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Zinc 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:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 1 atom

Zinc Binding Sites:

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

Zinc binding site 1 out of 2 in 3n3z

Go back to Zinc Binding Sites List in 3n3z
Zinc 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 Zinc with other atoms in the Zn 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:Zn507

b:69.7
occ:1.00
OD2 A:ASP293 2.2 30.4 1.0
NE2 A:HIS292 2.4 39.3 1.0
OD1 A:ASP402 2.5 38.7 1.0
NE2 A:HIS256 2.7 33.3 1.0
CG A:ASP293 3.1 30.4 1.0
CD2 A:HIS292 3.3 37.1 1.0
CE1 A:HIS292 3.4 39.0 1.0
CD2 A:HIS256 3.4 31.9 1.0
OD1 A:ASP293 3.4 31.5 1.0
CG A:ASP402 3.4 37.4 1.0
MG A:MG508 3.5 46.2 1.0
O A:HOH92 3.5 52.9 1.0
OD2 A:ASP402 3.7 36.5 1.0
CE1 A:HIS256 3.8 31.6 1.0
O A:HOH90 3.8 36.6 1.0
CD2 A:HIS252 4.2 33.2 1.0
NE2 A:HIS252 4.4 34.1 1.0
CG A:HIS292 4.4 34.9 1.0
O A:HOH93 4.4 35.1 1.0
ND1 A:HIS292 4.4 38.3 1.0
CB A:ASP293 4.5 30.3 1.0
CG A:HIS256 4.6 31.5 1.0
O A:HOH91 4.7 68.9 1.0
O A:ASP402 4.8 38.2 1.0
CB A:ASP402 4.8 36.8 1.0
ND1 A:HIS256 4.8 32.6 1.0

Zinc binding site 2 out of 2 in 3n3z

Go back to Zinc Binding Sites List in 3n3z
Zinc 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 Zinc with other atoms in the Zn 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:Zn2

b:83.7
occ:1.00
O B:HOH94 2.0 56.3 1.0
OD2 B:ASP293 2.1 32.9 1.0
OD1 B:ASP402 2.5 38.5 1.0
NE2 B:HIS292 2.5 42.0 1.0
NE2 B:HIS256 2.8 43.7 1.0
CD2 B:HIS292 3.1 39.5 1.0
CG B:ASP293 3.2 32.8 1.0
MG B:MG1 3.4 42.9 1.0
CD2 B:HIS256 3.5 41.5 1.0
CG B:ASP402 3.5 39.3 1.0
OD1 B:ASP293 3.6 32.2 1.0
CE1 B:HIS292 3.7 41.9 1.0
O B:HOH100 3.7 50.9 1.0
CE1 B:HIS256 3.8 41.8 1.0
OD2 B:ASP402 3.9 40.0 1.0
CD2 B:HIS252 4.0 35.0 1.0
NE2 B:HIS252 4.1 34.3 1.0
O B:HOH97 4.2 49.6 1.0
CG B:HIS292 4.4 38.0 1.0
CB B:ASP293 4.4 33.6 1.0
O B:ASP402 4.5 39.5 1.0
ND1 B:HIS292 4.6 41.1 1.0
O B:HOH51 4.6 33.3 1.0
CG B:HIS256 4.7 40.5 1.0
CB B:ASP402 4.8 38.7 1.0
ND1 B:HIS256 4.8 42.0 1.0
O B:HOH95 4.9 46.2 1.0
CG2 B:VAL260 5.0 34.3 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: Wed Dec 16 04:36:53 2020

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