Sodium in PDB 5svp: Anomalous Sulfur Signal Reveals the Position of Agonist 2-Methylthio- Atp Bound to the Atp-Gated Human P2X3 Ion Channel in the Desensitized State

The structure of Anomalous Sulfur Signal Reveals the Position of Agonist 2-Methylthio- Atp Bound to the Atp-Gated Human P2X3 Ion Channel in the Desensitized State, PDB code: 5svp 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)	47.96 / 3.30
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	172.930, 172.930, 172.930, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 22.7

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

Sodium binding site 1 out of 2 in the Anomalous Sulfur Signal Reveals the Position of Agonist 2-Methylthio- Atp Bound to the Atp-Gated Human P2X3 Ion Channel 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 Anomalous Sulfur Signal Reveals the Position of Agonist 2-Methylthio- Atp Bound to the Atp-Gated Human P2X3 Ion Channel in the Desensitized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:0.8 occ:1.00 OAI A:6AT404 2.8 95.1 1.0 OE1 A:GLU111 3.4 0.9 1.0 OE2 A:GLU111 3.4 1.0 1.0 OAC A:6AT404 3.5 84.1 1.0 OAE A:6AT404 3.6 84.6 1.0 PBE A:6AT404 3.7 96.4 1.0 CD A:GLU111 3.8 0.8 1.0 NZ A:LYS299 4.0 81.9 1.0 OD2 A:ASP158 4.1 0.6 1.0 OAS A:6AT404 4.7 57.4 1.0 PBG A:6AT404 4.7 63.5 1.0 H11 A:6AT404 4.8 0.5 1.0 CG A:ASP158 4.8 0.6 1.0 CB A:ASP158 4.8 0.1 1.0 OAH A:6AT404 4.9 72.1 1.0

Sodium binding site 2 out of 2 in the Anomalous Sulfur Signal Reveals the Position of Agonist 2-Methylthio- Atp Bound to the Atp-Gated Human P2X3 Ion Channel 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 Anomalous Sulfur Signal Reveals the Position of Agonist 2-Methylthio- Atp Bound to the Atp-Gated Human P2X3 Ion Channel in the Desensitized State within 5.0Å range: probe atom residue distance (Å) B Occ B:Na405 b:97.4 occ:1.00 O1G B:ATP401 3.4 90.1 1.0 OD2 B:ASP158 3.6 0.9 1.0 O2G B:ATP401 3.6 0.5 1.0 O2B B:ATP401 4.0 75.9 1.0 PG B:ATP401 4.1 81.8 1.0 CG B:ASP158 4.2 0.4 1.0 CB B:ASP158 4.5 0.9 1.0 NZ B:LYS299 4.7 83.8 1.0 O3B B:ATP401 4.8 62.8 1.0 HO2' B:ATP401 4.9 99.6 1.0 PB B:ATP401 5.0 62.5 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