Sodium in PDB 8t1v: Crystal Structure of Orphan G Protein-Coupled Receptor 6 with Bound Inverse Agonist 3H

The structure of Crystal Structure of Orphan G Protein-Coupled Receptor 6 with Bound Inverse Agonist 3H, PDB code: 8t1v was solved by M.Barekatain, L.Johansson, J.H.Lam, A.V.Sadybekov, G.W.Han, P.Popov, J.Russo, J.Bliesath, N.Brice, M.Beresford, L.Carlson, K.S.Saikatendu, H.Sun, S.Murphy, H.Monenschein, H.H.Schiffer, C.Lutomski, C.V.Robinson, Z.Liu, T.Hua, V.Katritch, V.Cherezov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.13 / 2.60
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	63.136, 63.136, 249.67, 90, 90, 120
R / Rfree (%)	23 / 25.8

The structure of Crystal Structure of Orphan G Protein-Coupled Receptor 6 with Bound Inverse Agonist 3H also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Orphan G Protein-Coupled Receptor 6 with Bound Inverse Agonist 3H (pdb code 8t1v). 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 Orphan G Protein-Coupled Receptor 6 with Bound Inverse Agonist 3H, PDB code: 8t1v:

Sodium binding site 1 out of 1 in the Crystal Structure of Orphan G Protein-Coupled Receptor 6 with Bound Inverse Agonist 3H


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 Orphan G Protein-Coupled Receptor 6 with Bound Inverse Agonist 3H within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1202 b:55.5 occ:1.00 OD1 A:ASN321 2.4 31.8 1.0 OD1 A:ASP118 2.9 44.9 1.0 CE1 A:PHE288 3.1 40.0 1.0 CD1 A:PHE288 3.4 48.3 1.0 ND2 A:ASN325 3.4 46.8 1.0 CG A:ASN321 3.6 42.5 1.0 CG A:ASP118 3.6 52.0 1.0 OD2 A:ASP118 3.7 43.7 1.0 CB A:SER155 3.8 39.6 1.0 OG A:SER322 4.0 53.7 1.0 NE1 A:TRP292 4.1 39.3 1.0 OG A:SER155 4.1 42.6 1.0 CD1 A:LEU114 4.2 32.7 1.0 CG A:ASN325 4.3 45.6 1.0 CZ A:PHE288 4.4 32.8 1.0 ND2 A:ASN321 4.4 47.8 1.0 N A:SER322 4.6 45.5 1.0 OD1 A:ASN325 4.6 41.2 1.0 CD1 A:TRP292 4.7 37.4 1.0 CB A:ASN321 4.7 50.7 1.0 CA A:SER322 4.7 51.1 1.0 C A:ASN321 4.8 50.8 1.0 CG A:PHE288 4.8 27.5 1.0 O A:ASN321 4.9 53.5 1.0 CB A:SER322 5.0 58.4 1.0

M.Barekatain, L.Johansson, J.H.Lam, A.V.Sadybekov, G.W.Han, P.Popov, J.Russo, J.Bliesath, N.Brice, M.Beresford, L.Carlson, K.S.Saikatendu, H.Sun, S.Murphy, H.Monenschein, H.H.Schiffer, C.Lutomski, C.V.Robinson, Z.Liu, T.Hua, V.Katritch, V.Cherezov. Structural Insights Into the High Basal Activity and Inverse Agonism of the Orphan Receptor GPR6 Implicated in Parkinson'S Disease Sci.Signal. 2024.
ISSN: ESSN 1937-9145
DOI: 10.1126/SCISIGNAL.ADO8741