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Calcium 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
Sodium (Na) 7 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 5 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 6v4s

Go back to Calcium Binding Sites List in 6v4s
Calcium binding site 1 out of 5 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 Calcium with other atoms in the Ca 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:Ca701

b:0.6
occ:0.00
 CD A:GLU479 1.6 0.8 1.0
CG A:GLU479 1.9 0.2 1.0
OE2 B:GLU347 2.2 77.1 1.0
OE2 A:GLU479 2.2 0.0 1.0
OE1 A:GLU479 2.3 0.7 1.0
OE1 B:GLU347 2.3 84.5 1.0
O B:PRO434 2.6 0.7 1.0
CD B:GLU347 2.7 77.8 1.0
CB A:GLU479 2.7 0.6 1.0
O B:PHE436 2.7 74.2 1.0
CA A:GLU479 3.4 0.3 1.0
C B:PRO434 3.6 0.2 1.0
N A:GLU479 3.7 0.4 1.0
C B:PHE436 3.9 0.2 1.0
CB A:GLN476 4.1 0.0 1.0
CA B:PRO434 4.2 98.7 1.0
CG B:GLU347 4.2 98.2 1.0
CB B:PRO434 4.5 0.1 1.0
N B:PHE436 4.6 0.9 1.0
N B:ASP435 4.7 0.0 1.0
CA B:PHE436 4.8 96.3 1.0
CG A:GLN476 4.8 0.3 1.0
C A:GLY478 4.9 0.5 1.0
C A:GLU479 4.9 0.1 1.0
N B:ASP437 5.0 0.7 1.0
C B:ASP435 5.0 0.9 1.0

Calcium binding site 2 out of 5 in 6v4s

Go back to Calcium Binding Sites List in 6v4s
Calcium binding site 2 out of 5 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 Calcium with other atoms in the Ca 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:Ca702

b:0.6
occ:0.00
 CD E:GLU479 1.9 0.8 1.0
CG E:GLU479 2.2 0.4 1.0
OE1 E:GLU479 2.2 0.3 1.0
OE2 E:GLU479 2.5 0.6 1.0
O A:PRO434 2.6 0.2 1.0
OE2 A:GLU347 2.8 72.3 1.0
OE1 A:GLU347 2.8 68.0 1.0
O A:PHE436 3.0 83.1 1.0
CB E:GLU479 3.0 0.5 1.0
CD A:GLU347 3.3 70.5 1.0
C A:PRO434 3.8 0.6 1.0
CA E:GLU479 3.8 0.5 1.0
N E:GLU479 4.1 0.5 1.0
CB E:GLN476 4.2 0.5 1.0
C A:PHE436 4.2 0.6 1.0
CA A:PRO434 4.5 98.5 1.0
CB A:PRO434 4.6 99.2 1.0
CG E:GLN476 4.7 0.3 1.0
N A:ASP435 4.8 0.0 1.0
CG A:GLU347 4.8 99.0 1.0
N A:PHE436 4.9 0.7 1.0

Calcium binding site 3 out of 5 in 6v4s

Go back to Calcium Binding Sites List in 6v4s
Calcium binding site 3 out of 5 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 Calcium with other atoms in the Ca 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
E:Ca701

b:0.3
occ:1.00
 OE2 E:GLU347 2.1 77.5 1.0
O E:PHE436 2.1 86.5 1.0
O E:PRO434 2.2 0.2 1.0
OE1 E:GLU347 2.3 82.5 1.0
CD E:GLU347 2.4 82.8 1.0
CD D:GLU479 2.6 0.2 1.0
OE2 D:GLU479 2.9 0.6 1.0
CG D:GLU479 3.0 0.1 1.0
OE1 D:GLU479 3.0 0.2 1.0
C E:PRO434 3.1 98.3 1.0
C E:PHE436 3.3 0.4 1.0
CB D:GLU479 3.5 0.7 1.0
CA E:PRO434 3.8 91.9 1.0
N E:PHE436 3.8 0.8 1.0
CG E:GLU347 3.9 88.4 1.0
CA E:PHE436 4.0 93.5 1.0
CA D:GLU479 4.1 0.5 1.0
N E:ASP435 4.2 0.4 1.0
CB E:PRO434 4.3 99.5 1.0
C E:ASP435 4.3 0.3 1.0
N E:ASP437 4.4 0.9 1.0
CB E:PHE436 4.4 85.6 1.0
N D:GLU479 4.5 0.1 1.0
CA E:ASP435 4.5 0.9 1.0
CB E:GLU347 4.7 90.0 1.0
CA E:ASP437 4.8 0.9 1.0

