190
|
3.5
|
24.9
|
1.0
|
HA
|
C:THR188
|
3.7
|
37.6
|
1.0
|
HA
|
C:VAL191
|
3.7
|
29.1
|
1.0
|
N
|
C:ALA190
|
4.0
|
29.1
|
1.0
|
CA
|
C:THR188
|
4.1
|
31.3
|
1.0
|
H
|
C:ALA190
|
4.1
|
34.9
|
1.0
|
C
|
C:ARG189
|
4.1
|
34.3
|
1.0
|
HA
|
C:ARG189
|
4.2
|
43.2
|
1.0
|
N
|
C:GLY192
|
4.3
|
22.4
|
1.0
|
N
|
C:ARG189
|
4.3
|
34.3
|
1.0
|
CA
|
C:ALA190
|
4.4
|
26.9
|
1.0
|
N
|
C:VAL191
|
4.4
|
25.0
|
1.0
|
CA
|
C:ARG189
|
4.5
|
36.0
|
1.0
|
CA
|
C:VAL191
|
4.5
|
24.3
|
1.0
|
O
|
C:HOH427
|
4.5
|
45.2
|
1.0
|
HB
|
C:THR188
|
4.5
|
39.3
|
1.0
|
O
|
C:ARG189
|
4.5
|
35.5
|
1.0
|
O
|
C:ASP187
|
4.6
|
29.2
|
1.0
|
O
|
C:HOH421
|
4.7
|
32.2
|
1.0
|
CB
|
C:THR188
|
4.9
|
32.8
|
1.0
|
C
|
C:VAL191
|
5.0
|
24.4
|
1.0
|
HA
|
C:ALA190
|
5.0
|
32.3
|
1.0
|
|
Sodium binding site 4 out
of 8 in 7cjs
Go back to
Sodium Binding Sites List in 7cjs
Sodium binding site 4 out
of 8 in the Structure of Aquaporin
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Structure of Aquaporin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na301
b:43.7
occ:1.00
|
O
|
D:HOH484
|
2.3
|
46.4
|
1.0
|
O
|
D:HOH482
|
2.4
|
48.5
|
1.0
|
O
|
D:ALA190
|
2.4
|
24.6
|
1.0
|
O
|
D:HOH490
|
2.6
|
36.6
|
1.0
|
O
|
D:HOH483
|
2.6
|
37.2
|
1.0
|
O
|
D:THR188
|
2.7
|
25.5
|
1.0
|
H
|
D:GLY192
|
3.3
|
31.0
|
1.0
|
C
|
D:ALA190
|
3.6
|
25.0
|
1.0
|
C
|
D:THR188
|
3.6
|
24.6
|
1.0
|
HA
|
D:VAL191
|
3.7
|
27.8
|
1.0
|
HA
|
D:THR188
|
3.9
|
30.1
|
1.0
|
N
|
D:GLY192
|
4.1
|
25.8
|
1.0
|
N
|
D:ALA190
|
4.2
|
25.9
|
1.0
|
C
|
D:ARG189
|
4.3
|
24.4
|
1.0
|
HA
|
D:ARG189
|
4.3
|
28.1
|
1.0
|
O
|
D:HOH425
|
4.4
|
30.1
|
1.0
|
CA
|
D:THR188
|
4.4
|
25.1
|
1.0
|
H
|
D:ALA190
|
4.4
|
31.0
|
1.0
|
CA
|
D:VAL191
|
4.4
|
23.1
|
1.0
|
N
|
D:VAL191
|
4.5
|
23.5
|
1.0
|
N
|
D:ARG189
|
4.5
|
23.1
|
1.0
|
O
|
D:ASP187
|
4.5
|
24.1
|
1.0
|
CA
|
D:ALA190
|
4.5
|
26.1
|
1.0
|
CA
|
D:ARG189
|
4.6
|
23.4
|
1.0
|
O
|
D:ARG189
|
4.7
|
24.3
|
1.0
|
HA3
|
D:GLY192
|
4.7
|
32.9
|
1.0
|
HB
|
D:THR188
|
4.8
|
32.0
|
1.0
|
C
|
D:VAL191
|
4.8
|
23.9
|
1.0
|
OE2
|
D:GLU193
|
4.8
|
30.8
|
1.0
|
|
Sodium binding site 5 out
of 8 in 7cjs
Go back to
Sodium Binding Sites List in 7cjs
Sodium binding site 5 out
of 8 in the Structure of Aquaporin
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Structure of Aquaporin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Na301
b:42.8
occ:1.00
|
O
|
E:ALA190
|
2.2
|
26.5
|
1.0
|
O
|
E:HOH435
|
2.4
|
50.8
|
1.0
|
O
|
E:THR188
|
2.5
|
29.2
|
1.0
|
O
|
E:HOH490
|
2.5
|
56.2
|
1.0
|
O
|
E:HOH447
|
2.6
|
66.9
|
1.0
|
O
|
E:HOH476
|
2.6
|
36.2
|
