Sodium in PDB 3b3b: Crystal Structure of E. Coli Aminopeptidase N in Complex with Tryptophan

All present enzymatic activity of Crystal Structure of E. Coli Aminopeptidase N in Complex with Tryptophan:
3.4.11.2;

The structure of Crystal Structure of E. Coli Aminopeptidase N in Complex with Tryptophan, PDB code: 3b3b was solved by A.Addlagatta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.27 / 1.85
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	120.640, 120.640, 170.640, 90.00, 90.00, 120.00
R / Rfree (%)	15.1 / 17.8

The structure of Crystal Structure of E. Coli Aminopeptidase N in Complex with Tryptophan also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Sodium atom in the Crystal Structure of E. Coli Aminopeptidase N in Complex with Tryptophan (pdb code 3b3b). 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 E. Coli Aminopeptidase N in Complex with Tryptophan, PDB code: 3b3b:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with Tryptophan


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 E. Coli Aminopeptidase N in Complex with Tryptophan within 5.0Å range: probe atom residue distance (Å) B Occ A:Na951 b:19.5 occ:1.00 O A:HOH1502 2.2 24.8 1.0 O A:GLY335 2.3 12.7 1.0 O A:SER332 2.4 10.8 1.0 O A:HOH1119 2.5 14.6 1.0 O A:HOH1265 2.5 24.5 1.0 O A:ASP333 2.8 11.7 1.0 O A:HOH1818 3.3 51.8 1.0 C A:ASP333 3.4 11.2 1.0 C A:GLY335 3.4 12.7 1.0 C A:SER332 3.5 10.8 1.0 CA A:ASP333 3.7 11.1 1.0 N A:GLY335 3.9 11.9 1.0 N A:ARG337 3.9 12.4 1.0 N A:ASP333 4.1 10.5 1.0 O A:HOH1360 4.2 25.2 1.0 N A:LEU334 4.2 10.9 1.0 CA A:GLY335 4.3 12.4 1.0 C A:LEU334 4.3 12.1 1.0 N A:SER336 4.4 12.8 1.0 CA A:SER336 4.5 12.9 1.0 O A:HOH1403 4.5 34.5 1.0 C A:SER336 4.5 12.4 1.0 O A:HOH1888 4.6 26.8 0.5 CB A:ARG337 4.6 12.6 1.0 O A:HOH1375 4.6 30.3 1.0 CA A:ARG337 4.7 12.5 1.0 CA A:SER332 4.7 10.5 1.0 O A:LEU334 4.7 11.6 1.0 CA A:LEU334 4.8 11.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with Tryptophan


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 E. Coli Aminopeptidase N in Complex with Tryptophan within 5.0Å range: probe atom residue distance (Å) B Occ A:Na952 b:31.5 occ:1.00 OD1 A:ASP452 2.4 16.2 1.0 O A:ASP452 2.5 15.4 1.0 O A:HOH1506 2.6 26.3 1.0 C A:ASP452 3.4 16.8 1.0 CG A:ASP452 3.6 17.9 1.0 O A:HOH1567 3.6 37.0 1.0 N A:ASP452 3.9 17.1 1.0 CA A:ASP452 4.0 16.6 1.0 N A:ASP453 4.3 17.2 1.0 CB A:ASP452 4.4 16.6 1.0 OD2 A:ASP452 4.5 17.3 1.0 CA A:ASP453 4.7 18.7 1.0 O A:HOH1187 4.7 28.2 1.0

A.Addlagatta, L.Gay, B.W.Matthews. Structural Basis For the Unusual Specificity of Escherichia Coli Aminopeptidase N. Biochemistry V. 47 5303 2008.
ISSN: ISSN 0006-2960
PubMed: 18416562
DOI: 10.1021/BI7022333