Sodium in PDB 5cdv: Proline Dipeptidase From Deinococcus Radiodurans R1

The structure of Proline Dipeptidase From Deinococcus Radiodurans R1, PDB code: 5cdv was solved by A.Kumar, V.Are, B.Ghosh, S.Jamdar, R.Makde, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.48 / 1.45
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	60.619, 60.619, 202.784, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 19.8

The structure of Proline Dipeptidase From Deinococcus Radiodurans R1 also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Sodium atom in the Proline Dipeptidase From Deinococcus Radiodurans R1 (pdb code 5cdv). 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 Proline Dipeptidase From Deinococcus Radiodurans R1, PDB code: 5cdv:

Sodium binding site 1 out of 1 in the Proline Dipeptidase From Deinococcus Radiodurans R1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Proline Dipeptidase From Deinococcus Radiodurans R1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:42.2 occ:1.00 O A:ASP221 2.4 10.1 1.0 CG A:GLU328 2.6 9.4 1.0 OE1 A:GLU328 2.7 17.1 1.0 C A:ASP329 2.8 8.6 1.0 CD A:GLU328 2.8 24.0 1.0 O A:ASP329 3.0 8.6 1.0 N A:LEU330 3.1 7.9 1.0 C A:ASP221 3.2 7.6 1.0 CA A:ASP329 3.3 8.3 1.0 CA A:MET222 3.3 10.3 1.0 N A:ASP329 3.4 7.5 1.0 CG2 A:THR312 3.4 9.8 1.0 C A:GLU328 3.5 8.1 1.0 O A:GLU328 3.7 9.1 1.0 CA A:LEU330 3.7 6.3 1.0 N A:MET222 3.7 8.3 1.0 CB A:GLU328 3.7 9.3 1.0 CB A:THR312 3.8 7.9 1.0 OE2 A:GLU328 3.8 22.8 1.0 CB A:LEU330 4.0 7.5 1.0 CB A:MET222 4.1 13.9 1.0 CA A:GLU328 4.2 8.5 1.0 CA A:THR312 4.3 8.5 1.0 C A:MET222 4.3 10.1 1.0 CB A:ASP221 4.4 10.3 1.0 CA A:ASP221 4.4 9.0 1.0 CD1 A:LEU330 4.6 8.2 1.0 N A:THR223 4.6 9.5 1.0 CG A:ASP221 4.7 8.8 1.0 CB A:ASP329 4.8 8.5 1.0 OD1 A:ASP221 4.8 10.9 1.0 N A:ILE313 4.9 7.4 1.0 MN A:MN401 4.9 9.7 0.4 OG A:SER342 4.9 10.0 1.0 CG A:LEU330 5.0 7.1 1.0

A.Kumar, V.Are, B.Ghosh, S.Jamdar, R.Makde. Proline Dipeptidase From Deinococcus Radiodurans R1 at 1.45 Angstrom Resolution To Be Published.