Sodium in PDB 5nv9: 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: 5nv9 was solved by W.Y.Wahlgren, R.A.North, E.Dunevall, A.Paz, P.Goyal, P.Bisignano, 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)	78.40 / 1.95
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	130.590, 98.070, 54.780, 90.00, 92.15, 90.00
R / Rfree (%)	19.9 / 24.3

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 5nv9). 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: 5nv9:
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:19.2 occ:1.00 O A:ALA56 2.1 22.6 1.0 O A:ALA339 2.3 20.9 1.0 O A:LEU59 2.3 19.1 1.0 OG A:SER343 2.4 18.7 1.0 OG A:SER342 2.4 22.4 1.0 N A:SER343 3.2 17.8 1.0 C A:LEU59 3.3 21.8 1.0 C A:ALA339 3.3 21.1 1.0 C A:ALA56 3.3 20.8 1.0 CB A:SER343 3.4 18.6 1.0 CB A:SER342 3.5 18.9 1.0 CA A:SER60 3.7 20.7 1.0 C A:SER342 3.7 18.4 1.0 CA A:SER343 3.7 19.4 1.0 CA A:ALA339 3.8 20.4 1.0 N A:SER60 3.9 20.4 1.0 CA A:SER342 4.1 17.2 1.0 CA A:ALA56 4.2 21.4 1.0 O A:THR57 4.2 21.3 1.0 O A:ALA338 4.2 22.0 1.0 N A:SER342 4.3 16.4 1.0 CB A:SER60 4.3 20.0 1.0 N A:THR57 4.3 23.4 1.0 CA A:LEU59 4.4 21.9 1.0 N A:LEU59 4.4 18.8 1.0 C A:THR57 4.5 21.2 1.0 O A:SER342 4.5 18.5 1.0 N A:ALA340 4.5 19.6 1.0 CA A:THR57 4.6 22.1 1.0 CB A:ALA56 4.6 21.5 1.0 CB A:ALA339 4.6 20.4 1.0 O A:ALA340 4.6 18.7 1.0 C A:ALA340 4.8 19.3 1.0 CD2 A:LEU189 4.8 20.7 1.0 C A:SER60 4.9 21.9 1.0 N A:ALA339 4.9 20.4 1.0 CA A:ALA340 4.9 18.5 1.0 CB A:LEU59 5.0 24.6 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:39.0 occ:1.00 OD1 A:ASP182 2.1 19.5 1.0 OG A:SER346 2.2 17.1 1.0 OD2 A:ASP182 2.3 21.1 1.0 O A:SER342 2.4 18.5 1.0 OG A:SER345 2.5 22.3 1.0 CG A:ASP182 2.6 23.0 1.0 N A:SER346 3.2 19.0 1.0 CG1 A:VAL178 3.2 16.2 1.0 CB A:SER346 3.3 19.3 1.0 C A:SER342 3.3 18.4 1.0 CA A:SER346 3.6 18.1 1.0 CA A:SER342 3.7 17.2 1.0 O A:VAL178 3.8 18.6 1.0 OG1 A:THR57 3.9 19.1 1.0 NH2 A:ARG260 3.9 27.0 1.0 CB A:SER345 3.9 21.8 1.0 O A:HOH609 4.0 23.6 1.0 CB A:ASP182 4.1 20.8 1.0 C A:SER345 4.1 20.2 1.0 CB A:SER342 4.3 18.9 1.0 CA A:SER345 4.4 21.0 1.0 N A:SER343 4.5 17.8 1.0 C A:VAL178 4.5 19.5 1.0 CB A:VAL178 4.6 16.2 1.0 O A:GLN341 4.6 16.5 1.0 N A:SER345 4.6 21.7 1.0 CA A:ASP182 4.9 22.2 1.0 OG A:SER53 4.9 30.8 1.0 CA A:THR57 4.9 22.1 1.0 CA A:VAL178 4.9 17.2 1.0 CB A:THR57 4.9 20.1 1.0 N A:SER342 5.0 16.4 1.0 CA A:SER343 5.0 19.4 1.0 CZ A:ARG260 5.0 29.5 1.0 O A:SER345 5.0 18.9 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