Sodium in PDB 5tzr: GPR40 in Complex with Partial Agonist Mk-8666

All present enzymatic activity of GPR40 in Complex with Partial Agonist Mk-8666:
3.2.1.17;

The structure of GPR40 in Complex with Partial Agonist Mk-8666, PDB code: 5tzr was solved by J.Lu, N.Byrne, S.Patel, S.Sharma, S.M.Soisson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.17 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	100.620, 62.600, 106.150, 90.00, 108.93, 90.00
R / Rfree (%)	20 / 22.8

The binding sites of Sodium atom in the GPR40 in Complex with Partial Agonist Mk-8666 (pdb code 5tzr). 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 GPR40 in Complex with Partial Agonist Mk-8666, PDB code: 5tzr:

Sodium binding site 1 out of 1 in the GPR40 in Complex with Partial Agonist Mk-8666


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of GPR40 in Complex with Partial Agonist Mk-8666 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2401 b:36.4 occ:1.00 OG A:SER1117 2.9 59.5 1.0 O A:HOH2549 3.0 47.7 1.0 CB A:PHE1114 3.6 43.7 1.0 N A:SER1117 3.6 42.6 1.0 CA A:PHE1114 3.7 42.3 1.0 CB A:SER1117 3.7 44.6 1.0 CB A:ASN1132 3.7 41.8 1.0 C A:PHE1114 3.9 45.4 1.0 CD1 A:PHE1114 3.9 46.4 1.0 O A:PHE1114 4.1 46.5 1.0 CG A:PHE1114 4.2 45.0 1.0 CA A:SER1117 4.3 42.3 1.0 OD1 A:ASN1132 4.3 44.8 1.0 N A:ASN1116 4.3 42.2 1.0 CB A:ASN1116 4.3 45.2 1.0 C A:ASN1132 4.4 48.9 1.0 CG A:ASN1132 4.4 51.6 1.0 O A:ASN1132 4.4 49.2 1.0 C A:ASN1116 4.5 46.7 1.0 CA A:ASN1116 4.6 42.6 1.0 N A:THR1115 4.6 39.7 1.0 CA A:ASN1132 4.7 42.7 1.0 CD2 A:LEU1133 4.7 49.6 1.0 N A:LEU1133 4.7 46.1 1.0

J.Lu, N.Byrne, J.Wang, G.Bricogne, F.K.Brown, H.R.Chobanian, S.L.Colletti, J.Di Salvo, B.Thomas-Fowlkes, Y.Guo, D.L.Hall, J.Hadix, N.B.Hastings, J.D.Hermes, T.Ho, A.D.Howard, H.Josien, M.Kornienko, K.J.Lumb, M.W.Miller, S.B.Patel, B.Pio, C.W.Plummer, B.S.Sherborne, P.Sheth, S.Souza, S.Tummala, C.Vonrhein, M.Webb, S.J.Allen, J.M.Johnston, A.B.Weinglass, S.Sharma, S.M.Soisson. Structural Basis For the Cooperative Allosteric Activation of the Free Fatty Acid Receptor GPR40. Nat. Struct. Mol. Biol. V. 24 570 2017.
ISSN: ESSN 1545-9985
PubMed: 28581512
DOI: 10.1038/NSMB.3417