Sodium in PDB 7m8w: Xfel Crystal Structure of the Prostaglandin D2 Receptor CRTH2 in Complex with 15R-Methyl-PGD2

The structure of Xfel Crystal Structure of the Prostaglandin D2 Receptor CRTH2 in Complex with 15R-Methyl-PGD2, PDB code: 7m8w was solved by A.Shiriaeva, G.W.Han, V.Cherezov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.43 / 2.61
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.4, 67.8, 265.4, 90, 90, 90
R / Rfree (%)	22.9 / 26.7

The binding sites of Sodium atom in the Xfel Crystal Structure of the Prostaglandin D2 Receptor CRTH2 in Complex with 15R-Methyl-PGD2 (pdb code 7m8w). 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 Xfel Crystal Structure of the Prostaglandin D2 Receptor CRTH2 in Complex with 15R-Methyl-PGD2, PDB code: 7m8w:

Sodium binding site 1 out of 1 in the Xfel Crystal Structure of the Prostaglandin D2 Receptor CRTH2 in Complex with 15R-Methyl-PGD2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Xfel Crystal Structure of the Prostaglandin D2 Receptor CRTH2 in Complex with 15R-Methyl-PGD2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2402 b:31.3 occ:1.00 OD1 A:ASP77 2.4 31.4 1.0 OG A:SER118 2.4 35.6 1.0 CG A:ASP77 3.1 32.1 1.0 OD1 A:ASN114 3.2 30.3 1.0 OG A:SER76 3.2 37.0 1.0 OD2 A:ASP77 3.3 32.8 1.0 CB A:SER118 3.4 24.8 1.0 O A:HOH2502 3.5 37.6 1.0 O A:LEU73 3.7 37.5 1.0 ND2 A:ASN300 3.7 42.6 1.0 O A:HOH2507 4.1 22.7 1.0 CD1 A:LEU73 4.1 35.1 1.0 OD1 A:ASN296 4.2 38.9 1.0 CG A:ASN114 4.2 27.4 1.0 N A:ASP77 4.4 24.6 1.0 CA A:SER118 4.4 19.1 1.0 CG A:LEU73 4.4 27.6 1.0 CB A:ASP77 4.4 23.2 1.0 CB A:SER76 4.4 31.4 1.0 ND2 A:ASN114 4.5 34.5 1.0 CA A:ASP77 4.6 33.0 1.0 C A:LEU73 4.8 35.9 1.0 O A:ASN114 4.8 38.8 1.0 OG A:SER297 4.8 40.6 1.0 C A:SER76 5.0 35.0 1.0

H.Liu, R.N.V.K.Deepak, A.Shiriaeva, C.Gati, A.Batyuk, H.Hu, U.Weierstall, W.Liu, L.Wang, V.Cherezov, H.Fan, C.Zhang. Molecular Basis For Lipid Recognition By the Prostaglandin D 2 Receptor CRTH2. Proc.Natl.Acad.Sci.Usa V. 118 2021.
ISSN: ESSN 1091-6490
PubMed: 34341104
DOI: 10.1073/PNAS.2102813118