Sodium in PDB 6v4s: A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain
Protein crystallography data
The structure of A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain, PDB code: 6v4s
was solved by
M.Delarue,
H.D.Hu,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.04 /
3.55
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
159.406,
337.254,
111.812,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.4 /
26.8
|
Other elements in 6v4s:
The structure of A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain
(pdb code 6v4s). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the
A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain, PDB code: 6v4s:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
Sodium binding site 1 out
of 7 in 6v4s
Go back to
Sodium Binding Sites List in 6v4s
Sodium binding site 1 out
of 7 in the A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na703
b:66.7
occ:1.00
|
OE1
|
C:GLU547
|
3.2
|
0.7
|
1.0
|
OE1
|
D:GLU547
|
3.3
|
0.4
|
1.0
|
OE1
|
A:GLU547
|
3.5
|
0.5
|
1.0
|
OE1
|
E:GLU547
|
3.5
|
1.0
|
1.0
|
CD
|
C:GLU547
|
4.3
|
0.9
|
1.0
|
OE1
|
B:GLU547
|
4.3
|
0.3
|
1.0
|
CD
|
D:GLU547
|
4.4
|
0.8
|
1.0
|
CD
|
A:GLU547
|
4.4
|
0.3
|
1.0
|
OE2
|
B:GLU547
|
4.5
|
0.3
|
1.0
|
OE2
|
C:GLU547
|
4.5
|
0.0
|
1.0
|
CD
|
E:GLU547
|
4.6
|
0.5
|
1.0
|
OE2
|
A:GLU547
|
4.6
|
0.6
|
1.0
|
OE2
|
D:GLU547
|
4.8
|
0.2
|
1.0
|
CD
|
B:GLU547
|
4.8
|
0.2
|
1.0
|
OE2
|
E:GLU547
|
4.9
|
0.8
|
1.0
|
|
Sodium binding site 2 out
of 7 in 6v4s
Go back to
Sodium Binding Sites List in 6v4s
Sodium binding site 2 out
of 7 in the A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na704
b:0.8
occ:1.00
|
C
|
A:VAL340
|
3.7
|
85.1
|
1.0
|
N
|
A:GLY341
|
3.7
|
81.0
|
1.0
|
O
|
A:VAL340
|
3.8
|
0.9
|
1.0
|
CA
|
A:GLY341
|
3.9
|
93.0
|
1.0
|
O
|
A:ILE339
|
4.1
|
0.1
|
1.0
|
OE1
|
A:GLU481
|
4.1
|
0.9
|
1.0
|
O
|
B:ARG345
|
4.2
|
0.8
|
1.0
|
CA
|
A:VAL340
|
4.3
|
87.7
|
1.0
|
CG
|
B:ARG345
|
4.5
|
0.8
|
1.0
|
C
|
A:GLY341
|
4.5
|
97.7
|
1.0
|
N
|
A:VAL342
|
4.6
|
91.0
|
1.0
|
CD
|
A:GLU481
|
4.7
|
0.5
|
1.0
|
C
|
A:ILE339
|
4.8
|
88.0
|
1.0
|
C
|
B:ARG345
|
4.9
|
0.5
|
1.0
|
NE
|
B:ARG345
|
5.0
|
0.0
|
1.0
|
N
|
A:VAL340
|
5.0
|
79.2
|
1.0
|
|
Sodium binding site 3 out
of 7 in 6v4s
Go back to
Sodium Binding Sites List in 6v4s
Sodium binding site 3 out
of 7 in the A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na705
b:71.5
occ:1.00
|
OE1
|
E:GLU481
|
3.3
|
0.9
|
1.0
|
O
|
A:ARG345
|
3.4
|
0.0
|
1.0
|
CG
|
A:ARG345
|
4.1
|
0.8
|
1.0
|
CD
|
E:GLU481
|
4.1
|
0.9
|
1.0
|
C
|
A:ARG345
|
4.2
|
0.1
|
1.0
|
O
|
E:ILE339
|
4.5
|
0.6
|
1.0
|
CB
|
E:GLU481
|
4.7
|
86.0
|
1.0
|
C
|
E:VAL340
|
4.7
|
92.1
|
1.0
|
CG
|
E:GLU481
|
4.8
|
94.5
|
1.0
|
O
|
E:VAL340
|
4.8
|
0.3
|
1.0
|
NE
|
A:ARG345
|
4.8
|
0.7
|
1.0
|
CA
|
A:SER346
|
4.8
|
0.9
|
1.0
|
N
|
E:GLY341
|
4.9
|
90.1
|
1.0
|
N
|
A:SER346
|
4.9
|
0.5
|
1.0
|
CD
|
A:ARG345
|
4.9
