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Magnesium in PDB 5e33: Structure of Human DPP3 in Complex with Met-Enkephalin

Enzymatic activity of Structure of Human DPP3 in Complex with Met-Enkephalin

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

Protein crystallography data

The structure of Structure of Human DPP3 in Complex with Met-Enkephalin, PDB code: 5e33 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) 45.42 / 1.84
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 119.790, 105.760, 65.167, 90.00, 93.49, 90.00
R / Rfree (%) 18.2 / 22.4

Other elements in 5e33:

The structure of Structure of Human DPP3 in Complex with Met-Enkephalin also contains other interesting chemical elements:

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Human DPP3 in Complex with Met-Enkephalin (pdb code 5e33). 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 Met-Enkephalin, PDB code: 5e33:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5e33

Go back to Magnesium Binding Sites List in 5e33
Magnesium binding site 1 out of 2 in the Structure of Human DPP3 in Complex with Met-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 Met-Enkephalin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:24.1
occ:1.00
O A:SER384 2.6 22.8 1.0
O A:HOH1278 2.7 26.2 1.0
OG A:SER108 2.9 26.4 1.0
OD1 A:ASN102 2.9 23.2 1.0
O A:HOH1291 3.1 42.2 1.0
O A:SER101 3.2 25.4 1.0
CG A:ASN102 3.6 20.7 1.0
CA A:GLY385 3.7 27.1 1.0
C A:SER384 3.7 24.3 1.0
O A:HOH1319 3.9 25.6 1.0
O A:HOH1099 4.0 24.0 1.0
C A:SER101 4.0 20.3 1.0
CB A:SER108 4.0 24.9 1.0
CA A:ASN102 4.0 21.4 1.0
O A:HOH1268 4.0 34.9 1.0
O A:HOH1274 4.0 33.7 1.0
N A:GLY385 4.2 21.3 1.0
N A:ASN102 4.3 19.4 1.0
ND2 A:ASN102 4.3 18.9 1.0
CB A:ASN102 4.4 18.2 1.0
O A:HOH1214 4.5 42.7 1.0
O A:HOH1322 4.6 27.6 1.0
O A:HOH1092 4.8 31.7 1.0
OG A:SER101 4.8 23.8 1.0
N A:SER108 4.9 22.4 1.0
CB A:SER101 5.0 19.1 1.0
CA A:SER384 5.0 23.2 1.0
C A:GLY385 5.0 31.3 1.0

Magnesium binding site 2 out of 2 in 5e33

Go back to Magnesium Binding Sites List in 5e33
Magnesium binding site 2 out of 2 in the Structure of Human DPP3 in Complex with Met-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 Met-Enkephalin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:21.8
occ:1.00
O A:GLY167 2.6 22.8 1.0
O A:GLY164 2.7 33.0 1.0
O A:HOH1156 2.8 26.0 1.0
O A:HOH1028 2.8 24.5 1.0
O A:HOH1239 2.9 33.0 1.0
O A:GLY162 3.0 23.8 1.0
C A:GLY167 3.5 25.7 1.0
C A:GLY164 3.8 35.6 1.0
N A:GLY164 3.9 28.9 1.0
CG2 A:THR169 3.9 22.4 1.0
C A:LEU163 3.9 30.3 1.0
N A:THR169 4.0 21.2 1.0
C A:GLY162 4.1 26.0 1.0
CA A:LEU163 4.1 28.2 1.0
CA A:ILE168 4.1 25.8 1.0
O A:GLY174 4.1 26.6 1.0
N A:ILE168 4.2 26.4 1.0
C A:ILE168 4.3 21.9 1.0
O A:HOH1400 4.4 26.8 1.0
O A:LEU163 4.4 28.9 1.0
CA A:GLY164 4.4 31.8 1.0
CA A:GLY174 4.5 25.7 1.0
N A:LEU163 4.6 25.1 1.0
O A:HOH1283 4.6 36.5 1.0
CA A:GLY167 4.6 29.9 1.0
N A:GLY167 4.6 29.5 1.0
C A:GLY174 4.7 28.6 1.0
CB A:THR169 4.8 24.7 1.0
O A:CYS176 4.9 30.4 1.0
O A:HOH1112 4.9 32.7 1.0
N A:LYS165 4.9 33.7 1.0
CA A:THR169 4.9 23.5 1.0
O A:THR169 5.0 21.1 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: Mon Dec 14 20:13:38 2020

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