Zinc in PDB 5xev: Crystal Structure of A Novel Xaa-Pro Dipeptidase From Deinococcus Radiodurans

All present enzymatic activity of Crystal Structure of A Novel Xaa-Pro Dipeptidase From Deinococcus Radiodurans:
3.4.13.9;

The structure of Crystal Structure of A Novel Xaa-Pro Dipeptidase From Deinococcus Radiodurans, PDB code: 5xev was solved by V.N.Are, A.Kumar, B.Ghosh, R.D.Makde, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.96 / 1.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	90.670, 91.879, 53.849, 90.00, 98.78, 90.00
R / Rfree (%)	14.6 / 16.4

The structure of Crystal Structure of A Novel Xaa-Pro Dipeptidase From Deinococcus Radiodurans also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of A Novel Xaa-Pro Dipeptidase From Deinococcus Radiodurans (pdb code 5xev). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of A Novel Xaa-Pro Dipeptidase From Deinococcus Radiodurans, PDB code: 5xev:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of A Novel Xaa-Pro Dipeptidase From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A Novel Xaa-Pro Dipeptidase From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:12.6 occ:1.00 O1 A:PO4503 2.0 11.5 1.0 NE2 A:HIS323 2.0 10.4 1.0 OE2 A:GLU377 2.1 12.4 1.0 OD2 A:ASP252 2.1 12.1 1.0 OE2 A:GLU356 2.3 12.8 1.0 CE1 A:HIS323 3.0 12.5 1.0 HG21 A:THR354 3.0 13.6 1.0 CD2 A:HIS323 3.0 11.1 1.0 CG A:ASP252 3.0 11.1 1.0 HG1 A:THR354 3.0 13.7 1.0 P A:PO4503 3.1 14.5 1.0 CD A:GLU377 3.1 11.2 1.0 O2 A:PO4503 3.2 16.9 1.0 ZN A:ZN502 3.2 11.7 1.0 HE1 A:HIS323 3.2 15.1 1.0 HD2 A:HIS323 3.2 13.3 1.0 CD A:GLU356 3.3 16.6 1.0 OD1 A:ASP252 3.4 11.2 1.0 OE1 A:GLU377 3.5 10.3 1.0 OE1 A:GLU356 3.7 18.3 1.0 O4 A:PO4503 3.8 20.4 1.0 OG1 A:THR354 3.8 11.4 1.0 CG2 A:THR354 3.9 11.3 1.0 HB A:THR354 4.0 12.5 1.0 ND1 A:HIS323 4.1 10.5 1.0 HE2 A:HIS330 4.1 20.2 1.0 CG A:HIS323 4.1 11.1 1.0 CB A:THR354 4.2 10.4 1.0 HB3 A:ASP252 4.2 12.3 1.0 CB A:ASP252 4.3 10.3 1.0 O3 A:PO4503 4.3 18.2 1.0 HG3 A:GLU377 4.3 14.4 1.0 HG23 A:THR354 4.4 13.6 1.0 CG A:GLU377 4.4 12.0 1.0 HG22 A:THR354 4.5 13.6 1.0 CG A:GLU356 4.5 14.2 1.0 HD2 A:HIS330 4.5 20.8 1.0 HG2 A:GLU356 4.5 17.0 1.0 HG12 A:ILE329 4.6 19.0 1.0 HD11 A:ILE329 4.6 20.6 1.0 HB3 A:GLU356 4.7 14.3 1.0 NE2 A:HIS330 4.8 16.9 1.0 HB2 A:ASP252 4.8 12.3 1.0 O A:HOH647 4.8 21.3 1.0 HG2 A:GLU377 4.8 14.4 1.0 HD1 A:HIS323 4.9 12.6 1.0 CD2 A:HIS330 5.0 17.4 1.0 HD13 A:LEU325 5.0 15.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of A Novel Xaa-Pro Dipeptidase From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A Novel Xaa-Pro Dipeptidase From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:11.7 occ:1.00 OD1 A:ASP240 2.0 11.8 1.0 O1 A:PO4503 2.0 11.5 1.0 OE1 A:GLU377 2.0 10.3 1.0 OD1 A:ASP252 2.0 11.2 1.0 CG A:ASP240 2.7 11.6 1.0 OD2 A:ASP240 2.7 12.1 1.0 CD A:GLU377 2.9 11.2 1.0 CG A:ASP252 3.0 11.1 1.0 OE2 A:GLU377 3.0 12.4 1.0 HG1 A:THR254 3.1 13.0 1.0 ZN A:ZN501 3.2 12.6 1.0 P A:PO4503 3.2 14.5 1.0 OD2 A:ASP252 3.3 12.1 1.0 HE3 A:TRP242 3.3 17.8 1.0 O3 A:PO4503 3.5 18.2 1.0 OG1 A:THR254 3.6 10.9 1.0 O4 A:PO4503 3.9 20.4 1.0 O A:VAL253 3.9 10.6 1.0 HZ3 A:TRP242 4.0 17.5 1.0 CE3 A:TRP242 4.1 14.8 1.0 N A:VAL253 4.1 10.4 1.0 H A:VAL253 4.1 12.5 1.0 CB A:ASP240 4.1 11.8 1.0 C A:ASP252 4.2 11.3 1.0 C A:VAL253 4.2 10.5 1.0 CG A:GLU377 4.3 12.0 1.0 CB A:ASP252 4.3 10.3 1.0 HE A:ARG375 4.3 14.9 1.0 CZ3 A:TRP242 4.4 14.6 1.0 O2 A:PO4503 4.4 16.9 1.0 HA A:ASP240 4.4 13.0 1.0 HD11 A:ILE329 4.5 20.6 1.0 HB3 A:GLU377 4.5 12.4 1.0 OE2 A:GLU356 4.5 12.8 1.0 HA A:ASP252 4.5 12.5 1.0 OE1 A:GLU356 4.5 18.3 1.0 HA A:VAL253 4.6 13.2 1.0 CA A:VAL253 4.6 11.0 1.0 HG2 A:GLU377 4.6 14.4 1.0 CA A:ASP252 4.6 10.4 1.0 HB3 A:TRP242 4.6 15.3 1.0 O A:ASP252 4.6 11.2 1.0 HB3 A:ASP240 4.6 14.2 1.0 H A:LEU241 4.6 13.0 1.0 HB2 A:ASP240 4.6 14.2 1.0 HB2 A:GLU377 4.6 12.4 1.0 CA A:ASP240 4.7 10.8 1.0 HH21 A:ARG375 4.7 16.1 1.0 O A:LEU241 4.8 10.9 1.0 CB A:GLU377 4.8 10.4 1.0 HB3 A:ASP252 4.8 12.3 1.0 CD A:GLU356 4.8 16.6 1.0 HB2 A:ASP252 4.8 12.3 1.0 N A:LEU241 4.9 10.8 1.0 HG3 A:GLU377 4.9 14.4 1.0 N A:THR254 4.9 10.6 1.0 C A:ASP240 4.9 10.9 1.0 CB A:THR254 4.9 11.2 1.0

V.N.Are, S.N.Jamdar, B.Ghosh, V.D.Goyal, A.Kumar, S.Neema, R.Gadre, R.D.Makde. Crystal Structure of A Novel Prolidase From Deinococcus Radiodurans Identifies New Subfamily of Bacterial Prolidases. Proteins V. 85 2239 2017.
ISSN: ESSN 1097-0134
PubMed: 28929533
DOI: 10.1002/PROT.25389