Magnesium in PDB 6iag: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-637

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-637

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-637:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-637, PDB code: 6iag was solved by A.K.Singh, D.G.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 84.50 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.108, 110.311, 160.722, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 24.6

Other elements in 6iag:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-637 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-637 (pdb code 6iag). 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-637, PDB code: 6iag:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6iag

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-637


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-637 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:19.4
occ:1.00
 O A:HOH634 1.9 19.8 1.0
O A:HOH703 1.9 25.3 1.0
O A:HOH665 1.9 21.1 1.0
OD1 A:ASP201 2.0 22.6 1.0
O A:HOH629 2.1 23.2 1.0
O A:HOH682 2.1 24.9 1.0
CG A:ASP201 3.0 22.2 1.0
OD2 A:ASP201 3.4 25.2 1.0
O A:HOH742 3.5 42.9 1.0
ZN A:ZN501 3.7 29.2 1.0
O A:HOH690 3.9 29.3 1.0
O A:HOH661 4.0 33.6 1.0
NE2 A:HIS233 4.1 23.9 1.0
CD2 A:HIS200 4.2 22.8 1.0
O A:HIS200 4.2 20.1 1.0
OE2 A:GLU230 4.2 27.4 1.0
OG1 A:THR271 4.2 24.1 1.0
CD2 A:HIS233 4.3 24.5 1.0
CB A:ASP201 4.4 23.6 1.0
OD2 A:ASP318 4.4 39.2 1.0
NE2 A:HIS200 4.5 25.2 1.0
CD2 A:HIS204 4.5 25.9 1.0
CD2 A:HIS160 4.7 28.4 1.0
CA A:ASP201 4.7 24.8 1.0
CB A:THR271 4.8 24.4 1.0
NE2 A:HIS204 4.8 24.6 1.0
NE2 A:HIS160 4.9 29.3 1.0
CG A:GLU230 4.9 24.0 1.0
O A:THR271 4.9 34.0 1.0
C A:HIS200 4.9 21.0 1.0
CD A:GLU230 4.9 24.6 1.0

Magnesium binding site 2 out of 4 in 6iag

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Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-637


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-637 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:17.8
occ:1.00
 O B:HOH701 1.8 21.0 1.0
O B:HOH708 1.9 26.6 1.0
O B:HOH623 1.9 20.6 1.0
O B:HOH648 1.9 23.5 1.0
OD1 B:ASP201 1.9 25.9 1.0
O B:HOH665 1.9 25.3 1.0
CG B:ASP201 2.9 25.5 1.0
OD2 B:ASP201 3.3 31.2 1.0
ZN B:ZN501 3.7 31.3 1.0
O B:HOH729 3.9 25.6 1.0
O B:HIS200 4.1 20.8 1.0
CD2 B:HIS200 4.1 26.2 1.0
NE2 B:HIS233 4.2 28.7 1.0
OE2 B:GLU230 4.2 26.7 1.0
O B:HOH731 4.2 27.5 1.0
CB B:ASP201 4.3 29.4 1.0
OG1 B:THR271 4.3 29.4 1.0
CD2 B:HIS233 4.4 27.4 1.0
NE2 B:HIS200 4.5 25.7 1.0
OD2 B:ASP318 4.5 29.9 1.0
CD2 B:HIS204 4.6 25.4 1.0
CA B:ASP201 4.6 26.6 1.0
CD2 B:HIS160 4.7 28.1 1.0
O B:HOH612 4.7 43.2 1.0
O B:THR271 4.8 30.7 1.0
CB B:THR271 4.8 29.7 1.0
CG B:GLU230 4.8 25.6 1.0
NE2 B:HIS204 4.8 24.5 1.0
NE2 B:HIS160 4.9 24.9 1.0
C B:HIS200 4.9 23.4 1.0
CD B:GLU230 5.0 29.2 1.0

Magnesium binding site 3 out of 4 in 6iag

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Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-637


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-637 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:17.3
occ:1.00
 O C:HOH624 1.9 22.5 1.0
O C:HOH695 1.9 21.7 1.0
O C:HOH666 1.9 20.2 1.0
O C:HOH641 1.9 22.9 1.0
O C:HOH667 1.9 22.9 1.0
OD1 C:ASP201 2.0 23.0 1.0
CG C:ASP201 3.0 22.1 1.0
OD2 C:ASP201 3.3 26.5 1.0
ZN C:ZN501 3.7 31.0 1.0
O C:HOH680 4.0 27.7 1.0
O C:HOH705 4.1 31.4 1.0
O C:HIS200 4.1 22.1 1.0
CD2 C:HIS200 4.1 24.7 1.0
OE2 C:GLU230 4.1 24.0 1.0
NE2 C:HIS233 4.2 21.2 1.0
OG1 C:THR271 4.3 25.9 1.0
CB C:ASP201 4.3 21.8 1.0
CD2 C:HIS233 4.4 21.3 1.0
NE2 C:HIS200 4.5 25.8 1.0
CD2 C:HIS204 4.6 21.0 1.0
O C:HOH623 4.6 34.9 1.0
O C:THR271 4.6 27.1 1.0
OD2 C:ASP318 4.7 31.9 1.0
CD2 C:HIS160 4.7 24.4 1.0
CB C:THR271 4.7 25.2 1.0
CA C:ASP201 4.7 23.7 1.0
NE2 C:HIS160 4.8 24.6 1.0
O C:HOH699 4.8 50.8 1.0
NE2 C:HIS204 4.9 19.1 1.0
C C:HIS200 5.0 22.1 1.0
CG C:GLU230 5.0 27.1 1.0
CD C:GLU230 5.0 27.7 1.0

Magnesium binding site 4 out of 4 in 6iag

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Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-637


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-637 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:15.5
occ:1.00
 O D:HOH692 1.8 21.8 1.0
O D:HOH613 1.9 17.9 1.0
O D:HOH740 1.9 24.4 1.0
O D:HOH659 1.9 20.7 1.0
O D:HOH642 1.9 22.1 1.0
OD1 D:ASP201 2.0 19.0 1.0
CG D:ASP201 3.1 21.0 1.0
OD2 D:ASP201 3.4 21.8 1.0
ZN D:ZN501 3.7 26.1 1.0
O D:HOH742 4.0 25.3 1.0
OE2 D:GLU230 4.0 28.7 1.0
CD2 D:HIS200 4.1 19.8 1.0
O D:HOH705 4.2 32.6 1.0
O D:HIS200 4.2 20.0 1.0
NE2 D:HIS233 4.2 20.9 1.0
OG1 D:THR271 4.3 22.3 1.0
CD2 D:HIS233 4.4 20.7 1.0
CB D:ASP201 4.4 22.3 1.0
OD2 D:ASP318 4.4 25.1 1.0
NE2 D:HIS200 4.4 20.8 1.0
CD2 D:HIS204 4.6 26.1 1.0
O D:HOH674 4.6 47.8 1.0
O D:THR271 4.7 25.1 1.0
CD2 D:HIS160 4.7 29.3 1.0
CG D:GLU230 4.7 24.6 1.0
NE2 D:HIS160 4.8 29.8 1.0
CA D:ASP201 4.8 21.2 1.0
NE2 D:HIS204 4.8 25.5 1.0
CD D:GLU230 4.9 25.4 1.0
CB D:THR271 4.9 22.4 1.0

Reference:

A.K.Singh, D.G.Brown. HPDE4D2 Structure with Inhibitor Npd-637 To Be Published.
Page generated: Mon Dec 14 22:56:33 2020

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