Sodium in PDB 5nva: Substrate-Bound Outward-Open State of A Na+-Coupled Sialic Acid Symporter Reveals A Novel Na+-Site

The structure of Substrate-Bound Outward-Open State of A Na+-Coupled Sialic Acid Symporter Reveals A Novel Na+-Site, PDB code: 5nva was solved by W.Y.Wahlgren, R.A.North, E.Dunevall, P.Goyal, M.Grabe, R.Dobson, J.Abramson, S.Ramaswamy, R.Friemann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	82.18 / 2.26
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.788, 97.764, 151.690, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 26.1

The binding sites of Sodium atom in the Substrate-Bound Outward-Open State of A Na+-Coupled Sialic Acid Symporter Reveals A Novel Na+-Site (pdb code 5nva). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Substrate-Bound Outward-Open State of A Na+-Coupled Sialic Acid Symporter Reveals A Novel Na+-Site, PDB code: 5nva:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Substrate-Bound Outward-Open State of A Na+-Coupled Sialic Acid Symporter Reveals A Novel Na+-Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Substrate-Bound Outward-Open State of A Na+-Coupled Sialic Acid Symporter Reveals A Novel Na+-Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:22.0 occ:1.00 O A:ALA56 2.3 24.8 1.0 O A:ALA339 2.3 22.7 1.0 O A:LEU59 2.3 25.6 1.0 OG A:SER342 2.4 25.8 1.0 OG A:SER343 2.4 18.9 1.0 N A:SER343 3.0 20.8 1.0 C A:ALA339 3.3 21.2 1.0 C A:LEU59 3.3 25.9 1.0 CB A:SER343 3.4 19.5 1.0 CB A:SER342 3.5 19.7 1.0 C A:ALA56 3.5 22.3 1.0 C A:SER342 3.6 23.4 1.0 CA A:SER343 3.7 20.0 1.0 CA A:SER60 3.7 20.2 1.0 CA A:ALA339 3.8 25.8 1.0 N A:SER60 3.9 23.4 1.0 CA A:SER342 3.9 25.0 1.0 O A:ALA338 4.1 23.1 1.0 N A:SER342 4.2 22.5 1.0 O A:THR57 4.2 19.7 1.0 CA A:ALA56 4.3 17.1 1.0 CB A:SER60 4.3 25.4 1.0 O A:SER342 4.4 23.2 1.0 N A:ALA340 4.4 20.5 1.0 C A:THR57 4.5 25.5 1.0 N A:THR57 4.5 21.4 1.0 CA A:LEU59 4.5 25.7 1.0 N A:LEU59 4.6 20.5 1.0 CA A:THR57 4.6 24.4 1.0 O A:ALA340 4.6 20.6 1.0 CB A:ALA339 4.7 19.5 1.0 C A:ALA340 4.7 22.4 1.0 CB A:ALA56 4.7 19.8 1.0 C A:SER60 4.8 30.2 1.0 CA A:ALA340 4.8 23.9 1.0 CD2 A:LEU189 4.9 24.2 1.0 N A:ALA339 4.9 23.4 1.0 C A:ALA338 4.9 23.2 1.0

Sodium binding site 2 out of 2 in the Substrate-Bound Outward-Open State of A Na+-Coupled Sialic Acid Symporter Reveals A Novel Na+-Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Substrate-Bound Outward-Open State of A Na+-Coupled Sialic Acid Symporter Reveals A Novel Na+-Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:42.1 occ:1.00 O A:SER342 2.4 23.2 1.0 OG A:SER346 2.4 23.1 1.0 OG A:SER345 2.4 25.6 1.0 OD1 A:ASP182 2.4 26.1 1.0 OD2 A:ASP182 2.4 26.6 1.0 CG A:ASP182 2.7 23.5 1.0 N A:SER346 3.1 20.1 1.0 CG1 A:VAL178 3.1 20.6 1.0 CB A:SER346 3.3 19.8 1.0 C A:SER342 3.4 23.4 1.0 CA A:SER346 3.5 20.4 1.0 O A:HOH631 3.7 23.9 1.0 CB A:SER345 3.7 20.6 1.0 CA A:SER342 3.8 25.0 1.0 NH2 A:ARG260 3.8 28.0 1.0 C A:SER345 3.8 21.4 1.0 O A:VAL178 3.9 23.1 1.0 OG1 A:THR57 4.1 20.5 1.0 CA A:SER345 4.2 22.5 1.0 CB A:ASP182 4.2 25.2 1.0 CB A:VAL178 4.4 23.2 1.0 N A:SER345 4.5 21.8 1.0 CB A:SER342 4.5 19.7 1.0 O A:GLN341 4.5 22.9 1.0 C A:VAL178 4.5 25.1 1.0 N A:SER343 4.5 20.8 1.0 O A:SER345 4.7 20.2 1.0 CA A:VAL178 4.8 23.2 1.0 CA A:SER343 4.9 20.0 1.0 CZ A:ARG260 4.9 27.0 1.0

W.Y.Wahlgren, E.Dunevall, R.A.North, A.Paz, M.Scalise, P.Bisignano, J.Bengtsson-Palme, P.Goyal, E.Claesson, R.Caing-Carlsson, R.Andersson, K.Beis, U.J.Nilsson, A.Farewell, L.Pochini, C.Indiveri, M.Grabe, R.C.J.Dobson, J.Abramson, S.Ramaswamy, R.Friemann. Substrate-Bound Outward-Open Structure of A Na+-Coupled Sialic Acid Symporter Reveals A New Na+Site. Nat Commun V. 9 1753 2018.
ISSN: ESSN 2041-1723
PubMed: 29717135
DOI: 10.1038/S41467-018-04045-7