Manganese 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:

Sodium

(Na)

1 atom

The binding sites of Manganese atom in the Proline Dipeptidase From Deinococcus Radiodurans R1 (pdb code 5cdv). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the Proline Dipeptidase From Deinococcus Radiodurans R1, PDB code: 5cdv:

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Proline Dipeptidase From Deinococcus Radiodurans R1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:9.7 occ:0.36 OE1 A:GLU328 2.3 17.1 1.0 OD1 A:ASP210 2.3 12.2 1.0 OD1 A:ASP221 2.3 10.9 1.0 O1 A:PO4403 2.4 17.7 1.0 OG1 A:THR223 2.5 10.3 1.0 O A:MET222 2.6 9.9 1.0 C A:MET222 3.0 10.1 1.0 CG A:ASP210 3.1 16.7 1.0 CD A:GLU328 3.2 24.0 1.0 CG A:ASP221 3.4 8.8 1.0 OD2 A:ASP210 3.5 29.4 1.0 N A:MET222 3.5 8.3 1.0 OE2 A:GLU328 3.6 22.8 1.0 P A:PO4403 3.6 12.7 1.0 CA A:MET222 3.7 10.3 1.0 N A:THR223 3.7 9.5 1.0 O4 A:PO4403 3.8 21.4 1.0 CB A:THR223 3.8 11.3 1.0 OD2 A:ASP221 4.0 11.4 1.0 CA A:THR223 4.1 10.3 1.0 C A:ASP221 4.2 7.6 1.0 O3 A:PO4403 4.2 21.5 1.0 CB A:ASP210 4.2 13.6 1.0 CZ A:PHE179 4.2 9.7 1.0 N A:MET211 4.2 8.6 1.0 OE2 A:GLU314 4.3 16.4 1.0 CA A:ASP210 4.3 11.2 1.0 CG A:GLU328 4.3 9.4 1.0 O A:MET211 4.4 8.5 1.0 OE1 A:GLU314 4.4 26.5 1.0 CB A:GLU328 4.4 9.3 1.0 CB A:ASP221 4.5 10.3 1.0 C A:ASP210 4.5 9.7 1.0 CA A:ASP221 4.6 9.0 1.0 CD A:GLU314 4.6 20.9 1.0 O2 A:PO4403 4.8 25.5 1.0 CG2 A:THR223 4.8 10.9 1.0 NA A:NA402 4.9 42.2 1.0 O A:ASP221 4.9 10.1 1.0 CE2 A:PHE179 4.9 10.3 1.0 C A:MET211 5.0 8.4 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.