Sodium in PDB 8t1b: Cryo-Em Structure of Full-Length Human TRPV4 in Apo State
Sodium Binding Sites:
The binding sites of Sodium atom in the Cryo-Em Structure of Full-Length Human TRPV4 in Apo State
(pdb code 8t1b). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
Cryo-Em Structure of Full-Length Human TRPV4 in Apo State, PDB code: 8t1b:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 8t1b
Go back to
Sodium Binding Sites List in 8t1b
Sodium binding site 1 out
of 4 in the Cryo-Em Structure of Full-Length Human TRPV4 in Apo State
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Cryo-Em Structure of Full-Length Human TRPV4 in Apo State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1214
b:27.7
occ:1.00
|
NA
|
A:NA1215
|
3.6
|
28.9
|
1.0
|
CA
|
D:GLY679
|
4.7
|
47.2
|
1.0
|
CA
|
C:GLY679
|
4.7
|
46.7
|
1.0
|
O
|
D:ILE678
|
4.7
|
45.4
|
1.0
|
O
|
C:ILE678
|
4.7
|
45.1
|
1.0
|
O
|
C:GLY679
|
4.7
|
46.7
|
1.0
|
O
|
D:GLY679
|
4.7
|
47.2
|
1.0
|
O
|
B:ILE678
|
4.7
|
45.7
|
1.0
|
CA
|
B:GLY679
|
4.7
|
47.3
|
1.0
|
O
|
A:ILE678
|
4.7
|
30.1
|
1.0
|
CA
|
A:GLY679
|
4.8
|
30.8
|
1.0
|
O
|
B:GLY679
|
4.8
|
47.3
|
1.0
|
O
|
A:GLY679
|
4.8
|
30.8
|
1.0
|
C
|
C:GLY679
|
4.9
|
46.7
|
1.0
|
C
|
D:GLY679
|
4.9
|
47.2
|
1.0
|
C
|
B:GLY679
|
4.9
|
47.3
|
1.0
|
C
|
A:GLY679
|
5.0
|
30.8
|
1.0
|
|
Sodium binding site 2 out
of 4 in 8t1b
Go back to
Sodium Binding Sites List in 8t1b
Sodium binding site 2 out
of 4 in the Cryo-Em Structure of Full-Length Human TRPV4 in Apo State
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Cryo-Em Structure of Full-Length Human TRPV4 in Apo State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1215
b:28.9
occ:1.00
|
O
|
D:GLY679
|
3.3
|
47.2
|
1.0
|
O
|
C:GLY679
|
3.3
|
46.7
|
1.0
|
O
|
B:GLY679
|
3.3
|
47.3
|
1.0
|
O
|
A:GLY679
|
3.4
|
30.8
|
1.0
|
NA
|
A:NA1214
|
3.6
|
27.7
|
1.0
|
O
|
D:HOH1311
|
4.0
|
100.1
|
1.0
|
O
|
A:HOH1311
|
4.0
|
76.7
|
1.0
|
O
|
B:HOH1311
|
4.0
|
119.3
|
1.0
|
O
|
C:HOH1311
|
4.0
|
113.2
|
1.0
|
C
|
D:GLY679
|
4.1
|
47.2
|
1.0
|
C
|
C:GLY679
|
4.1
|
46.7
|
1.0
|
C
|
B:GLY679
|
4.2
|
47.3
|
1.0
|
C
|
A:GLY679
|
4.2
|
30.8
|
1.0
|
CA
|
D:MET680
|
4.6
|
49.2
|
1.0
|
CA
|
C:MET680
|
4.6
|
48.9
|
1.0
|
CA
|
A:MET680
|
4.7
|
32.8
|
1.0
|
CA
|
B:MET680
|
4.7
|
49.6
|
1.0
|
N
|
D:MET680
|
4.7
|
