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Magnesium in PDB 4y87: Crystal Structure of Phosphodiesterase 9 in Complex with (R)-C33 (6- {[(1R)-1-(4-Chlorophenyl)Ethyl]Amino}-1-Cyclopentyl-1,5-Dihydro-4H- Pyrazolo[3,4-D]Pyrimidin-4-One)

Enzymatic activity of Crystal Structure of Phosphodiesterase 9 in Complex with (R)-C33 (6- {[(1R)-1-(4-Chlorophenyl)Ethyl]Amino}-1-Cyclopentyl-1,5-Dihydro-4H- Pyrazolo[3,4-D]Pyrimidin-4-One)

All present enzymatic activity of Crystal Structure of Phosphodiesterase 9 in Complex with (R)-C33 (6- {[(1R)-1-(4-Chlorophenyl)Ethyl]Amino}-1-Cyclopentyl-1,5-Dihydro-4H- Pyrazolo[3,4-D]Pyrimidin-4-One):
3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of Phosphodiesterase 9 in Complex with (R)-C33 (6- {[(1R)-1-(4-Chlorophenyl)Ethyl]Amino}-1-Cyclopentyl-1,5-Dihydro-4H- Pyrazolo[3,4-D]Pyrimidin-4-One), PDB code: 4y87 was solved by M.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 98.22 / 3.10
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 105.436, 105.436, 270.056, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 24.7

Other elements in 4y87:

The structure of Crystal Structure of Phosphodiesterase 9 in Complex with (R)-C33 (6- {[(1R)-1-(4-Chlorophenyl)Ethyl]Amino}-1-Cyclopentyl-1,5-Dihydro-4H- Pyrazolo[3,4-D]Pyrimidin-4-One) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Phosphodiesterase 9 in Complex with (R)-C33 (6- {[(1R)-1-(4-Chlorophenyl)Ethyl]Amino}-1-Cyclopentyl-1,5-Dihydro-4H- Pyrazolo[3,4-D]Pyrimidin-4-One) (pdb code 4y87). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Phosphodiesterase 9 in Complex with (R)-C33 (6- {[(1R)-1-(4-Chlorophenyl)Ethyl]Amino}-1-Cyclopentyl-1,5-Dihydro-4H- Pyrazolo[3,4-D]Pyrimidin-4-One), PDB code: 4y87:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4y87

Go back to Magnesium Binding Sites List in 4y87
Magnesium binding site 1 out of 2 in the Crystal Structure of Phosphodiesterase 9 in Complex with (R)-C33 (6- {[(1R)-1-(4-Chlorophenyl)Ethyl]Amino}-1-Cyclopentyl-1,5-Dihydro-4H- Pyrazolo[3,4-D]Pyrimidin-4-One)


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 Phosphodiesterase 9 in Complex with (R)-C33 (6- {[(1R)-1-(4-Chlorophenyl)Ethyl]Amino}-1-Cyclopentyl-1,5-Dihydro-4H- Pyrazolo[3,4-D]Pyrimidin-4-One) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:54.3
occ:1.00
 O A:HOH705 2.0 41.3 1.0
O A:HOH706 2.1 50.4 1.0
OD1 A:ASP293 2.2 50.8 1.0
O A:HOH702 2.3 37.1 1.0
O A:HOH704 2.4 20.2 1.0
O A:HOH703 2.7 34.8 1.0
CG A:ASP293 3.0 48.8 1.0
OD2 A:ASP293 3.3 54.8 1.0
ZN A:ZN602 3.8 74.1 1.0
CD2 A:HIS292 4.0 56.9 1.0
CE1 A:HIS325 4.0 47.4 1.0
OG1 A:THR363 4.0 48.1 1.0
OE2 A:GLU322 4.2 44.2 1.0
ND1 A:HIS325 4.2 48.7 1.0
NE2 A:HIS292 4.3 62.9 1.0
O A:HIS292 4.3 42.8 1.0
CB A:ASP293 4.4 47.1 1.0
OD2 A:ASP402 4.5 60.5 1.0
CD2 A:HIS296 4.5 44.9 1.0
CB A:THR363 4.6 50.2 1.0
NE2 A:HIS252 4.7 55.4 1.0
CA A:ASP293 4.7 45.3 1.0
CG A:GLU322 4.7 46.4 1.0
CD2 A:HIS252 4.7 53.3 1.0
OD1 A:ASP402 4.8 61.7 1.0
CD A:GLU322 4.8 44.8 1.0
NE2 A:HIS296 4.9 45.6 1.0
C A:HIS292 5.0 44.9 1.0

Magnesium binding site 2 out of 2 in 4y87

Go back to Magnesium Binding Sites List in 4y87
Magnesium binding site 2 out of 2 in the Crystal Structure of Phosphodiesterase 9 in Complex with (R)-C33 (6- {[(1R)-1-(4-Chlorophenyl)Ethyl]Amino}-1-Cyclopentyl-1,5-Dihydro-4H- Pyrazolo[3,4-D]Pyrimidin-4-One)


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 Phosphodiesterase 9 in Complex with (R)-C33 (6- {[(1R)-1-(4-Chlorophenyl)Ethyl]Amino}-1-Cyclopentyl-1,5-Dihydro-4H- Pyrazolo[3,4-D]Pyrimidin-4-One) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:46.9
occ:1.00
 O B:HOH701 2.0 31.1 1.0
O B:HOH705 2.1 86.4 1.0
OD1 B:ASP293 2.2 47.1 1.0
O B:HOH703 2.3 32.3 1.0
O B:HOH706 2.4 36.5 1.0
CG B:ASP293 3.1 47.5 1.0
OD2 B:ASP293 3.2 51.6 1.0
O B:HOH704 3.6 39.6 1.0
ZN B:ZN602 3.9 69.4 1.0
NE2 B:HIS325 3.9 48.9 1.0
OE2 B:GLU322 4.0 43.9 1.0
CD2 B:HIS296 4.1 50.8 1.0
CD2 B:HIS325 4.3 49.1 1.0
O B:HOH702 4.3 70.6 1.0
OG1 B:THR363 4.3 45.1 1.0
NE2 B:HIS252 4.4 51.3 1.0
CD2 B:HIS292 4.4 51.6 1.0
CB B:ASP293 4.5 46.2 1.0
NE2 B:HIS296 4.5 51.8 1.0
O B:HIS292 4.5 47.1 1.0
CD2 B:HIS252 4.6 48.6 1.0
NE2 B:HIS292 4.6 55.6 1.0
CA B:ASP293 4.8 45.2 1.0
CB B:THR363 4.9 47.3 1.0
CD B:GLU322 4.9 44.9 1.0
OD2 B:ASP402 4.9 56.2 1.0
CE1 B:HIS325 5.0 48.7 1.0

Reference:

M.Huang, Y.Shao, J.Hou, W.Cui, B.Liang, Y.Huang, Z.Li, Y.Wu, X.Zhu, P.Liu, Y.Wan, H.Ke, H.B.Luo. Structural Asymmetry of Phosphodiesterase-9A and A Unique Pocket For Selective Binding of A Potent Enantiomeric Inhibitor. Mol.Pharmacol. V. 88 836 2015.
ISSN: ESSN 1521-0111
PubMed: 26316540
DOI: 10.1124/MOL.115.099747
Page generated: Sat Sep 28 22:56:18 2024

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