Magnesium in PDB 5e3a: Structure of Human DPP3 in Complex with Opioid Peptide Leu-Enkephalin

All present enzymatic activity of Structure of Human DPP3 in Complex with Opioid Peptide Leu-Enkephalin:
3.4.14.4;

The structure of Structure of Human DPP3 in Complex with Opioid Peptide Leu-Enkephalin, PDB code: 5e3a 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)	39.58 / 2.05
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	119.558, 105.757, 64.992, 90.00, 93.43, 90.00
R / Rfree (%)	20.9 / 26

The structure of Structure of Human DPP3 in Complex with Opioid Peptide Leu-Enkephalin 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 Opioid Peptide Leu-Enkephalin (pdb code 5e3a). 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 Opioid Peptide Leu-Enkephalin, PDB code: 5e3a:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Human DPP3 in Complex with Opioid Peptide Leu-Enkephalin


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 Opioid Peptide Leu-Enkephalin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:19.9 occ:1.00 O A:HOH1206 2.3 28.1 1.0 O A:SER384 2.6 26.6 1.0 OD1 A:ASN102 2.8 24.8 1.0 OG A:SER108 2.9 28.2 1.0 O A:SER101 3.2 20.2 1.0 O A:HOH924 3.2 38.0 1.0 CG A:ASN102 3.4 23.0 1.0 C A:SER384 3.7 21.7 1.0 CA A:GLY385 3.8 23.9 1.0 C A:SER101 3.9 19.2 1.0 CA A:ASN102 3.9 21.7 1.0 O A:HOH1101 4.0 34.6 1.0 O A:HOH1213 4.0 26.2 1.0 O A:HOH1081 4.0 23.0 1.0 CB A:SER108 4.0 27.8 1.0 ND2 A:ASN102 4.1 23.7 1.0 O A:HOH1112 4.1 30.2 1.0 N A:ASN102 4.2 20.6 1.0 N A:GLY385 4.2 23.4 1.0 CB A:ASN102 4.3 21.4 1.0 O A:HOH1196 4.5 21.5 1.0 OG A:SER101 4.7 27.7 1.0 CB A:SER101 4.8 18.7 1.0 N A:SER108 4.8 26.1 1.0 CA A:SER384 4.9 22.4 1.0 CA A:SER101 4.9 21.0 1.0

Magnesium binding site 2 out of 2 in the Structure of Human DPP3 in Complex with Opioid Peptide Leu-Enkephalin


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 Opioid Peptide Leu-Enkephalin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg803 b:19.2 occ:1.00 O A:GLY167 2.5 27.9 1.0 O A:GLY164 2.7 31.9 1.0 O A:HOH1046 2.7 25.6 1.0 O A:GLY162 3.0 23.6 1.0 O A:HOH1005 3.0 21.0 1.0 O A:HOH1204 3.0 29.9 1.0 C A:GLY167 3.4 28.5 1.0 C A:LEU163 3.8 27.6 1.0 N A:GLY164 3.8 27.1 1.0 C A:GLY164 3.8 31.8 1.0 CA A:LEU163 3.9 24.4 1.0 CG2 A:THR169 4.0 21.6 1.0 N A:THR169 4.0 20.1 1.0 O A:GLY174 4.0 26.6 1.0 C A:GLY162 4.0 23.9 1.0 CA A:ILE168 4.1 22.3 1.0 N A:ILE168 4.2 23.9 1.0 O A:LEU163 4.2 28.4 1.0 O A:HOH1018 4.3 34.0 1.0 C A:ILE168 4.3 23.3 1.0 O A:HOH1255 4.4 23.0 1.0 CA A:GLY167 4.4 27.7 1.0 CA A:GLY164 4.4 28.2 1.0 N A:LEU163 4.5 28.6 1.0 N A:GLY167 4.5 30.5 1.0 CA A:GLY174 4.7 23.2 1.0 CB A:THR169 4.7 28.6 1.0 C A:GLY174 4.8 22.5 1.0 O A:HOH1110 4.8 29.3 1.0 O A:CYS176 4.8 29.4 1.0 CA A:THR169 4.9 23.6 1.0 N A:LYS165 4.9 36.9 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