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Magnesium in PDB 7abd: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-768

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-768

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-768:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-768, PDB code: 7abd 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) 84.24 / 2.41
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.703, 110.935, 160.626, 90, 90, 90
R / Rfree (%) 17.3 / 22.7

Other elements in 7abd:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-768 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-768 (pdb code 7abd). 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-768, PDB code: 7abd:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7abd

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-768


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-768 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:26.7
occ:1.00
 O A:HOH603 2.0 34.5 1.0
O A:HOH650 2.0 33.6 1.0
O A:HOH661 2.0 38.5 1.0
O A:HOH619 2.1 27.2 1.0
OD1 A:ASP201 2.1 32.1 1.0
O A:HOH613 2.2 27.9 1.0
CG A:ASP201 3.1 34.6 1.0
OD2 A:ASP201 3.5 35.8 1.0
O A:HOH609 3.6 47.2 1.0
ZN A:ZN501 3.7 40.9 1.0
OE2 A:GLU230 4.1 40.9 1.0
O A:HIS200 4.1 30.8 1.0
CD2 A:HIS200 4.1 35.0 1.0
OG1 A:THR271 4.2 33.6 1.0
O A:HOH610 4.2 40.6 1.0
OD2 A:ASP318 4.4 44.2 1.0
NE2 A:HIS233 4.4 35.0 1.0
CD2 A:HIS233 4.5 31.4 1.0
CB A:ASP201 4.5 32.3 1.0
NE2 A:HIS200 4.5 35.6 1.0
CD2 A:HIS204 4.6 37.8 1.0
CB A:THR271 4.6 35.9 1.0
CD2 A:HIS160 4.6 37.1 1.0
NE2 A:HIS160 4.6 34.7 1.0
O A:THR271 4.7 42.0 1.0
CG A:GLU230 4.8 38.1 1.0
NE2 A:HIS204 4.8 33.6 1.0
CA A:ASP201 4.9 34.7 1.0
CD A:GLU230 4.9 40.9 1.0
C A:HIS200 5.0 29.6 1.0

Magnesium binding site 2 out of 4 in 7abd

Go back to Magnesium Binding Sites List in 7abd
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-768


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-768 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:28.8
occ:1.00
 O B:HOH620 1.9 34.9 1.0
O B:HOH640 2.0 24.3 1.0
OD1 B:ASP201 2.0 31.2 1.0
O B:HOH660 2.1 39.5 1.0
O B:HOH659 2.1 35.9 1.0
O B:HOH618 2.2 28.7 1.0
CG B:ASP201 3.1 34.9 1.0
OD2 B:ASP201 3.5 38.5 1.0
ZN B:ZN501 3.9 41.8 1.0
OE2 B:GLU230 3.9 45.4 1.0
O B:HIS200 4.0 37.7 1.0
O B:HOH631 4.1 41.9 1.0
OG1 B:THR271 4.1 42.9 1.0
NE2 B:HIS233 4.2 38.0 1.0
CD2 B:HIS200 4.2 40.0 1.0
O2 B:EDO509 4.2 57.2 1.0
CD2 B:HIS233 4.2 40.7 1.0
CB B:ASP201 4.4 34.7 1.0
CD2 B:HIS204 4.5 30.4 1.0
NE2 B:HIS200 4.6 40.3 1.0
CG B:GLU230 4.6 43.2 1.0
OD2 B:ASP318 4.6 56.8 1.0
NE2 B:HIS204 4.6 27.8 1.0
CB B:THR271 4.6 44.0 1.0
CD B:GLU230 4.7 43.0 1.0
CA B:ASP201 4.7 34.8 1.0
O B:THR271 4.8 47.8 1.0
O B:HOH697 4.8 57.4 1.0
CD2 B:HIS160 4.8 38.0 1.0
NE2 B:HIS160 4.8 38.8 1.0
C B:HIS200 4.9 36.9 1.0

Magnesium binding site 3 out of 4 in 7abd

Go back to Magnesium Binding Sites List in 7abd
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-768


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-768 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:25.2
occ:1.00
 O C:HOH604 2.0 29.9 1.0
O C:HOH601 2.0 24.7 1.0
OD1 C:ASP201 2.0 33.8 1.0
O C:HOH633 2.1 40.4 1.0
O C:HOH619 2.1 33.3 1.0
O C:HOH631 2.2 34.9 1.0
CG C:ASP201 3.0 35.7 1.0
OD2 C:ASP201 3.3 44.3 1.0
O C:HOH642 3.3 39.3 1.0
ZN C:ZN501 3.5 42.3 1.0
CD2 C:HIS200 4.1 36.0 1.0
OE2 C:GLU230 4.2 39.8 1.0
OD2 C:ASP318 4.3 45.4 1.0
O C:HIS200 4.3 31.0 1.0
OG1 C:THR271 4.3 42.0 1.0
O C:HOH658 4.3 40.3 1.0
NE2 C:HIS200 4.4 37.7 1.0
CB C:ASP201 4.4 32.2 1.0
CD2 C:HIS160 4.4 43.2 1.0
NE2 C:HIS160 4.4 40.5 1.0
CD2 C:HIS204 4.5 33.6 1.0
NE2 C:HIS233 4.6 30.7 1.0
O C:HOH650 4.6 56.6 1.0
O C:THR271 4.7 41.6 1.0
CD2 C:HIS233 4.7 30.7 1.0
CB C:THR271 4.7 39.6 1.0
NE2 C:HIS204 4.7 31.1 1.0
CA C:ASP201 4.9 29.4 1.0

Magnesium binding site 4 out of 4 in 7abd

Go back to Magnesium Binding Sites List in 7abd
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-768


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-768 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:23.6
occ:1.00
 O D:HOH610 2.0 22.1 1.0
OD1 D:ASP201 2.0 37.1 1.0
O D:HOH665 2.1 36.6 1.0
O D:HOH634 2.1 40.4 1.0
O D:HOH640 2.1 23.8 1.0
O D:HOH618 2.1 23.1 1.0
CG D:ASP201 3.0 35.6 1.0
OD2 D:ASP201 3.4 39.4 1.0
O D:HOH661 3.6 43.3 1.0
ZN D:ZN501 3.7 35.8 1.0
OE2 D:GLU230 4.1 35.0 1.0
CD2 D:HIS200 4.2 28.7 1.0
O D:HIS200 4.2 33.6 1.0
NE2 D:HIS233 4.3 31.4 1.0
OG1 D:THR271 4.3 34.2 1.0
O D:HOH683 4.3 52.4 1.0
OD2 D:ASP318 4.4 39.1 1.0
CB D:ASP201 4.4 36.9 1.0
NE2 D:HIS200 4.5 33.0 1.0
CD2 D:HIS204 4.5 36.0 1.0
NE2 D:HIS160 4.5 36.4 1.0
CD2 D:HIS160 4.5 40.2 1.0
CD2 D:HIS233 4.5 32.1 1.0
NE2 D:HIS204 4.7 33.9 1.0
CB D:THR271 4.8 39.1 1.0
O D:THR271 4.8 41.9 1.0
CG D:GLU230 4.8 39.8 1.0
CA D:ASP201 4.8 33.5 1.0
CD D:GLU230 4.9 41.4 1.0

Reference:

A.K.Singh, D.G.Brown. HPDE4D2 Structure with Inhibitor Npd-768 To Be Published.
Page generated: Wed Oct 2 09:08:55 2024

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