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Magnesium in PDB 7abe: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-769

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-769

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-769:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-769, PDB code: 7abe 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) 84.16 / 1.83
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.701, 111.245, 160.084, 90, 90, 90
R / Rfree (%) 17.9 / 20.8

Other elements in 7abe:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-769 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-769 (pdb code 7abe). 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-769, PDB code: 7abe:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7abe

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-769


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-769 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:21.1
occ:1.00
 O A:HOH654 1.9 27.1 1.0
OD1 A:ASP201 2.1 25.5 1.0
O A:HOH697 2.1 24.0 1.0
O A:HOH676 2.1 26.3 1.0
O A:HOH698 2.1 29.3 1.0
O A:HOH647 2.2 26.1 1.0
CG A:ASP201 3.1 24.1 1.0
OD2 A:ASP201 3.4 24.0 1.0
ZN A:ZN501 3.7 29.3 1.0
O A:HOH713 4.0 31.5 1.0
O A:HOH705 4.1 30.7 1.0
OE2 A:GLU230 4.1 28.9 1.0
NE2 A:HIS233 4.1 24.5 1.0
CD2 A:HIS200 4.2 26.7 1.0
O A:HIS200 4.2 22.0 1.0
OG1 A:THR271 4.2 26.3 1.0
CD2 A:HIS233 4.4 23.1 1.0
OD2 A:ASP318 4.4 37.3 1.0
CB A:ASP201 4.5 24.4 1.0
O A:HOH615 4.5 44.9 1.0
NE2 A:HIS200 4.5 24.4 1.0
CD2 A:HIS204 4.6 28.1 1.0
O A:THR271 4.7 30.4 1.0
NE2 A:HIS160 4.7 30.2 1.0
CD2 A:HIS160 4.7 32.5 1.0
CB A:THR271 4.8 26.1 1.0
NE2 A:HIS204 4.8 25.1 1.0
CG A:GLU230 4.8 24.6 1.0
CA A:ASP201 4.8 23.9 1.0
CD A:GLU230 4.9 28.3 1.0
C A:HIS200 5.0 22.8 1.0

Magnesium binding site 2 out of 4 in 7abe

Go back to Magnesium Binding Sites List in 7abe
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-769


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-769 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:22.7
occ:1.00
 OD1 B:ASP201 2.1 26.2 1.0
O B:HOH672 2.1 25.3 1.0
O B:HOH645 2.1 26.1 1.0
O B:HOH727 2.1 29.2 1.0
O B:HOH675 2.2 24.6 1.0
O B:HOH616 2.3 27.0 1.0
CG B:ASP201 3.1 23.9 1.0
OD2 B:ASP201 3.5 25.5 1.0
O B:HOH764 3.8 56.0 1.0
ZN B:ZN501 3.8 30.6 1.0
O B:HOH748 4.0 28.0 1.0
OE2 B:GLU230 4.1 31.4 1.0
NE2 B:HIS233 4.1 25.1 1.0
O B:HOH720 4.2 27.5 1.0
O B:HIS200 4.2 25.8 1.0
OG1 B:THR271 4.2 31.2 1.0
CD2 B:HIS200 4.2 24.5 1.0
CD2 B:HIS233 4.4 28.2 1.0
CB B:ASP201 4.4 26.6 1.0
OD2 B:ASP318 4.5 31.7 1.0
CD2 B:HIS204 4.5 23.6 1.0
NE2 B:HIS200 4.6 24.8 1.0
O B:THR271 4.7 32.9 1.0
CB B:THR271 4.7 31.1 1.0
NE2 B:HIS160 4.7 26.9 1.0
CD2 B:HIS160 4.7 28.9 1.0
NE2 B:HIS204 4.8 24.1 1.0
CG B:GLU230 4.8 28.4 1.0
CA B:ASP201 4.8 26.7 1.0
O B:HOH622 4.8 42.3 1.0
CD B:GLU230 4.9 30.7 1.0

