Sodium in PDB 6to7: Crystal Structure of the Orexin-1 Receptor in Complex with Suvorexant at 2.29 A Resolution

The structure of Crystal Structure of the Orexin-1 Receptor in Complex with Suvorexant at 2.29 A Resolution, PDB code: 6to7 was solved by M.Rappas, A.Ali, K.A.Bennett, J.D.Brown, S.J.Bucknell, M.Congreve, R.M.Cooke, G.Cseke, C.De Graaf, A.S.Dore, J.C.Errey, A.Jazayeri, F.H.Marshall, J.S.Mason, R.Mould, J.C.Patel, B.G.Tehan, M.Weir, J.A.Christopher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.38 / 2.26
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	57.900, 158.470, 183.620, 90.00, 95.31, 90.00
R / Rfree (%)	18.6 / 21.1

The structure of Crystal Structure of the Orexin-1 Receptor in Complex with Suvorexant at 2.29 A Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of the Orexin-1 Receptor in Complex with Suvorexant at 2.29 A Resolution (pdb code 6to7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Orexin-1 Receptor in Complex with Suvorexant at 2.29 A Resolution, PDB code: 6to7:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Orexin-1 Receptor in Complex with Suvorexant at 2.29 A Resolution


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 the Orexin-1 Receptor in Complex with Suvorexant at 2.29 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na427 b:50.7 occ:1.00 OH A:TYR311 2.5 39.1 1.0 OD1 A:ASP92 2.8 41.0 1.0 ND2 A:ASN350 3.1 21.6 1.0 O A:HOH508 3.3 26.6 1.0 CZ A:TYR311 3.4 33.9 1.0 CE2 A:TYR311 3.5 23.7 1.0 CG A:ASP92 3.6 41.0 1.0 OD2 A:ASP92 3.7 45.8 1.0 CG A:ASN350 3.9 37.6 1.0 CE1 A:PHE307 4.0 28.4 1.0 CB A:ASN350 4.0 24.9 1.0 O A:HOH522 4.2 36.0 1.0 OG A:SER351 4.3 42.6 1.0 CB A:ALA133 4.3 18.4 1.0 CD1 A:PHE307 4.4 27.5 1.0 O A:VAL347 4.4 34.6 1.0 N A:SER351 4.6 27.8 1.0 CE1 A:TYR311 4.7 26.0 1.0 C A:ASN350 4.8 31.8 1.0 CD2 A:TYR311 4.9 23.4 1.0 CB A:ASP92 4.9 29.4 1.0 ND2 A:ASN354 4.9 35.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Orexin-1 Receptor in Complex with Suvorexant at 2.29 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Orexin-1 Receptor in Complex with Suvorexant at 2.29 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na427 b:44.6 occ:1.00 OH B:TYR311 2.6 27.4 1.0 OD1 B:ASP92 2.6 39.6 1.0 ND2 B:ASN350 3.2 19.1 1.0 O B:HOH502 3.3 32.8 1.0 CG B:ASP92 3.4 37.2 1.0 OD2 B:ASP92 3.5 36.3 1.0 CZ B:TYR311 3.6 29.6 1.0 CE2 B:TYR311 3.7 22.2 1.0 O B:HOH536 3.9 24.9 1.0 CE1 B:PHE307 3.9 23.6 1.0 CB B:ALA133 4.0 17.8 1.0 CG B:ASN350 4.1 39.8 1.0 CB B:ASN350 4.3 33.5 1.0 OG B:SER351 4.4 33.3 1.0 CD1 B:PHE307 4.4 22.5 1.0 O B:VAL347 4.7 36.0 1.0 CD1 B:LEU88 4.8 17.9 1.0 CB B:ASP92 4.8 29.1 1.0 N B:SER351 4.8 28.1 1.0 CE1 B:TYR311 4.8 26.5 1.0 ND2 B:ASN354 4.9 29.8 1.0 CZ B:PHE307 5.0 23.6 1.0

M.Rappas, A.Ali, K.A.Bennett, J.D.Brown, S.J.Bucknell, M.Congreve, R.M.Cooke, G.Cseke, C.De Graaf, A.S.Dore, J.C.Errey, A.Jazayeri, F.H.Marshall, J.S.Mason, R.Mould, J.C.Patel, B.Tehan, M.Weir, J.A.Christopher. Comparison of Orexin 1 and Orexin 2 Ligand Binding Modes Using X-Ray Crystallography and Computational Analysis. J.Med.Chem. 2019.
ISSN: ISSN 0022-2623
PubMed: 31860301
DOI: 10.1021/ACS.JMEDCHEM.9B01787