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Zinc in PDB 5e3c: Structure of Human DPP3 in Complex with Hemorphin Like Opioid Peptide Ivypw

Enzymatic activity of Structure of Human DPP3 in Complex with Hemorphin Like Opioid Peptide Ivypw

All present enzymatic activity of Structure of Human DPP3 in Complex with Hemorphin Like Opioid Peptide Ivypw:
3.4.14.4;

Protein crystallography data

The structure of Structure of Human DPP3 in Complex with Hemorphin Like Opioid Peptide Ivypw, PDB code: 5e3c was solved by P.Kumar, V.Reithofer, M.Reisinger, T.Pavkov-Keller, S.Wallner, P.Macheroux, K.Gruber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.56 / 2.77
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 120.669, 106.386, 65.121, 90.00, 93.44, 90.00
R / Rfree (%) 20.4 / 25.3

Other elements in 5e3c:

The structure of Structure of Human DPP3 in Complex with Hemorphin Like Opioid Peptide Ivypw also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Potassium (K) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Human DPP3 in Complex with Hemorphin Like Opioid Peptide Ivypw (pdb code 5e3c). 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 Structure of Human DPP3 in Complex with Hemorphin Like Opioid Peptide Ivypw, PDB code: 5e3c:

Zinc binding site 1 out of 1 in 5e3c

Go back to Zinc Binding Sites List in 5e3c
Zinc binding site 1 out of 1 in the Structure of Human DPP3 in Complex with Hemorphin Like Opioid Peptide Ivypw


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human DPP3 in Complex with Hemorphin Like Opioid Peptide Ivypw within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:70.7
occ:0.54
 NE2 A:HIS450 2.0 63.4 1.0
OE2 A:GLU508 2.1 59.1 1.0
NE2 A:HIS455 2.1 61.7 1.0
O B:VAL2 2.1 70.7 1.0
CD A:GLU508 2.8 57.7 1.0
OE1 A:GLU508 2.9 59.6 1.0
CD2 A:HIS450 2.9 65.8 1.0
CE1 A:HIS455 3.0 63.0 1.0
C B:VAL2 3.0 68.7 1.0
CE1 A:HIS450 3.1 61.4 1.0
CD2 A:HIS455 3.1 65.9 1.0
N B:VAL2 3.7 63.8 1.0
N B:TYR3 3.8 70.0 1.0
CA B:VAL2 3.9 66.3 1.0
CA B:TYR3 4.1 70.7 1.0
CG A:HIS450 4.1 57.3 1.0
ND1 A:HIS455 4.1 62.6 1.0
CB B:TYR3 4.2 65.0 1.0
ND1 A:HIS450 4.2 61.3 1.0
CG2 B:ILE1 4.2 64.9 1.0
CG A:HIS455 4.2 64.2 1.0
CG A:GLU508 4.3 50.9 1.0
NE2 A:HIS568 4.3 52.9 1.0
CB B:ILE1 4.4 71.9 1.0
CD2 A:HIS568 4.6 44.9 1.0
OH A:TYR318 4.7 61.2 1.0
C B:ILE1 4.7 65.2 1.0
CB A:GLU508 4.8 40.0 1.0
CD1 B:TYR3 4.9 75.6 1.0
CA A:GLU508 4.9 50.9 1.0

Reference:

P.Kumar, V.Reithofer, M.Reisinger, S.Wallner, T.Pavkov-Keller, P.Macheroux, K.Gruber. Substrate Complexes of Human Dipeptidyl Peptidase III Reveal the Mechanism of Enzyme Inhibition. Sci Rep V. 6 23787 2016.
ISSN: ESSN 2045-2322
PubMed: 27025154
DOI: 10.1038/SREP23787
Page generated: Wed Dec 16 06:09:03 2020

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