Magnesium in PDB 5ehh: Structure of Human DPP3 in Complex with Endomorphin-2.

All present enzymatic activity of Structure of Human DPP3 in Complex with Endomorphin-2.:
3.4.14.4;

The structure of Structure of Human DPP3 in Complex with Endomorphin-2., PDB code: 5ehh 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)	49.09 / 2.38
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	120.035, 105.457, 64.719, 90.00, 93.49, 90.00
R / Rfree (%)	19.4 / 23.7

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

Magnesium binding site 1 out of 2 in the Structure of Human DPP3 in Complex with Endomorphin-2.


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 Endomorphin-2. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:21.6 occ:1.00 O A:HOH1034 2.4 25.2 1.0 OD1 A:ASN102 2.6 23.5 1.0 O A:SER384 2.6 23.7 1.0 OG A:SER108 2.8 24.4 1.0 O A:SER101 3.1 24.2 1.0 O A:HOH1165 3.2 32.7 1.0 CG A:ASN102 3.4 22.2 1.0 CA A:GLY385 3.7 26.8 1.0 C A:SER384 3.7 23.2 1.0 O A:HOH1129 3.8 26.9 1.0 CB A:SER108 3.9 25.6 1.0 C A:SER101 3.9 23.2 1.0 O A:HOH929 3.9 20.1 1.0 CA A:ASN102 4.0 21.7 1.0 O A:HOH1114 4.1 28.1 1.0 ND2 A:ASN102 4.1 17.6 1.0 N A:GLY385 4.2 22.8 1.0 O A:HOH1130 4.2 21.8 1.0 N A:ASN102 4.3 22.2 1.0 CB A:ASN102 4.3 20.3 1.0 OG A:SER101 4.6 28.8 1.0 CB A:SER101 4.8 18.3 1.0 O A:HOH1125 4.8 31.8 1.0 N A:SER108 4.8 21.7 1.0 CA A:SER108 4.9 27.2 1.0 CA A:SER101 4.9 18.7 1.0 C A:GLY385 5.0 25.5 1.0 CA A:SER384 5.0 23.4 1.0

Magnesium binding site 2 out of 2 in the Structure of Human DPP3 in Complex with Endomorphin-2.


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 Endomorphin-2. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg804 b:17.3 occ:1.00 O A:GLY167 2.5 27.7 1.0 O A:GLY164 2.6 34.3 1.0 O A:HOH1029 2.8 27.1 1.0 O A:HOH1059 2.9 20.9 1.0 O A:HOH1046 3.0 33.3 1.0 O A:GLY162 3.0 22.1 1.0 C A:GLY167 3.4 29.8 1.0 C A:GLY164 3.7 30.7 1.0 C A:LEU163 3.8 26.5 1.0 N A:GLY164 3.8 22.6 1.0 CA A:LEU163 4.0 23.7 1.0 O A:GLY174 4.0 27.9 1.0 C A:GLY162 4.1 25.0 1.0 N A:ILE168 4.1 27.9 1.0 N A:THR169 4.1 22.1 1.0 CA A:ILE168 4.1 22.1 1.0 CG2 A:THR169 4.1 23.2 1.0 O A:LEU163 4.2 31.0 1.0 CA A:GLY167 4.3 28.3 1.0 O A:HOH1168 4.3 24.1 1.0 CA A:GLY164 4.4 27.8 1.0 C A:ILE168 4.4 22.2 1.0 N A:LEU163 4.5 27.4 1.0 O A:HOH1053 4.5 34.4 1.0 N A:GLY167 4.5 34.5 1.0 CA A:GLY174 4.7 21.4 1.0 C A:GLY174 4.7 20.9 1.0 O A:HOH1078 4.8 29.6 1.0 N A:LYS165 4.8 33.6 1.0 O A:CYS176 4.8 27.4 1.0 CB A:THR169 4.9 20.2 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