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Magnesium in PDB 6fdi: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-226

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-226

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-226:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-226, PDB code: 6fdi 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) 67.10 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.804, 111.042, 161.089, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 20

Other elements in 6fdi:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-226 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-226 (pdb code 6fdi). 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-226, PDB code: 6fdi:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6fdi

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-226


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-226 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:17.1
occ:1.00
 O A:HOH634 2.0 18.6 1.0
OD1 A:ASP201 2.1 20.4 1.0
O A:HOH755 2.1 18.6 1.0
O A:HOH721 2.1 15.7 1.0
O A:HOH636 2.1 18.1 1.0
O A:HOH704 2.2 17.9 1.0
CG A:ASP201 3.2 19.6 1.0
OD2 A:ASP201 3.5 17.7 1.0
ZN A:ZN501 3.8 23.4 1.0
OE2 A:GLU230 4.1 20.6 1.0
NE2 A:HIS233 4.1 17.3 1.0
O A:HIS200 4.1 15.9 1.0
O A:HOH729 4.1 21.6 1.0
OG1 A:THR271 4.2 19.5 1.0
CD2 A:HIS200 4.2 17.3 1.0
O A:HOH707 4.2 20.2 1.0
CD2 A:HIS233 4.4 17.1 1.0
OD2 A:ASP318 4.5 22.6 1.0
C24 A:D5T514 4.5 21.8 1.0
CB A:ASP201 4.5 18.3 1.0
C23 A:D5T514 4.6 22.3 1.0
NE2 A:HIS200 4.6 17.8 1.0
CD2 A:HIS204 4.6 18.6 1.0
O A:THR271 4.7 19.6 1.0
O A:HOH693 4.7 27.9 1.0
CB A:THR271 4.7 19.2 1.0
CG A:GLU230 4.8 18.8 1.0
NE2 A:HIS160 4.8 19.3 1.0
CD A:GLU230 4.8 19.3 1.0
CD2 A:HIS160 4.8 20.8 1.0
CA A:ASP201 4.9 17.4 1.0
NE2 A:HIS204 4.9 18.6 1.0
C A:HIS200 5.0 16.7 1.0

Magnesium binding site 2 out of 4 in 6fdi

Go back to Magnesium Binding Sites List in 6fdi
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-226


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-226 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:20.3
occ:1.00
 O B:HOH632 2.0 22.4 1.0
O B:HOH676 2.1 24.0 1.0
OD1 B:ASP201 2.1 21.6 1.0
O B:HOH738 2.1 20.2 1.0
O B:HOH660 2.2 18.3 1.0
O B:HOH621 2.3 20.4 1.0
CG B:ASP201 3.1 20.5 1.0
OD2 B:ASP201 3.5 21.3 1.0
ZN B:ZN501 3.9 26.2 1.0
OE2 B:GLU230 4.1 25.2 1.0
NE2 B:HIS233 4.1 23.5 1.0
OG1 B:THR271 4.1 26.3 1.0
O B:HOH705 4.2 19.6 1.0
O B:HIS200 4.2 19.8 1.0
O B:HOH725 4.2 20.0 1.0
CD2 B:HIS200 4.3 21.5 1.0
CD2 B:HIS233 4.4 25.7 1.0
C24 B:D5T512 4.5 21.4 1.0
CB B:ASP201 4.5 21.7 1.0
O B:HOH661 4.5 27.2 1.0
O B:THR271 4.6 25.0 1.0
OD2 B:ASP318 4.6 21.6 1.0
CD2 B:HIS204 4.6 19.7 1.0
C23 B:D5T512 4.6 20.1 1.0
CB B:THR271 4.7 27.2 1.0
NE2 B:HIS200 4.7 19.8 1.0
NE2 B:HIS160 4.8 23.6 1.0
CG B:GLU230 4.8 23.1 1.0
NE2 B:HIS204 4.9 18.1 1.0
CA B:ASP201 4.9 22.7 1.0
CD2 B:HIS160 4.9 23.6 1.0
CD B:GLU230 4.9 23.6 1.0
C B:HIS200 5.0 18.7 1.0

