Sodium in PDB 3zpq: Thermostabilised Turkey BETA1 Adrenergic Receptor with 4-(Piperazin-1- Yl)-1H-Indole Bound (Compound 19)

The structure of Thermostabilised Turkey BETA1 Adrenergic Receptor with 4-(Piperazin-1- Yl)-1H-Indole Bound (Compound 19), PDB code: 3zpq 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)	95.36 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.852, 61.441, 100.784, 90.00, 108.89, 90.00
R / Rfree (%)	22 / 27.4

The binding sites of Sodium atom in the Thermostabilised Turkey BETA1 Adrenergic Receptor with 4-(Piperazin-1- Yl)-1H-Indole Bound (Compound 19) (pdb code 3zpq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Thermostabilised Turkey BETA1 Adrenergic Receptor with 4-(Piperazin-1- Yl)-1H-Indole Bound (Compound 19), PDB code: 3zpq:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Thermostabilised Turkey BETA1 Adrenergic Receptor with 4-(Piperazin-1- Yl)-1H-Indole Bound (Compound 19)


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-(Piperazin-1- Yl)-1H-Indole Bound (Compound 19) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1360 b:61.9 occ:1.00 O A:ASP195 2.4 70.6 1.0 O A:CYS192 2.4 58.0 1.0 O A:HOH2010 2.5 58.4 1.0 O A:CYS198 2.5 57.6 1.0 O A:TYR193 3.3 69.0 1.0 C A:CYS192 3.6 62.6 1.0 C A:ASP195 3.6 72.3 1.0 C A:CYS198 3.6 55.2 1.0 C A:TYR193 3.7 73.0 1.0 CA A:TYR193 3.8 69.2 1.0 CB A:CYS198 4.1 58.9 1.0 N A:TYR193 4.2 63.5 1.0 CA A:CYS198 4.2 58.0 1.0 N A:CYS198 4.3 55.9 1.0 SG A:CYS192 4.3 73.9 1.0 N A:PRO196 4.4 72.8 1.0 CA A:PRO196 4.4 70.6 1.0 N A:ASP195 4.5 81.1 1.0 CA A:ASP195 4.6 72.3 1.0 N A:GLN194 4.6 80.1 1.0 C A:GLN194 4.7 83.8 1.0 C A:PRO196 4.7 66.2 1.0 N A:CYS199 4.7 54.0 1.0 CA A:CYS192 4.8 67.0 1.0 O A:GLN194 5.0 84.4 1.0

Sodium binding site 2 out of 3 in the Thermostabilised Turkey BETA1 Adrenergic Receptor with 4-(Piperazin-1- Yl)-1H-Indole Bound (Compound 19)


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-(Piperazin-1- Yl)-1H-Indole Bound (Compound 19) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1359 b:47.0 occ:1.00 OD1 B:ASP87 2.3 45.8 1.0 OG B:SER128 2.4 32.3 1.0 O B:HOH2004 2.4 53.5 1.0 O B:HOH2003 2.4 40.8 1.0 CG B:ASP87 3.2 49.4 1.0 CB B:SER128 3.4 31.1 1.0 OD2 B:ASP87 3.6 48.2 1.0 OG B:SER336 4.2 42.1 1.0 OD1 B:ASN335 4.2 40.7 1.0 CE2 B:PHE299 4.3 39.8 1.0 CB B:ALA86 4.4 41.0 1.0 N B:ASP87 4.4 42.1 1.0 O B:HOH2016 4.4 40.0 1.0 CB B:ASP87 4.5 44.8 1.0 O B:CYS124 4.5 31.6 1.0 O B:HOH2002 4.5 35.7 1.0 CA B:ASP87 4.5 42.7 1.0 O B:LEU83 4.6 44.0 1.0 O B:HOH2017 4.6 43.9 1.0 CA B:SER128 4.6 31.5 1.0 C B:ALA86 4.7 43.8 1.0 CD2 B:PHE299 4.8 39.1 1.0 CD1 B:LEU83 4.8 43.2 1.0

Sodium binding site 3 out of 3 in the Thermostabilised Turkey BETA1 Adrenergic Receptor with 4-(Piperazin-1- Yl)-1H-Indole Bound (Compound 19)


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-(Piperazin-1- Yl)-1H-Indole Bound (Compound 19) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1361 b:56.0 occ:1.00 O B:CYS198 2.3 51.3 1.0 O B:ASP195 2.4 56.4 1.0 O B:CYS192 2.5 58.9 1.0 O B:HOH2012 2.5 48.5 1.0 C B:CYS198 3.5 52.9 1.0 C B:ASP195 3.5 54.3 1.0 O B:TYR193 3.5 59.5 1.0 C B:CYS192 3.6 61.7 1.0 C B:TYR193 3.9 58.8 1.0 CA B:TYR193 3.9 59.1 1.0 CB B:CYS198 4.0 59.4 1.0 CA B:CYS198 4.1 56.5 1.0 N B:CYS198 4.1 55.6 1.0 N B:ASP195 4.2 56.0 1.0 N B:TYR193 4.2 61.5 1.0 CA B:PRO196 4.3 53.4 1.0 N B:PRO196 4.3 54.9 1.0 CA B:ASP195 4.4 54.8 1.0 SG B:CYS192 4.4 72.2 1.0 C B:PRO196 4.5 51.0 1.0 N B:CYS199 4.6 52.2 1.0 O B:PRO196 4.7 50.7 1.0 CA B:CYS192 4.8 63.3 1.0 N B:GLN194 4.8 59.3 1.0 CB B:ASP195 4.9 53.7 1.0 CA B:CYS199 4.9 55.6 1.0 C B:GLN194 5.0 60.3 1.0 SG B:CYS198 5.0 69.8 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