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Magnesium in PDB 6fta: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-3098

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-3098

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-3098:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-3098, PDB code: 6fta 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) 80.67 / 2.34
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.990, 110.760, 161.340, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 24

Other elements in 6fta:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-3098 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-3098 (pdb code 6fta). 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-3098, PDB code: 6fta:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6fta

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-3098


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-3098 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:29.2
occ:1.00
 O A:HOH629 1.8 37.0 1.0
O A:HOH659 1.8 43.4 1.0
O A:HOH624 1.9 27.7 1.0
OD1 A:ASP201 2.0 37.4 1.0
O A:HOH605 2.1 30.0 1.0
O A:HOH627 2.1 34.1 1.0
CG A:ASP201 3.0 39.8 1.0
OD2 A:ASP201 3.3 42.3 1.0
ZN A:ZN501 3.7 43.8 1.0
O A:HOH654 3.9 41.6 1.0
OG1 A:THR271 4.0 35.6 1.0
O A:HIS200 4.0 33.7 1.0
O A:HOH631 4.1 44.6 1.0
CD2 A:HIS200 4.1 39.7 1.0
OE2 A:GLU230 4.2 42.5 1.0
NE2 A:HIS233 4.3 34.6 1.0
C27 A:E6N510 4.4 63.3 1.0
CB A:ASP201 4.4 36.2 1.0
OD2 A:ASP318 4.5 46.1 1.0
CD2 A:HIS233 4.5 35.9 1.0
NE2 A:HIS200 4.5 41.5 1.0
CD2 A:HIS204 4.6 38.0 1.0
O A:THR271 4.6 45.8 1.0
CD2 A:HIS160 4.6 44.5 1.0
CB A:THR271 4.6 38.8 1.0
NE2 A:HIS160 4.7 41.8 1.0
CA A:ASP201 4.8 36.5 1.0
O A:HOH621 4.8 50.8 1.0
C26 A:E6N510 4.8 71.2 1.0
NE2 A:HIS204 4.8 41.0 1.0
CG A:GLU230 4.9 40.2 1.0
C A:HIS200 4.9 36.6 1.0

Magnesium binding site 2 out of 4 in 6fta

Go back to Magnesium Binding Sites List in 6fta
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-3098


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-3098 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:28.4
occ:1.00
 O B:HOH652 1.9 31.6 1.0
O B:HOH664 1.9 32.0 1.0
OD1 B:ASP201 1.9 37.6 1.0
O B:HOH615 2.0 30.4 1.0
O B:HOH627 2.1 33.7 1.0
O B:HOH650 2.2 33.6 1.0
CG B:ASP201 2.9 40.5 1.0
OD2 B:ASP201 3.2 46.1 1.0
ZN B:ZN501 3.8 44.1 1.0
OE2 B:GLU230 3.9 41.2 1.0
O B:HOH680 3.9 39.4 1.0
O B:HIS200 4.0 33.6 1.0
O B:HOH660 4.1 36.5 1.0
CD2 B:HIS200 4.1 34.0 1.0
OG1 B:THR271 4.1 39.2 1.0
C27 B:E6N508 4.3 56.2 1.0
CB B:ASP201 4.3 38.2 1.0
NE2 B:HIS233 4.4 31.4 1.0
O B:THR271 4.5 40.1 1.0
CD2 B:HIS233 4.5 33.5 1.0
NE2 B:HIS200 4.6 32.8 1.0
C26 B:E6N508 4.6 60.6 1.0
OD2 B:ASP318 4.6 37.6 1.0
CD2 B:HIS204 4.6 35.8 1.0
O B:HOH623 4.7 58.4 1.0
CB B:THR271 4.7 43.2 1.0
CA B:ASP201 4.8 34.5 1.0
CD2 B:HIS160 4.8 43.9 1.0
CD B:GLU230 4.8 43.2 1.0
NE2 B:HIS204 4.8 37.4 1.0
NE2 B:HIS160 4.9 39.4 1.0
CG B:GLU230 4.9 42.1 1.0
C B:HIS200 5.0 32.8 1.0

Magnesium binding site 3 out of 4 in 6fta

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Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-3098


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-3098 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:23.9
occ:1.00
 O C:HOH621 1.9 27.2 1.0
OD1 C:ASP201 1.9 32.7 1.0
O C:HOH609 1.9 31.0 1.0
O C:HOH641 2.0 26.6 1.0
O C:HOH648 2.0 25.3 1.0
O C:HOH635 2.1 34.6 1.0
CG C:ASP201 3.0 36.9 1.0
OD2 C:ASP201 3.3 43.1 1.0
ZN C:ZN501 3.8 42.8 1.0
O C:HIS200 3.8 35.5 1.0
OG1 C:THR271 3.9 40.2 1.0
OE2 C:GLU230 4.0 43.1 1.0
O C:HOH661 4.0 35.8 1.0
CD2 C:HIS200 4.1 34.4 1.0
NE2 C:HIS233 4.2 32.1 1.0
CD2 C:HIS233 4.3 31.7 1.0
CB C:ASP201 4.3 35.5 1.0
OD2 C:ASP318 4.4 39.1 1.0
O C:HOH674 4.5 35.0 1.0
C27 C:E6N506 4.5 58.2 1.0
CB C:THR271 4.5 36.3 1.0
O C:THR271 4.5 39.6 1.0
NE2 C:HIS200 4.6 34.2 1.0
CA C:ASP201 4.7 33.9 1.0
CD2 C:HIS204 4.7 30.3 1.0
C C:HIS200 4.7 37.7 1.0
O C:HOH617 4.8 43.4 1.0
CG C:GLU230 4.8 41.4 1.0
CD C:GLU230 4.9 45.5 1.0
CD2 C:HIS160 4.9 45.9 1.0
C26 C:E6N506 4.9 57.6 1.0
NE2 C:HIS160 5.0 38.5 1.0

Magnesium binding site 4 out of 4 in 6fta

Go back to Magnesium Binding Sites List in 6fta
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-3098


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-3098 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:22.0
occ:1.00
 O D:HOH606 2.0 24.7 1.0
O D:HOH628 2.0 31.6 1.0
O D:HOH699 2.0 30.6 1.0
OD1 D:ASP201 2.0 32.4 1.0
O D:HOH621 2.1 26.4 1.0
O D:HOH648 2.1 29.9 1.0
CG D:ASP201 3.1 34.8 1.0
OD2 D:ASP201 3.4 35.0 1.0
ZN D:ZN502 3.7 38.6 1.0
O D:HOH669 4.0 35.0 1.0
OG1 D:THR271 4.0 27.2 1.0
OE2 D:GLU230 4.0 35.4 1.0
CD2 D:HIS200 4.1 29.9 1.0
O D:HIS200 4.1 32.6 1.0
C27 D:E6N514 4.3 60.5 1.0
NE2 D:HIS233 4.3 27.5 1.0
O D:HOH689 4.4 37.4 1.0
CB D:ASP201 4.4 35.0 1.0
O D:THR271 4.5 40.1 1.0
CD2 D:HIS233 4.5 31.8 1.0
NE2 D:HIS200 4.5 31.8 1.0
OD2 D:ASP318 4.5 40.6 1.0
CD2 D:HIS204 4.6 36.6 1.0
CB D:THR271 4.7 35.5 1.0
C26 D:E6N514 4.7 64.7 1.0
NE2 D:HIS204 4.8 36.1 1.0
O D:HOH653 4.8 48.9 1.0
CG D:GLU230 4.8 37.1 1.0
CA D:ASP201 4.8 34.9 1.0
CD2 D:HIS160 4.9 44.1 1.0
NE2 D:HIS160 4.9 40.0 1.0
CD D:GLU230 4.9 41.5 1.0
C D:HIS200 5.0 35.0 1.0

Reference:

A.K.Singh, D.G.Brown. HPDE4D2 Structure with Inhibitor Npd-3098 To Be Published.
Page generated: Wed Aug 13 06:12:59 2025

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