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Magnesium in PDB 3n3z: Crystal Structure of PDE9A (E406A) Mutant in Complex with Ibmx

Enzymatic activity of Crystal Structure of PDE9A (E406A) Mutant in Complex with Ibmx

All present enzymatic activity of Crystal Structure of PDE9A (E406A) Mutant in Complex with Ibmx:
3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of PDE9A (E406A) Mutant in Complex with Ibmx, PDB code: 3n3z was solved by J.Hou, H.-B.Luo, Y.Chen, J.Xu, R.Zhao, L.Zou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.33 / 2.75
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 104.090, 104.090, 270.210, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 23

Other elements in 3n3z:

The structure of Crystal Structure of PDE9A (E406A) Mutant in Complex with Ibmx also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of PDE9A (E406A) Mutant in Complex with Ibmx (pdb code 3n3z). 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 PDE9A (E406A) Mutant in Complex with Ibmx, PDB code: 3n3z:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3n3z

Go back to Magnesium Binding Sites List in 3n3z
Magnesium binding site 1 out of 2 in the Crystal Structure of PDE9A (E406A) Mutant in Complex with Ibmx


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 PDE9A (E406A) Mutant in Complex with Ibmx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg508

b:46.2
occ:1.00
O A:HOH91 2.0 68.9 1.0
OD1 A:ASP293 2.0 31.5 1.0
O A:HOH90 2.1 36.6 1.0
O A:HOH89 2.3 35.5 1.0
O A:HOH92 2.3 52.9 1.0
O A:HOH93 2.4 35.1 1.0
CG A:ASP293 3.1 30.4 1.0
ZN A:ZN507 3.5 69.7 1.0
OD2 A:ASP293 3.5 30.4 1.0
NE2 A:HIS325 3.9 29.4 1.0
CD2 A:HIS296 4.1 30.8 1.0
CD2 A:HIS325 4.3 28.1 1.0
OE2 A:GLU322 4.3 33.7 1.0
O A:HIS292 4.3 32.1 1.0
CD2 A:HIS292 4.4 37.1 1.0
CB A:ASP293 4.4 30.3 1.0
NE2 A:HIS296 4.4 29.8 1.0
CD2 A:HIS252 4.5 33.2 1.0
OG1 A:THR363 4.5 28.7 1.0
NE2 A:HIS252 4.5 34.1 1.0
NE2 A:HIS292 4.6 39.3 1.0
CA A:ASP293 4.7 30.5 1.0
CB A:THR363 5.0 29.5 1.0
CE1 A:HIS325 5.0 28.4 1.0
OD2 A:ASP402 5.0 36.5 1.0

Magnesium binding site 2 out of 2 in 3n3z

Go back to Magnesium Binding Sites List in 3n3z
Magnesium binding site 2 out of 2 in the Crystal Structure of PDE9A (E406A) Mutant in Complex with Ibmx


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 PDE9A (E406A) Mutant in Complex with Ibmx within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1

b:42.9
occ:1.00
O B:HOH96 2.0 37.6 1.0
O B:HOH100 2.1 50.9 1.0
OD1 B:ASP293 2.2 32.2 1.0
O B:HOH94 2.3 56.3 1.0
O B:HOH95 2.3 46.2 1.0
O B:HOH97 2.4 49.6 1.0
CG B:ASP293 3.1 32.8 1.0
OD2 B:ASP293 3.3 32.9 1.0
ZN B:ZN2 3.4 83.7 1.0
O B:HOH48 4.1 32.0 1.0
NE2 B:HIS325 4.2 29.2 1.0
CD2 B:HIS296 4.3 32.7 1.0
NE2 B:HIS252 4.3 34.3 1.0
CD2 B:HIS292 4.3 39.5 1.0
CD2 B:HIS252 4.4 35.0 1.0
O B:HOH51 4.4 33.3 1.0
OE2 B:GLU322 4.4 35.2 1.0
O B:HIS292 4.4 35.7 1.0
NE2 B:HIS296 4.5 31.5 1.0
CB B:ASP293 4.5 33.6 1.0
OG1 B:THR363 4.5 30.2 1.0
CD2 B:HIS325 4.5 29.6 1.0
O B:HOH33 4.7 43.5 1.0
NE2 B:HIS292 4.7 42.0 1.0
OD2 B:ASP402 4.8 40.0 1.0
O B:THR363 4.8 31.6 1.0
OD1 B:ASP402 4.8 38.5 1.0
CB B:THR363 4.9 30.9 1.0
CA B:ASP293 4.9 33.5 1.0

Reference:

J.Hou, H.-B.Luo, Y.Chen, J.Xu, R.Zhao, L.Zou. Crystal Structure of PDE9A (E406A) Mutation in Complex with Ibmx To Be Published.
Page generated: Mon Dec 14 08:27:35 2020

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