Sodium in PDB 5cnx: Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12

The structure of Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12, PDB code: 5cnx was solved by A.Kumar, V.Are, B.Ghosh, S.Jamdar, R.D.Makde, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.90 / 2.60
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	224.202, 224.202, 74.636, 90.00, 90.00, 120.00
R / Rfree (%)	21.9 / 24

The structure of Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12 also contains other interesting chemical elements:

Arsenic	(As)	3 atoms
Zinc	(Zn)	6 atoms

The binding sites of Sodium atom in the Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12 (pdb code 5cnx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12, PDB code: 5cnx:

Sodium binding site 1 out of 1 in the Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12


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 Xaa-Pro Aminopeptidase From Escherichia Coli K12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:66.5 occ:1.00 O A:GLN109 2.3 68.2 1.0 O A:ALA114 2.4 56.1 1.0 O A:LEU112 2.5 58.0 1.0 OE1 A:GLN109 2.9 63.7 1.0 C A:GLN109 3.3 67.4 1.0 C A:ALA114 3.5 55.7 1.0 N A:ALA114 3.7 58.0 1.0 C A:LEU112 3.7 57.7 1.0 CD A:GLN109 3.9 64.0 1.0 CA A:GLN109 4.0 64.9 1.0 CA A:ALA114 4.2 56.6 1.0 CG A:GLN109 4.3 65.1 1.0 N A:SER110 4.4 72.2 1.0 CD1 A:LEU116 4.4 52.2 1.0 N A:LYS115 4.5 60.3 1.0 O A:TRP108 4.6 55.8 1.0 CA A:LEU112 4.6 56.9 1.0 CA A:LYS115 4.6 59.9 1.0 N A:LEU112 4.6 57.9 1.0 CA A:SER110 4.6 75.1 1.0 C A:ASN113 4.7 62.6 1.0 N A:ASN113 4.7 62.2 1.0 CA A:ASN113 4.7 63.5 1.0 CB A:LEU112 4.8 55.1 1.0 CB A:GLN109 4.8 64.6 1.0 C A:SER110 4.8 75.7 1.0 N A:LEU116 4.9 51.7 1.0 O A:SER110 5.0 77.0 1.0

V.N.Are, A.Kumar, V.D.Goyal, S.S.Gotad, B.Ghosh, R.Gadre, S.N.Jamdar, R.D.Makde. Structures and Activities of Widely Conserved Small Prokaryotic Aminopeptidases-P Clarify Classification of M24B Peptidases Proteins 2018.
ISSN: ESSN 1097-0134
PubMed: 30536999
DOI: 10.1002/PROT.25641