49.2
|
1.0
|
N
|
C:MET680
|
4.7
|
48.9
|
1.0
|
N
|
B:MET680
|
4.8
|
49.6
|
1.0
|
N
|
A:MET680
|
4.8
|
32.8
|
1.0
|
CA
|
D:GLY679
|
5.0
|
47.2
|
1.0
|
CA
|
C:GLY679
|
5.0
|
46.7
|
1.0
|
CA
|
B:GLY679
|
5.0
|
47.3
|
1.0
|
|
Sodium binding site 3 out
of 4 in 8t1b
Go back to
Sodium Binding Sites List in 8t1b
Sodium binding site 3 out
of 4 in the Cryo-Em Structure of Full-Length Human TRPV4 in Apo State
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Cryo-Em Structure of Full-Length Human TRPV4 in Apo State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1216
b:30.3
occ:1.00
|
CG2
|
A:ILE715
|
4.5
|
21.4
|
1.0
|
CG2
|
C:ILE715
|
4.5
|
34.4
|
1.0
|
CG2
|
D:ILE715
|
4.5
|
34.6
|
1.0
|
CG2
|
B:ILE715
|
4.6
|
34.9
|
1.0
|
O
|
A:ILE715
|
4.7
|
21.4
|
1.0
|
O
|
D:ILE715
|
4.8
|
34.6
|
1.0
|
O
|
C:ILE715
|
4.8
|
34.4
|
1.0
|
O
|
B:ILE715
|
4.8
|
34.9
|
1.0
|
|
Sodium binding site 4 out
of 4 in 8t1b
Go back to
Sodium Binding Sites List in 8t1b
Sodium binding site 4 out
of 4 in the Cryo-Em Structure of Full-Length Human TRPV4 in Apo State
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Cryo-Em Structure of Full-Length Human TRPV4 in Apo State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1217
b:98.2
occ:1.00
|
O
|
D:HOH1310
|
2.5
|
102.8
|
1.0
|
O
|
A:HOH1310
|
2.5
|
78.2
|
1.0
|
O
|
C:HOH1308
|
2.5
|
116.5
|
1.0
|
O
|
B:HOH1310
|
2.5
|
114.3
|
1.0
|
O
|
B:HOH1311
|
3.1
|
119.3
|
1.0
|
O
|
C:HOH1311
|
3.2
|
113.2
|
1.0
|
O
|
A:HOH1311
|
3.2
|
76.7
|
1.0
|
O
|
D:HOH1311
|
3.2
|
100.1
|
1.0
|
OD1
|
B:ASP682
|
4.1
|
55.1
|
1.0
|
OD1
|
C:ASP682
|
4.2
|
54.5
|
1.0
|
OD1
|
D:ASP682
|
4.2
|
54.5
|
1.0
|
OD1
|
A:ASP682
|
4.4
|
38.2
|
1.0
|
OD2
|
B:ASP682
|
4.5
|
55.1
|
1.0
|
OD2
|
C:ASP682
|
4.5
|
54.5
|
1.0
|
OD2
|
D:ASP682
|
4.6
|
54.5
|
1.0
|
OD2
|
A:ASP682
|
4.7
|
38.2
|
1.0
|
CG
|
B:ASP682
|
4.8
|
55.1
|
1.0
|
CG
|
C:ASP682
|
4.8
|
54.5
|
1.0
|
CG
|
D:ASP682
|
4.9
|
54.5
|
1.0
|
CG
|
A:ASP682
|
5.0
|
38.2
|
1.0
|
|
Reference:
K.D.Nadezhdin,
I.A.Talyzina,
A.Parthasarathy,
A.Neuberger,
D.X.Zhang,
A.I.Sobolevsky.
Structure of Human TRPV4 in Complex with Gtpase Rhoa. Nat Commun V. 14 3733 2023.
ISSN: ESSN 2041-1723
PubMed: 37353478
DOI: 10.1038/S41467-023-39346-Z
Page generated: Fri Jul 28 03:42:50 2023
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