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Magnesium in PDB 7ab9: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-656

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-656

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-656:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-656, PDB code: 7ab9 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) 91.69 / 2.19
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.168, 111.797, 160.261, 90, 90, 90
R / Rfree (%) 18.5 / 22.3

Other elements in 7ab9:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-656 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-656 (pdb code 7ab9). 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-656, PDB code: 7ab9:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7ab9

Go back to Magnesium Binding Sites List in 7ab9
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-656


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-656 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:24.4
occ:1.00
 O A:HOH613 2.0 33.3 1.0
OD1 A:ASP201 2.0 28.9 1.0
O A:HOH660 2.1 31.9 1.0
O A:HOH615 2.1 27.4 1.0
O A:HOH693 2.1 34.2 1.0
O A:HOH629 2.2 31.1 1.0
CG A:ASP201 3.1 30.6 1.0
OD2 A:ASP201 3.5 30.6 1.0
O A:HOH705 3.6 62.5 1.0
ZN A:ZN501 3.8 37.5 1.0
O A:HOH659 3.8 40.0 1.0
OE2 A:GLU230 4.1 38.9 1.0
NE2 A:HIS233 4.1 29.4 1.0
O A:HOH681 4.1 35.8 1.0
O A:HIS200 4.1 27.3 1.0
CD2 A:HIS200 4.2 33.5 1.0
OG1 A:THR271 4.3 35.5 1.0
CD2 A:HIS233 4.4 30.1 1.0
CB A:ASP201 4.4 31.9 1.0
OD2 A:ASP318 4.4 43.5 1.0
O A:HOH609 4.5 44.5 1.0
NE2 A:HIS200 4.6 36.9 1.0
CD2 A:HIS204 4.6 31.3 1.0
CB A:THR271 4.7 34.1 1.0
O A:THR271 4.7 43.8 1.0
CD2 A:HIS160 4.8 33.1 1.0
NE2 A:HIS160 4.8 35.0 1.0
CA A:ASP201 4.8 28.1 1.0
CG A:GLU230 4.9 35.1 1.0
NE2 A:HIS204 4.9 33.0 1.0
CD A:GLU230 5.0 37.8 1.0
C A:HIS200 5.0 26.3 1.0

Magnesium binding site 2 out of 4 in 7ab9

Go back to Magnesium Binding Sites List in 7ab9
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-656


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-656 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:29.2
occ:1.00
 OD1 B:ASP201 2.0 32.8 1.0
O B:HOH640 2.0 30.3 1.0
O B:HOH616 2.0 38.0 1.0
O B:HOH659 2.1 37.6 1.0
O B:HOH622 2.1 33.2 1.0
O B:HOH645 2.2 38.4 1.0
CG B:ASP201 3.1 34.1 1.0
OD2 B:ASP201 3.5 41.8 1.0
ZN B:ZN501 3.8 43.5 1.0
O B:HOH680 3.9 32.5 1.0
OE2 B:GLU230 4.1 40.9 1.0
O B:HIS200 4.1 37.0 1.0
NE2 B:HIS233 4.2 37.9 1.0
CD2 B:HIS200 4.2 32.4 1.0
O B:HOH657 4.2 39.7 1.0
OG1 B:THR271 4.3 41.8 1.0
CB B:ASP201 4.4 38.1 1.0
CD2 B:HIS233 4.4 36.8 1.0
OD2 B:ASP318 4.5 47.0 1.0
CD2 B:HIS204 4.6 34.2 1.0
NE2 B:HIS200 4.6 38.1 1.0
O B:THR271 4.7 49.8 1.0
CB B:THR271 4.7 47.8 1.0
CA B:ASP201 4.7 37.2 1.0
CD2 B:HIS160 4.8 37.0 1.0
NE2 B:HIS160 4.8 34.8 1.0
O B:HOH644 4.8 49.9 1.0
CG B:GLU230 4.8 37.9 1.0
NE2 B:HIS204 4.9 32.5 1.0
CD B:GLU230 4.9 38.4 1.0
C B:HIS200 5.0 35.6 1.0

