Sodium in PDB 5svm: Crystal Structure of the Atp-Gated Human P2X3 Ion Channel Bound to Agonist 2-Methylthio-Atp in the Desensitized State

The structure of Crystal Structure of the Atp-Gated Human P2X3 Ion Channel Bound to Agonist 2-Methylthio-Atp in the Desensitized State, PDB code: 5svm 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)	47.88 / 3.09
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	172.640, 172.640, 172.640, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 22.8

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

Sodium binding site 1 out of 2 in the Crystal Structure of the Atp-Gated Human P2X3 Ion Channel Bound to Agonist 2-Methylthio-Atp in the 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 Bound to Agonist 2-Methylthio-Atp in the Desensitized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:0.3 occ:1.00 O A:HOH518 2.3 93.6 1.0 O A:HOH514 2.5 83.8 1.0 OAI A:6AT404 2.6 72.2 1.0 O A:HOH511 2.6 87.4 1.0 O A:HOH505 2.9 74.7 1.0 OAC A:6AT404 3.0 87.2 1.0 PBE A:6AT404 3.3 66.8 1.0 OAE A:6AT404 3.3 65.6 1.0 OE1 A:GLU111 3.8 0.9 1.0 OE2 A:GLU111 3.8 0.9 1.0 NZ A:LYS299 4.1 70.5 1.0 OAS A:6AT404 4.2 64.8 1.0 CD A:GLU111 4.2 0.7 1.0 PBG A:6AT404 4.3 64.1 1.0 H11 A:6AT404 4.3 89.8 1.0 OAH A:6AT404 4.6 78.5 1.0 NH2 A:ARG281 4.7 57.5 1.0 OAK A:6AT404 4.8 66.8 1.0 H22 A:TRS406 4.8 0.4 1.0 OD2 A:ASP158 4.8 0.2 1.0 H11 A:TRS406 4.9 0.7 1.0 H9 A:6AT404 4.9 88.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Atp-Gated Human P2X3 Ion Channel Bound to Agonist 2-Methylthio-Atp in the 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 Bound to Agonist 2-Methylthio-Atp in the Desensitized State within 5.0Å range: probe atom residue distance (Å) B Occ B:Na405 b:90.7 occ:1.00 OD2 B:ASP158 2.7 0.8 1.0 O B:HOH512 3.0 75.5 1.0 O B:HOH508 3.0 87.5 1.0 O1G B:ATP401 3.3 69.6 1.0 CG B:ASP158 3.4 0.2 1.0 CB B:ASP158 3.4 0.2 1.0 O2G B:ATP401 4.0 90.6 1.0 NZ B:LYS299 4.1 75.3 1.0 PG B:ATP401 4.2 80.4 1.0 NH2 B:ARG281 4.5 54.6 1.0 NH1 B:ARG281 4.5 85.7 1.0 OD1 B:ASP158 4.5 0.4 1.0 OE2 B:GLU156 4.6 96.1 1.0 CZ B:ARG281 4.9 69.1 1.0 CA B:ASP158 5.0 0.3 1.0 O2B B:ATP401 5.0 66.2 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