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Magnesium in PDB 5wh5: Crystal Structure of the PDE4D2 Catalytic Domain in Complex with Inhibitor (R)-Zl-N-91

Enzymatic activity of Crystal Structure of the PDE4D2 Catalytic Domain in Complex with Inhibitor (R)-Zl-N-91

All present enzymatic activity of Crystal Structure of the PDE4D2 Catalytic Domain in Complex with Inhibitor (R)-Zl-N-91:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of the PDE4D2 Catalytic Domain in Complex with Inhibitor (R)-Zl-N-91, PDB code: 5wh5 was solved by H.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.467, 79.883, 163.444, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 21.4

Other elements in 5wh5:

The structure of Crystal Structure of the PDE4D2 Catalytic Domain in Complex with Inhibitor (R)-Zl-N-91 also contains other interesting chemical elements:

Fluorine (F) 4 atoms
Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the PDE4D2 Catalytic Domain in Complex with Inhibitor (R)-Zl-N-91 (pdb code 5wh5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the PDE4D2 Catalytic Domain in Complex with Inhibitor (R)-Zl-N-91, PDB code: 5wh5:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5wh5

Go back to Magnesium Binding Sites List in 5wh5
Magnesium binding site 1 out of 3 in the Crystal Structure of the PDE4D2 Catalytic Domain in Complex with Inhibitor (R)-Zl-N-91


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 the PDE4D2 Catalytic Domain in Complex with Inhibitor (R)-Zl-N-91 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:17.1
occ:1.00
 O A:HOH601 2.1 15.0 1.0
O A:HOH628 2.1 16.3 1.0
O A:HOH612 2.1 15.9 1.0
O A:HOH729 2.1 13.5 1.0
OD1 A:ASP201 2.2 16.7 1.0
O A:HOH684 2.2 15.3 1.0
CG A:ASP201 3.2 16.7 1.0
OD2 A:ASP201 3.5 17.2 1.0
ZN A:ZN502 3.9 19.0 1.0
OE2 A:GLU230 4.1 18.2 1.0
O A:HOH717 4.1 16.9 1.0
CD2 A:HIS200 4.2 16.1 1.0
O A:HIS200 4.2 15.6 1.0
NE2 A:HIS233 4.2 15.9 1.0
O A:HOH708 4.3 22.5 1.0
OG1 A:THR271 4.3 17.9 1.0
OD2 A:ASP318 4.4 17.0 1.0
CD2 A:HIS233 4.4 15.7 1.0
CB A:ASP201 4.5 16.4 1.0
CD2 A:HIS204 4.6 17.8 1.0
O A:THR271 4.6 20.2 1.0
NE2 A:HIS200 4.6 16.4 1.0
CB A:THR271 4.8 18.2 1.0
NE2 A:HIS160 4.8 18.9 1.0
NE2 A:HIS204 4.8 17.9 1.0
CD2 A:HIS160 4.8 18.9 1.0
CG A:GLU230 4.8 17.6 1.0
CA A:ASP201 4.9 16.3 1.0
CD A:GLU230 4.9 18.0 1.0

Magnesium binding site 2 out of 3 in 5wh5

Go back to Magnesium Binding Sites List in 5wh5
Magnesium binding site 2 out of 3 in the Crystal Structure of the PDE4D2 Catalytic Domain in Complex with Inhibitor (R)-Zl-N-91


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 the PDE4D2 Catalytic Domain in Complex with Inhibitor (R)-Zl-N-91 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:22.0
occ:1.00
 O A:HOH712 2.0 24.2 1.0
O A:ASP151 2.2 20.5 1.0
O A:TYR153 2.2 19.7 1.0
C A:ASP151 3.3 20.3 1.0
C A:TYR153 3.3 18.8 1.0
CA A:HIS154 3.9 20.7 1.0
N A:HIS154 4.0 19.9 1.0
N A:ALA155 4.0 23.1 1.0
CA A:ASP151 4.1 21.4 1.0
N A:TYR153 4.1 18.3 1.0
N A:HIS152 4.2 19.5 1.0
O A:HOH670 4.2 20.6 1.0
C A:HIS152 4.3 18.7 1.0
CA A:HIS152 4.3 19.0 1.0
CA A:TYR153 4.4 18.2 1.0
C A:HIS154 4.4 21.6 1.0
O A:GLU150 4.6 19.0 1.0
O A:HOH731 4.6 29.5 1.0
O A:HIS152 4.9 18.6 1.0
CB A:ASP151 5.0 22.6 1.0
CB A:ALA155 5.0 24.4 1.0

Magnesium binding site 3 out of 3 in 5wh5

Go back to Magnesium Binding Sites List in 5wh5
Magnesium binding site 3 out of 3 in the Crystal Structure of the PDE4D2 Catalytic Domain in Complex with Inhibitor (R)-Zl-N-91


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the PDE4D2 Catalytic Domain in Complex with Inhibitor (R)-Zl-N-91 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:17.6
occ:1.00
 O B:HOH605 2.1 19.6 1.0
O B:HOH620 2.1 16.5 1.0
O B:HOH634 2.1 15.2 1.0
O B:HOH723 2.1 14.5 1.0
OD1 B:ASP201 2.2 16.7 1.0
O B:HOH688 2.2 15.4 1.0
CG B:ASP201 3.2 17.0 1.0
OD2 B:ASP201 3.5 17.5 1.0
ZN B:ZN502 4.0 20.4 1.0
OE2 B:GLU230 4.0 18.3 1.0
O B:HOH663 4.1 18.2 1.0
O B:HIS200 4.1 17.4 1.0
O B:HOH675 4.1 20.9 1.0
OG1 B:THR271 4.2 18.6 1.0
CD2 B:HIS200 4.2 18.1 1.0
NE2 B:HIS233 4.2 17.4 1.0
CD2 B:HIS233 4.4 17.0 1.0
OD2 B:ASP318 4.4 19.5 1.0
CB B:ASP201 4.5 17.1 1.0
CD2 B:HIS204 4.6 17.9 1.0
O B:HOH652 4.6 44.4 1.0
O B:THR271 4.6 19.1 1.0
NE2 B:HIS200 4.7 18.4 1.0
NE2 B:HIS160 4.7 18.6 1.0
CB B:THR271 4.7 19.1 1.0
NE2 B:HIS204 4.8 17.4 1.0
CD2 B:HIS160 4.8 18.6 1.0
CG B:GLU230 4.8 17.4 1.0
CD B:GLU230 4.9 18.0 1.0
CA B:ASP201 4.9 17.3 1.0

Reference:

X.Feng, H.Wang, M.Ye, X.T.Xu, Y.Xu, W.Yang, H.T.Zhang, G.Song, H.Ke. Identification of A PDE4-Specific Pocket For the Design of Selective Inhibitors. Biochemistry V. 57 4518 2018.
ISSN: ISSN 0006-2960
PubMed: 29975048
DOI: 10.1021/ACS.BIOCHEM.8B00336
Page generated: Mon Sep 30 06:34:43 2024

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