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Magnesium in PDB 3fvy: Crystal Structure of Human Dipeptidyl Peptidase III

Enzymatic activity of Crystal Structure of Human Dipeptidyl Peptidase III

All present enzymatic activity of Crystal Structure of Human Dipeptidyl Peptidase III:
3.4.14.4;

Protein crystallography data

The structure of Crystal Structure of Human Dipeptidyl Peptidase III, PDB code: 3fvy was solved by A.Dong, E.Dobrovetsky, A.Seitova, B.Duncan, L.Crombet, M.Sundstrom, C.H.Arrowsmith, A.M.Edwards, C.Bountra, A.Bochkarev, D.Cossar, Structuralgenomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.59 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.812, 151.378, 53.721, 90.00, 100.04, 90.00
R / Rfree (%) 17.2 / 21.9

Other elements in 3fvy:

The structure of Crystal Structure of Human Dipeptidyl Peptidase III also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Dipeptidyl Peptidase III (pdb code 3fvy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Human Dipeptidyl Peptidase III, PDB code: 3fvy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3fvy

Go back to Magnesium Binding Sites List in 3fvy
Magnesium binding site 1 out of 2 in the Crystal Structure of Human Dipeptidyl Peptidase III


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Dipeptidyl Peptidase III within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg738

b:29.9
occ:1.00
O A:HOH924 2.0 27.6 1.0
O A:HOH948 2.1 25.5 1.0
O A:HOH830 2.1 16.9 1.0
O A:HOH868 2.2 24.7 1.0
O A:HOH899 2.2 21.2 1.0
O A:HOH900 2.3 19.7 1.0
O A:HOH1198 4.0 26.8 1.0
O A:HOH1026 4.1 26.3 1.0
OD1 A:ASP444 4.1 22.8 1.0
OD1 A:ASP377 4.2 16.6 1.0
OD2 A:ASP377 4.2 17.3 1.0
CB A:ASN411 4.3 14.3 1.0
O A:ASP18 4.4 19.7 1.0
O A:HOH1282 4.5 34.3 1.0
OD2 A:ASP18 4.5 22.9 1.0
CA A:ASN411 4.6 14.0 1.0
CG A:ASP377 4.6 16.6 1.0
OD2 A:ASP444 4.7 25.2 1.0
CG A:ASP444 4.9 21.3 1.0
CG A:ASP18 4.9 21.0 1.0
CB A:ALA414 4.9 19.6 1.0
O A:HOH742 5.0 13.9 1.0
CB A:ASP18 5.0 20.2 1.0

Magnesium binding site 2 out of 2 in 3fvy

Go back to Magnesium Binding Sites List in 3fvy
Magnesium binding site 2 out of 2 in the Crystal Structure of Human Dipeptidyl Peptidase III


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Dipeptidyl Peptidase III within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg739

b:26.1
occ:1.00
O A:GLY167 2.2 17.8 1.0
O A:HOH1230 2.3 21.6 1.0
O A:GLY164 2.3 24.9 1.0
O A:HOH998 2.4 28.0 1.0
O A:HOH812 2.4 23.7 1.0
C A:GLY164 3.2 25.5 1.0
N A:GLY164 3.2 25.0 1.0
C A:GLY167 3.4 18.4 1.0
CA A:GLY164 3.5 25.1 1.0
C A:LEU163 3.8 24.8 1.0
CA A:ILE168 3.9 16.9 1.0
O A:HOH988 3.9 31.0 1.0
N A:ILE168 4.1 17.4 1.0
O A:HOH961 4.2 23.7 1.0
O A:LEU163 4.3 25.2 1.0
CA A:LEU163 4.4 23.6 1.0
O A:ARG157 4.5 19.3 1.0
N A:LYS165 4.5 25.3 1.0
NE A:ARG157 4.5 30.1 1.0
O A:GLY162 4.5 18.2 1.0
O A:GLY174 4.5 17.7 1.0
N A:GLY167 4.5 21.4 1.0
CA A:GLY167 4.5 19.2 1.0
O A:HOH912 4.6 26.7 1.0
CD1 A:ILE168 4.6 14.3 1.0
O A:HOH879 4.7 23.3 1.0
CB A:ILE168 4.8 16.8 1.0
CB A:ARG157 4.9 18.7 1.0
C A:ILE168 5.0 16.0 1.0

Reference:

G.A.Bezerra, E.Dobrovetsky, R.Viertlmayr, A.Dong, A.Binter, M.Abramic, P.Macheroux, S.Dhe-Paganon, K.Gruber. Entropy-Driven Binding of Opioid Peptides Induces A Large Domain Motion in Human Dipeptidyl Peptidase III. Proc.Natl.Acad.Sci.Usa V. 109 6525 2012.
ISSN: ISSN 0027-8424
PubMed: 22493238
DOI: 10.1073/PNAS.1118005109
Page generated: Mon Dec 14 08:09:22 2020

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