Magnesium binding site 3 out of 4 in 7ab9

Go back to Magnesium Binding Sites List in 7ab9
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-656


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-656 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:27.1
occ:1.00
 O C:HOH621 2.0 32.8 1.0
O C:HOH611 2.0 29.9 1.0
OD1 C:ASP201 2.0 34.0 1.0
O C:HOH664 2.0 32.7 1.0
O C:HOH628 2.1 31.2 1.0
O C:HOH636 2.2 37.2 1.0
CG C:ASP201 3.1 35.1 1.0
OD2 C:ASP201 3.5 38.1 1.0
ZN C:ZN501 3.7 42.6 1.0
O C:HOH662 3.9 34.2 1.0
OE2 C:GLU230 4.0 38.3 1.0
O C:HOH651 4.1 47.9 1.0
NE2 C:HIS233 4.2 28.0 1.0
O C:HIS200 4.2 34.0 1.0
CD2 C:HIS200 4.2 33.0 1.0
OG1 C:THR271 4.3 36.2 1.0
CD2 C:HIS233 4.4 29.6 1.0
CB C:ASP201 4.4 35.3 1.0
OD2 C:ASP318 4.5 41.1 1.0
CD2 C:HIS204 4.6 29.0 1.0
NE2 C:HIS200 4.6 34.2 1.0
O C:THR271 4.7 41.9 1.0
O C:HOH623 4.7 51.5 1.0
NE2 C:HIS160 4.7 34.8 1.0
CD2 C:HIS160 4.7 35.2 1.0
CB C:THR271 4.7 37.8 1.0
CA C:ASP201 4.8 31.5 1.0
NE2 C:HIS204 4.9 26.0 1.0
CG C:GLU230 4.9 36.2 1.0
CD C:GLU230 4.9 40.4 1.0
O C:HOH632 4.9 60.6 1.0

Magnesium binding site 4 out of 4 in 7ab9

Go back to Magnesium Binding Sites List in 7ab9
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-656


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-656 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:26.8
occ:1.00
 O D:HOH687 1.9 33.1 1.0
O D:HOH682 2.0 34.8 1.0
OD1 D:ASP201 2.1 30.5 1.0
O D:HOH645 2.1 30.4 1.0
O D:HOH649 2.1 32.5 1.0
O D:HOH610 2.1 32.6 1.0
CG D:ASP201 3.1 33.1 1.0
OD2 D:ASP201 3.5 30.9 1.0
ZN D:ZN501 3.8 37.4 1.0
OE2 D:GLU230 4.0 41.1 1.0
O D:HOH688 4.1 37.3 1.0
NE2 D:HIS233 4.1 31.2 1.0
CD2 D:HIS200 4.3 27.7 1.0
OG1 D:THR271 4.3 31.8 1.0
O D:HIS200 4.3 31.9 1.0
O D:HOH674 4.4 42.2 1.0
CD2 D:HIS233 4.4 29.5 1.0
O D:HOH623 4.5 54.8 1.0
CB D:ASP201 4.5 33.3 1.0
OD2 D:ASP318 4.5 39.5 1.0
NE2 D:HIS200 4.6 29.5 1.0
CD2 D:HIS204 4.6 39.0 1.0
O D:THR271 4.7 37.0 1.0
CB D:THR271 4.7 35.6 1.0
CG D:GLU230 4.7 36.7 1.0
CA D:ASP201 4.8 31.4 1.0
CD2 D:HIS160 4.8 43.0 1.0
CD D:GLU230 4.8 44.2 1.0
NE2 D:HIS160 4.8 42.4 1.0
NE2 D:HIS204 4.9 38.4 1.0

Reference:

A.K.Singh, D.G.Brown. HPDE4D2 Structure with Inhibitor Npd-656 To Be Published.
Page generated: Thu Aug 14 00:37:54 2025

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