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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:

Chlorine (Cl) 5 atoms
Calcium (Ca) 5 atoms

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

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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

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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

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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

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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

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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

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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

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