Sodium in PDB 6ibl: Activated Turkey BETA1 Adrenoceptor with Bound Agonist Formoterol and Nanobody NB80

The structure of Activated Turkey BETA1 Adrenoceptor with Bound Agonist Formoterol and Nanobody NB80, PDB code: 6ibl was solved by T.Warne, P.C.Edwards, A.S.Dore, A.G.W.Leslie, C.G.Tate, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.32 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	116.650, 121.120, 129.840, 90.00, 90.00, 90.00
R / Rfree (%)	24 / 27.7

The binding sites of Sodium atom in the Activated Turkey BETA1 Adrenoceptor with Bound Agonist Formoterol and Nanobody NB80 (pdb code 6ibl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Activated Turkey BETA1 Adrenoceptor with Bound Agonist Formoterol and Nanobody NB80, PDB code: 6ibl:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Activated Turkey BETA1 Adrenoceptor with Bound Agonist Formoterol and Nanobody NB80


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Activated Turkey BETA1 Adrenoceptor with Bound Agonist Formoterol and Nanobody NB80 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:79.1 occ:1.00 O A:HOH608 2.4 68.5 1.0 O A:CYS192 2.4 93.3 1.0 O A:CYS198 2.4 78.2 1.0 O A:ASP195 2.4 0.4 1.0 C A:ASP195 3.5 0.7 1.0 C A:CYS198 3.6 83.9 1.0 C A:CYS192 3.6 0.8 1.0 O A:TYR193 3.9 92.1 1.0 CA A:TYR193 4.1 0.4 1.0 C A:TYR193 4.1 0.5 1.0 CA A:PRO196 4.1 92.3 1.0 N A:PRO196 4.2 91.0 1.0 N A:TYR193 4.3 1.0 1.0 CB A:CYS198 4.3 94.8 1.0 CA A:CYS198 4.3 85.3 1.0 C A:PRO196 4.4 88.5 1.0 N A:CYS198 4.4 83.4 1.0 O A:PRO196 4.5 77.4 1.0 SG A:CYS192 4.5 0.9 1.0 N A:ASP195 4.5 0.7 1.0 CA A:ASP195 4.6 0.9 1.0 N A:CYS199 4.6 83.9 1.0 OG A:SER111 4.6 0.1 1.0 CA A:CYS192 4.7 0.0 1.0 CA A:CYS199 4.8 79.7 1.0 N A:GLN194 4.9 0.9 1.0 C A:GLN194 5.0 0.1 1.0

Sodium binding site 2 out of 2 in the Activated Turkey BETA1 Adrenoceptor with Bound Agonist Formoterol and Nanobody NB80


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Activated Turkey BETA1 Adrenoceptor with Bound Agonist Formoterol and Nanobody NB80 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:68.9 occ:1.00 O B:CYS198 2.4 57.0 1.0 O B:HOH611 2.4 61.9 1.0 O B:ASP195 2.4 74.7 1.0 O B:CYS192 2.4 73.0 1.0 O B:HOH608 2.4 70.6 1.0 C B:ASP195 3.5 71.6 1.0 C B:CYS198 3.5 59.7 1.0 C B:CYS192 3.6 77.8 1.0 O B:TYR193 3.8 66.2 1.0 CA B:TYR193 4.0 84.6 1.0 O B:HOH610 4.0 38.8 1.0 C B:TYR193 4.1 74.9 1.0 CA B:PRO196 4.1 73.8 1.0 N B:TYR193 4.2 81.1 1.0 N B:PRO196 4.2 73.8 1.0 CA B:CYS198 4.3 59.8 1.0 CB B:CYS198 4.3 64.1 1.0 N B:CYS198 4.4 55.2 1.0 C B:PRO196 4.4 74.4 1.0 SG B:CYS192 4.5 87.8 1.0 O B:PRO196 4.5 82.5 1.0 N B:ASP195 4.5 72.4 1.0 N B:CYS199 4.5 62.0 1.0 CA B:ASP195 4.6 67.7 1.0 CA B:CYS192 4.7 88.8 1.0 CA B:CYS199 4.8 65.6 1.0 OG B:SER111 4.9 81.3 1.0 N B:GLN194 4.9 77.7 1.0

T.Warne, P.C.Edwards, A.S.Dore, A.G.W.Leslie, C.G.Tate. Molecular Basis For High Affinity Agonist Binding in Gpcrs Biorxiv 2018.
DOI: 10.1101/436212