Sodium in PDB 4rwd: Xfel Structure of the Human Delta Opioid Receptor in Complex with A Bifunctional Peptide

The structure of Xfel Structure of the Human Delta Opioid Receptor in Complex with A Bifunctional Peptide, PDB code: 4rwd was solved by G.Fenalti, N.A.Zatsepin, C.Betti, P.Giguere, G.W.Han, A.Ishchenko, W.Liu, K.Guillemyn, H.Zhang, D.James, D.Wang, U.Weierstall, J.C.H.Spence, S.Boutet, M.Messerschmidt, G.J.Williams, C.Gati, O.M.Yefanov, T.A.White, D.Oberthuer, M.Metz, C.H.Yoon, A.Barty, H.N.Chapman, S.Basu, J.Coe, C.E.Conrad, R.Fromme, P.Fromme, D.Tourwe, P.W.Schiller, B.L.Roth, S.Ballet, V.Katritch, R.C.Stevens, V.Cherezov, Gpcr Network (Gpcr), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.45 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	156.230, 89.290, 96.420, 90.00, 92.30, 90.00
R / Rfree (%)	20.8 / 23.8

The binding sites of Sodium atom in the Xfel Structure of the Human Delta Opioid Receptor in Complex with A Bifunctional Peptide (pdb code 4rwd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Xfel Structure of the Human Delta Opioid Receptor in Complex with A Bifunctional Peptide, PDB code: 4rwd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Xfel Structure of the Human Delta Opioid Receptor in Complex with A Bifunctional Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Xfel Structure of the Human Delta Opioid Receptor in Complex with A Bifunctional Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1202 b:66.2 occ:1.00 O A:HOH1309 2.4 54.5 1.0 OD1 A:ASP95 2.4 53.6 1.0 OG A:SER135 2.5 45.5 1.0 OD1 A:ASN131 2.6 52.4 1.0 CG A:ASP95 3.3 51.6 1.0 CB A:SER135 3.5 46.6 1.0 CG A:ASN131 3.7 50.0 1.0 OD2 A:ASP95 3.7 53.4 1.0 ND2 A:ASN131 4.0 48.9 1.0 OD1 A:ASN310 4.1 51.5 1.0 OG A:SER311 4.2 48.5 1.0 O A:ASN131 4.3 53.4 1.0 O A:HOH1310 4.3 49.7 1.0 CE2 A:PHE270 4.3 57.5 1.0 CB A:ASP95 4.6 50.2 1.0 N A:ASP95 4.7 49.4 1.0 ND2 A:ASN314 4.7 56.9 1.0 CB A:ALA94 4.7 47.9 1.0 CA A:ASP95 4.7 50.4 1.0 CA A:SER135 4.8 46.3 1.0 O A:LEU91 4.8 48.8 1.0 CD2 A:PHE270 4.8 57.3 1.0 C A:ASN131 4.9 52.6 1.0 CB A:ASN131 5.0 51.4 1.0

Sodium binding site 2 out of 2 in the Xfel Structure of the Human Delta Opioid Receptor in Complex with A Bifunctional Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Xfel Structure of the Human Delta Opioid Receptor in Complex with A Bifunctional Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1202 b:62.1 occ:1.00 OD1 B:ASP95 2.3 51.7 1.0 O B:HOH1313 2.3 46.4 1.0 OD1 B:ASN131 2.4 50.8 1.0 OG B:SER135 2.4 48.1 1.0 CG B:ASP95 3.3 52.0 1.0 CG B:ASN131 3.5 50.4 1.0 CB B:SER135 3.5 49.4 1.0 OD2 B:ASP95 3.7 53.3 1.0 ND2 B:ASN131 3.9 51.6 1.0 O B:ASN131 4.1 54.6 1.0 OG B:SER311 4.2 51.2 1.0 O B:HOH1304 4.2 50.5 1.0 ND2 B:ASN310 4.2 48.0 1.0 N B:ASP95 4.5 51.1 1.0 CB B:ALA94 4.5 48.0 1.0 CB B:ASP95 4.5 52.2 1.0 CE2 B:PHE270 4.5 55.8 1.0 CA B:ASP95 4.6 51.0 1.0 O B:LEU91 4.7 46.5 1.0 C B:ASN131 4.8 51.6 1.0 CB B:ASN131 4.8 50.5 1.0 CA B:SER135 4.8 49.5 1.0 C B:ALA94 4.8 48.1 1.0 ND2 B:ASN314 4.9 63.3 1.0 CA B:ASN131 5.0 49.9 1.0

G.Fenalti, N.A.Zatsepin, C.Betti, P.Giguere, G.W.Han, A.Ishchenko, W.Liu, K.Guillemyn, H.Zhang, D.James, D.Wang, U.Weierstall, J.C.H Spence, S.Boutet, M.Messerschmidt, G.J.Williams, C.Gati, O.M.Yefanov, T.A.White, D.Oberthuer, M.Metz, C.H.Yoon, A.Barty, H.N.Chapman, S.Basu, J.Coe, C.E.Conrad, R.Fromme, P.Fromme, D.Tourwe, P.W.Schiller, B.L.Roth, S.Ballet, V.Katritch, R.C.Stevens, V.Cherezov. Structural Basis For the Bi-Functional Recognition at Human Delta-Opioid Receptor To Be Published.