Sodium in PDB 3ked: Crystal Structure of Aminopeptidase N in Complex with 2,4- Diaminobutyric Acid

All present enzymatic activity of Crystal Structure of Aminopeptidase N in Complex with 2,4- Diaminobutyric Acid:
3.4.11.2;

The structure of Crystal Structure of Aminopeptidase N in Complex with 2,4- Diaminobutyric Acid, PDB code: 3ked was solved by A.Addlagatta, R.Gumpena, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.94 / 2.30
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	120.601, 120.601, 170.479, 90.00, 90.00, 120.00
R / Rfree (%)	15.4 / 19.8

The structure of Crystal Structure of Aminopeptidase N in Complex with 2,4- Diaminobutyric Acid also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Aminopeptidase N in Complex with 2,4- Diaminobutyric Acid (pdb code 3ked). 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 Aminopeptidase N in Complex with 2,4- Diaminobutyric Acid, PDB code: 3ked:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Aminopeptidase N in Complex with 2,4- Diaminobutyric Acid


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 Aminopeptidase N in Complex with 2,4- Diaminobutyric Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na951 b:40.4 occ:1.00 O A:SER332 2.5 23.5 1.0 O A:GLY335 2.5 23.0 1.0 O A:HOH1126 2.6 47.3 1.0 O A:HOH949 2.8 35.1 1.0 O A:ASP333 2.8 24.6 1.0 C A:ASP333 3.4 23.6 1.0 O A:HOH1329 3.5 68.3 1.0 C A:GLY335 3.6 24.5 1.0 C A:SER332 3.6 22.9 1.0 CA A:ASP333 3.7 22.9 1.0 N A:ARG337 3.9 24.1 1.0 O A:HOH1295 4.0 54.2 1.0 N A:GLY335 4.0 25.7 1.0 N A:ASP333 4.2 22.4 1.0 N A:LEU334 4.3 23.7 1.0 C A:LEU334 4.3 24.7 1.0 CA A:SER336 4.4 26.8 1.0 C A:SER336 4.4 25.8 1.0 N A:SER336 4.4 26.6 1.0 CA A:GLY335 4.5 23.5 1.0 CB A:ARG337 4.6 24.6 1.0 CA A:ARG337 4.6 24.7 1.0 CA A:LEU334 4.8 24.2 1.0 CA A:SER332 4.8 22.8 1.0 O A:LEU334 4.8 25.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Aminopeptidase N in Complex with 2,4- Diaminobutyric Acid


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 Aminopeptidase N in Complex with 2,4- Diaminobutyric Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na952 b:40.7 occ:1.00 OD1 A:ASP452 2.3 29.9 1.0 O A:ASP452 2.3 25.8 1.0 O A:HOH1210 2.7 33.9 1.0 C A:ASP452 3.1 27.4 1.0 CG A:ASP452 3.4 28.7 1.0 N A:ASP452 3.7 27.8 1.0 CA A:ASP452 3.8 27.7 1.0 N A:ASP453 4.1 28.1 1.0 O A:HOH1278 4.1 62.6 1.0 CB A:ASP452 4.2 28.3 1.0 OD2 A:ASP452 4.2 32.4 1.0 CA A:ASP453 4.3 29.9 1.0 O A:HOH1085 4.8 28.7 1.0 C A:LYS451 4.9 29.7 1.0

R.Gumpena, C.Kishor, R.J.Ganji, A.Addlagatta. Discovery of Alpha, Beta- and Alpha, Gamma-Diamino Acid Scaffolds For the Inhibition of M1 Family Aminopeptidases Chemmedchem V. 6 1971 2011.
ISSN: ISSN 1860-7179
PubMed: 22025387
DOI: 10.1002/CMDC.201100298