Sodium in PDB 3b2p: Crystal Structure of E. Coli Aminopeptidase N in Complex with Arginine

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

The structure of Crystal Structure of E. Coli Aminopeptidase N in Complex with Arginine, PDB code: 3b2p was solved by A.Anthony, G.Leslie, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.37 / 2.00
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	120.204, 120.204, 169.655, 90.00, 90.00, 120.00
R / Rfree (%)	15.3 / 18.8

The structure of Crystal Structure of E. Coli Aminopeptidase N in Complex with Arginine 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 Arginine (pdb code 3b2p). 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 Arginine, PDB code: 3b2p:
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 Arginine


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 Arginine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na951 b:23.0 occ:1.00 O A:HOH1050 2.2 31.7 1.0 O A:GLY335 2.3 16.2 1.0 O A:SER332 2.4 15.8 1.0 O A:HOH1132 2.4 20.1 1.0 O A:HOH1281 2.5 27.9 1.0 O A:ASP333 2.9 16.5 1.0 O A:HOH1624 3.4 43.2 1.0 C A:GLY335 3.5 16.4 1.0 C A:ASP333 3.5 16.5 1.0 C A:SER332 3.6 15.5 1.0 N A:ARG337 3.8 18.6 1.0 CA A:ASP333 3.8 16.7 1.0 O A:HOH1399 4.0 29.8 1.0 N A:GLY335 4.0 15.5 1.0 O A:HOH1715 4.1 22.2 0.5 N A:ASP333 4.2 15.9 1.0 CA A:GLY335 4.3 16.2 1.0 O A:HOH1716 4.3 17.2 0.5 N A:SER336 4.3 17.2 1.0 N A:LEU334 4.4 15.4 1.0 CA A:SER336 4.4 18.5 1.0 C A:SER336 4.4 18.2 1.0 C A:LEU334 4.4 16.7 1.0 CB A:ARG337 4.5 17.5 1.0 O A:HOH1493 4.5 31.0 1.0 CA A:ARG337 4.6 17.8 1.0 CA A:SER332 4.8 15.4 1.0 CA A:LEU334 4.9 16.1 1.0 O A:LEU334 4.9 16.2 1.0

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


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 Arginine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na952 b:33.2 occ:1.00 OD1 A:ASP452 2.4 21.1 1.0 O A:HOH1717 2.5 13.7 0.5 O A:HOH1553 2.5 15.4 0.5 O A:ASP452 2.5 21.2 1.0 O A:HOH1203 2.6 23.9 1.0 O A:HOH1455 3.3 31.9 1.0 O A:HOH1718 3.4 27.7 0.5 C A:ASP452 3.4 22.0 1.0 O A:HOH1626 3.5 44.9 1.0 CG A:ASP452 3.6 21.8 1.0 O A:HOH1458 3.6 33.7 1.0 N A:ASP452 3.9 21.9 1.0 CA A:ASP452 4.0 21.6 1.0 O A:HOH1457 4.1 32.6 1.0 O A:HOH1680 4.2 39.5 1.0 N A:ASP453 4.3 22.2 1.0 CB A:ASP452 4.4 21.4 1.0 OD2 A:ASP452 4.5 22.9 1.0 O A:HOH1043 4.5 21.0 1.0 CA A:ASP453 4.7 23.3 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