Zinc in PDB 3fvy: Crystal Structure of Human Dipeptidyl Peptidase III

All present enzymatic activity of Crystal Structure of Human Dipeptidyl Peptidase III:
3.4.14.4;

The structure of Crystal Structure of Human Dipeptidyl Peptidase III, PDB code: 3fvy was solved by A.Dong, E.Dobrovetsky, A.Seitova, B.Duncan, L.Crombet, M.Sundstrom, C.H.Arrowsmith, A.M.Edwards, C.Bountra, A.Bochkarev, D.Cossar, Structuralgenomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	75.59 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.812, 151.378, 53.721, 90.00, 100.04, 90.00
R / Rfree (%)	17.2 / 21.9

The structure of Crystal Structure of Human Dipeptidyl Peptidase III also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Zinc atom in the Crystal Structure of Human Dipeptidyl Peptidase III (pdb code 3fvy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Human Dipeptidyl Peptidase III, PDB code: 3fvy:

Zinc binding site 1 out of 1 in the Crystal Structure of Human Dipeptidyl Peptidase III


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 Human Dipeptidyl Peptidase III within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1000 b:26.7 occ:1.00 NE2 A:HIS455 2.0 16.9 1.0 OE2 A:GLU508 2.1 17.0 1.0 NE2 A:HIS450 2.1 19.5 1.0 O A:HOH874 2.4 24.8 1.0 O A:HOH1320 2.6 37.5 1.0 CD A:GLU508 2.9 19.7 1.0 CE1 A:HIS450 3.0 19.8 1.0 CE1 A:HIS455 3.0 18.0 1.0 CD2 A:HIS455 3.1 18.0 1.0 CD2 A:HIS450 3.1 17.6 1.0 OE1 A:GLU508 3.1 23.4 1.0 OE2 A:GLU451 3.9 25.4 1.0 ND1 A:HIS450 4.1 18.9 1.0 ND1 A:HIS455 4.1 17.7 1.0 CG A:HIS455 4.2 16.4 1.0 CG A:HIS450 4.2 17.7 1.0 CG A:GLU508 4.4 17.1 1.0 NE2 A:HIS568 4.4 30.3 1.0 CD A:GLU451 4.4 23.6 1.0 OE1 A:GLU451 4.4 23.6 1.0 CB A:ALA511 4.7 14.4 1.0 CB A:GLU508 4.8 15.0 1.0 CA A:GLU508 4.8 14.8 1.0

G.A.Bezerra, E.Dobrovetsky, R.Viertlmayr, A.Dong, A.Binter, M.Abramic, P.Macheroux, S.Dhe-Paganon, K.Gruber. Entropy-Driven Binding of Opioid Peptides Induces A Large Domain Motion in Human Dipeptidyl Peptidase III. Proc.Natl.Acad.Sci.Usa V. 109 6525 2012.
ISSN: ISSN 0027-8424
PubMed: 22493238
DOI: 10.1073/PNAS.1118005109