Atomistry » Magnesium » PDB 5dql-5e5s » 5e3c
Atomistry »
  Magnesium »
    PDB 5dql-5e5s »
      5e3c »

Magnesium 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:

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 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 5e3c

Go back to Magnesium Binding Sites List in 5e3c
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 5e3c

Go back to Magnesium Binding Sites List in 5e3c
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

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 20:13:40 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy