Sodium in PDB 6dmi: A Multiconformer Ligand Model of 5T5 Bound to Bace-1

All present enzymatic activity of A Multiconformer Ligand Model of 5T5 Bound to Bace-1:
3.4.23.46;

The structure of A Multiconformer Ligand Model of 5T5 Bound to Bace-1, PDB code: 6dmi was solved by B.M.Hudson, G.Van Zundert, D.Keedy, R.Fonseca, A.Heliou, P.Suresh, K.Borrelli, T.Day, J.S.Fraser, H.Van Den Bedem, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.70 / 1.90
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	102.320, 102.320, 169.820, 90.00, 90.00, 120.00
R / Rfree (%)	19.2 / 22.6

The structure of A Multiconformer Ligand Model of 5T5 Bound to Bace-1 also contains other interesting chemical elements:

Fluorine	(F)	6 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Sodium atom in the A Multiconformer Ligand Model of 5T5 Bound to Bace-1 (pdb code 6dmi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the A Multiconformer Ligand Model of 5T5 Bound to Bace-1, PDB code: 6dmi:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the A Multiconformer Ligand Model of 5T5 Bound to Bace-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of A Multiconformer Ligand Model of 5T5 Bound to Bace-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:44.0 occ:1.00 O A:TYR245 2.3 25.1 1.0 O A:HOH699 2.3 33.8 1.0 O A:HOH720 2.4 46.3 1.0 O A:HIS242 2.5 29.5 1.0 C A:TYR245 3.4 24.0 1.0 O A:HOH923 3.5 48.3 1.0 C A:HIS242 3.6 28.6 1.0 O A:HOH804 3.7 38.4 1.0 CD2 A:TYR245 3.9 24.6 1.0 CE2 A:TYR245 3.9 26.2 1.0 CG A:TYR245 4.1 21.1 1.0 N A:THR246 4.2 27.1 1.0 CB A:HIS242 4.2 31.8 1.0 CZ A:TYR245 4.2 29.6 1.0 CA A:THR246 4.2 27.6 1.0 CA A:HIS242 4.2 29.8 1.0 CD1 A:TYR245 4.4 27.9 1.0 CA A:TYR245 4.4 26.7 1.0 CE1 A:TYR245 4.4 27.0 1.0 N A:TYR245 4.4 27.8 1.0 O A:HOH809 4.7 44.3 1.0 N A:SER243 4.7 29.4 1.0 O A:GLY247 4.7 27.3 1.0 C A:THR246 4.8 32.6 1.0 OH A:TYR245 4.8 30.6 1.0 CB A:TYR245 4.8 22.7 1.0 CA A:SER243 4.9 29.0 1.0 O A:HOH665 4.9 47.1 1.0 N A:GLY247 4.9 31.7 1.0

Sodium binding site 2 out of 2 in the A Multiconformer Ligand Model of 5T5 Bound to Bace-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of A Multiconformer Ligand Model of 5T5 Bound to Bace-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:40.5 occ:1.00 O A:HOH875 2.0 46.1 1.0 O A:HOH754 2.3 50.4 1.0 O A:HOH694 2.3 34.1 1.0 O A:VAL202 2.3 37.0 1.0 O A:THR205 2.4 36.3 1.0 O A:HOH886 2.5 48.2 1.0 C A:VAL202 3.5 35.1 1.0 C A:THR205 3.6 34.3 1.0 O A:HOH920 3.7 42.3 1.0 CA A:HIS206 4.1 40.8 1.0 CG1 A:VAL202 4.2 24.5 1.0 O A:LYS203 4.3 39.3 1.0 N A:HIS206 4.4 32.8 1.0 CA A:VAL202 4.4 32.2 1.0 N A:THR205 4.4 32.3 1.0 C A:LYS203 4.5 34.8 1.0 N A:LYS203 4.5 30.9 1.0 CA A:LYS203 4.6 33.6 1.0 O A:VAL207 4.7 27.6 1.0 C A:HIS206 4.7 41.2 1.0 CA A:THR205 4.7 33.9 1.0 CD2 A:HIS206 4.8 59.9 1.0 N A:VAL207 5.0 28.8 1.0 CB A:VAL202 5.0 24.5 1.0

G.C.P.Van Zundert, B.M.Hudson, S.H.P.De Oliveira, D.A.Keedy, R.Fonseca, A.Heliou, P.Suresh, K.Borrelli, T.Day, J.S.Fraser, H.Van Den Bedem. Qfit-Ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps. J. Med. Chem. V. 61 11183 2018.
ISSN: ISSN 1520-4804
PubMed: 30457858
DOI: 10.1021/ACS.JMEDCHEM.8B01292