Magnesium in PDB 5e3c: 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;

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

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

Potassium	(K)	1 atom
Zinc	(Zn)	1 atom

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Human DPP3 in Complex with Hemorphin Like Opioid Peptide Ivypw, PDB code: 5e3c:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Human DPP3 in Complex with Hemorphin Like Opioid Peptide Ivypw


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg802 b:46.4 occ:1.00 O A:GLY164 2.4 54.4 1.0 O A:GLY167 2.8 42.3 1.0 O A:GLY162 3.3 44.4 1.0 C A:GLY164 3.6 54.9 1.0 C A:GLY167 3.7 41.1 1.0 N A:GLY164 3.9 44.1 1.0 C A:LEU163 3.9 41.9 1.0 O A:GLY174 4.0 46.9 1.0 CG2 A:THR169 4.1 40.7 1.0 CA A:ILE168 4.2 36.0 1.0 CA A:LEU163 4.2 35.7 1.0 N A:ILE168 4.3 41.0 1.0 N A:THR169 4.3 39.7 1.0 CA A:GLY164 4.3 47.5 1.0 O A:LEU163 4.3 46.8 1.0 C A:GLY162 4.4 44.4 1.0 C A:ILE168 4.5 36.2 1.0 N A:GLY167 4.6 53.1 1.0 N A:LYS165 4.7 52.2 1.0 CA A:GLY167 4.7 45.0 1.0 N A:LEU163 4.8 46.1 1.0 C A:GLY174 4.8 37.6 1.0 CA A:GLY174 4.9 39.9 1.0 CA A:LYS165 4.9 47.2 1.0 O A:CYS176 5.0 52.2 1.0 O A:SER173 5.0 45.6 1.0

Magnesium binding site 2 out of 2 in the Structure of Human DPP3 in Complex with Hemorphin Like Opioid Peptide Ivypw


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 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:Mg804 b:38.2 occ:1.00 O A:SER384 2.9 43.5 1.0 OG A:SER108 2.9 48.1 1.0 OD1 A:ASN102 3.0 41.8 1.0 O A:SER101 3.4 30.3 1.0 CG A:ASN102 3.5 39.0 1.0 ND2 A:ASN102 4.0 40.3 1.0 C A:SER101 4.0 28.9 1.0 CA A:GLY385 4.0 37.9 1.0 C A:SER384 4.0 39.4 1.0 CB A:SER108 4.1 34.4 1.0 CA A:ASN102 4.2 30.1 1.0 N A:ASN102 4.3 34.2 1.0 CB A:ASN102 4.4 31.9 1.0 N A:GLY385 4.5 34.4 1.0 OG A:SER101 4.6 40.2 1.0 CB A:SER101 4.7 28.1 1.0 N A:SER108 5.0 38.2 1.0 CA A:SER101 5.0 28.3 1.0

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