Sodium in PDB 3qjx: Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Serine

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

The structure of Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Serine, PDB code: 3qjx was solved by A.Addlagatta, R.Gumpena, C.Kishor, R.J.Ganji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.74 / 1.45
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	120.230, 120.230, 170.801, 90.00, 90.00, 120.00
R / Rfree (%)	12 / 14.7

The structure of Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Serine 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 L-Serine (pdb code 3qjx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Serine, PDB code: 3qjx:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Serine


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 L-Serine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na890 b:15.9 occ:1.00 O A:HOH1689 2.2 27.6 1.0 O A:SER332 2.3 9.7 1.0 O A:GLY335 2.4 11.7 1.0 O A:HOH1643 2.4 23.1 1.0 O A:HOH1444 2.5 17.0 1.0 O A:ASP333 2.8 11.2 1.0 C A:ASP333 3.4 7.1 1.0 C A:GLY335 3.4 9.4 1.0 C A:SER332 3.5 7.7 1.0 CA A:ASP333 3.7 7.4 1.0 N A:GLY335 3.9 9.0 1.0 N A:ARG337 4.0 9.6 1.0 O A:HOH1659 4.1 27.5 1.0 N A:ASP333 4.1 8.0 1.0 N A:LEU334 4.2 8.1 1.0 C A:LEU334 4.3 9.4 1.0 CA A:GLY335 4.3 9.8 1.0 N A:SER336 4.4 11.8 1.0 O A:HOH1137 4.4 39.3 1.0 O A:HOH1138 4.5 43.0 1.0 CA A:SER336 4.5 11.4 1.0 C A:SER336 4.6 10.3 1.0 CB A:ARG337 4.6 10.3 1.0 O A:HOH1715 4.6 25.3 1.0 CA A:SER332 4.7 8.1 1.0 CA A:ARG337 4.7 9.8 1.0 CA A:LEU334 4.7 9.5 1.0 O A:LEU334 4.8 11.6 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Serine


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 L-Serine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na891 b:28.0 occ:1.00 O A:HOH1289 2.2 23.6 0.5 O A:ASP452 2.4 15.4 1.0 OD1 A:ASP452 2.4 19.6 1.0 O A:HOH1640 2.6 28.7 1.0 O A:HOH1288 2.6 37.5 0.5 C A:ASP452 3.3 13.5 1.0 CG A:ASP452 3.5 18.8 1.0 O A:HOH1103 3.5 31.4 1.0 O A:HOH1749 3.7 24.7 1.0 N A:ASP452 3.8 13.6 1.0 CA A:ASP452 3.8 12.9 1.0 N A:ASP453 4.2 13.0 1.0 CB A:ASP452 4.2 15.4 1.0 OD2 A:ASP452 4.5 18.3 1.0 CA A:ASP453 4.5 15.5 1.0 O A:HOH877 4.7 25.0 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Serine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Serine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na892 b:21.8 occ:0.80 O A:HOH1506 2.1 19.7 1.0 OE1 A:GLN821 2.2 19.2 1.0 OD1 A:ASN373 2.5 14.8 1.0 O A:HOH1530 2.7 20.8 1.0 CG A:ASN373 2.8 12.0 1.0 O A:HOH1574 2.9 23.8 1.0 SD A:MET260 3.1 17.4 1.0 CD A:GLN821 3.3 14.8 1.0 CB A:ASN373 3.6 13.2 1.0 ND2 A:ASN373 3.6 19.8 1.0 CG A:MET260 3.8 14.2 1.0 O A:GLU121 3.8 8.9 1.0 NE2 A:GLN821 3.8 16.1 1.0 CE A:MET260 3.9 20.2 1.0 O A:HOH930 4.1 31.4 1.0 OE2 A:GLU107 4.2 12.5 0.4 CA A:ASN373 4.2 10.1 1.0 O A:HOH1425 4.3 13.6 1.0 O A:HOH1397 4.4 15.2 1.0 CG A:GLN821 4.4 11.5 1.0 N A:ALA122 4.5 8.0 1.0 O A:HOH882 4.6 12.8 0.5 C A:GLU121 4.6 7.7 1.0 O A:ASN373 4.8 12.1 1.0 O A:HOH1270 4.9 12.3 0.5 CD1 A:TYR376 4.9 7.9 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