Sodium in PDB 6tq4: Crystal Structure of the Orexin-1 Receptor in Complex with Compound 16

The structure of Crystal Structure of the Orexin-1 Receptor in Complex with Compound 16, PDB code: 6tq4 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)	34.69 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.339, 145.892, 71.341, 90.00, 112.33, 90.00
R / Rfree (%)	20.9 / 23.6

The binding sites of Sodium atom in the Crystal Structure of the Orexin-1 Receptor in Complex with Compound 16 (pdb code 6tq4). 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 the Orexin-1 Receptor in Complex with Compound 16, PDB code: 6tq4:

Sodium binding site 1 out of 1 in the Crystal Structure of the Orexin-1 Receptor in Complex with Compound 16


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 Compound 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na413 b:82.3 occ:1.00 ND2 A:ASN350 2.5 54.3 1.0 OH A:TYR311 2.8 59.6 1.0 OD1 A:ASP92 3.0 70.4 1.0 CE1 A:TYR311 3.5 48.1 1.0 CZ A:TYR311 3.6 56.4 1.0 CG A:ASN350 3.6 62.0 1.0 CE2 A:PHE307 3.8 48.8 1.0 CG A:ASP92 3.9 78.0 1.0 CB A:ASN350 3.9 56.3 1.0 OD2 A:ASP92 4.1 86.2 1.0 CD2 A:PHE307 4.1 60.7 1.0 O A:HOH512 4.2 76.4 1.0 OG A:SER351 4.2 78.0 1.0 CB A:ALA133 4.4 47.5 1.0 N A:SER351 4.6 60.8 1.0 O A:VAL347 4.6 64.8 1.0 ND2 A:ASN354 4.6 68.0 1.0 C A:ASN350 4.7 66.5 1.0 OD1 A:ASN350 4.7 63.1 1.0 CD1 A:TYR311 4.8 50.0 1.0 CZ A:PHE307 4.9 46.5 1.0 CD1 A:LEU88 4.9 53.7 1.0 CE2 A:TYR311 4.9 52.0 1.0 CA A:ASN350 4.9 64.0 1.0 CA A:SER351 5.0 61.8 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