Sodium in PDB 3b37: Crystal Structure of E. Coli Aminopeptidase N in Complex with Tyrosine

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

The structure of Crystal Structure of E. Coli Aminopeptidase N in Complex with Tyrosine, PDB code: 3b37 was solved by A.Addlagatta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.88 / 1.70
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	120.324, 120.324, 170.345, 90.00, 90.00, 120.00
R / Rfree (%)	16.2 / 18.4

The structure of Crystal Structure of E. Coli Aminopeptidase N in Complex with Tyrosine 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 Tyrosine (pdb code 3b37). 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 Tyrosine, PDB code: 3b37:
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 Tyrosine


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 Tyrosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na951 b:17.5 occ:1.00 OD1 A:ASP356 2.8 11.2 1.0 OG1 A:THR379 2.8 6.6 1.0 N A:HIS362 3.0 8.4 1.0 O A:HIS362 3.2 8.8 1.0 CA A:ALA361 3.4 9.1 1.0 CG A:ASP356 3.4 10.9 1.0 CA A:ASP356 3.6 11.2 1.0 C A:ALA361 3.6 8.8 1.0 CB A:THR379 3.7 6.7 1.0 ND1 A:HIS362 3.8 8.7 1.0 CG2 A:THR379 3.8 7.9 1.0 N A:ASP356 3.9 9.8 1.0 O A:GLU355 3.9 9.8 1.0 CG A:GLU355 3.9 9.6 1.0 CB A:ALA361 4.0 8.7 1.0 C A:GLU355 4.0 9.6 1.0 O A:HOH989 4.0 8.9 1.0 CE1 A:HIS362 4.0 9.5 1.0 CA A:HIS362 4.0 8.1 1.0 C A:HIS362 4.0 8.2 1.0 CB A:ASP356 4.1 11.6 1.0 CG A:HIS362 4.2 7.4 1.0 OD2 A:ASP356 4.2 11.4 1.0 OE1 A:GLU355 4.3 8.9 1.0 NE2 A:GLN352 4.3 8.4 1.0 O A:MET360 4.4 10.8 1.0 N A:ALA361 4.4 9.3 1.0 CD A:GLU355 4.5 11.0 1.0 NE2 A:HIS362 4.6 7.2 1.0 CB A:GLU355 4.6 8.7 1.0 CD2 A:HIS362 4.7 8.9 1.0 CB A:HIS362 4.7 7.9 1.0 C A:ASP356 4.8 12.5 1.0 C A:MET360 4.8 10.6 1.0 O A:ALA361 4.9 9.2 1.0 CA A:GLU355 5.0 9.4 1.0

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


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 Tyrosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na952 b:23.4 occ:1.00 O A:HOH1731 2.3 14.7 0.5 O A:HOH1730 2.4 24.3 0.5 OD1 A:ASP452 2.4 16.4 1.0 O A:ASP452 2.4 13.2 1.0 O A:HOH1295 2.6 24.7 1.0 C A:ASP452 3.3 14.4 1.0 O A:HOH1617 3.3 28.5 1.0 CG A:ASP452 3.5 15.4 1.0 O A:HOH1460 3.6 28.2 1.0 N A:ASP452 3.8 14.7 1.0 CA A:ASP452 3.9 14.3 1.0 N A:ASP453 4.3 14.4 1.0 CB A:ASP452 4.3 14.7 1.0 OD2 A:ASP452 4.4 16.5 1.0 CA A:ASP453 4.6 15.7 1.0 O A:HOH1103 4.8 20.9 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