Atomistry » Magnesium » PDB 7a1w-7ads » 7a9v
Atomistry »
  Magnesium »
    PDB 7a1w-7ads »
      7a9v »

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

Go back to Magnesium Binding Sites List in 7a9v
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: Wed Oct 2 09:06:40 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy