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Magnesium in PDB 7abj: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1361

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1361

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1361:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1361, PDB code: 7abj 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) 84.41 / 2.11
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.999, 111.037, 160.565, 90, 90, 90
R / Rfree (%) 18.1 / 21.8

Other elements in 7abj:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1361 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-1361 (pdb code 7abj). 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-1361, PDB code: 7abj:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7abj

Go back to Magnesium Binding Sites List in 7abj
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1361


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-1361 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:29.3
occ:1.00
 O A:HOH668 1.8 33.9 1.0
OD1 A:ASP201 2.0 32.3 1.0
O A:HOH646 2.0 35.4 1.0
O A:HOH623 2.1 32.5 1.0
O A:HOH695 2.1 36.8 1.0
O A:HOH638 2.2 33.6 1.0
CG A:ASP201 3.0 34.2 1.0
OD2 A:ASP201 3.4 31.6 1.0
O A:HOH703 3.7 66.7 1.0
ZN A:ZN501 3.8 40.4 1.0
O A:HOH655 3.9 44.4 1.0
O A:HOH673 4.0 37.8 1.0
OE2 A:GLU230 4.1 42.7 1.0
O A:HIS200 4.1 35.9 1.0
NE2 A:HIS233 4.1 36.9 1.0
CD2 A:HIS200 4.2 36.0 1.0
OG1 A:THR271 4.2 37.9 1.0
CD2 A:HIS233 4.4 36.5 1.0
CB A:ASP201 4.4 33.2 1.0
OD2 A:ASP318 4.6 48.8 1.0
CD2 A:HIS204 4.6 36.5 1.0
NE2 A:HIS200 4.7 39.0 1.0
O A:THR271 4.7 43.7 1.0
CB A:THR271 4.8 37.2 1.0
CA A:ASP201 4.8 30.8 1.0
CD2 A:HIS160 4.8 40.8 1.0
CG A:GLU230 4.8 35.8 1.0
NE2 A:HIS204 4.8 35.3 1.0
NE2 A:HIS160 4.8 38.0 1.0
O A:HOH716 4.8 63.4 1.0
CD A:GLU230 4.9 38.8 1.0
C A:HIS200 5.0 32.7 1.0

Magnesium binding site 2 out of 4 in 7abj

Go back to Magnesium Binding Sites List in 7abj
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1361


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-1361 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:31.8
occ:1.00
 OD1 B:ASP201 2.0 36.7 1.0
O B:HOH632 2.0 30.8 1.0
O B:HOH613 2.0 37.2 1.0
O B:HOH684 2.0 36.4 1.0
O B:HOH665 2.1 36.4 1.0
O B:HOH623 2.3 33.2 1.0
CG B:ASP201 3.1 33.8 1.0
OD2 B:ASP201 3.5 39.2 1.0
O B:HOH699 3.7 38.1 1.0
ZN B:ZN501 3.8 44.6 1.0
OE2 B:GLU230 4.1 42.7 1.0
NE2 B:HIS233 4.2 35.5 1.0
O B:HIS200 4.2 37.8 1.0
O B:HOH642 4.3 39.1 1.0
OG1 B:THR271 4.3 45.8 1.0
CD2 B:HIS200 4.3 35.5 1.0
CB B:ASP201 4.4 37.1 1.0
CD2 B:HIS233 4.5 37.5 1.0
O B:HOH607 4.5 60.2 1.0
OD2 B:ASP318 4.5 48.2 1.0
CD2 B:HIS204 4.6 35.3 1.0
O B:THR271 4.7 47.5 1.0
NE2 B:HIS200 4.7 39.1 1.0
CB B:THR271 4.7 48.0 1.0
NE2 B:HIS160 4.7 37.0 1.0
CD2 B:HIS160 4.7 41.2 1.0
NE2 B:HIS204 4.8 33.1 1.0
CA B:ASP201 4.8 39.0 1.0
CG B:GLU230 4.9 39.7 1.0
CD B:GLU230 4.9 41.2 1.0

