Sodium in PDB 6lpk: A2AR Crystallized in EROCOC17+4, Lcp-Sfx at 293 K

The structure of A2AR Crystallized in EROCOC17+4, Lcp-Sfx at 293 K, PDB code: 6lpk was solved by K.Ihara, M.Hato, T.Nakane, K.Yamashita, T.Kimura-Someya, T.Hosaka, Y.Ishizuka-Katsura, R.Tanaka, T.Tanaka, M.Sugahara, K.Hirata, M.Yamamoto, O.Nureki, K.Tono, E.Nango, S.Iwata, M.Shirouzu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.40 / 1.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	40.500, 179.200, 142.900, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 20.9

The binding sites of Sodium atom in the A2AR Crystallized in EROCOC17+4, Lcp-Sfx at 293 K (pdb code 6lpk). 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 A2AR Crystallized in EROCOC17+4, Lcp-Sfx at 293 K, PDB code: 6lpk:

Sodium binding site 1 out of 1 in the A2AR Crystallized in EROCOC17+4, Lcp-Sfx at 293 K


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of A2AR Crystallized in EROCOC17+4, Lcp-Sfx at 293 K within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2402 b:31.5 occ:1.00 O A:HOH2522 2.4 31.2 1.0 OD1 A:ASP52 2.4 28.4 1.0 O A:HOH2579 2.5 33.0 1.0 OG A:SER91 2.5 27.1 1.0 O A:HOH2546 2.5 34.4 1.0 CG A:ASP52 3.3 26.4 1.0 CB A:SER91 3.5 27.2 1.0 OD2 A:ASP52 3.6 28.4 1.0 OD1 A:ASN280 4.0 31.2 1.0 O A:HOH2563 4.1 37.4 1.0 CD1 A:LEU48 4.1 33.7 1.0 OG A:SER281 4.2 27.6 1.0 O A:HOH2519 4.4 29.9 1.0 CB A:ASP52 4.6 27.1 1.0 N A:ASP52 4.7 27.5 1.0 CB A:ALA51 4.7 28.4 1.0 CA A:ASP52 4.7 26.7 1.0 CA A:SER91 4.7 28.0 1.0 O A:LEU87 4.7 28.4 1.0 CE2 A:PHE242 4.7 32.0 1.0 O A:HOH2572 4.8 44.7 1.0 O A:LEU48 4.8 29.2 1.0 C A:ALA51 4.9 28.2 1.0 CD2 A:PHE242 5.0 31.6 1.0

K.Ihara, M.Hato, T.Nakane, K.Yamashita, T.Kimura-Someya, T.Hosaka, Y.Ishizuka-Katsura, R.Tanaka, T.Tanaka, M.Sugahara, K.Hirata, M.Yamamoto, O.Nureki, K.Tono, E.Nango, S.Iwata, M.Shirouzu. Isoprenoid-Chained Lipid Erococ 17+4 : A New Matrix For Membrane Protein Crystallization and A Crystal Delivery Medium in Serial Femtosecond Crystallography. Sci Rep V. 10 19305 2020.
ISSN: ESSN 2045-2322
PubMed: 33168855
DOI: 10.1038/S41598-020-76277-X