Magnesium binding site 3 out of 4 in 7abe

Go back to Magnesium Binding Sites List in 7abe
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-769


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-769 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:20.8
occ:1.00
 OD1 C:ASP201 2.0 26.2 1.0
O C:HOH661 2.1 24.7 1.0
O C:HOH708 2.1 27.6 1.0
O C:HOH641 2.1 26.3 1.0
O C:HOH664 2.2 26.4 1.0
O C:HOH603 2.2 26.4 1.0
CG C:ASP201 3.1 23.6 1.0
OD2 C:ASP201 3.4 25.5 1.0
ZN C:ZN501 3.8 30.6 1.0
O C:HOH703 4.0 28.5 1.0
OE2 C:GLU230 4.0 30.3 1.0
O C:HOH612 4.1 29.4 1.0
NE2 C:HIS233 4.1 22.8 1.0
O C:HIS200 4.2 25.2 1.0
CD2 C:HIS200 4.2 24.3 1.0
OG1 C:THR271 4.2 26.8 1.0
CD2 C:HIS233 4.4 20.9 1.0
CB C:ASP201 4.4 23.7 1.0
CD2 C:HIS204 4.5 25.3 1.0
OD2 C:ASP318 4.6 32.1 1.0
NE2 C:HIS200 4.6 25.4 1.0
O C:THR271 4.6 29.3 1.0
O C:HOH637 4.7 39.0 1.0
CD2 C:HIS160 4.7 27.3 1.0
CB C:THR271 4.7 32.5 1.0
NE2 C:HIS160 4.7 27.5 1.0
NE2 C:HIS204 4.8 25.6 1.0
CG C:GLU230 4.8 27.1 1.0
CA C:ASP201 4.8 26.0 1.0
CD C:GLU230 4.9 30.2 1.0
C C:HIS200 5.0 23.2 1.0

Magnesium binding site 4 out of 4 in 7abe

Go back to Magnesium Binding Sites List in 7abe
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-769


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-769 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:18.9
occ:1.00
 O D:HOH673 2.0 21.8 1.0
O D:HOH646 2.0 25.8 1.0
O D:HOH757 2.0 26.1 1.0
O D:HOH735 2.1 21.6 1.0
OD1 D:ASP201 2.1 21.2 1.0
O D:HOH691 2.1 23.9 1.0
CG D:ASP201 3.1 25.5 1.0
OD2 D:ASP201 3.4 22.9 1.0
ZN D:ZN502 3.8 26.7 1.0
O D:HOH754 4.0 28.5 1.0
OE2 D:GLU230 4.1 28.9 1.0
O D:HOH729 4.1 31.7 1.0
NE2 D:HIS233 4.1 21.1 1.0
CD2 D:HIS200 4.2 19.5 1.0
OG1 D:THR271 4.2 23.4 1.0
O D:HIS200 4.3 21.3 1.0
CD2 D:HIS233 4.4 20.6 1.0
CB D:ASP201 4.5 23.1 1.0
OD2 D:ASP318 4.5 29.8 1.0
CD2 D:HIS204 4.6 25.7 1.0
NE2 D:HIS200 4.6 20.8 1.0
NE2 D:HIS160 4.7 30.8 1.0
O D:THR271 4.7 28.6 1.0
CG D:GLU230 4.7 25.6 1.0
CD2 D:HIS160 4.7 28.0 1.0
CB D:THR271 4.8 24.3 1.0
O D:HOH669 4.8 37.2 1.0
NE2 D:HIS204 4.8 27.2 1.0
CA D:ASP201 4.8 22.1 1.0
CD D:GLU230 4.9 25.9 1.0

Reference:

A.K.Singh, D.G.Brown. HPDE4D2 Structure with Inhibitor Npd-769 To Be Published.
Page generated: Wed Oct 2 09:09:23 2024

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