Sodium in PDB 6zdv: Crystal Structure of Stabilized A2A Adenosine Receptor A2AR-STAR2-Bril in Complex with Chromone 5D

The structure of Crystal Structure of Stabilized A2A Adenosine Receptor A2AR-STAR2-Bril in Complex with Chromone 5D, PDB code: 6zdv was solved by G.Verdon, W.Jespers, J.Azuaje, M.Majellaro, H.Keranen, X.Garcia-Mera, M.Congreve, F.Deflorian, C.De Graaf, A.Zhukov, A.Dore, J.Mason, J.Aqvist, R.Cooke, E.Sotelo, H.Gutierrez-De-Teran, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.80 / 2.13
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	39.414, 179.833, 140.085, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 22.4

The binding sites of Sodium atom in the Crystal Structure of Stabilized A2A Adenosine Receptor A2AR-STAR2-Bril in Complex with Chromone 5D (pdb code 6zdv). 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 Crystal Structure of Stabilized A2A Adenosine Receptor A2AR-STAR2-Bril in Complex with Chromone 5D, PDB code: 6zdv:

Sodium binding site 1 out of 1 in the Crystal Structure of Stabilized A2A Adenosine Receptor A2AR-STAR2-Bril in Complex with Chromone 5D


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 Stabilized A2A Adenosine Receptor A2AR-STAR2-Bril in Complex with Chromone 5D within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1202 b:47.0 occ:1.00 OD1 A:ASP52 2.4 31.5 1.0 O A:HOH1338 2.7 35.1 1.0 OG A:SER91 2.7 25.0 1.0 O A:HOH1354 2.8 54.5 1.0 CG A:ASP52 3.3 30.9 1.0 OD2 A:ASP52 3.5 32.6 1.0 CB A:SER91 3.5 22.9 1.0 ND2 A:ASN280 3.6 27.5 1.0 O A:HOH1331 3.7 46.2 1.0 CD1 A:LEU48 3.9 29.1 1.0 CE2 A:PHE242 4.4 24.9 1.0 CD2 A:PHE242 4.4 24.2 1.0 OG A:SER281 4.5 28.2 1.0 O A:HOH1313 4.6 27.0 1.0 CB A:ASP52 4.7 26.0 1.0 O A:LEU48 4.7 28.0 1.0 CA A:SER91 4.8 23.0 1.0 CG A:ASN280 4.8 30.0 1.0 CG A:LEU48 5.0 29.3 1.0 N A:ASP52 5.0 25.9 1.0 CB A:ALA51 5.0 24.1 1.0

W.Jespers, G.Verdon, J.Azuaje, M.Majellaro, H.Keranen, X.Garcia-Mera, M.Congreve, F.Deflorian, C.De Graaf, A.Zhukov, A.S.Dore, J.S.Mason, J.Aqvist, R.M.Cooke, E.Sotelo, H.Gutierrez-De-Teran. X-Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A2AADENOSINE Receptor Antagonists. Angew.Chem.Int.Ed.Engl. 2020.
ISSN: ESSN 1521-3773
PubMed: 32542862
DOI: 10.1002/ANIE.202003788