Calcium binding site 4 out of 5 in 6v4s

Go back to Calcium Binding Sites List in 6v4s
Calcium binding site 4 out of 5 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 Calcium with other atoms in the Ca 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
C:Ca701

b:0.6
occ:0.00
 OE2 D:GLU347 1.9 74.2 1.0
OE1 D:GLU347 2.5 83.2 1.0
O D:PHE436 2.5 84.1 1.0
O D:PRO434 2.5 0.7 1.0
CD D:GLU347 2.6 91.0 1.0
CD C:GLU479 2.7 0.2 1.0
CB C:GLU479 2.8 0.8 1.0
OE2 C:GLU479 2.9 0.5 1.0
OE1 C:GLU479 3.2 0.7 1.0
CG C:GLU479 3.2 0.6 1.0
CA C:GLU479 3.4 0.3 1.0
C D:PRO434 3.5 97.3 1.0
N C:GLU479 3.6 1.0 1.0
C D:PHE436 3.7 0.5 1.0
CG D:GLU347 4.1 98.4 1.0
CA D:PRO434 4.1 95.2 1.0
N D:PHE436 4.4 0.4 1.0
CB D:PRO434 4.4 97.6 1.0
CA D:PHE436 4.5 93.0 1.0
N D:ASP435 4.6 0.4 1.0
C C:GLY478 4.7 0.7 1.0
CB C:GLN476 4.7 0.8 1.0
N D:ASP437 4.8 0.2 1.0
C D:ASP435 4.8 0.2 1.0
C C:GLU479 4.9 0.4 1.0
CA D:ASP435 4.9 0.2 1.0
CB D:PHE436 4.9 83.0 1.0
CB D:GLU347 5.0 0.8 1.0

Calcium binding site 5 out of 5 in 6v4s

Go back to Calcium Binding Sites List in 6v4s
Calcium binding site 5 out of 5 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 Calcium with other atoms in the Ca 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
B:Ca701

b:0.6
occ:0.00
 CD B:GLU479 1.6 0.3 1.0
CG B:GLU479 1.9 0.4 1.0
OE2 B:GLU479 2.0 0.4 1.0
OE2 C:GLU347 2.1 76.9 1.0
OE1 C:GLU347 2.2 76.2 1.0
OE1 B:GLU479 2.3 0.8 1.0
CD C:GLU347 2.4 78.8 1.0
CB B:GLU479 2.6 0.1 1.0
O C:PHE436 2.7 67.1 1.0
O C:PRO434 2.7 1.0 1.0
CA B:GLU479 3.2 0.2 1.0
N B:GLU479 3.5 0.9 1.0
C C:PRO434 3.7 94.6 1.0
C C:PHE436 3.9 0.2 1.0
CG C:GLU347 4.0 0.3 1.0
CA C:PRO434 4.2 95.5 1.0
CB B:GLN476 4.4 0.4 1.0
CB C:PRO434 4.5 0.9 1.0
C B:GLY478 4.6 0.7 1.0
N C:PHE436 4.6 0.1 1.0
CA C:PHE436 4.7 90.5 1.0
C B:GLU479 4.7 97.3 1.0
N C:ASP435 4.8 0.2 1.0
CB C:GLU347 4.9 0.6 1.0
N C:ASP437 4.9 0.1 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: Wed Jul 9 18:59:56 2025

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