Magnesium binding site 3 out of 4 in 7abj

Go back to Magnesium Binding Sites List in 7abj
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1361


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-1361 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg504

b:27.9
occ:1.00
 OD1 C:ASP201 1.9 33.0 1.0
O C:HOH646 2.0 31.6 1.0
O C:HOH640 2.0 32.8 1.0
O C:HOH616 2.0 34.5 1.0
O C:HOH613 2.1 32.3 1.0
O C:HOH638 2.2 37.3 1.0
CG C:ASP201 3.0 34.9 1.0
OD2 C:ASP201 3.4 36.6 1.0
ZN C:ZN503 3.7 41.8 1.0
O C:HOH658 3.9 39.1 1.0
O C:HIS200 4.1 33.2 1.0
OE2 C:GLU230 4.1 41.6 1.0
CD2 C:HIS200 4.1 34.5 1.0
O2 C:EDO511 4.2 46.8 1.0
NE2 C:HIS233 4.2 28.5 1.0
OG1 C:THR271 4.2 37.8 1.0
CB C:ASP201 4.3 32.9 1.0
CD2 C:HIS233 4.4 27.0 1.0
CD2 C:HIS204 4.5 29.4 1.0
NE2 C:HIS200 4.6 37.7 1.0
OD2 C:ASP318 4.6 43.3 1.0
CB C:THR271 4.7 43.3 1.0
CD2 C:HIS160 4.7 34.4 1.0
O C:THR271 4.7 38.9 1.0
CA C:ASP201 4.7 34.6 1.0
NE2 C:HIS160 4.7 32.6 1.0
NE2 C:HIS204 4.8 27.5 1.0
CG C:GLU230 4.9 37.5 1.0
O C:HOH614 4.9 49.6 1.0
O C:HOH681 4.9 58.4 1.0
C C:HIS200 4.9 35.3 1.0
CD C:GLU230 5.0 42.3 1.0

Magnesium binding site 4 out of 4 in 7abj

Go back to Magnesium Binding Sites List in 7abj
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1361


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-1361 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:26.3
occ:1.00
 O D:HOH658 2.0 27.1 1.0
O D:HOH660 2.0 28.9 1.0
OD1 D:ASP201 2.0 29.6 1.0
O D:HOH677 2.2 33.9 1.0
O D:HOH689 2.2 36.5 1.0
O D:HOH604 2.3 32.8 1.0
CG D:ASP201 3.1 33.9 1.0
OD2 D:ASP201 3.5 32.5 1.0
O D:HOH744 3.7 67.6 1.0
ZN D:ZN501 3.8 36.9 1.0
OE2 D:GLU230 4.0 39.5 1.0
O D:HOH722 4.0 36.7 1.0
O D:HIS200 4.1 33.0 1.0
NE2 D:HIS233 4.2 28.3 1.0
O D:HOH696 4.2 39.8 1.0
OG1 D:THR271 4.2 32.0 1.0
CD2 D:HIS200 4.2 29.7 1.0
CD2 D:HIS233 4.4 26.4 1.0
CB D:ASP201 4.4 33.0 1.0
OD2 D:ASP318 4.5 42.5 1.0
CD2 D:HIS204 4.6 38.7 1.0
O D:HOH614 4.6 50.2 1.0
NE2 D:HIS200 4.7 32.2 1.0
CG D:GLU230 4.7 34.0 1.0
O D:THR271 4.7 40.0 1.0
CB D:THR271 4.7 34.7 1.0
CD D:GLU230 4.8 39.6 1.0
CA D:ASP201 4.8 31.4 1.0
NE2 D:HIS160 4.8 41.0 1.0
CD2 D:HIS160 4.8 39.2 1.0
NE2 D:HIS204 4.9 35.1 1.0
C D:HIS200 5.0 27.8 1.0

Reference:

A.K.Singh, D.G.Brown. HPDE4D2 Structure with Inhibitor Npd-1361 To Be Published.
Page generated: Wed Oct 2 09:09:47 2024

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