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Magnesium in PDB 6ft0: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-425

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-425

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-425:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-425, PDB code: 6ft0 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) 91.28 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.939, 110.812, 160.983, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 22.2

Other elements in 6ft0:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-425 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-425 (pdb code 6ft0). 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-425, PDB code: 6ft0:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6ft0

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-425


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-425 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:18.4
occ:1.00
 O A:HOH611 2.2 25.8 1.0
OD1 A:ASP201 2.2 29.5 1.0
O A:HOH696 2.2 26.8 1.0
O A:HOH697 2.2 29.0 1.0
O A:HOH675 2.2 30.7 1.0
O A:HOH608 2.2 27.0 1.0
CG A:ASP201 3.1 28.4 1.0
OD2 A:ASP201 3.3 26.4 1.0
ZN A:ZN501 3.9 35.8 1.0
O A:HOH657 4.1 39.8 1.0
O A:HOH680 4.1 37.6 1.0
O A:HIS200 4.1 27.2 1.0
CD2 A:HIS200 4.2 27.1 1.0
OE2 A:GLU230 4.2 34.0 1.0
OG1 A:THR271 4.2 33.2 1.0
NE2 A:HIS233 4.3 31.8 1.0
CD2 A:HIS233 4.3 31.7 1.0
CB A:ASP201 4.5 28.0 1.0
CD2 A:HIS204 4.6 31.9 1.0
OD2 A:ASP318 4.6 38.9 1.0
NE2 A:HIS200 4.6 27.5 1.0
C27 A:E6E509 4.6 46.9 1.0
O A:HOH648 4.7 44.7 1.0
O A:THR271 4.8 36.3 1.0
CB A:THR271 4.8 33.8 1.0
C26 A:E6E509 4.8 49.0 1.0
NE2 A:HIS204 4.8 31.6 1.0
CG A:GLU230 4.8 31.9 1.0
CA A:ASP201 4.8 29.3 1.0
CD2 A:HIS160 4.9 34.7 1.0
CD A:GLU230 4.9 33.3 1.0
NE2 A:HIS160 4.9 39.7 1.0
C A:HIS200 5.0 26.3 1.0

Magnesium binding site 2 out of 4 in 6ft0

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Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-425


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-425 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:18.8
occ:1.00
 O B:HOH620 2.0 23.9 1.0
OD1 B:ASP201 2.0 29.4 1.0
O B:HOH649 2.0 27.6 1.0
O B:HOH678 2.0 27.5 1.0
O B:HOH622 2.1 31.0 1.0
O B:HOH672 2.2 27.9 1.0
CG B:ASP201 3.1 27.7 1.0
OD2 B:ASP201 3.5 28.0 1.0
ZN B:ZN501 3.8 35.8 1.0
OE2 B:GLU230 4.0 31.4 1.0
O B:HOH677 4.1 27.1 1.0
O B:HIS200 4.1 29.6 1.0
O B:HOH696 4.2 27.4 1.0
NE2 B:HIS233 4.2 24.5 1.0
OG1 B:THR271 4.2 34.8 1.0
CD2 B:HIS200 4.2 26.5 1.0
CB B:ASP201 4.4 29.3 1.0
CD2 B:HIS233 4.4 26.9 1.0
O B:THR271 4.5 30.8 1.0
OD2 B:ASP318 4.5 31.7 1.0
C27 B:E6E509 4.6 38.8 1.0
C26 B:E6E509 4.6 37.7 1.0
CD2 B:HIS204 4.6 28.3 1.0
O B:HOH607 4.6 36.2 1.0
NE2 B:HIS200 4.7 27.0 1.0
CB B:THR271 4.7 35.5 1.0
CA B:ASP201 4.8 30.7 1.0
CG B:GLU230 4.8 30.4 1.0
NE2 B:HIS160 4.8 31.4 1.0
NE2 B:HIS204 4.8 31.3 1.0
CD B:GLU230 4.8 32.3 1.0
CD2 B:HIS160 4.9 31.5 1.0
C B:HIS200 5.0 26.4 1.0

