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Sodium in PDB 6lpl: A2AR Crystallized in EROCOC17+4, Ss-Rox at 100 K

Protein crystallography data

The structure of A2AR Crystallized in EROCOC17+4, Ss-Rox at 100 K, PDB code: 6lpl 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) 42.75 / 2.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 39.890, 179.276, 140.956, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 20.8

Sodium Binding Sites:

The binding sites of Sodium atom in the A2AR Crystallized in EROCOC17+4, Ss-Rox at 100 K (pdb code 6lpl). 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, Ss-Rox at 100 K, PDB code: 6lpl:

Sodium binding site 1 out of 1 in 6lpl

Go back to Sodium Binding Sites List in 6lpl
Sodium binding site 1 out of 1 in the A2AR Crystallized in EROCOC17+4, Ss-Rox 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 A2AR Crystallized in EROCOC17+4, Ss-Rox at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2402

b:35.1
occ:1.00
OD1 A:ASP52 2.4 30.0 1.0
O A:HOH2524 2.4 38.9 1.0
OG A:SER91 2.5 24.6 1.0
O A:HOH2546 2.5 28.7 1.0
O A:HOH2589 2.5 34.5 1.0
CG A:ASP52 3.3 28.0 1.0
CB A:SER91 3.4 22.8 1.0
OD2 A:ASP52 3.6 30.6 1.0
O A:HOH2540 4.0 39.0 1.0
OD1 A:ASN280 4.0 32.5 1.0
OG A:SER281 4.1 25.4 1.0
CD1 A:LEU48 4.4 27.8 1.0
O A:HOH2530 4.4 30.0 1.0
CE2 A:PHE242 4.6 30.2 1.0
CB A:ASP52 4.7 27.8 1.0
O A:LEU87 4.7 26.7 1.0
CA A:SER91 4.7 23.7 1.0
N A:ASP52 4.7 26.6 1.0
O A:HOH2577 4.7 36.3 1.0
CB A:ALA51 4.8 24.7 1.0
CA A:ASP52 4.8 27.8 1.0
CD2 A:PHE242 4.9 28.5 1.0
O A:LEU48 4.9 25.8 1.0
C A:ALA51 5.0 26.4 1.0

Reference:

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
Page generated: Tue Dec 15 12:34:10 2020

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