Magnesium binding site 3 out of 4 in 6fdi

Go back to Magnesium Binding Sites List in 6fdi
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-226


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-226 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg505

b:20.1
occ:1.00
 O C:HOH643 2.0 19.7 1.0
O C:HOH718 2.1 20.2 1.0
OD1 C:ASP201 2.1 20.4 1.0
O C:HOH634 2.1 18.0 1.0
O C:HOH615 2.2 19.1 1.0
O C:HOH668 2.2 20.6 1.0
CG C:ASP201 3.1 20.2 1.0
OD2 C:ASP201 3.5 21.8 1.0
ZN C:ZN504 3.8 26.4 1.0
OE2 C:GLU230 4.0 21.9 1.0
O C:HOH680 4.1 20.2 1.0
O C:HOH707 4.1 19.3 1.0
OG1 C:THR271 4.2 22.5 1.0
O C:HIS200 4.2 19.7 1.0
NE2 C:HIS233 4.2 20.4 1.0
CD2 C:HIS200 4.2 18.3 1.0
CD2 C:HIS233 4.4 20.6 1.0
C24 C:D5T513 4.4 25.6 1.0
CB C:ASP201 4.5 20.5 1.0
OD2 C:ASP318 4.5 24.4 1.0
CD2 C:HIS204 4.6 18.4 1.0
O C:THR271 4.6 22.0 1.0
NE2 C:HIS200 4.6 20.7 1.0
C23 C:D5T513 4.7 23.1 1.0
O C:HOH682 4.7 27.4 1.0
CB C:THR271 4.7 24.7 1.0
CG C:GLU230 4.8 21.4 1.0
NE2 C:HIS160 4.8 23.4 1.0
CD2 C:HIS160 4.8 21.8 1.0
CD C:GLU230 4.8 23.4 1.0
NE2 C:HIS204 4.9 19.5 1.0
CA C:ASP201 4.9 21.2 1.0

Magnesium binding site 4 out of 4 in 6fdi

Go back to Magnesium Binding Sites List in 6fdi
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-226


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-226 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg504

b:15.8
occ:1.00
 O D:HOH677 2.1 16.4 1.0
OD1 D:ASP201 2.1 18.7 1.0
O D:HOH746 2.1 15.1 1.0
O D:HOH625 2.2 19.7 1.0
O D:HOH776 2.2 18.4 1.0
O D:HOH661 2.2 18.3 1.0
CG D:ASP201 3.1 18.2 1.0
OD2 D:ASP201 3.5 15.9 1.0
ZN D:ZN503 3.9 21.8 1.0
OE2 D:GLU230 4.0 20.7 1.0
NE2 D:HIS233 4.1 15.1 1.0
O D:HIS200 4.1 16.8 1.0
O D:HOH733 4.2 21.9 1.0
OG1 D:THR271 4.2 21.5 1.0
CD2 D:HIS200 4.2 14.3 1.0
O D:HOH762 4.2 18.3 1.0
CD2 D:HIS233 4.3 15.3 1.0
CB D:ASP201 4.5 17.1 1.0
C24 D:D5T512 4.6 20.9 1.0
CD2 D:HIS204 4.6 18.6 1.0
OD2 D:ASP318 4.6 21.4 1.0
C23 D:D5T512 4.6 20.5 1.0
NE2 D:HIS200 4.7 15.5 1.0
O D:THR271 4.7 21.2 1.0
O D:HOH682 4.7 24.9 1.0
CG D:GLU230 4.7 20.5 1.0
CD D:GLU230 4.8 19.6 1.0
CB D:THR271 4.8 21.0 1.0
CA D:ASP201 4.8 16.3 1.0
NE2 D:HIS204 4.8 20.1 1.0
NE2 D:HIS160 4.9 20.3 1.0
CD2 D:HIS160 4.9 20.5 1.0
C D:HIS200 5.0 16.1 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-226 To Be Published.
Page generated: Tue Oct 1 00:25:03 2024

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