Magnesium binding site 3 out of 4 in 6ft0

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Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-425


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-425 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg503

b:19.2
occ:1.00
 OD1 C:ASP201 2.0 26.9 1.0
O C:HOH664 2.0 24.1 1.0
O C:HOH633 2.0 25.1 1.0
O C:HOH628 2.0 25.7 1.0
O C:HOH678 2.1 28.1 1.0
O C:HOH655 2.1 29.3 1.0
CG C:ASP201 3.0 27.9 1.0
OD2 C:ASP201 3.4 27.9 1.0
ZN C:ZN502 3.9 35.7 1.0
OE2 C:GLU230 4.0 33.9 1.0
NE2 C:HIS233 4.1 26.4 1.0
O C:HIS200 4.1 30.3 1.0
O C:HOH669 4.2 30.6 1.0
O C:HOH666 4.2 32.5 1.0
CD2 C:HIS200 4.2 26.8 1.0
OG1 C:THR271 4.2 34.7 1.0
CD2 C:HIS233 4.3 24.1 1.0
CB C:ASP201 4.4 26.3 1.0
CD2 C:HIS204 4.5 24.6 1.0
OD2 C:ASP318 4.6 35.5 1.0
O C:THR271 4.6 30.2 1.0
NE2 C:HIS200 4.7 28.8 1.0
CB C:THR271 4.7 35.6 1.0
CA C:ASP201 4.7 29.2 1.0
O C:HOH626 4.8 34.0 1.0
C27 C:E6E510 4.8 41.8 1.0
CG C:GLU230 4.8 33.4 1.0
CD2 C:HIS160 4.8 35.4 1.0
NE2 C:HIS204 4.8 22.6 1.0
NE2 C:HIS160 4.8 30.1 1.0
CD C:GLU230 4.8 36.7 1.0
C26 C:E6E510 4.9 42.7 1.0
C C:HIS200 4.9 29.7 1.0

Magnesium binding site 4 out of 4 in 6ft0

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Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-425


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-425 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:16.9
occ:1.00
 O D:HOH648 2.0 23.9 1.0
O D:HOH663 2.0 21.6 1.0
O D:HOH699 2.0 29.6 1.0
O D:HOH727 2.0 26.5 1.0
O D:HOH666 2.0 29.9 1.0
OD1 D:ASP201 2.1 24.0 1.0
CG D:ASP201 3.1 28.7 1.0
OD2 D:ASP201 3.6 25.2 1.0
ZN D:ZN502 3.9 31.0 1.0
OE2 D:GLU230 4.0 30.1 1.0
O D:HOH697 4.1 30.8 1.0
NE2 D:HIS233 4.1 22.1 1.0
O D:HOH702 4.1 30.2 1.0
CD2 D:HIS200 4.2 20.5 1.0
O D:HIS200 4.2 25.1 1.0
OG1 D:THR271 4.3 26.2 1.0
C27 D:E6E517 4.4 42.3 1.0
CD2 D:HIS233 4.4 22.9 1.0
OD2 D:ASP318 4.5 27.6 1.0
CB D:ASP201 4.5 27.3 1.0
CD2 D:HIS204 4.6 31.6 1.0
O D:THR271 4.6 31.4 1.0
NE2 D:HIS200 4.6 22.2 1.0
CG D:GLU230 4.7 27.5 1.0
O D:HOH638 4.7 34.9 1.0
C26 D:E6E517 4.7 38.9 1.0
CB D:THR271 4.7 29.8 1.0
NE2 D:HIS204 4.8 28.8 1.0
CD D:GLU230 4.8 30.2 1.0
NE2 D:HIS160 4.8 34.2 1.0
CA D:ASP201 4.8 27.0 1.0
CD2 D:HIS160 4.9 30.5 1.0
C D:HIS200 5.0 25.2 1.0

Reference:

A.K.Singh, D.G.Brown. HPDE4D2 Structure with Inhibitor Npd-425 To Be Published.
Page generated: Wed Aug 13 06:12:47 2025

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