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Magnesium in PDB 7a8q: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-654

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-654

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-654:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-654, PDB code: 7a8q 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) 91.49 / 2.24
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.349, 111.441, 160.227, 90, 90, 90
R / Rfree (%) 18.7 / 22.9

Other elements in 7a8q:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-654 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-654 (pdb code 7a8q). 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-654, PDB code: 7a8q:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7a8q

Go back to Magnesium Binding Sites List in 7a8q
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-654


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-654 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:32.8
occ:1.00
 O A:HOH613 2.0 34.9 1.0
O A:HOH641 2.0 37.8 1.0
OD1 A:ASP201 2.1 40.0 1.0
O A:HOH662 2.1 43.0 1.0
O A:HOH625 2.1 37.5 1.0
O A:HOH606 2.3 35.9 1.0
CG A:ASP201 3.2 40.5 1.0
O A:HOH718 3.5 59.9 1.0
OD2 A:ASP201 3.6 35.2 1.0
O A:HOH627 3.7 42.0 1.0
ZN A:ZN501 3.9 44.1 1.0
O A:HOH657 4.0 45.6 1.0
OE2 A:GLU230 4.1 47.6 1.0
O A:HIS200 4.2 35.6 1.0
OG1 A:THR271 4.2 40.0 1.0
CD2 A:HIS200 4.2 38.3 1.0
NE2 A:HIS233 4.3 39.7 1.0
O A:HOH609 4.4 59.5 1.0
OD2 A:ASP318 4.4 45.0 1.0
CD2 A:HIS233 4.5 40.5 1.0
CB A:ASP201 4.5 39.4 1.0
NE2 A:HIS200 4.6 40.3 1.0
CD2 A:HIS204 4.7 41.7 1.0
O A:THR271 4.7 52.8 1.0
CB A:THR271 4.7 43.8 1.0
NE2 A:HIS160 4.7 42.3 1.0
CD2 A:HIS160 4.8 38.8 1.0
NE2 A:HIS204 4.9 37.2 1.0
CG A:GLU230 4.9 38.2 1.0
CA A:ASP201 4.9 33.7 1.0
O A:HOH675 4.9 70.3 1.0
CD A:GLU230 4.9 41.3 1.0

Magnesium binding site 2 out of 4 in 7a8q

Go back to Magnesium Binding Sites List in 7a8q
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-654


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-654 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:33.7
occ:1.00
 OD1 B:ASP201 1.9 39.7 1.0
O B:HOH654 2.0 34.0 1.0
O B:HOH660 2.0 40.1 1.0
O B:HOH612 2.1 41.2 1.0
O B:HOH633 2.2 45.8 1.0
O B:HOH607 2.2 32.6 1.0
CG B:ASP201 3.0 42.1 1.0
OD2 B:ASP201 3.5 49.7 1.0
O B:HOH682 3.5 60.1 1.0
ZN B:ZN501 3.8 53.0 1.0
O B:HOH655 3.9 39.6 1.0
O B:HIS200 4.1 46.3 1.0
NE2 B:HIS233 4.2 42.4 1.0
CD2 B:HIS200 4.2 42.9 1.0
OE2 B:GLU230 4.2 46.3 1.0
OG1 B:THR271 4.3 47.7 1.0
CB B:ASP201 4.3 44.9 1.0
CD2 B:HIS233 4.4 41.9 1.0
O B:HOH621 4.4 47.9 1.0
OD2 B:ASP318 4.5 57.0 1.0
NE2 B:HIS200 4.5 49.9 1.0
CD2 B:HIS204 4.6 41.4 1.0
CB B:THR271 4.7 56.2 1.0
CD2 B:HIS160 4.7 42.9 1.0
CA B:ASP201 4.7 44.7 1.0
O B:THR271 4.8 53.2 1.0
NE2 B:HIS160 4.8 43.7 1.0
O B:HOH626 4.8 61.2 1.0
NE2 B:HIS204 4.9 40.5 1.0
CG B:GLU230 4.9 46.6 1.0
C B:HIS200 4.9 43.9 1.0

