Sodium in PDB 3zpr: Thermostabilised Turkey BETA1 Adrenergic Receptor with 4-Methyl-2- (Piperazin-1-Yl) Quinoline Bound

The structure of Thermostabilised Turkey BETA1 Adrenergic Receptor with 4-Methyl-2- (Piperazin-1-Yl) Quinoline Bound, PDB code: 3zpr was solved by J.A.Christopher, M.Congreve, A.S.Dore, F.H.Marshall, D.G.Myszka, J.Brown, M.Koglin, B.Tehan, J.C.Errey, C.G.Tate, T.Warne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	95.55 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.968, 60.812, 101.178, 90.00, 109.20, 90.00
R / Rfree (%)	22.4 / 26.6

The binding sites of Sodium atom in the Thermostabilised Turkey BETA1 Adrenergic Receptor with 4-Methyl-2- (Piperazin-1-Yl) Quinoline Bound (pdb code 3zpr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Thermostabilised Turkey BETA1 Adrenergic Receptor with 4-Methyl-2- (Piperazin-1-Yl) Quinoline Bound, PDB code: 3zpr:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Thermostabilised Turkey BETA1 Adrenergic Receptor with 4-Methyl-2- (Piperazin-1-Yl) Quinoline Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thermostabilised Turkey BETA1 Adrenergic Receptor with 4-Methyl-2- (Piperazin-1-Yl) Quinoline Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1 b:53.8 occ:1.00 O A:HOH2003 2.4 57.4 1.0 O A:HOH2001 2.4 42.4 1.0 OD1 A:ASP87 2.4 48.0 1.0 O A:HOH2002 2.5 57.3 1.0 OG A:SER128 2.5 43.2 1.0 CB A:SER128 3.4 37.2 1.0 CG A:ASP87 3.5 49.7 1.0 O A:HOH2004 3.8 57.7 1.0 OD2 A:ASP87 3.9 56.8 1.0 OD1 A:ASN335 3.9 46.3 1.0 OG A:SER336 4.0 41.7 1.0 CE2 A:PHE299 4.1 41.2 1.0 O A:HOH2017 4.3 38.2 1.0 O A:HOH2018 4.5 58.0 1.0 CD2 A:PHE299 4.6 39.9 1.0 O A:CYS124 4.7 40.7 1.0 CA A:SER128 4.7 35.7 1.0 CB A:ALA86 4.7 38.9 1.0 CB A:ASP87 4.7 45.4 1.0 N A:ASP87 4.8 43.4 1.0 CA A:ASP87 4.8 44.4 1.0 O A:LEU83 5.0 45.8 1.0

Sodium binding site 2 out of 4 in the Thermostabilised Turkey BETA1 Adrenergic Receptor with 4-Methyl-2- (Piperazin-1-Yl) Quinoline Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Thermostabilised Turkey BETA1 Adrenergic Receptor with 4-Methyl-2- (Piperazin-1-Yl) Quinoline Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2 b:57.8 occ:1.00 O A:CYS198 2.4 49.8 1.0 O A:ASP195 2.4 63.0 1.0 O A:HOH2005 2.4 50.0 1.0 O A:CYS192 2.4 63.4 1.0 O A:TYR193 3.4 55.9 1.0 C A:ASP195 3.5 68.2 1.0 C A:CYS198 3.5 49.8 1.0 C A:CYS192 3.6 67.3 1.0 C A:TYR193 3.8 64.0 1.0 CA A:TYR193 3.8 64.1 1.0 CB A:CYS198 4.1 53.4 1.0 CA A:CYS198 4.2 52.9 1.0 N A:TYR193 4.2 65.1 1.0 N A:CYS198 4.3 50.6 1.0 N A:ASP195 4.3 72.4 1.0 SG A:CYS192 4.3 70.8 1.0 N A:PRO196 4.3 67.9 1.0 CA A:PRO196 4.4 65.0 1.0 CA A:ASP195 4.4 68.5 1.0 N A:CYS199 4.6 53.3 1.0 C A:PRO196 4.6 60.4 1.0 C A:GLN194 4.7 73.4 1.0 N A:GLN194 4.7 73.6 1.0 CA A:CYS192 4.7 67.9 1.0 O A:PRO196 4.8 62.4 1.0 CB A:ASP195 4.9 69.3 1.0 CA A:CYS199 4.9 51.5 1.0 SG A:CYS198 5.0 63.8 1.0

