Sodium in PDB 5vra: 2.35-Angstrom in Situ Mylar Structure of Human A2A Adenosine Receptor at 100 K

The structure of 2.35-Angstrom in Situ Mylar Structure of Human A2A Adenosine Receptor at 100 K, PDB code: 5vra was solved by J.Broecker, T.Morizumi, W.-L.Ou, V.Klingel, A.Kuo, D.J.Kissick, A.Ishchenko, M.-Y.Lee, S.Xu, O.Makarov, V.Cherezov, C.M.Ogata, O.P.Ernst, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.42 / 2.35
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	39.820, 178.900, 140.190, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 22.3

The binding sites of Sodium atom in the 2.35-Angstrom in Situ Mylar Structure of Human A2A Adenosine Receptor at 100 K (pdb code 5vra). 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 2.35-Angstrom in Situ Mylar Structure of Human A2A Adenosine Receptor at 100 K, PDB code: 5vra:

Sodium binding site 1 out of 1 in the 2.35-Angstrom in Situ Mylar Structure of Human A2A Adenosine Receptor at 100 K


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 2.35-Angstrom in Situ Mylar Structure of Human A2A Adenosine Receptor at 100 K within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2402 b:35.5 occ:1.00 OD1 A:ASP52 2.4 25.9 1.0 O A:HOH2561 2.4 25.1 1.0 O A:HOH2530 2.4 17.8 1.0 O A:HOH2576 2.6 44.2 1.0 OG A:SER91 2.7 16.8 1.0 HG A:SER91 3.2 20.2 1.0 HG A:SER281 3.4 30.8 1.0 HB3 A:SER91 3.4 21.4 1.0 CG A:ASP52 3.5 25.1 1.0 CB A:SER91 3.6 17.8 1.0 HE2 A:PHE242 3.7 22.1 1.0 HB2 A:SER91 3.8 21.4 1.0 OD2 A:ASP52 3.8 26.3 1.0 HD11 A:LEU48 3.9 25.7 1.0 HD12 A:LEU48 4.0 25.7 1.0 OD1 A:ASN280 4.1 22.3 1.0 OG A:SER281 4.1 25.6 1.0 O A:HOH2539 4.2 12.7 1.0 HA A:THR88 4.3 25.3 0.5 HA A:THR88 4.3 25.3 0.5 HG21 A:VAL55 4.3 17.5 1.0 HA A:ASP52 4.3 23.9 1.0 HD2 A:PHE242 4.3 22.7 1.0 HB3 A:ALA51 4.4 30.4 1.0 CD1 A:LEU48 4.4 21.4 1.0 HE1 A:TRP246 4.5 19.4 1.0 HB1 A:ALA51 4.5 30.4 1.0 CE2 A:PHE242 4.5 18.4 1.0 HA A:SER281 4.5 27.0 1.0 O A:HOH2554 4.6 26.6 1.0 O A:LEU87 4.7 20.1 1.0 CB A:ASP52 4.7 22.0 1.0 HG22 A:THR88 4.8 25.2 0.5 HG23 A:VAL55 4.8 17.5 1.0 CD2 A:PHE242 4.9 18.9 1.0 CA A:ASP52 4.9 19.8 1.0 N A:ASP52 4.9 20.4 1.0 CB A:ALA51 4.9 25.3 1.0 HD13 A:LEU48 4.9 25.7 1.0 CA A:SER91 4.9 18.4 1.0 HB3 A:ASN280 4.9 26.5 1.0 CG2 A:VAL55 5.0 14.7 1.0

J.Broecker, T.Morizumi, W.L.Ou, V.Klingel, A.Kuo, D.J.Kissick, A.Ishchenko, M.Y.Lee, S.Xu, O.Makarov, V.Cherezov, C.M.Ogata, O.P.Ernst. High-Throughput in Situ X-Ray Screening of and Data Collection From Protein Crystals at Room Temperature and Under Cryogenic Conditions. Nat Protoc V. 13 260 2018.
ISSN: ESSN 1750-2799
PubMed: 29300389
DOI: 10.1038/NPROT.2017.135