Sodium in PDB 5k2d: 1.9A Angstrom A2A Adenosine Receptor Structure with Mr Phasing Using Xfel Data

The structure of 1.9A Angstrom A2A Adenosine Receptor Structure with Mr Phasing Using Xfel Data, PDB code: 5k2d was solved by A.Batyuk, L.Galli, A.Ishchenko, G.W.Han, C.Gati, P.Popov, M.-Y.Lee, B.Stauch, T.A.White, A.Barty, A.Aquila, M.S.Hunter, M.Liang, S.Boutet, M.Pu, Z.-J.Liu, G.Nelson, D.James, C.Li, Y.Zhao, J.C.H.Spence, W.Liu, P.Fromme, V.Katritch, U.Weierstall, R.C.Stevens, V.Cherezov, Gpcr Network(Gpcr), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.44 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	40.360, 180.740, 142.800, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 20.7

The binding sites of Sodium atom in the 1.9A Angstrom A2A Adenosine Receptor Structure with Mr Phasing Using Xfel Data (pdb code 5k2d). 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 1.9A Angstrom A2A Adenosine Receptor Structure with Mr Phasing Using Xfel Data, PDB code: 5k2d:

Sodium binding site 1 out of 1 in the 1.9A Angstrom A2A Adenosine Receptor Structure with Mr Phasing Using Xfel Data


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1.9A Angstrom A2A Adenosine Receptor Structure with Mr Phasing Using Xfel Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1202 b:35.5 occ:1.00 O A:HOH1375 2.4 36.6 1.0 OD1 A:ASP52 2.4 30.1 1.0 O A:HOH1339 2.4 33.8 1.0 OG A:SER91 2.5 30.0 1.0 O A:HOH1315 2.5 35.8 1.0 CG A:ASP52 3.3 29.8 1.0 CB A:SER91 3.4 29.5 1.0 OD2 A:ASP52 3.6 30.8 1.0 ND2 A:ASN280 4.0 28.5 1.0 CD1 A:LEU48 4.2 39.5 1.0 O A:HOH1355 4.2 39.6 1.0 OG A:SER281 4.3 32.6 1.0 O A:HOH1323 4.5 32.6 1.0 O A:HOH1360 4.6 50.5 1.0 CB A:ASP52 4.6 26.5 1.0 CE2 A:PHE242 4.7 30.6 1.0 N A:ASP52 4.7 29.6 1.0 CB A:ALA51 4.7 30.0 1.0 CA A:SER91 4.8 26.8 1.0 O A:LEU87 4.8 32.8 1.0 CA A:ASP52 4.8 29.3 1.0 O A:LEU48 4.8 32.8 1.0 CD2 A:PHE242 4.9 30.2 1.0 C A:ALA51 5.0 32.5 1.0

A.Batyuk, L.Galli, A.Ishchenko, G.W.Han, C.Gati, P.A.Popov, M.Y.Lee, B.Stauch, T.A.White, A.Barty, A.Aquila, M.S.Hunter, M.Liang, S.Boutet, M.Pu, Z.J.Liu, G.Nelson, D.James, C.Li, Y.Zhao, J.C.Spence, W.Liu, P.Fromme, V.Katritch, U.Weierstall, R.C.Stevens, V.Cherezov. Native Phasing of X-Ray Free-Electron Laser Data For A G Protein-Coupled Receptor. Sci Adv V. 2 00292 2016.
ISSN: ESSN 2375-2548
PubMed: 27679816
DOI: 10.1126/SCIADV.1600292