Sodium in PDB 4bfd: Crystal Structure of Bace-1 in Complex with Chemical Ligand

All present enzymatic activity of Crystal Structure of Bace-1 in Complex with Chemical Ligand:
3.4.23.46;

The structure of Crystal Structure of Bace-1 in Complex with Chemical Ligand, PDB code: 4bfd was solved by D.W.Banner, J.Benz, M.Stihle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.90 / 2.30
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	102.008, 102.008, 171.040, 90.00, 90.00, 120.00
R / Rfree (%)	17.9 / 23.5

The structure of Crystal Structure of Bace-1 in Complex with Chemical Ligand also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Crystal Structure of Bace-1 in Complex with Chemical Ligand (pdb code 4bfd). 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 Bace-1 in Complex with Chemical Ligand, PDB code: 4bfd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Bace-1 in Complex with Chemical Ligand


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 Bace-1 in Complex with Chemical Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1448 b:26.8 occ:1.00 O A:HIS242 2.3 24.1 1.0 O A:TYR245 2.3 24.2 1.0 O A:HOH2192 2.3 27.2 1.0 O A:HOH2196 2.5 31.9 1.0 O A:HOH2193 2.8 49.8 1.0 O A:HOH2316 2.9 48.7 1.0 C A:HIS242 3.4 23.7 1.0 C A:TYR245 3.4 23.9 1.0 CD2 A:TYR245 3.9 20.1 1.0 CE2 A:TYR245 4.0 20.1 1.0 CA A:HIS242 4.1 23.8 1.0 O A:HOH2195 4.1 45.1 1.0 CB A:HIS242 4.2 23.9 1.0 CA A:THR246 4.2 24.8 1.0 CG A:TYR245 4.2 20.4 1.0 N A:THR246 4.2 24.0 1.0 CZ A:TYR245 4.3 20.3 1.0 N A:TYR245 4.4 23.2 1.0 CA A:TYR245 4.4 23.0 1.0 N A:SER243 4.4 23.8 1.0 CD1 A:TYR245 4.5 18.8 1.0 CE1 A:TYR245 4.5 19.1 1.0 CA A:SER243 4.7 24.6 1.0 O A:GLY247 4.8 23.8 1.0 C A:THR246 4.8 25.1 1.0 O A:HOH2200 4.8 31.1 1.0 C A:SER243 4.9 24.4 1.0 CB A:TYR245 4.9 22.5 1.0 OH A:TYR245 4.9 21.7 1.0 N A:GLY247 5.0 24.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Bace-1 in Complex with Chemical Ligand


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 Bace-1 in Complex with Chemical Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1449 b:33.7 occ:1.00 O A:THR205 2.2 32.5 1.0 O A:VAL202 2.2 30.8 1.0 O A:HOH2169 2.4 45.5 1.0 O A:HOH2168 2.4 29.9 1.0 O A:HOH2171 2.7 44.3 1.0 C A:THR205 3.4 32.1 1.0 C A:VAL202 3.5 30.0 1.0 O A:LYS203 4.2 32.2 1.0 N A:THR205 4.2 31.2 1.0 CA A:HIS206 4.3 32.8 1.0 N A:HIS206 4.3 32.1 1.0 C A:LYS203 4.3 31.1 1.0 CG1 A:VAL202 4.4 27.6 1.0 CA A:VAL202 4.4 29.2 1.0 N A:LYS203 4.4 30.6 1.0 CA A:THR205 4.4 31.6 1.0 CA A:LYS203 4.5 31.2 1.0 O A:VAL207 4.6 25.8 1.0 C A:HIS206 4.8 31.5 1.0 N A:GLN204 4.9 30.6 1.0

T.J.Woltering, W.Wostl, H.Hilpert, M.Rogers-Evans, E.Pinard, A.Mayweg, M.Gobel, D.W.Banner, J.Benz, M.Travagli, M.Pollastrini, G.Marconi, E.Gabellieri, W.Guba, H.Mauser, M.Andreini, H.Jacobsen, E.Power, R.Narquizian. BACE1 Inhibitors: A Head Group Scan on A Series of Amides. Bioorg.Med.Chem.Lett. V. 23 4239 2013.
ISSN: ISSN 0960-894X
PubMed: 23735744
DOI: 10.1016/J.BMCL.2013.05.003