Sodium in PDB 3zmg: 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: 3zmg was solved by D.W.Banner, A.Kuglstatter, J.Benz, M.Stihle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.12 / 1.74
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	102.519, 102.519, 171.805, 90.00, 90.00, 120.00
R / Rfree (%)	17.5 / 20.3

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

Fluorine

(F)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of Bace-1 in Complex with Chemical Ligand (pdb code 3zmg). 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: 3zmg:
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:Na1449 b:37.5 occ:1.00 O A:HOH2240 2.1 51.9 1.0 O A:TYR245 2.3 19.9 1.0 O A:HIS242 2.5 24.2 1.0 O A:HOH2245 2.5 34.5 1.0 O A:HOH2244 2.5 46.9 1.0 C A:TYR245 3.4 20.0 1.0 C A:HIS242 3.6 23.0 1.0 O A:HOH2246 3.7 44.7 1.0 CD2 A:TYR245 4.0 18.4 1.0 CE2 A:TYR245 4.1 19.8 1.0 CA A:THR246 4.1 22.9 1.0 N A:THR246 4.2 20.8 1.0 CG A:TYR245 4.2 18.0 1.0 CB A:HIS242 4.3 24.6 1.0 O A:HOH2242 4.3 46.1 1.0 CA A:HIS242 4.3 22.9 1.0 CZ A:TYR245 4.4 20.0 1.0 N A:TYR245 4.4 19.9 1.0 CA A:TYR245 4.4 18.7 1.0 CD1 A:TYR245 4.5 18.2 1.0 CE1 A:TYR245 4.6 20.0 1.0 N A:SER243 4.6 24.4 1.0 O A:HOH2251 4.8 35.4 1.0 CA A:SER243 4.8 24.8 1.0 C A:THR246 4.8 23.5 1.0 CB A:TYR245 4.9 19.1 1.0 O A:GLY247 4.9 19.9 1.0 C A:SER243 5.0 24.6 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:Na1450 b:34.0 occ:1.00 O A:HOH2212 2.3 32.4 1.0 O A:THR205 2.3 29.2 1.0 O A:HOH2214 2.3 45.2 1.0 O A:HOH2213 2.4 47.6 1.0 O A:VAL202 2.4 28.7 1.0 O A:HOH2218 2.4 38.9 1.0 C A:THR205 3.5 28.6 1.0 C A:VAL202 3.6 25.2 1.0 CA A:HIS206 4.1 32.9 1.0 CG1 A:VAL202 4.2 24.2 1.0 N A:HIS206 4.3 30.7 1.0 CA A:VAL202 4.3 23.4 1.0 O A:LYS203 4.4 28.3 1.0 N A:THR205 4.4 26.1 1.0 O A:VAL207 4.5 21.4 1.0 C A:LYS203 4.5 29.4 1.0 O A:HOH2217 4.5 55.5 1.0 N A:LYS203 4.5 25.1 1.0 C A:HIS206 4.6 30.4 1.0 CA A:THR205 4.6 27.7 1.0 O A:HOH2221 4.6 43.9 1.0 CA A:LYS203 4.7 28.9 1.0 N A:VAL207 4.8 25.4 1.0 ND1 A:HIS206 4.9 50.9 1.0 CB A:VAL202 4.9 22.9 1.0

H.Hilpert, W.Guba, T.J.Woltering, W.Wostl, E.Pinard, H.Mauser, A.V.Mayweg, M.Rogers-Evans, R.Humm, D.Krummenacher, T.Muser, C.Schnider, H.Jacobsen, L.Ozmen, A.Bergadano, D.W.Banner, R.Hochstrasser, A.Kuglstatter, P.David-Pierson, H.Fischer, A.Polara, R.Narquizian. Beta-Secretase (BACE1) Inhibitors with High in Vivo Efficacy Suitable For Clinical Evaluation in Alzheimer'S Disease. J.Med.Chem. V. 56 3980 2013.
ISSN: ISSN 0022-2623
PubMed: 23590342
DOI: 10.1021/JM400225M