Zinc in PDB 5giq: Xaa-Pro Peptidase From Deinococcus Radiodurans, Zinc Bound

The structure of Xaa-Pro Peptidase From Deinococcus Radiodurans, Zinc Bound, PDB code: 5giq was solved by V.N.Are, R.Singh, A.Kumar, B.Ghosh, S.N.Jamdar, R.D.Makde, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.14 / 1.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	60.007, 60.007, 202.841, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 19.5

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

Zinc binding site 1 out of 2 in the Xaa-Pro Peptidase From Deinococcus Radiodurans, Zinc Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Xaa-Pro Peptidase From Deinococcus Radiodurans, Zinc Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:17.9 occ:1.00 O3 A:PO4401 2.0 15.8 1.0 NE2 A:HIS285 2.1 12.5 1.0 OE1 A:GLU328 2.1 12.5 1.0 OD2 A:ASP221 2.2 15.0 1.0 OE2 A:GLU314 2.3 16.6 1.0 CE1 A:HIS285 3.0 13.4 1.0 CD2 A:HIS285 3.1 13.7 1.0 P A:PO4401 3.1 21.1 1.0 CD A:GLU328 3.1 14.5 1.0 ZN A:ZN403 3.1 16.1 1.0 CG A:ASP221 3.2 14.7 1.0 CD A:GLU314 3.2 18.7 1.0 O2 A:PO4401 3.3 20.8 1.0 OE2 A:GLU328 3.5 13.7 1.0 OD1 A:ASP221 3.5 14.2 1.0 OE1 A:GLU314 3.6 20.9 1.0 O1 A:PO4401 3.7 23.0 1.0 OG1 A:THR312 3.8 16.1 1.0 CG2 A:THR312 4.0 13.9 1.0 ND1 A:HIS285 4.1 11.9 1.0 CB A:THR312 4.2 13.7 1.0 CG A:HIS285 4.2 12.9 1.0 CG A:GLU314 4.3 14.9 1.0 CB A:ASP221 4.4 13.8 1.0 O4 A:PO4401 4.4 23.4 1.0 CG A:GLU328 4.5 12.3 1.0 NE2 A:HIS292 4.6 19.4 1.0 CD2 A:HIS292 4.8 19.1 1.0 CB A:GLU314 4.9 14.8 1.0

Zinc binding site 2 out of 2 in the Xaa-Pro Peptidase From Deinococcus Radiodurans, Zinc Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Xaa-Pro Peptidase From Deinococcus Radiodurans, Zinc Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:16.1 occ:1.00 O3 A:PO4401 1.9 15.8 1.0 OD1 A:ASP210 1.9 15.1 1.0 OD1 A:ASP221 2.0 14.2 1.0 OE2 A:GLU328 2.0 13.7 1.0 CG A:ASP210 2.8 14.2 1.0 CD A:GLU328 2.9 14.5 1.0 CG A:ASP221 2.9 14.7 1.0 OD2 A:ASP210 3.0 15.7 1.0 OE1 A:GLU328 3.1 12.5 1.0 OD2 A:ASP221 3.1 15.0 1.0 ZN A:ZN402 3.1 17.9 1.0 P A:PO4401 3.1 21.1 1.0 O4 A:PO4401 3.4 23.4 1.0 OG1 A:THR223 3.5 11.9 1.0 CZ A:PHE179 3.8 16.1 1.0 O A:MET222 3.9 14.6 1.0 O1 A:PO4401 3.9 23.0 1.0 C A:MET222 4.2 14.1 1.0 CB A:ASP210 4.2 13.6 1.0 N A:MET222 4.3 12.0 1.0 O2 A:PO4401 4.3 20.8 1.0 CB A:ASP221 4.3 13.8 1.0 CG A:GLU328 4.3 12.3 1.0 CE2 A:PHE179 4.4 15.6 1.0 CE1 A:PHE179 4.5 16.4 1.0 OE1 A:GLU314 4.5 20.9 1.0 C A:ASP221 4.6 11.4 1.0 OE2 A:GLU314 4.6 16.6 1.0 CA A:MET222 4.7 13.8 1.0 CA A:ASP221 4.7 11.7 1.0 CA A:ASP210 4.7 13.4 1.0 CB A:GLU328 4.7 12.1 1.0 N A:MET211 4.8 14.6 1.0 CD A:GLU314 4.8 18.7 1.0 CB A:THR223 4.9 12.5 1.0 N A:THR223 4.9 12.5 1.0 C A:ASP210 4.9 14.8 1.0

V.N.Are, A.Kumar, V.D.Goyal, S.S.Gotad, B.Ghosh, R.Gadre, S.N.Jamdar, R.D.Makde. Structures and Activities of Widely Conserved Small Prokaryotic Aminopeptidases-P Clarify Classification of M24B Peptidases. Proteins 2018.
ISSN: ESSN 1097-0134
PubMed: 30536999
DOI: 10.1002/PROT.25641