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Magnesium in PDB 2qyn: Crystal Structure of PDE4D2 in Complex with Inhibitor Npv

Enzymatic activity of Crystal Structure of PDE4D2 in Complex with Inhibitor Npv

All present enzymatic activity of Crystal Structure of PDE4D2 in Complex with Inhibitor Npv:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of PDE4D2 in Complex with Inhibitor Npv, PDB code: 2qyn was solved by H.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.57
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.100, 80.626, 163.315, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 24.8

Other elements in 2qyn:

The structure of Crystal Structure of PDE4D2 in Complex with Inhibitor Npv also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of PDE4D2 in Complex with Inhibitor Npv (pdb code 2qyn). 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 PDE4D2 in Complex with Inhibitor Npv, PDB code: 2qyn:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2qyn

Go back to Magnesium Binding Sites List in 2qyn
Magnesium binding site 1 out of 2 in the Crystal Structure of PDE4D2 in Complex with Inhibitor Npv


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 PDE4D2 in Complex with Inhibitor Npv within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:12.6
occ:1.00
O A:HOH503 2.1 14.3 1.0
OD1 A:ASP201 2.1 10.8 1.0
O A:HOH508 2.2 11.3 1.0
O A:HOH505 2.2 11.7 1.0
O A:HOH506 2.2 13.9 1.0
O A:HOH507 2.2 12.9 1.0
CG A:ASP201 3.1 10.4 1.0
OD2 A:ASP201 3.4 9.3 1.0
ZN A:ZN501 3.8 14.8 1.0
OE2 A:GLU230 4.1 15.2 1.0
O A:HOH504 4.1 11.9 1.0
NE2 A:HIS233 4.2 13.6 1.0
O2 A:NPV1 4.2 21.3 1.0
CD2 A:HIS200 4.2 12.4 1.0
O A:HIS200 4.2 10.8 1.0
O A:HOH647 4.2 29.3 1.0
OG1 A:THR271 4.3 13.5 1.0
CD2 A:HIS233 4.4 10.6 1.0
CB A:ASP201 4.5 10.7 1.0
CD2 A:HIS204 4.5 11.8 1.0
OD2 A:ASP318 4.5 16.9 1.0
NE2 A:HIS200 4.6 9.7 1.0
O A:THR271 4.7 14.5 1.0
CD2 A:HIS160 4.8 12.5 1.0
NE2 A:HIS160 4.8 14.0 1.0
CA A:ASP201 4.8 12.1 1.0
NE2 A:HIS204 4.8 14.3 1.0
CB A:THR271 4.8 14.2 1.0
CG A:GLU230 4.9 14.5 1.0
CD A:GLU230 4.9 12.7 1.0

Magnesium binding site 2 out of 2 in 2qyn

Go back to Magnesium Binding Sites List in 2qyn
Magnesium binding site 2 out of 2 in the Crystal Structure of PDE4D2 in Complex with Inhibitor Npv


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 PDE4D2 in Complex with Inhibitor Npv within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:15.0
occ:1.00
OD1 B:ASP201 2.1 13.2 1.0
O B:HOH508 2.2 12.7 1.0
O B:HOH505 2.2 13.9 1.0
O B:HOH503 2.2 15.6 1.0
O B:HOH507 2.2 14.3 1.0
O B:HOH506 2.3 15.3 1.0
CG B:ASP201 3.1 11.9 1.0
OD2 B:ASP201 3.5 13.5 1.0
ZN B:ZN501 3.8 18.1 1.0
OE2 B:GLU230 4.0 16.2 1.0
O B:HIS200 4.1 13.3 1.0
O B:HOH618 4.1 34.6 1.0
CD2 B:HIS200 4.1 13.9 1.0
O B:HOH504 4.2 13.5 1.0
NE2 B:HIS233 4.2 14.3 1.0
O2 B:NPV1 4.2 22.8 1.0
OG1 B:THR271 4.3 13.6 1.0
CD2 B:HIS233 4.4 12.4 1.0
CB B:ASP201 4.5 13.0 1.0
OD2 B:ASP318 4.5 21.2 1.0
NE2 B:HIS200 4.6 11.5 1.0
CD2 B:HIS204 4.6 14.2 1.0
O B:THR271 4.7 15.8 1.0
CD2 B:HIS160 4.7 13.4 1.0
NE2 B:HIS160 4.7 16.1 1.0
CA B:ASP201 4.8 12.4 1.0
CB B:THR271 4.8 15.7 1.0
CD B:GLU230 4.9 14.9 1.0
CG B:GLU230 4.9 15.0 1.0
NE2 B:HIS204 4.9 15.4 1.0
C B:HIS200 4.9 13.9 1.0

Reference:

H.Wang, M.S.Peng, Y.Chen, J.Geng, H.Robinson, M.D.Houslay, J.Cai, H.Ke. Structures of the Four Subfamilies of Phosphodiesterase-4 Provide Insight Into the Selectivity of Their Inhibitors. Biochem.J. V. 408 193 2007.
ISSN: ISSN 0264-6021
PubMed: 17727341
DOI: 10.1042/BJ20070970
Page generated: Mon Dec 14 07:37:41 2020

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