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Magnesium in PDB 6fe7: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-356

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-356

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-356:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-356, PDB code: 6fe7 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) 54.30 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.220, 111.030, 160.960, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 20

Other elements in 6fe7:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-356 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-356 (pdb code 6fe7). 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-356, PDB code: 6fe7:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6fe7

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-356


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-356 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:19.3
occ:1.00
 O A:HOH629 2.0 25.6 1.0
O A:HOH719 2.0 24.8 1.0
O A:HOH669 2.1 24.6 1.0
O A:HOH634 2.1 23.8 1.0
O A:HOH710 2.1 25.2 1.0
OD1 A:ASP201 2.1 29.2 1.0
CG A:ASP201 3.1 28.1 1.0
OD2 A:ASP201 3.4 26.7 1.0
ZN A:ZN501 3.8 33.4 1.0
OE2 A:GLU230 3.9 28.8 1.0
O A:HOH677 4.1 29.7 1.0
OG1 A:THR271 4.2 28.8 1.0
NE2 A:HIS233 4.2 27.0 1.0
O A:HOH688 4.2 31.3 1.0
O A:HIS200 4.2 25.6 1.0
CD2 A:HIS200 4.3 26.7 1.0
CD2 A:HIS233 4.3 26.3 1.0
OD2 A:ASP318 4.4 32.8 1.0
CB A:ASP201 4.4 25.2 1.0
C21 A:D62520 4.5 33.5 1.0
O A:THR271 4.6 29.2 1.0
CD2 A:HIS204 4.6 27.9 1.0
O A:HOH639 4.7 34.8 1.0
CB A:THR271 4.7 27.8 1.0
C20 A:D62520 4.7 33.0 1.0
CG A:GLU230 4.7 27.4 1.0
CA A:ASP201 4.7 26.4 1.0
NE2 A:HIS200 4.8 25.9 1.0
CD A:GLU230 4.8 27.8 1.0
NE2 A:HIS160 4.8 29.6 1.0
CD2 A:HIS160 4.9 31.9 1.0
NE2 A:HIS204 4.9 28.0 1.0
C A:HIS200 4.9 24.2 1.0

Magnesium binding site 2 out of 4 in 6fe7

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Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-356


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-356 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:22.4
occ:1.00
 O B:HOH645 2.0 24.7 1.0
O B:HOH649 2.0 24.7 1.0
O B:HOH724 2.1 27.0 1.0
OD1 B:ASP201 2.1 28.8 1.0
O B:HOH670 2.2 24.7 1.0
O B:HOH616 2.3 25.9 1.0
CG B:ASP201 3.1 26.9 1.0
OD2 B:ASP201 3.4 29.2 1.0
ZN B:ZN501 3.8 33.4 1.0
OE2 B:GLU230 3.9 29.8 1.0
O B:HOH688 4.1 24.7 1.0
O B:HIS200 4.1 28.9 1.0
NE2 B:HIS233 4.2 25.0 1.0
OG1 B:THR271 4.2 34.9 1.0
CD2 B:HIS200 4.2 30.4 1.0
O B:HOH700 4.2 26.4 1.0
CD2 B:HIS233 4.4 28.4 1.0
CB B:ASP201 4.5 28.8 1.0
O B:THR271 4.5 29.4 1.0
OD2 B:ASP318 4.5 29.1 1.0
O B:HOH642 4.6 31.2 1.0
CD2 B:HIS204 4.6 26.5 1.0
C21 B:D62516 4.6 32.0 1.0
C20 B:D62516 4.6 31.6 1.0
CB B:THR271 4.6 31.7 1.0
NE2 B:HIS200 4.6 26.6 1.0
CG B:GLU230 4.7 29.5 1.0
CD B:GLU230 4.8 29.2 1.0
NE2 B:HIS160 4.8 34.0 1.0
NE2 B:HIS204 4.8 27.0 1.0
CA B:ASP201 4.8 27.3 1.0
CD2 B:HIS160 4.8 32.6 1.0
C B:HIS200 5.0 27.6 1.0

Magnesium binding site 3 out of 4 in 6fe7

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Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-356


