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

Resolution Low / High (Å)	44.41 / 2.10
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	102.571, 102.571, 171.320, 90.00, 90.00, 120.00
R / Rfree (%)	21.9 / 27.2

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 3zov). 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: 3zov:
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:32.4 occ:1.00 O A:TYR245 2.2 27.9 1.0 O A:HIS242 2.2 29.3 1.0 O A:HOH2185 2.3 37.7 1.0 O A:HOH2181 2.6 54.0 1.0 O A:HOH2186 2.6 26.8 1.0 C A:HIS242 3.4 27.5 1.0 C A:TYR245 3.4 26.7 1.0 O A:HOH2187 3.8 50.8 1.0 O A:HOH2182 3.8 44.6 1.0 CA A:HIS242 4.1 27.3 1.0 CB A:HIS242 4.2 27.3 1.0 CD2 A:TYR245 4.2 19.7 1.0 N A:THR246 4.3 27.3 1.0 CA A:THR246 4.3 27.5 1.0 CE2 A:TYR245 4.3 18.1 1.0 CG A:TYR245 4.3 21.7 1.0 N A:TYR245 4.4 24.9 1.0 N A:SER243 4.4 27.6 1.0 CA A:TYR245 4.4 25.6 1.0 O A:HOH2190 4.5 39.2 1.0 CZ A:TYR245 4.5 19.5 1.0 CD1 A:TYR245 4.5 20.4 1.0 CA A:SER243 4.5 27.7 1.0 CE1 A:TYR245 4.6 20.0 1.0 C A:SER243 4.8 26.9 1.0 CB A:TYR245 4.9 25.1 1.0 C A:THR246 5.0 27.2 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:34.3 occ:1.00 O A:THR205 2.2 33.6 1.0 O A:VAL202 2.3 33.1 1.0 O A:HOH2162 2.4 39.3 1.0 O A:HOH2164 2.4 39.3 1.0 O A:HOH2169 2.5 30.5 1.0 C A:THR205 3.5 33.7 1.0 C A:VAL202 3.5 32.8 1.0 O A:HOH2096 3.9 49.4 1.0 N A:THR205 4.3 33.0 1.0 CA A:VAL202 4.3 32.1 1.0 CA A:HIS206 4.3 34.8 1.0 N A:HIS206 4.3 34.2 1.0 CG1 A:VAL202 4.3 31.7 1.0 CA A:THR205 4.5 33.4 1.0 N A:LYS203 4.5 33.2 1.0 C A:LYS203 4.5 33.6 1.0 O A:LYS203 4.5 34.3 1.0 O A:VAL207 4.5 27.5 1.0 CA A:LYS203 4.6 33.9 1.0 C A:HIS206 4.7 33.7 1.0 N A:GLN204 4.9 32.8 1.0 CB A:VAL202 5.0 32.0 1.0

D.W.Banner, B.Gsell, J.Benz, J.Bertschinger, D.Burger, S.Brack, S.Cuppuleri, M.Debulpaep, A.Gast, D.Grabulovski, M.Hennig, H.Hilpert, W.Huber, A.Kuglstatter, E.Kusznir, T.Laeremans, H.Matile, C.Miscenic, A.Rufer, D.Schlatter, J.Steyeart, M.Stihle, R.Thoma, M.Weber, A.Ruf. Mapping the Conformational Space Accessible to BACE2 Using Surface Mutants and Co-Crystals with Fab-Fragments, Fynomers, and Xaperones Acta Crystallogr.,Sect.D V. 69 1124 2013.
ISSN: ISSN 0907-4449
PubMed: 23695257
DOI: 10.1107/S0907444913006574