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Magnesium in PDB 7aag: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-617

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-617

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-617:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-617, PDB code: 7aag was solved by A.K.Singh, A.R.Blaazer, L.Zara, I.J.P.De Esch, R.Leurs, D.G.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.94 / 1.79
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.44, 110.82, 161.03, 90, 90, 90
R / Rfree (%) 16.7 / 19.7

Other elements in 7aag:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-617 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-617 (pdb code 7aag). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-617, PDB code: 7aag:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 7aag

Go back to Magnesium Binding Sites List in 7aag
Magnesium binding site 1 out of 5 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-617


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-617 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:13.8
occ:1.00
 O A:HOH675 2.0 19.6 1.0
O A:HOH770 2.0 21.5 1.0
OD1 A:ASP201 2.1 19.8 1.0
O A:HOH673 2.1 16.9 1.0
O A:HOH709 2.1 19.5 1.0
O A:HOH639 2.2 20.9 1.0
CG A:ASP201 3.1 19.0 1.0
OD2 A:ASP201 3.5 17.1 1.0
ZN A:ZN501 3.7 22.9 1.0
OE2 A:GLU230 4.1 22.8 1.0
NE2 A:HIS233 4.1 17.5 1.0
O A:HOH716 4.1 23.1 1.0
CD2 A:HIS200 4.1 20.4 1.0
O A:HOH722 4.1 23.3 1.0
O A:HIS200 4.1 18.3 1.0
OG1 A:THR271 4.2 21.1 1.0
CD2 A:HIS233 4.3 16.7 1.0
CB A:ASP201 4.4 18.8 1.0
NE2 A:HIS200 4.5 18.8 1.0
OD2 A:ASP318 4.5 28.4 1.0
CD2 A:HIS204 4.6 20.0 1.0
O A:HOH642 4.6 38.9 1.0
O A:THR271 4.7 24.9 1.0
NE2 A:HIS160 4.7 21.5 1.0
CB A:THR271 4.7 20.1 1.0
CD2 A:HIS160 4.8 23.7 1.0
CA A:ASP201 4.8 17.8 1.0
NE2 A:HIS204 4.8 19.4 1.0
CG A:GLU230 4.8 19.9 1.0
CD A:GLU230 4.9 21.9 1.0
C A:HIS200 5.0 17.3 1.0

Magnesium binding site 2 out of 5 in 7aag

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Magnesium binding site 2 out of 5 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-617


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-617 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg525

b:8.9
occ:1.00
 O C:HOH662 2.0 23.3 1.0
O A:HOH681 2.0 32.5 1.0
OD1 A:ASP156 2.0 30.0 1.0
ND1 C:HIS154 2.1 39.2 1.0
ND1 A:HIS154 2.3 32.5 1.0
CG A:ASP156 2.8 31.0 1.0
OD2 A:ASP156 2.9 29.9 1.0
CE1 C:HIS154 2.9 42.4 1.0
CG A:HIS154 3.2 30.2 1.0
CG C:HIS154 3.2 35.9 1.0
CE1 A:HIS154 3.3 36.1 1.0
CB A:HIS154 3.4 23.0 1.0
CB C:HIS154 3.7 24.9 1.0
OD1 C:ASP156 3.9 33.8 1.0
NE2 C:HIS154 4.1 39.1 1.0
CB A:ASP156 4.2 28.6 1.0
CD2 C:HIS154 4.2 38.1 1.0
CD2 A:HIS154 4.3 32.5 1.0
NE2 A:HIS154 4.4 35.6 1.0
CA C:HIS154 4.4 24.1 1.0
CA A:HIS154 4.4 23.4 1.0
N A:ASP156 4.6 26.4 1.0
O1 A:EDO520 4.8 43.5 1.0
CA A:ASP156 4.9 27.7 1.0
O2 A:EDO520 4.9 46.2 1.0
CG C:ASP156 5.0 30.2 1.0

Magnesium binding site 3 out of 5 in 7aag

Go back to Magnesium Binding Sites List in 7aag
Magnesium binding site 3 out of 5 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-617


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-617 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:13.4
occ:1.00
 O B:HOH675 2.0 20.9 1.0
OD1 B:ASP201 2.0 19.1 1.0
O B:HOH673 2.1 19.8 1.0
O B:HOH764 2.1 20.2 1.0
O B:HOH681 2.1 19.2 1.0
O B:HOH635 2.2 19.4 1.0
CG B:ASP201 3.1 18.8 1.0
OD2 B:ASP201 3.5 18.8 1.0
ZN B:ZN502 3.8 23.6 1.0
O B:HOH738 4.1 20.2 1.0
NE2 B:HIS233 4.1 17.5 1.0
OE2 B:GLU230 4.1 23.3 1.0
O B:HOH744 4.1 21.0 1.0
CD2 B:HIS200 4.2 19.1 1.0
O B:HIS200 4.2 19.7 1.0
OG1 B:THR271 4.2 22.5 1.0
CD2 B:HIS233 4.3 19.3 1.0
CB B:ASP201 4.4 20.0 1.0
NE2 B:HIS200 4.6 17.6 1.0
OD2 B:ASP318 4.6 25.3 1.0
CD2 B:HIS204 4.6 18.9 1.0
O B:THR271 4.6 24.7 1.0
O B:HOH648 4.7 33.0 1.0
NE2 B:HIS160 4.7 22.0 1.0
CB B:THR271 4.7 22.3 1.0
CD2 B:HIS160 4.8 21.2 1.0
CA B:ASP201 4.8 19.5 1.0
CG B:GLU230 4.8 19.8 1.0
NE2 B:HIS204 4.9 18.3 1.0
CD B:GLU230 4.9 21.4 1.0
C B:HIS200 5.0 17.0 1.0

