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Magnesium in PDB 7a9v: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-635

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-635

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-635:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-635, PDB code: 7a9v was solved by A.K.Singh, A.R.Blaazer, L.Zara, I.J.P.De Esch, R.Leurs, D.G.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 91.29 / 2.17
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.199, 111.155, 159.684, 90, 90, 90
R / Rfree (%) 18.9 / 22.9

Other elements in 7a9v:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-635 also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-635 (pdb code 7a9v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-635, PDB code: 7a9v:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7a9v

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-635


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 Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-635 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:27.0
occ:1.00
 O A:HOH625 2.1 30.0 1.0
OD1 A:ASP201 2.1 29.8 1.0
O A:HOH661 2.1 32.3 1.0
O A:HOH696 2.2 33.5 1.0
O A:HOH622 2.2 26.4 1.0
O A:HOH620 2.4 32.6 1.0
CG A:ASP201 3.1 30.5 1.0
OD2 A:ASP201 3.5 29.9 1.0
ZN A:ZN501 3.8 36.4 1.0
O A:HOH707 3.9 59.2 1.0
O A:HOH655 4.0 37.9 1.0
O A:HOH679 4.1 33.9 1.0
OE2 A:GLU230 4.1 37.2 1.0
NE2 A:HIS233 4.1 29.3 1.0
O A:HIS200 4.2 24.6 1.0
CD2 A:HIS200 4.2 33.1 1.0
OG1 A:THR271 4.2 32.4 1.0
CD2 A:HIS233 4.4 32.6 1.0
CB A:ASP201 4.4 29.8 1.0
O A:HOH609 4.5 48.0 1.0
OD2 A:ASP318 4.5 44.1 1.0
CD2 A:HIS204 4.6 30.4 1.0
NE2 A:HIS200 4.6 35.8 1.0
CD2 A:HIS160 4.7 32.4 1.0
CB A:THR271 4.8 34.1 1.0
O A:THR271 4.8 40.1 1.0
NE2 A:HIS160 4.8 30.3 1.0
CA A:ASP201 4.8 28.7 1.0
CG A:GLU230 4.8 34.9 1.0
NE2 A:HIS204 4.8 33.9 1.0
CD A:GLU230 4.9 32.9 1.0

Magnesium binding site 2 out of 4 in 7a9v

Go back to Magnesium Binding Sites List in 7a9v
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-635


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 Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-635 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:34.3
occ:1.00
 O B:HOH670 2.0 39.1 1.0
OD1 B:ASP201 2.0 36.7 1.0
O B:HOH645 2.1 34.2 1.0
O B:HOH616 2.2 37.4 1.0
O B:HOH612 2.2 33.6 1.0
O B:HOH630 2.3 39.3 1.0
CG B:ASP201 3.1 35.9 1.0
OD2 B:ASP201 3.5 40.3 1.0
O B:HOH702 3.7 50.2 1.0
ZN B:ZN501 3.8 43.3 1.0
OE2 B:GLU230 4.1 40.0 1.0
CD2 B:HIS200 4.2 36.1 1.0
NE2 B:HIS233 4.2 40.1 1.0
O B:HOH651 4.2 35.3 1.0
O B:HIS200 4.2 39.7 1.0
OG1 B:THR271 4.3 40.9 1.0
O B:HOH667 4.3 32.9 1.0
CD2 B:HIS233 4.4 37.0 1.0
OD2 B:ASP318 4.4 46.2 1.0
CB B:ASP201 4.5 39.9 1.0
O B:HOH654 4.5 56.0 1.0
NE2 B:HIS200 4.5 39.4 1.0
CD2 B:HIS204 4.6 36.0 1.0
O B:THR271 4.7 45.2 1.0
CB B:THR271 4.7 47.4 1.0
CD2 B:HIS160 4.8 40.6 1.0
NE2 B:HIS160 4.8 34.9 1.0
CA B:ASP201 4.8 39.7 1.0
CG B:GLU230 4.8 42.4 1.0
NE2 B:HIS204 4.9 35.2 1.0
CD B:GLU230 4.9 39.8 1.0

