Sodium in PDB 6tod: Crystal Structure of the Orexin-1 Receptor in Complex with Empa

The structure of Crystal Structure of the Orexin-1 Receptor in Complex with Empa, PDB code: 6tod 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)	30.62 / 2.11
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	57.907, 158.891, 182.354, 90.00, 95.77, 90.00
R / Rfree (%)	18.8 / 20.8

The binding sites of Sodium atom in the Crystal Structure of the Orexin-1 Receptor in Complex with Empa (pdb code 6tod). 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 Empa, PDB code: 6tod:
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 Empa


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 Empa within 5.0Å range: probe atom residue distance (Å) B Occ A:Na430 b:52.7 occ:1.00 OD1 A:ASN350 2.8 36.9 1.0 OH A:TYR311 2.8 33.7 1.0 OD1 A:ASP92 2.9 43.2 1.0 O A:HOH513 3.3 34.9 1.0 CG A:ASP92 3.6 41.8 1.0 CE1 A:TYR311 3.6 26.9 1.0 OD2 A:ASP92 3.6 44.6 1.0 CZ A:TYR311 3.6 33.6 1.0 CG A:ASN350 3.7 42.4 1.0 CB A:ASN350 3.9 33.8 1.0 OG A:SER351 4.1 42.8 1.0 O A:HOH565 4.1 43.6 1.0 CE2 A:PHE307 4.2 30.4 1.0 O A:VAL347 4.3 36.5 1.0 N A:SER351 4.3 31.1 1.0 CD2 A:PHE307 4.4 28.1 1.0 C A:ASN350 4.4 33.8 1.0 CB A:ALA133 4.5 21.8 1.0 ND2 A:ASN354 4.7 35.4 1.0 CA A:SER351 4.7 31.0 1.0 CA A:ASN350 4.8 31.1 1.0 O A:ASN350 4.9 31.8 1.0 ND2 A:ASN350 4.9 33.9 1.0 CD1 A:TYR311 4.9 27.4 1.0 CE2 A:TYR311 5.0 27.8 1.0 CB A:ASP92 5.0 31.5 1.0 CD1 A:LEU88 5.0 32.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Orexin-1 Receptor in Complex with Empa


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 Empa within 5.0Å range: probe atom residue distance (Å) B Occ B:Na432 b:45.2 occ:1.00 OD1 B:ASP92 2.6 37.7 1.0 OH B:TYR311 2.8 32.8 1.0 OD1 B:ASN350 3.1 28.1 1.0 CG B:ASP92 3.4 39.0 1.0 OD2 B:ASP92 3.5 42.5 1.0 O B:HOH511 3.7 43.8 1.0 CZ B:TYR311 3.7 32.7 1.0 CE1 B:TYR311 3.8 29.1 1.0 CB B:ALA133 4.0 20.0 1.0 CE2 B:PHE307 4.0 28.7 1.0 O B:HOH561 4.0 38.0 1.0 CG B:ASN350 4.0 33.9 1.0 CD2 B:PHE307 4.3 26.6 1.0 OG B:SER351 4.4 45.8 1.0 CB B:ASN350 4.4 27.3 1.0 CD1 B:LEU88 4.6 28.5 1.0 ND2 B:ASN354 4.7 34.5 1.0 N B:SER351 4.7 31.3 1.0 O B:VAL347 4.8 35.6 1.0 CB B:ASP92 4.8 31.8 1.0 C B:ASN350 4.9 32.7 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