Sodium in PDB 5svl: Crystal Structure of the Atp-Gated Human P2X3 Ion Channel in the Atp- Bound, Closed (Desensitized) State

The structure of Crystal Structure of the Atp-Gated Human P2X3 Ion Channel in the Atp- Bound, Closed (Desensitized) State, PDB code: 5svl was solved by S.E.Mansoor, W.Lu, W.Oosterheert, M.Shekhar, E.Tajkhorshid, E.Gouaux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	76.98 / 2.90
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	172.140, 172.140, 172.140, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 24

The binding sites of Sodium atom in the Crystal Structure of the Atp-Gated Human P2X3 Ion Channel in the Atp- Bound, Closed (Desensitized) State (pdb code 5svl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Atp-Gated Human P2X3 Ion Channel in the Atp- Bound, Closed (Desensitized) State, PDB code: 5svl:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the Atp-Gated Human P2X3 Ion Channel in the Atp- Bound, Closed (Desensitized) State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Atp-Gated Human P2X3 Ion Channel in the Atp- Bound, Closed (Desensitized) State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na412 b:76.8 occ:1.00 O A:HOH543 2.3 85.2 1.0 O A:HOH547 2.3 76.9 1.0 OD1 A:ASP210 2.8 77.2 1.0 OD2 A:ASP210 3.3 88.9 1.0 CG A:ASP210 3.4 77.4 1.0 O A:HOH548 4.1 68.3 1.0 C A:PHE212 4.1 61.5 1.0 O A:PHE212 4.1 89.3 1.0 N A:CYS213 4.2 71.2 1.0 CB A:CYS203 4.3 73.2 1.0 CA A:CYS213 4.5 61.4 1.0 CB A:PHE212 4.5 63.4 1.0 CB A:CYS213 4.7 50.0 1.0 CA A:PHE212 4.7 63.7 1.0 SG A:CYS203 4.9 72.6 1.0 CB A:ASP210 4.9 69.3 1.0 N A:PHE212 5.0 66.2 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of the Atp-Gated Human P2X3 Ion Channel in the Atp- Bound, Closed (Desensitized) State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Atp-Gated Human P2X3 Ion Channel in the Atp- Bound, Closed (Desensitized) State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na413 b:0.9 occ:1.00 O A:HOH542 2.3 99.3 1.0 O A:HOH516 2.5 96.4 1.0 O1G A:ATP401 2.5 64.0 1.0 O A:HOH518 2.9 87.3 1.0 O2G A:ATP401 2.9 61.5 1.0 PG A:ATP401 3.2 63.4 1.0 OE2 A:GLU111 3.5 0.8 1.0 O2B A:ATP401 3.6 71.5 1.0 O3B A:ATP401 4.1 63.0 1.0 CD A:GLU111 4.3 0.8 1.0 HO2' A:ATP401 4.3 0.7 1.0 OE1 A:GLU111 4.3 0.8 1.0 PB A:ATP401 4.4 60.1 1.0 O3G A:ATP401 4.5 73.1 1.0 NH2 A:ARG281 4.6 57.4 1.0 NZ A:LYS299 4.7 68.7 1.0 OD2 A:ASP158 4.8 0.8 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the Atp-Gated Human P2X3 Ion Channel in the Atp- Bound, Closed (Desensitized) State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Atp-Gated Human P2X3 Ion Channel in the Atp- Bound, Closed (Desensitized) State within 5.0Å range: probe atom residue distance (Å) B Occ B:Na408 b:0.5 occ:1.00 O B:HOH526 2.5 86.9 1.0 OD2 B:ASP158 2.9 0.6 1.0 O1G B:ATP401 3.0 55.1 1.0 O2G B:ATP401 3.3 66.8 1.0 PG B:ATP401 3.7 66.7 1.0 CG B:ASP158 3.9 0.5 1.0 CB B:ASP158 4.1 0.9 1.0 NH2 B:ARG281 4.1 66.1 1.0 NZ B:LYS299 4.5 67.9 1.0 O3G B:ATP401 4.6 67.0 1.0 O2B B:ATP401 4.7 77.7 1.0 NH1 B:ARG281 4.7 78.6 1.0 OE2 B:GLU156 4.8 96.6 1.0 CZ B:ARG281 4.9 67.2 1.0 OD1 B:ASP158 4.9 0.6 1.0 O3B B:ATP401 4.9 57.8 1.0

S.E.Mansoor, W.Lu, W.Oosterheert, M.Shekhar, E.Tajkhorshid, E.Gouaux. X-Ray Structures Define Human P2X3 Receptor Gating Cycle and Antagonist Action. Nature V. 538 66 2016.
ISSN: ESSN 1476-4687
PubMed: 27626375
DOI: 10.1038/NATURE19367