Magnesium binding site 3 out of 4 in 7a9v

Go back to Magnesium Binding Sites List in 7a9v
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-635


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 Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-635 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:28.2
occ:1.00
 O C:HOH619 1.9 34.9 1.0
OD1 C:ASP201 1.9 33.0 1.0
O C:HOH682 2.0 31.5 1.0
O C:HOH661 2.0 34.8 1.0
O C:HOH617 2.1 29.8 1.0
O C:HOH647 2.1 35.0 1.0
CG C:ASP201 3.0 34.2 1.0
OD2 C:ASP201 3.4 37.8 1.0
ZN C:ZN501 3.7 41.3 1.0
O C:HOH673 3.9 31.6 1.0
CD2 C:HIS200 4.1 33.9 1.0
O C:HIS200 4.1 30.1 1.0
OE2 C:GLU230 4.1 40.5 1.0
NE2 C:HIS233 4.2 28.3 1.0
O C:HOH618 4.2 43.8 1.0
OG1 C:THR271 4.2 40.6 1.0
CB C:ASP201 4.3 34.4 1.0
CD2 C:HIS233 4.4 29.4 1.0
NE2 C:HIS200 4.5 33.9 1.0
OD2 C:ASP318 4.5 44.8 1.0
CD2 C:HIS204 4.6 28.7 1.0
CD2 C:HIS160 4.7 31.1 1.0
CA C:ASP201 4.7 33.4 1.0
CB C:THR271 4.7 39.7 1.0
O C:THR271 4.8 40.9 1.0
NE2 C:HIS160 4.8 29.8 1.0
O C:HOH604 4.8 53.7 1.0
NE2 C:HIS204 4.8 27.1 1.0
CG C:GLU230 4.9 36.5 1.0
C C:HIS200 4.9 34.1 1.0
CD C:GLU230 5.0 38.6 1.0

Magnesium binding site 4 out of 4 in 7a9v

Go back to Magnesium Binding Sites List in 7a9v
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-635


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-635 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:30.9
occ:1.00
 O D:HOH699 1.9 41.2 1.0
O D:HOH648 2.0 29.7 1.0
O D:HOH613 2.0 30.0 1.0
OD1 D:ASP201 2.1 31.9 1.0
O D:HOH667 2.2 31.1 1.0
O D:HOH675 2.2 33.0 1.0
CG D:ASP201 3.1 31.9 1.0
O D:HOH743 3.2 69.0 1.0
OD2 D:ASP201 3.4 31.2 1.0
ZN D:ZN501 3.7 35.7 1.0
O D:HOH698 3.8 35.1 1.0
OE2 D:GLU230 4.2 36.2 1.0
O D:HOH689 4.2 42.2 1.0
CD2 D:HIS200 4.2 28.4 1.0
NE2 D:HIS233 4.3 28.4 1.0
O D:HIS200 4.3 31.4 1.0
OG1 D:THR271 4.3 34.6 1.0
OD2 D:ASP318 4.4 39.1 1.0
CB D:ASP201 4.5 32.1 1.0
CD2 D:HIS233 4.5 27.1 1.0
CD2 D:HIS204 4.5 36.5 1.0
NE2 D:HIS200 4.6 30.5 1.0
O D:HOH687 4.6 56.4 1.0
NE2 D:HIS160 4.7 41.8 1.0
CD2 D:HIS160 4.7 39.8 1.0
O D:THR271 4.7 37.0 1.0
NE2 D:HIS204 4.8 36.5 1.0
CB D:THR271 4.8 36.9 1.0
CA D:ASP201 4.9 29.7 1.0
CG D:GLU230 4.9 37.8 1.0
CD D:GLU230 5.0 42.1 1.0

Reference:

A.K.Singh, D.G.Brown. HPDE4D2 Structure with Inhibitor Npd-635 To Be Published.
Page generated: Thu Aug 14 00:35:43 2025

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