Sodium in PDB 4x2l: Crystal Structure of Human Bace-1 Bound to Compound 6

All present enzymatic activity of Crystal Structure of Human Bace-1 Bound to Compound 6:
3.4.23.46;

The structure of Crystal Structure of Human Bace-1 Bound to Compound 6, PDB code: 4x2l was solved by F.F.Vajdos, K.Parris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	89.57 / 2.55
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	103.420, 103.420, 168.330, 90.00, 90.00, 120.00
R / Rfree (%)	18.8 / 23.9

The structure of Crystal Structure of Human Bace-1 Bound to Compound 6 also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Iodine	(I)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of Human Bace-1 Bound to Compound 6 (pdb code 4x2l). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Human Bace-1 Bound to Compound 6, PDB code: 4x2l:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human Bace-1 Bound to Compound 6


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Bace-1 Bound to Compound 6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:55.7 occ:1.00 O A:HOH509 2.2 65.4 1.0 OG A:SER328 2.3 52.2 1.0 O A:HOH522 2.8 47.4 1.0 CB A:SER328 3.0 44.5 1.0 N A:SER328 3.1 40.9 1.0 O A:HOH526 3.4 79.6 0.5 CA A:SER328 3.6 40.6 1.0 C A:SER327 4.0 45.4 1.0 CA A:SER327 4.3 40.7 1.0 C A:SER328 4.3 45.1 1.0 NH2 A:ARG235 4.4 76.2 1.0 N A:THR329 4.6 42.7 1.0 O A:SER327 5.0 46.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human Bace-1 Bound to Compound 6


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Human Bace-1 Bound to Compound 6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:56.7 occ:1.00 O A:TYR184 2.6 32.5 1.0 O A:HIS181 2.7 35.9 1.0 C A:TYR184 3.7 32.4 1.0 CE2 A:TYR184 3.8 21.9 1.0 C A:HIS181 3.8 35.3 1.0 CD2 A:TYR184 3.9 22.8 1.0 CZ A:TYR184 4.0 29.5 1.0 CB A:HIS181 4.2 35.2 1.0 CG A:TYR184 4.2 24.5 1.0 CA A:HIS181 4.2 34.1 1.0 CE1 A:TYR184 4.4 28.4 1.0 CA A:THR185 4.4 28.9 1.0 O A:GLY186 4.5 34.1 1.0 N A:THR185 4.5 28.8 1.0 CD1 A:TYR184 4.5 27.0 1.0 OH A:TYR184 4.6 33.8 1.0 CA A:TYR184 4.7 26.3 1.0 N A:TYR184 4.8 26.5 1.0 C A:THR185 4.9 33.6 1.0 N A:SER182 4.9 29.6 1.0 N A:GLY186 4.9 30.5 1.0

C.R.Butler, M.A.Brodney, E.M.Beck, G.Barreiro, C.E.Nolan, F.Pan, F.F.Vajdos, K.Parris, A.H.Varghese, C.J.Helal, R.Lira, S.D.Doran, D.Riddell, L.M.Buzon, J.K.Dutra, L.A.Martinez-Alsina, K.Ogilvie, J.C.Murray, J.M.Young, K.Atchison, A.Robshaw, C.Gonzales, J.Wang, Y.Zhang, B.T.O'neill. Discovery of A Series of Efficient, Centrally Efficacious BACE1 Inhibitors Through Structure-Based Drug Design. J.Med.Chem. 2015.
ISSN: ISSN 0022-2623
PubMed: 25695670
DOI: 10.1021/JM501833T