Sodium in PDB 4r60: Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris

All present enzymatic activity of Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris:
3.4.13.9;

The structure of Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris, PDB code: 4r60 was solved by A.Kumar, B.Ghosh, V.N.Are, S.N.Jamdar, R.D.Makde, S.M.Sharma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.46 / 1.83
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	84.324, 105.515, 111.352, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 20.6

The structure of Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris (pdb code 4r60). 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 Xaa-Pro Dipeptidase From Xanthomonas Campestris, PDB code: 4r60:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris


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 Dipeptidase From Xanthomonas Campestris within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:32.2 occ:1.00 OE1 B:GLN46 2.4 37.1 1.0 O B:ASP155 2.8 16.9 1.0 NE2 B:GLN46 2.9 38.2 1.0 CD B:GLN46 3.0 37.1 1.0 C B:ALA156 3.1 16.5 1.0 N B:ILE159 3.1 17.1 1.0 N B:ALA158 3.2 18.0 1.0 CA B:ALA156 3.3 15.8 1.0 O B:HOH740 3.3 26.6 1.0 O B:ALA156 3.4 16.1 1.0 CB B:ALA158 3.4 19.6 1.0 CG1 B:ILE159 3.5 19.1 1.0 N B:GLY157 3.6 16.6 1.0 CA B:ALA158 3.6 18.7 1.0 CD1 B:ILE159 3.7 19.3 1.0 C B:ASP155 3.8 16.4 1.0 C B:ALA158 3.9 18.9 1.0 CB B:ILE159 4.0 17.7 1.0 N B:ALA156 4.0 15.8 1.0 O B:HOH754 4.1 37.2 1.0 C B:GLY157 4.1 17.7 1.0 CA B:ILE159 4.1 16.9 1.0 O B:HOH817 4.4 43.0 1.0 CA B:GLY157 4.4 17.4 1.0 CG B:GLN46 4.5 34.8 1.0 CB B:ALA156 4.5 13.6 1.0 CB B:ALA132 5.0 13.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris


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 Xaa-Pro Dipeptidase From Xanthomonas Campestris within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:37.0 occ:1.00 O B:HOH503 2.6 21.6 1.0 O B:HOH666 2.6 33.5 1.0 O B:HOH562 3.1 32.5 1.0 CG1 B:VAL203 3.7 24.8 1.0 CB B:CYS222 3.8 22.4 1.0 CB B:SER219 3.8 21.8 1.0 O A:HOH822 4.2 54.0 1.0 OG B:SER219 4.3 23.0 1.0 CB B:ASP207 4.4 27.0 1.0 OD1 B:ASP207 4.4 26.2 1.0 N B:CYS222 4.4 22.1 1.0 O B:VAL203 4.5 25.3 1.0 C B:PHE221 4.6 21.8 1.0 CG B:ASP207 4.7 28.3 1.0 CA B:CYS222 4.7 22.4 1.0 O B:SER219 4.7 20.7 1.0 NH1 B:ARG204 4.8 31.2 0.6 O B:PHE221 4.9 21.1 1.0

A.Kumar, B.Ghosh, V.N.Are, S.N.Jamdar, R.D.Makde, S.M.Sharma. Crystal Structure of Xaa-Pro Dipeptidase From Xanthomonas Campestris To Be Published.