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-356 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg506

b:21.5
occ:1.00
 O C:HOH627 2.1 27.0 1.0
OD1 C:ASP201 2.1 27.0 1.0
O C:HOH634 2.1 24.7 1.0
O C:HOH681 2.1 26.9 1.0
O C:HOH667 2.1 28.6 1.0
O C:HOH611 2.1 24.7 1.0
CG C:ASP201 3.1 27.4 1.0
OD2 C:ASP201 3.4 25.8 1.0
ZN C:ZN505 3.8 33.7 1.0
OE2 C:GLU230 4.0 28.4 1.0
O C:HOH655 4.1 27.8 1.0
O C:HIS200 4.1 26.4 1.0
OG1 C:THR271 4.2 28.1 1.0
O C:HOH674 4.2 26.5 1.0
NE2 C:HIS233 4.2 23.8 1.0
CD2 C:HIS200 4.2 25.3 1.0
CD2 C:HIS233 4.4 22.7 1.0
CB C:ASP201 4.4 27.3 1.0
CD2 C:HIS204 4.5 29.8 1.0
O C:THR271 4.5 28.6 1.0
C21 C:D62520 4.5 37.0 1.0
OD2 C:ASP318 4.6 31.9 1.0
NE2 C:HIS200 4.6 29.0 1.0
CB C:THR271 4.7 30.9 1.0
C20 C:D62520 4.7 35.3 1.0
O C:HOH623 4.7 32.7 1.0
NE2 C:HIS160 4.7 30.3 1.0
CD2 C:HIS160 4.7 33.8 1.0
CG C:GLU230 4.8 29.1 1.0
NE2 C:HIS204 4.8 27.5 1.0
CA C:ASP201 4.8 25.7 1.0
CD C:GLU230 4.8 31.1 1.0
C C:HIS200 5.0 27.4 1.0

Magnesium binding site 4 out of 4 in 6fe7

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Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-356


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-356 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:19.0
occ:1.00
 O D:HOH637 2.0 24.0 1.0
O D:HOH749 2.0 24.9 1.0
OD1 D:ASP201 2.0 25.2 1.0
O D:HOH638 2.1 22.4 1.0
O D:HOH654 2.1 23.3 1.0
O D:HOH702 2.2 23.8 1.0
CG D:ASP201 3.0 25.6 1.0
OD2 D:ASP201 3.4 22.6 1.0
ZN D:ZN502 3.8 30.5 1.0
OE2 D:GLU230 3.9 25.4 1.0
O D:HIS200 4.1 23.4 1.0
O D:HOH705 4.1 25.6 1.0
NE2 D:HIS233 4.2 21.6 1.0
CD2 D:HIS200 4.2 22.8 1.0
O D:HOH666 4.2 28.6 1.0
OG1 D:THR271 4.2 27.0 1.0
CD2 D:HIS233 4.4 21.3 1.0
CB D:ASP201 4.4 24.7 1.0
OD2 D:ASP318 4.5 28.4 1.0
C21 D:D62517 4.5 30.2 1.0
CD2 D:HIS204 4.5 25.9 1.0
O D:THR271 4.6 27.8 1.0
NE2 D:HIS200 4.6 24.5 1.0
C20 D:D62517 4.7 30.8 1.0
O D:HOH649 4.7 33.8 1.0
CG D:GLU230 4.7 30.3 1.0
CB D:THR271 4.7 27.1 1.0
NE2 D:HIS160 4.8 30.0 1.0
CD D:GLU230 4.8 29.5 1.0
NE2 D:HIS204 4.8 27.2 1.0
CD2 D:HIS160 4.8 31.4 1.0
CA D:ASP201 4.8 24.8 1.0
C D:HIS200 5.0 25.6 1.0

Reference:

I.G.Salado, C.Moreno, G.Sakaine, A.K.Singh, A.R.Blaazer, M.Siderius, A.Matheeussen, S.Gul, L.Maes, R.Leurs, D.G.Brown, K.Augustyns. HPDE4D2 Structure with Inhibitor Npd-356 To Be Published.
Page generated: Tue Oct 1 00:25:29 2024

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