Sodium in PDB 7mzd: Cryo-Em Structure of Minimal TRPV1 with Rtx Bound in C2 State
Sodium Binding Sites:
The binding sites of Sodium atom in the Cryo-Em Structure of Minimal TRPV1 with Rtx Bound in C2 State
(pdb code 7mzd). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the
Cryo-Em Structure of Minimal TRPV1 with Rtx Bound in C2 State, PDB code: 7mzd:
Jump to Sodium binding site number:
1;
2;
Sodium binding site 1 out
of 2 in 7mzd
Go back to
Sodium Binding Sites List in 7mzd
Sodium binding site 1 out
of 2 in the Cryo-Em Structure of Minimal TRPV1 with Rtx Bound in C2 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 Minimal TRPV1 with Rtx Bound in C2 State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na902
b:31.2
occ:1.00
|
O
|
A:GLY643
|
2.3
|
45.1
|
1.0
|
O
|
B:GLY643
|
2.3
|
45.6
|
1.0
|
O
|
C:GLY643
|
2.3
|
45.4
|
1.0
|
O
|
D:GLY643
|
2.3
|
45.8
|
1.0
|
C
|
B:GLY643
|
3.4
|
45.6
|
1.0
|
C
|
C:GLY643
|
3.4
|
45.4
|
1.0
|
C
|
D:GLY643
|
3.4
|
45.8
|
1.0
|
C
|
A:GLY643
|
3.4
|
45.1
|
1.0
|
NA
|
A:NA903
|
3.7
|
35.0
|
1.0
|
CA
|
B:GLY643
|
3.9
|
45.6
|
1.0
|
CA
|
D:GLY643
|
4.0
|
45.8
|
1.0
|
CA
|
C:GLY643
|
4.0
|
45.4
|
1.0
|
CA
|
A:GLY643
|
4.0
|
45.1
|
1.0
|
SD
|
C:MET644
|
4.5
|
45.5
|
1.0
|
SD
|
A:MET644
|
4.5
|
45.7
|
1.0
|
SD
|
D:MET644
|
4.5
|
45.5
|
1.0
|
SD
|
B:MET644
|
4.5
|
46.2
|
1.0
|
N
|
B:MET644
|
4.6
|
46.2
|
1.0
|
N
|
C:MET644
|
4.6
|
45.5
|
1.0
|
N
|
D:MET644
|
4.6
|
45.5
|
1.0
|
N
|
A:MET644
|
4.6
|
45.7
|
1.0
|
O
|
A:ILE642
|
4.8
|
47.4
|
1.0
|
CG
|
C:MET644
|
4.8
|
45.5
|
1.0
|
CG
|
D:MET644
|
4.8
|
45.5
|
1.0
|
CG
|
A:MET644
|
4.8
|
45.7
|
1.0
|
O
|
D:ILE642
|
4.8
|
47.8
|
1.0
|
CG
|
B:MET644
|
4.8
|
46.2
|
1.0
|
O
|
C:ILE642
|
4.8
|
47.7
|
1.0
|
O
|
B:ILE642
|
4.8
|
48.0
|
1.0
|
CA
|
B:MET644
|
4.9
|
46.2
|
1.0
|
CA
|
C:MET644
|
4.9
|
45.5
|
1.0
|
CA
|
D:MET644
|
4.9
|
45.5
|
1.0
|
CA
|
A:MET644
|
4.9
|
45.7
|
1.0
|
|
Sodium binding site 2 out
of 2 in 7mzd
Go back to
Sodium Binding Sites List in 7mzd
Sodium binding site 2 out
of 2 in the Cryo-Em Structure of Minimal TRPV1 with Rtx Bound in C2 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 Minimal TRPV1 with Rtx Bound in C2 State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na903
b:35.0
occ:1.00
|
NA
|
A:NA902
|
3.7
|
31.2
|
1.0
|
CA
|
B:GLY643
|
4.0
|
45.6
|
1.0
|
CA
|
A:GLY643
|
4.0
|
45.1
|
1.0
|
CA
|
C:GLY643
|
4.0
|
45.4
|
1.0
|
CA
|
D:GLY643
|
4.0
|
45.8
|
1.0
|
O
|
B:HOH1001
|
4.3
|
51.4
|
1.0
|
O
|
A:HOH1001
|
4.3
|
52.2
|
1.0
|
O
|
D:HOH1001
|
4.3
|
50.8
|
1.0
|
O
|
C:HOH1001
|
4.4
|
51.5
|
1.0
|
O
|
A:GLY643
|
4.6
|
45.1
|
1.0
|
O
|
B:GLY643
|
4.6
|
45.6
|
1.0
|
O
|
C:GLY643
|
4.6
|
45.4
|
1.0
|
O
|
D:GLY643
|
4.6
|
45.8
|
1.0
|
O
|
B:ILE642
|
4.8
|
48.0
|
1.0
|
N
|
A:GLY643
|
4.8
|
45.1
|
1.0
|
O
|
C:ILE642
|
4.8
|
47.7
|
1.0
|
O
|
D:ILE642
|
4.8
|
47.8
|
1.0
|
N
|
B:GLY643
|
4.8
|
45.6
|
1.0
|
O
|
A:ILE642
|
4.8
|
47.4
|
1.0
|
C
|
B:GLY643
|
4.8
|
45.6
|
1.0
|
N
|
C:GLY643
|
4.8
|
45.4
|
1.0
|
C
|
A:GLY643
|
4.8
|
45.1
|
1.0
|
C
|
C:GLY643
|
4.8
|
45.4
|
1.0
|
N
|
D:GLY643
|
4.8
|
45.8
|
1.0
|
C
|
D:GLY643
|
4.8
|
45.8
|
1.0
|
|
Reference:
K.Zhang,
D.Julius,
Y.Cheng.
Structural Snapshots of TRPV1 Reveal Mechanism of Polymodal Functionality. Cell 2021.
ISSN: ISSN 1097-4172
PubMed: 34496225
DOI: 10.1016/J.CELL.2021.08.012
Page generated: Fri Sep 24 16:28:43 2021
|