Magnesium binding site 4 out of 5 in 7aag

Go back to Magnesium Binding Sites List in 7aag
Magnesium binding site 4 out of 5 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-617


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-617 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg505

b:14.4
occ:1.00
 OD1 C:ASP201 2.0 21.6 1.0
O C:HOH733 2.1 21.4 1.0
O C:HOH632 2.1 20.2 1.0
O C:HOH668 2.1 19.4 1.0
O C:HOH645 2.1 20.4 1.0
O C:HOH631 2.1 21.0 1.0
CG C:ASP201 3.1 19.6 1.0
OD2 C:ASP201 3.5 20.7 1.0
ZN C:ZN504 3.8 25.1 1.0
OE2 C:GLU230 4.0 24.7 1.0
NE2 C:HIS233 4.0 17.8 1.0
O C:HIS200 4.1 19.4 1.0
CD2 C:HIS200 4.1 20.1 1.0
O C:HOH702 4.1 21.7 1.0
O C:HOH649 4.2 24.2 1.0
OG1 C:THR271 4.2 21.1 1.0
CD2 C:HIS233 4.3 17.5 1.0
CB C:ASP201 4.4 20.1 1.0
NE2 C:HIS200 4.5 22.9 1.0
CD2 C:HIS204 4.6 20.6 1.0
OD2 C:ASP318 4.6 25.9 1.0
O C:HOH661 4.6 32.4 1.0
O C:THR271 4.6 24.3 1.0
CB C:THR271 4.7 24.8 1.0
NE2 C:HIS160 4.7 23.1 1.0
CD2 C:HIS160 4.8 24.7 1.0
CG C:GLU230 4.8 22.2 1.0
CA C:ASP201 4.8 19.9 1.0
CD C:GLU230 4.8 23.7 1.0
NE2 C:HIS204 4.9 20.4 1.0
C C:HIS200 5.0 18.1 1.0
O C:HOH735 5.0 48.0 1.0

Magnesium binding site 5 out of 5 in 7aag

Go back to Magnesium Binding Sites List in 7aag
Magnesium binding site 5 out of 5 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-617


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-617 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg504

b:11.6
occ:1.00
 O D:HOH687 2.0 15.8 1.0
O D:HOH777 2.0 20.2 1.0
OD1 D:ASP201 2.1 18.4 1.0
O D:HOH713 2.1 17.8 1.0
O D:HOH707 2.1 19.2 1.0
O D:HOH639 2.1 18.7 1.0
CG D:ASP201 3.1 20.0 1.0
OD2 D:ASP201 3.5 17.3 1.0
ZN D:ZN503 3.8 22.2 1.0
O D:HOH796 4.0 50.4 1.0
OE2 D:GLU230 4.1 23.2 1.0
NE2 D:HIS233 4.1 16.5 1.0
O D:HOH691 4.1 21.5 1.0
CD2 D:HIS200 4.1 14.6 1.0
O D:HIS200 4.2 17.3 1.0
OG1 D:THR271 4.2 20.4 1.0
O D:HOH715 4.2 22.5 1.0
CD2 D:HIS233 4.3 15.6 1.0
CB D:ASP201 4.4 18.6 1.0
NE2 D:HIS200 4.5 15.7 1.0
OD2 D:ASP318 4.5 24.6 1.0
CD2 D:HIS204 4.6 19.3 1.0
O D:THR271 4.7 21.8 1.0
O D:HOH669 4.7 33.5 1.0
CG D:GLU230 4.7 20.6 1.0
NE2 D:HIS160 4.8 22.1 1.0
CB D:THR271 4.8 20.0 1.0
CD2 D:HIS160 4.8 22.2 1.0
CA D:ASP201 4.8 17.4 1.0
CD D:GLU230 4.9 23.8 1.0
NE2 D:HIS204 4.9 20.7 1.0
C D:HIS200 5.0 17.4 1.0

Reference:

A.K.Singh, D.G.Brown. HPDE4D2 Structure with Inhibitor Npd-617 To Be Published.
Page generated: Wed Oct 2 09:07:08 2024

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