Magnesium binding site 3 out of 4 in 7a8q

Go back to Magnesium Binding Sites List in 7a8q
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-654


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-654 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:32.8
occ:1.00
 OD1 C:ASP201 1.9 36.5 1.0
O C:HOH612 1.9 38.1 1.0
O C:HOH616 2.0 33.8 1.0
O C:HOH655 2.0 34.1 1.0
O C:HOH630 2.0 39.1 1.0
O C:HOH645 2.2 40.4 1.0
CG C:ASP201 3.0 40.8 1.0
O C:HOH673 3.3 30.0 1.0
OD2 C:ASP201 3.4 47.0 1.0
ZN C:ZN501 3.7 48.9 1.0
O C:HOH631 3.9 40.9 1.0
O C:HIS200 4.0 37.3 1.0
CD2 C:HIS200 4.1 40.1 1.0
NE2 C:HIS233 4.2 33.1 1.0
OE2 C:GLU230 4.2 40.8 1.0
O C:HOH635 4.2 54.9 1.0
OG1 C:THR271 4.2 41.7 1.0
CB C:ASP201 4.3 38.0 1.0
CD2 C:HIS233 4.4 34.0 1.0
OD2 C:ASP318 4.5 51.3 1.0
NE2 C:HIS200 4.5 39.2 1.0
CD2 C:HIS204 4.5 31.6 1.0
CA C:ASP201 4.7 36.3 1.0
CB C:THR271 4.7 47.5 1.0
CD2 C:HIS160 4.7 39.4 1.0
O C:THR271 4.7 44.8 1.0
NE2 C:HIS160 4.7 36.7 1.0
NE2 C:HIS204 4.9 30.1 1.0
C C:HIS200 4.9 40.0 1.0
CG C:GLU230 5.0 42.3 1.0

Magnesium binding site 4 out of 4 in 7a8q

Go back to Magnesium Binding Sites List in 7a8q
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-654


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-654 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:33.2
occ:1.00
 O D:HOH686 1.9 40.6 1.0
O D:HOH620 2.0 33.1 1.0
O D:HOH628 2.0 30.6 1.0
OD1 D:ASP201 2.1 34.4 1.0
O D:HOH656 2.1 33.9 1.0
O D:HOH666 2.1 42.0 1.0
CG D:ASP201 3.1 36.2 1.0
O D:HOH685 3.4 30.0 1.0
OD2 D:ASP201 3.5 36.4 1.0
ZN D:ZN501 3.9 42.3 1.0
OE2 D:GLU230 4.1 46.5 1.0
O D:HIS200 4.2 36.6 1.0
NE2 D:HIS233 4.3 32.5 1.0
O D:HOH654 4.3 52.5 1.0
OG1 D:THR271 4.3 38.2 1.0
CD2 D:HIS200 4.3 38.9 1.0
OD2 D:ASP318 4.4 42.3 1.0
O D:HOH603 4.5 43.5 1.0
CD2 D:HIS233 4.5 28.9 1.0
CB D:ASP201 4.5 36.3 1.0
CD2 D:HIS204 4.6 45.5 1.0
NE2 D:HIS200 4.6 40.6 1.0
O D:THR271 4.7 40.3 1.0
CB D:THR271 4.7 42.3 1.0
NE2 D:HIS160 4.7 47.4 1.0
CD2 D:HIS160 4.8 44.7 1.0
CG D:GLU230 4.8 43.2 1.0
NE2 D:HIS204 4.9 44.0 1.0
CD D:GLU230 4.9 49.8 1.0
CA D:ASP201 4.9 33.0 1.0

Reference:

A.K.Singh, D.G.Brown. HPDE4D2 Structure with Inhibitor Npd-654 To Be Published.
Page generated: Wed Oct 2 09:06:26 2024

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