1.0
|
C
|
E:THR188
|
3.4
|
28.7
|
1.0
|
C
|
E:ALA190
|
3.4
|
23.0
|
1.0
|
H
|
E:GLY192
|
3.4
|
29.7
|
1.0
|
HA
|
E:VAL191
|
3.6
|
29.0
|
1.0
|
HA
|
E:THR188
|
3.7
|
34.8
|
1.0
|
C
|
E:ARG189
|
4.0
|
28.2
|
1.0
|
N
|
E:ALA190
|
4.0
|
24.1
|
1.0
|
CA
|
E:THR188
|
4.1
|
29.0
|
1.0
|
HA
|
E:ARG189
|
4.2
|
35.3
|
1.0
|
N
|
E:GLY192
|
4.2
|
24.7
|
1.0
|
N
|
E:ARG189
|
4.3
|
27.8
|
1.0
|
H
|
E:ALA190
|
4.3
|
28.9
|
1.0
|
O
|
E:ARG189
|
4.3
|
28.8
|
1.0
|
N
|
E:VAL191
|
4.3
|
23.7
|
1.0
|
CA
|
E:ALA190
|
4.3
|
22.4
|
1.0
|
CA
|
E:VAL191
|
4.4
|
24.2
|
1.0
|
O
|
E:HOH471
|
4.4
|
54.2
|
1.0
|
CA
|
E:ARG189
|
4.4
|
29.4
|
1.0
|
O
|
E:ASP187
|
4.4
|
23.1
|
1.0
|
HB
|
E:THR188
|
4.6
|
36.4
|
1.0
|
O
|
E:HOH409
|
4.8
|
36.1
|
1.0
|
C
|
E:VAL191
|
4.9
|
24.4
|
1.0
|
HA
|
E:ALA190
|
4.9
|
26.9
|
1.0
|
CB
|
E:THR188
|
5.0
|
30.4
|
1.0
|
HA3
|
E:GLY192
|
5.0
|
30.7
|
1.0
|
OE2
|
E:GLU193
|
5.0
|
31.5
|
1.0
|
|
Sodium binding site 6 out
of 8 in 7cjs
Go back to
Sodium Binding Sites List in 7cjs
Sodium binding site 6 out
of 8 in the Structure of Aquaporin
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Structure of Aquaporin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Na301
b:46.0
occ:1.00
|
O
|
F:HOH466
|
2.2
|
43.0
|
1.0
|
O
|
F:ALA190
|
2.3
|
21.8
|
1.0
|
O
|
F:THR188
|
2.5
|
25.2
|
1.0
|
O
|
F:HOH481
|
2.5
|
32.2
|
1.0
|
O
|
F:HOH489
|
2.5
|
49.1
|
1.0
|
O
|
F:HOH408
|
2.6
|
39.0
|
1.0
|
H
|
F:GLY192
|
3.4
|
28.7
|
1.0
|
C
|
F:THR188
|
3.5
|
24.6
|
1.0
|
C
|
F:ALA190
|
3.5
|
22.3
|
1.0
|
HA
|
F:VAL191
|
3.7
|
28.8
|
1.0
|
HA
|
F:THR188
|
3.8
|
29.6
|
1.0
|
O
|
F:HOH446
|
4.1
|
57.4
|
1.0
|
N
|
F:ALA190
|
4.1
|
21.8
|
1.0
|
C
|
F:ARG189
|
4.1
|
22.9
|
1.0
|
N
|
F:GLY192
|
4.2
|
23.9
|
1.0
|
CA
|
F:THR188
|
4.2
|
24.7
|
1.0
|
HA
|
F:ARG189
|
4.3
|
28.3
|
1.0
|
H
|
F:ALA190
|
4.3
|
26.2
|
1.0
|
N
|
F:ARG189
|
4.3
|
23.7
|
1.0
|
O
|
F:HOH429
|
4.4
|
27.5
|
1.0
|
CA
|
F:VAL191
|
4.4
|
24.0
|
1.0
|
N
|
F:VAL191
|
4.4
|
23.2
|
1.0
|
CA
|
F:ALA190
|
4.4
|
22.1
|
1.0
|
O
|
F:ARG189
|
4.5
|
22.9
|
1.0
|
CA
|
F:ARG189
|
4.5
|
23.6
|
1.0
|
O
|
F:ASP187
|
4.5
|
22.2
|
1.0
|
HB
|
F:THR188
|
4.6
|
31.8
|
1.0
|
C
|
F:VAL191
|
4.9
|
24.0
|
1.0
|
HA3
|
F:GLY192
|
4.9
|
29.1
|
1.0
|
|
Sodium binding site 7 out
of 8 in 7cjs
Go back to
Sodium Binding Sites List in 7cjs
Sodium binding site 7 out
of 8 in the Structure of Aquaporin
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Structure of Aquaporin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Na301
b:38.9
occ:1.00
|
O
|
G:HOH486
|
2.2
|
41.4
|
1.0
|
O
|
G:ALA190
