Sodium in PDB 8byj: The Structures of ACE2 in Complex with Bicyclic Peptide Inhibitor

The structure of The Structures of ACE2 in Complex with Bicyclic Peptide Inhibitor, PDB code: 8byj was solved by P.Brear, A.Lulla, M.Harman, R.Dods, L.Chen, G.Bezerra, Y.Demydchuk, S.Stanway, M.Hyvonen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	77.02 / 2.07
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	78.784, 75.958, 114.905, 90, 102.15, 90
R / Rfree (%)	22.4 / 30.4

The structure of The Structures of ACE2 in Complex with Bicyclic Peptide Inhibitor also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Sodium atom in the The Structures of ACE2 in Complex with Bicyclic Peptide Inhibitor (pdb code 8byj). 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 The Structures of ACE2 in Complex with Bicyclic Peptide Inhibitor, PDB code: 8byj:

Sodium binding site 1 out of 1 in the The Structures of ACE2 in Complex with Bicyclic Peptide Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structures of ACE2 in Complex with Bicyclic Peptide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na702 b:75.3 occ:1.00 OH B:TYR252 2.6 52.3 1.0 O B:SER155 3.4 52.9 1.0 CD1 B:LEU281 3.5 71.6 1.0 NH1 B:ARG161 3.5 48.4 1.0 CZ B:TYR252 3.6 60.1 1.0 CZ B:ARG161 3.9 54.0 1.0 CE1 B:TYR252 3.9 55.7 1.0 NE B:ARG161 4.1 45.6 1.0 CD B:ARG161 4.1 45.5 1.0 CD2 B:LEU278 4.3 59.0 1.0 CD2 B:LEU156 4.4 64.7 1.0 O B:LEU266 4.4 65.3 1.0 C B:SER155 4.5 50.2 1.0 CA B:LEU156 4.7 55.2 1.0 NH2 B:ARG161 4.7 51.5 1.0 C B:LEU266 4.9 54.1 1.0 CE2 B:TYR252 4.9 57.5 1.0 CA B:LEU266 5.0 49.2 1.0 CG B:LEU281 5.0 65.7 1.0 CG B:LEU156 5.0 63.6 1.0

M.A.J.Harman, S.J.Stanway, H.Scott, Y.Demydchuk, G.A.Bezerra, S.Pellegrino, L.Chen, P.Brear, A.Lulla, M.Hyvonen, P.J.Beswick, M.J.Skynner. Structure-Guided Chemical Optimization of Bicyclic Peptide ( Bicycle ) Inhibitors of Angiotensin-Converting Enzyme 2. J.Med.Chem. V. 66 9881 2023.
ISSN: ISSN 0022-2623
PubMed: 37433017
DOI: 10.1021/ACS.JMEDCHEM.3C00710