Sodium in PDB 7lgp: Dape Enzyme From Shigella Flexneri

All present enzymatic activity of Dape Enzyme From Shigella Flexneri:
3.5.1.18;

The structure of Dape Enzyme From Shigella Flexneri, PDB code: 7lgp was solved by J.Osipiuk, M.Endres, D.P.Becker, A.Joachimiak, Center For Structuralgenomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.68 / 1.91
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	180.141, 180.141, 200.091, 90, 90, 120
R / Rfree (%)	15.9 / 18.7

The structure of Dape Enzyme From Shigella Flexneri also contains other interesting chemical elements:

Chlorine	(Cl)	15 atoms
Zinc	(Zn)	2 atoms

The binding sites of Sodium atom in the Dape Enzyme From Shigella Flexneri (pdb code 7lgp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Dape Enzyme From Shigella Flexneri, PDB code: 7lgp:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Dape Enzyme From Shigella Flexneri


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dape Enzyme From Shigella Flexneri within 5.0Å range: probe atom residue distance (Å) B Occ A:Na509 b:61.0 occ:1.00 O A:HOH830 2.3 52.9 1.0 O A:HOH760 2.3 49.0 1.0 O A:THR122 2.4 44.3 1.0 O A:GLN57 2.5 46.8 1.0 C A:THR122 3.3 44.2 1.0 C A:GLN57 3.5 44.7 1.0 N A:GLN57 3.8 44.0 1.0 OE1 A:GLN57 3.9 57.6 0.6 CA A:THR122 3.9 45.5 1.0 CB A:GLN57 3.9 49.7 0.6 CA A:GLN57 4.0 46.6 0.6 CA A:GLN57 4.0 45.2 0.4 CB A:GLN57 4.1 46.5 0.4 O A:HOH906 4.1 60.9 1.0 N A:GLY123 4.3 41.9 1.0 O A:GLY123 4.3 39.1 1.0 O A:HOH799 4.5 44.8 1.0 O A:HIS121 4.5 43.2 1.0 CA A:GLY123 4.5 39.8 1.0 CD A:GLN57 4.6 54.8 0.6 C A:GLY123 4.6 38.7 1.0 N A:GLY58 4.6 44.0 1.0 CB A:THR122 4.8 48.5 1.0 CG A:GLN57 4.8 53.6 0.6 CA A:GLY58 5.0 45.8 1.0

Sodium binding site 2 out of 3 in the Dape Enzyme From Shigella Flexneri


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dape Enzyme From Shigella Flexneri within 5.0Å range: probe atom residue distance (Å) B Occ B:Na510 b:57.9 occ:1.00 O B:HOH650 2.2 52.2 1.0 O B:THR122 2.5 39.5 1.0 O B:HOH766 2.7 42.4 1.0 O B:GLN57 2.8 38.2 1.0 O B:HOH617 3.6 38.9 1.0 C B:THR122 3.7 35.9 1.0 C B:GLN57 3.8 36.4 1.0 OE1 B:GLN57 3.8 43.5 1.0 CA B:GLY58 4.1 37.7 1.0 O B:HOH770 4.2 38.8 1.0 N B:GLY58 4.4 35.8 1.0 O B:HOH858 4.4 59.0 1.0 O B:HOH829 4.5 54.5 1.0 CA B:THR122 4.6 36.8 1.0 N B:GLY123 4.6 35.3 1.0 CA B:GLY123 4.7 33.9 1.0 CD B:GLN57 4.7 43.1 1.0 N B:GLU59 4.9 37.0 1.0 CB B:THR122 4.9 39.5 1.0 CA B:GLN57 4.9 39.1 1.0

Sodium binding site 3 out of 3 in the Dape Enzyme From Shigella Flexneri


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Dape Enzyme From Shigella Flexneri within 5.0Å range: probe atom residue distance (Å) B Occ B:Na511 b:57.6 occ:1.00 O B:ASN223 2.3 44.2 1.0 O B:HOH816 2.5 53.2 1.0 O B:PHE226 2.5 42.4 1.0 O B:HOH857 2.7 57.4 1.0 O B:HOH846 2.7 61.4 1.0 C B:PHE226 3.3 43.3 1.0 C B:ASN223 3.5 52.0 1.0 N B:ASN223 3.8 55.3 1.0 N B:PRO227 4.0 43.2 1.0 N B:PHE226 4.1 45.1 1.0 CA B:PRO227 4.1 45.7 1.0 O B:GLU224 4.2 50.4 1.0 C B:GLU224 4.3 52.8 1.0 CA B:ASN223 4.3 53.2 1.0 CA B:PHE226 4.3 43.6 1.0 N B:GLU224 4.5 52.3 1.0 C B:GLY222 4.6 55.6 1.0 CA B:GLU224 4.6 54.9 1.0 N B:PHE225 4.7 49.3 1.0 C B:PHE225 4.7 47.9 1.0 O B:GLN221 4.8 61.8 1.0 CA B:GLY222 4.9 55.9 1.0 C B:PRO227 4.9 45.5 1.0

J.Osipiuk, M.Endres, D.P.Becker, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid). Dape Enzyme From Shigella Flexneri To Be Published.