Sodium in PDB 6rz5: Xfel Crystal Structure of the Human Cysteinyl Leukotriene Receptor 1 in Complex with Zafirlukast

The structure of Xfel Crystal Structure of the Human Cysteinyl Leukotriene Receptor 1 in Complex with Zafirlukast, PDB code: 6rz5 was solved by A.Luginina, A.Gusach, E.Marin, A.Mishin, R.Brouillette, P.Popov, A.Shiryaeva, E.Besserer-Offroy, J.M.Longpre, E.Lyapina, A.Ishchenko, N.Patel, V.Polovinkin, N.Safronova, A.Bogorodskiy, E.Edelweiss, W.Liu, A.Batyuk, V.Gordeliy, G.W.Han, P.Sarret, V.Katritch, V.Borshchevskiy, V.Cherezov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.84 / 2.53
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	41.590, 68.580, 87.390, 76.31, 76.68, 81.21
R / Rfree (%)	18.9 / 22.3

The binding sites of Sodium atom in the Xfel Crystal Structure of the Human Cysteinyl Leukotriene Receptor 1 in Complex with Zafirlukast (pdb code 6rz5). 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 Crystal Structure of the Human Cysteinyl Leukotriene Receptor 1 in Complex with Zafirlukast, PDB code: 6rz5:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Xfel Crystal Structure of the Human Cysteinyl Leukotriene Receptor 1 in Complex with Zafirlukast


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Xfel Crystal Structure of the Human Cysteinyl Leukotriene Receptor 1 in Complex with Zafirlukast within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2022 b:55.0 occ:1.00 OD1 A:ASN396 2.3 50.4 1.0 OG A:SER110 2.4 55.8 1.0 OD1 A:ASP69 2.4 51.7 1.0 OD2 A:ASP400 2.4 71.8 1.0 O A:HOH2105 2.5 61.1 1.0 CB A:SER110 3.1 53.4 1.0 CG A:ASP69 3.3 54.2 1.0 CG A:ASN396 3.5 62.0 1.0 OD2 A:ASP69 3.5 58.2 1.0 CG A:ASP400 3.5 65.7 1.0 O A:ASN396 3.7 60.4 1.0 C A:ASN396 3.9 60.5 1.0 ND2 A:ASN106 4.0 48.1 1.0 OD1 A:ASP400 4.0 65.5 1.0 N A:CYS397 4.0 57.9 1.0 CA A:CYS397 4.1 58.2 1.0 CB A:ASN396 4.2 49.2 1.0 CD2 A:LEU65 4.3 57.1 1.0 CA A:SER110 4.4 51.3 1.0 ND2 A:ASN396 4.5 56.0 1.0 CA A:ASN396 4.7 55.4 1.0 CB A:ASP69 4.7 56.5 1.0 O A:ASN106 4.8 55.5 1.0 CB A:ASP400 4.8 57.3 1.0 CB A:CYS397 4.8 58.5 1.0 O A:LEU65 4.8 55.4 1.0 CG A:ASN106 4.9 53.7 1.0

Sodium binding site 2 out of 2 in the Xfel Crystal Structure of the Human Cysteinyl Leukotriene Receptor 1 in Complex with Zafirlukast


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Xfel Crystal Structure of the Human Cysteinyl Leukotriene Receptor 1 in Complex with Zafirlukast within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2020 b:53.1 occ:1.00 OD1 B:ASP69 2.3 67.3 1.0 OD1 B:ASN396 2.3 52.0 1.0 OG B:SER110 2.4 67.4 1.0 OD2 B:ASP400 2.4 76.5 1.0 O B:HOH2105 2.4 59.0 1.0 CB B:SER110 3.2 59.6 1.0 CG B:ASP69 3.2 69.0 1.0 OD2 B:ASP69 3.5 69.1 1.0 CG B:ASN396 3.5 57.9 1.0 CG B:ASP400 3.6 70.1 1.0 O B:ASN396 3.7 65.8 1.0 C B:ASN396 3.9 67.4 1.0 ND2 B:ASN106 3.9 54.9 1.0 N B:CYS397 4.0 68.4 1.0 CA B:CYS397 4.0 69.4 1.0 OD1 B:ASP400 4.0 70.7 1.0 CB B:ASN396 4.2 53.6 1.0 CD2 B:LEU65 4.3 64.2 1.0 CA B:SER110 4.4 55.7 1.0 ND2 B:ASN396 4.5 52.2 1.0 CB B:ASP69 4.6 67.5 1.0 CA B:ASN396 4.7 60.2 1.0 CB B:CYS397 4.7 70.8 1.0 O B:LEU65 4.7 63.5 1.0 CB B:ASP400 4.8 61.7 1.0 O B:ASN106 4.8 59.5 1.0 CG B:ASN106 4.9 68.2 1.0

A.Luginina, A.Gusach, E.Marin, A.Mishin, R.Brouillette, P.Popov, A.Shiriaeva, E.Besserer-Offroy, J.M.Longpre, E.Lyapina, A.Ishchenko, N.Patel, V.Polovinkin, N.Safronova, A.Bogorodskiy, E.Edelweiss, H.Hu, U.Weierstall, W.Liu, A.Batyuk, V.Gordeliy, G.W.Han, P.Sarret, V.Katritch, V.Borshchevskiy, V.Cherezov. Structure-Based Mechanism of Cysteinyl Leukotriene Receptor Inhibition By Antiasthmatic Drugs. Sci Adv V. 5 X2518 2019.
ISSN: ESSN 2375-2548
PubMed: 31633023
DOI: 10.1126/SCIADV.AAX2518