|
0.2
|
1.0
|
OE2
|
E:GLU481
|
4.9
|
91.0
|
1.0
|
|
Sodium binding site 4 out
of 7 in 6v4s
Go back to
Sodium Binding Sites List in 6v4s
Sodium binding site 4 out
of 7 in the A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na701
b:63.9
occ:1.00
|
OE1
|
D:GLU481
|
3.4
|
0.0
|
1.0
|
O
|
E:ARG345
|
3.7
|
0.4
|
1.0
|
CD
|
D:GLU481
|
4.2
|
0.2
|
1.0
|
CG
|
E:ARG345
|
4.2
|
0.6
|
1.0
|
O
|
D:ILE339
|
4.3
|
0.8
|
1.0
|
C
|
D:VAL340
|
4.4
|
88.5
|
1.0
|
O
|
D:VAL340
|
4.4
|
95.1
|
1.0
|
C
|
E:ARG345
|
4.5
|
0.1
|
1.0
|
N
|
D:GLY341
|
4.5
|
93.9
|
1.0
|
CA
|
D:GLY341
|
4.6
|
99.1
|
1.0
|
CB
|
D:GLU481
|
4.8
|
91.4
|
1.0
|
CG
|
D:GLU481
|
4.8
|
99.9
|
1.0
|
CA
|
E:SER346
|
4.9
|
98.2
|
1.0
|
NE
|
E:ARG345
|
4.9
|
0.6
|
1.0
|
CA
|
D:VAL340
|
4.9
|
89.1
|
1.0
|
|
Sodium binding site 5 out
of 7 in 6v4s
Go back to
Sodium Binding Sites List in 6v4s
Sodium binding site 5 out
of 7 in the A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na702
b:0.6
occ:0.00
|
O
|
D:HOH801
|
2.1
|
0.8
|
1.0
|
O
|
C:HOH801
|
2.2
|
77.3
|
1.0
|
O
|
A:HOH801
|
2.3
|
0.2
|
1.0
|
O
|
E:HOH801
|
2.5
|
0.1
|
1.0
|
O
|
B:HOH801
|
2.6
|
0.9
|
1.0
|
|
Sodium binding site 6 out
of 7 in 6v4s
Go back to
Sodium Binding Sites List in 6v4s
Sodium binding site 6 out
of 7 in the A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na703
b:79.3
occ:1.00
|
OE1
|
C:GLU481
|
3.8
|
0.5
|
1.0
|
O
|
D:ARG345
|
4.1
|
0.8
|
1.0
|
C
|
C:VAL340
|
4.2
|
79.8
|
1.0
|
N
|
C:GLY341
|
4.2
|
86.6
|
1.0
|
CA
|
C:GLY341
|
4.3
|
0.2
|
1.0
|
O
|
C:VAL340
|
4.3
|
97.2
|
1.0
|
O
|
C:ILE339
|
4.3
|
0.3
|
1.0
|
CD
|
C:GLU481
|
4.4
|
0.4
|
1.0
|
CG
|
D:ARG345
|
4.4
|
95.8
|
1.0
|
CB
|
C:GLU481
|
4.7
|
94.9
|
1.0
|
CA
|
C:VAL340
|
4.8
|
86.4
|
1.0
|
CG
|
C:GLU481
|
4.8
|
97.6
|
1.0
|
C
|
D:ARG345
|
4.8
|
0.2
|
1.0
|
NE
|
D:ARG345
|
4.9
|
0.0
|
1.0
|
N
|
C:VAL342
|
4.9
|
81.8
|
1.0
|
C
|
C:GLY341
|
4.9
|
93.5
|
1.0
|
|
Sodium binding site 7 out
of 7 in 6v4s
Go back to
Sodium Binding Sites List in 6v4s
Sodium binding site 7 out
of 7 in the A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of A Closed Pore Conformation of A Pentameic Ligand-Gated Ion Channel with Additional N-Terminal Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na702
b:88.6
occ:1.00
|
OE1
|
B:GLU481
|
3.5
|
0.9
|
1.0
|
O
|
C:ARG345
|
3.7
|
0.0
|
1.0
|
O
|
B:ILE339
|
4.0
|
0.6
|
1.0
|
CB
|
B:GLU481
|
4.1
|
95.5
|
1.0
|
CD
|
B:GLU481
|
4.2
|
0.3
|
1.0
|
CG
|
B:GLU481
|
4.4
|
0.5
|
1.0
|
CG
|
C:ARG345
|
4.5
|
0.6
|
1.0
|
C
|
C:ARG345
|
4.6
|
0.4
|
1.0
|
C
|
B:VAL340
|
4.7
|
93.4
|
1.0
|
O
|
B:VAL340
|
4.9
|
0.5
|
1.0
|
N
|
B:GLY341
|
4.9
|
0.6
|
1.0
|
|
Reference:
H.Hu,
R.Howard,
U.Bastolla,
E.Lindahl,
M.Delarue.
Structural Basis For Allosteric Transitions of A Multi-Domain Pentameric Ligand-Gated Ion Channel Proc.Natl.Acad.Sci.Usa 2020.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.1922701117
Page generated: Tue Oct 8 14:17:12 2024
|