Sodium in PDB 5svq: Crystal Structure of the Atp-Gated Human P2X3 Ion Channel Bound to Competitive Antagonist Tnp-Atp

The structure of Crystal Structure of the Atp-Gated Human P2X3 Ion Channel Bound to Competitive Antagonist Tnp-Atp, PDB code: 5svq 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)	47.82 / 3.25
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	120.450, 120.450, 235.990, 90.00, 90.00, 120.00
R / Rfree (%)	24.9 / 28.9

The structure of Crystal Structure of the Atp-Gated Human P2X3 Ion Channel Bound to Competitive Antagonist Tnp-Atp also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Crystal Structure of the Atp-Gated Human P2X3 Ion Channel Bound to Competitive Antagonist Tnp-Atp (pdb code 5svq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of the Atp-Gated Human P2X3 Ion Channel Bound to Competitive Antagonist Tnp-Atp, PDB code: 5svq:

Sodium binding site 1 out of 1 in the Crystal Structure of the Atp-Gated Human P2X3 Ion Channel Bound to Competitive Antagonist Tnp-Atp


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 Bound to Competitive Antagonist Tnp-Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:0.9 occ:0.33 CG2 A:ILE323 3.7 0.4 1.0 O A:ILE323 3.9 0.3 1.0 CG1 A:VAL326 4.6 96.8 1.0 C A:ILE323 4.7 0.3 1.0 CB A:ALA327 4.7 0.7 1.0 CA A:ILE323 4.7 0.2 1.0 N A:ALA327 4.8 0.7 1.0 CB A:ILE323 4.8 0.8 1.0 CB A:VAL326 4.9 95.8 1.0 CA A:ALA327 5.0 0.6 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