|
2.3
|
23.9
|
1.0
|
O
|
G:HOH429
|
2.4
|
41.1
|
1.0
|
O
|
G:THR188
|
2.4
|
29.7
|
1.0
|
O
|
G:HOH500
|
2.5
|
35.1
|
1.0
|
O
|
G:HOH533
|
2.6
|
43.7
|
1.0
|
H
|
G:GLY192
|
3.4
|
23.1
|
1.0
|
C
|
G:THR188
|
3.4
|
29.6
|
1.0
|
C
|
G:ALA190
|
3.5
|
24.8
|
1.0
|
HA
|
G:THR188
|
3.7
|
34.6
|
1.0
|
HA
|
G:VAL191
|
3.7
|
26.8
|
1.0
|
N
|
G:ALA190
|
4.1
|
29.0
|
1.0
|
CA
|
G:THR188
|
4.1
|
28.9
|
1.0
|
H
|
G:ALA190
|
4.2
|
34.8
|
1.0
|
N
|
G:GLY192
|
4.2
|
19.3
|
1.0
|
C
|
G:ARG189
|
4.3
|
31.2
|
1.0
|
HA
|
G:ARG189
|
4.4
|
38.1
|
1.0
|
N
|
G:ARG189
|
4.4
|
30.4
|
1.0
|
N
|
G:VAL191
|
4.4
|
23.4
|
1.0
|
CA
|
G:VAL191
|
4.4
|
22.3
|
1.0
|
CA
|
G:ALA190
|
4.5
|
27.2
|
1.0
|
O
|
G:HOH432
|
4.5
|
28.5
|
1.0
|
HB
|
G:THR188
|
4.5
|
37.2
|
1.0
|
O
|
G:HOH406
|
4.6
|
44.0
|
1.0
|
O
|
G:ASP187
|
4.6
|
27.4
|
1.0
|
CA
|
G:ARG189
|
4.6
|
31.8
|
1.0
|
O
|
G:ARG189
|
4.7
|
31.7
|
1.0
|
C
|
G:VAL191
|
4.9
|
21.8
|
1.0
|
OE2
|
G:GLU193
|
4.9
|
29.5
|
1.0
|
HA3
|
G:GLY192
|
4.9
|
22.9
|
1.0
|
CB
|
G:THR188
|
5.0
|
31.0
|
1.0
|
|
Sodium binding site 8 out
of 8 in 7cjs
Go back to
Sodium Binding Sites List in 7cjs
Sodium binding site 8 out
of 8 in the Structure of Aquaporin
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of Structure of Aquaporin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Na301
b:44.3
occ:1.00
|
O
|
H:ALA190
|
2.2
|
23.4
|
1.0
|
O
|
H:HOH489
|
2.3
|
43.3
|
1.0
|
O
|
H:HOH499
|
2.4
|
44.4
|
1.0
|
O
|
H:HOH483
|
2.4
|
30.1
|
1.0
|
O
|
H:THR188
|
2.6
|
28.1
|
1.0
|
O
|
H:HOH462
|
2.7
|
44.7
|
1.0
|
H
|
H:GLY192
|
3.3
|
31.9
|
1.0
|
C
|
H:ALA190
|
3.4
|
23.9
|
1.0
|
C
|
H:THR188
|
3.5
|
26.5
|
1.0
|
HA
|
H:VAL191
|
3.7
|
26.2
|
1.0
|
HA
|
H:THR188
|
3.8
|
31.9
|
1.0
|
N
|
H:ALA190
|
4.0
|
23.8
|
1.0
|
C
|
H:ARG189
|
4.1
|
23.4
|
1.0
|
N
|
H:GLY192
|
4.1
|
26.6
|
1.0
|
H
|
H:ALA190
|
4.2
|
28.5
|
1.0
|
CA
|
H:THR188
|
4.2
|
26.6
|
1.0
|
HA
|
H:ARG189
|
4.2
|
28.3
|
1.0
|
N
|
H:VAL191
|
4.4
|
22.3
|
1.0
|
CA
|
H:ALA190
|
4.4
|
24.7
|
1.0
|
N
|
H:ARG189
|
4.4
|
24.6
|
1.0
|
O
|
H:ASP187
|
4.4
|
22.4
|
1.0
|
CA
|
H:VAL191
|
4.4
|
21.8
|
1.0
|
O
|
H:HOH424
|
4.4
|
32.0
|
1.0
|
CA
|
H:ARG189
|
4.5
|
23.6
|
1.0
|
O
|
H:ARG189
|
4.5
|
22.8
|
1.0
|
HB
|
H:THR188
|
4.7
|
33.5
|
1.0
|
HA3
|
H:GLY192
|
4.8
|
34.3
|
1.0
|
C
|
H:VAL191
|
4.9
|
22.9
|
1.0
|
OE2
|
H:GLU193
|
4.9
|
30.7
|
1.0
|
HA
|
H:ALA190
|
5.0
|
29.6
|
1.0
|
|
Reference:
Y.Saitoh,
J.F.Ma,
M.Suga.
Structure of Aquaporin Nat Commun 2021.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-021-26535-X
Page generated: Tue Oct 8 16:22:57 2024
|