Sodium binding site 3 out of 4 in the Thermostabilised Turkey BETA1 Adrenergic Receptor with 4-Methyl-2- (Piperazin-1-Yl) Quinoline Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Thermostabilised Turkey BETA1 Adrenergic Receptor with 4-Methyl-2- (Piperazin-1-Yl) Quinoline Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1 b:52.8 occ:1.00 OD1 B:ASP87 2.3 49.7 1.0 OG B:SER128 2.4 43.6 1.0 O B:HOH2002 2.4 40.2 1.0 O B:HOH2003 2.5 55.6 1.0 CG B:ASP87 3.4 52.6 1.0 CB B:SER128 3.5 40.0 1.0 O B:HOH2001 3.6 44.5 1.0 OG B:SER336 3.8 43.4 1.0 OD2 B:ASP87 3.9 52.4 1.0 OD1 B:ASN335 4.3 38.8 1.0 O B:HOH2016 4.3 34.9 1.0 CE2 B:PHE299 4.4 37.2 1.0 O B:CYS124 4.4 41.4 1.0 CB B:ALA86 4.5 41.2 1.0 N B:ASP87 4.5 47.1 1.0 O B:HOH2017 4.6 63.0 1.0 CA B:ASP87 4.6 47.6 1.0 CB B:ASP87 4.6 47.0 1.0 C B:ALA86 4.7 44.9 1.0 CA B:SER128 4.8 37.8 1.0 CD2 B:PHE299 4.9 38.3 1.0 O B:LEU83 4.9 46.4 1.0 CB B:SER336 5.0 41.8 1.0 O B:ALA86 5.0 50.3 1.0

Sodium binding site 4 out of 4 in the Thermostabilised Turkey BETA1 Adrenergic Receptor with 4-Methyl-2- (Piperazin-1-Yl) Quinoline Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Thermostabilised Turkey BETA1 Adrenergic Receptor with 4-Methyl-2- (Piperazin-1-Yl) Quinoline Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2 b:57.8 occ:1.00 O B:CYS198 2.4 54.2 1.0 O B:CYS192 2.4 58.7 1.0 O B:HOH2004 2.4 54.5 1.0 O B:ASP195 2.5 57.4 1.0 O B:TYR193 3.4 68.2 1.0 C B:ASP195 3.5 58.2 1.0 C B:CYS198 3.5 56.9 1.0 C B:CYS192 3.5 60.2 1.0 C B:TYR193 3.8 59.2 1.0 CA B:TYR193 3.8 58.4 1.0 CB B:CYS198 4.1 62.3 1.0 CA B:CYS198 4.2 61.2 1.0 N B:TYR193 4.2 57.2 1.0 N B:ASP195 4.2 62.5 1.0 N B:CYS198 4.3 59.1 1.0 SG B:CYS192 4.3 72.3 1.0 N B:PRO196 4.4 59.2 1.0 CA B:PRO196 4.4 58.1 1.0 CA B:ASP195 4.4 60.4 1.0 C B:PRO196 4.6 55.0 1.0 N B:CYS199 4.7 53.5 1.0 CA B:CYS192 4.7 63.7 1.0 N B:GLN194 4.7 62.5 1.0 O B:PRO196 4.8 52.6 1.0 CB B:ASP195 4.9 61.5 1.0 CA B:CYS199 4.9 55.5 1.0 SG B:CYS198 5.0 70.7 1.0

J.Christopher, J.Brown, A.Dore, J.Errey, M.Koglin, F.H.Marshall, D.Myszka, R.L.Rich, C.G.Tate, B.Tehan, T.Warne, M.Congreve. Biophysical Fragment Screening of the BETA1-Adrenergic Receptor: Identification of High Affinity Aryl Piperazine Leads Using Structure-Based Drug Design. J.Med.Chem. V. 56 3446 2013.
ISSN: ISSN 0022-2623
PubMed: 23517028
DOI: 10.1021/JM400140Q