Sodium in PDB 3b34: Crystal Structure of E. Coli Aminopeptidase N in Complex with Phenylalanine

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

The structure of Crystal Structure of E. Coli Aminopeptidase N in Complex with Phenylalanine, PDB code: 3b34 was solved by A.Addlagatta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.30
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	120.582, 120.582, 170.761, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 19.4

The structure of Crystal Structure of E. Coli Aminopeptidase N in Complex with Phenylalanine 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 Phenylalanine (pdb code 3b34). 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 Phenylalanine, PDB code: 3b34:
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 Phenylalanine


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 Phenylalanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na951 b:18.4 occ:1.00 O A:HOH1710 2.2 27.6 1.0 O A:GLY335 2.3 15.4 1.0 O A:HOH1268 2.4 25.6 1.0 O A:SER332 2.4 13.7 1.0 O A:HOH1166 2.5 21.3 1.0 O A:ASP333 2.8 14.2 1.0 O A:HOH1665 3.3 38.8 1.0 C A:ASP333 3.3 12.5 1.0 C A:GLY335 3.5 14.9 1.0 C A:SER332 3.5 12.1 1.0 CA A:ASP333 3.7 12.7 1.0 N A:GLY335 3.9 14.0 1.0 N A:ARG337 4.0 14.1 1.0 N A:ASP333 4.1 12.2 1.0 N A:LEU334 4.2 12.6 1.0 C A:LEU334 4.3 13.9 1.0 O A:HOH1355 4.3 26.6 1.0 CA A:GLY335 4.3 14.3 1.0 N A:SER336 4.4 15.2 1.0 CA A:SER336 4.5 15.1 1.0 O A:HOH1303 4.5 27.9 1.0 O A:HOH1985 4.6 28.6 0.5 CB A:ARG337 4.6 13.8 1.0 C A:SER336 4.6 14.5 1.0 O A:HOH1986 4.6 25.8 0.5 O A:LEU334 4.7 14.6 1.0 CA A:LEU334 4.7 13.8 1.0 O A:HOH1732 4.7 45.1 1.0 CA A:ARG337 4.8 13.9 1.0 CA A:SER332 4.8 11.9 1.0

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


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 Phenylalanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na952 b:19.6 occ:1.00 OD1 A:ASP452 2.3 20.8 1.0 O A:ASP452 2.4 17.2 1.0 O A:HOH1844 2.4 33.2 1.0 O A:HOH1282 2.6 24.4 1.0 O A:HOH1840 2.6 41.7 1.0 O A:HOH1817 2.7 58.9 1.0 C A:ASP452 3.2 17.1 1.0 O A:HOH1389 3.3 22.8 1.0 CG A:ASP452 3.5 18.7 1.0 N A:ASP452 3.8 17.1 1.0 O A:HOH1437 3.8 27.9 1.0 CA A:ASP452 3.9 17.4 1.0 O A:HOH1752 4.0 38.6 1.0 O A:HOH1845 4.1 39.2 1.0 N A:ASP453 4.2 17.5 1.0 O A:HOH1843 4.2 44.3 1.0 CB A:ASP452 4.2 17.6 1.0 OD2 A:ASP452 4.4 19.5 1.0 CA A:ASP453 4.6 18.3 1.0 O A:HOH1676 4.6 34.5 1.0 O A:HOH1198 4.7 25.1 1.0 O A:HOH2095 4.9 28.4 0.5

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