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Zinc in PDB 3qi3: Crystal Structure of PDE9A(Q453E) in Complex with Inhibitor BAY73-6691

Enzymatic activity of Crystal Structure of PDE9A(Q453E) in Complex with Inhibitor BAY73-6691

All present enzymatic activity of Crystal Structure of PDE9A(Q453E) in Complex with Inhibitor BAY73-6691:
3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of PDE9A(Q453E) in Complex with Inhibitor BAY73-6691, PDB code: 3qi3 was solved by J.Hou, J.Xu, M.Liu, R.Zhao, H.Lou, H.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.30
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 103.127, 103.127, 270.441, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 24.2

Other elements in 3qi3:

The structure of Crystal Structure of PDE9A(Q453E) in Complex with Inhibitor BAY73-6691 also contains other interesting chemical elements:

Fluorine (F) 6 atoms
Magnesium (Mg) 2 atoms
Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of PDE9A(Q453E) in Complex with Inhibitor BAY73-6691 (pdb code 3qi3). 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(Q453E) in Complex with Inhibitor BAY73-6691, PDB code: 3qi3:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3qi3

Go back to Zinc Binding Sites List in 3qi3
Zinc binding site 1 out of 2 in the Crystal Structure of PDE9A(Q453E) in Complex with Inhibitor BAY73-6691


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(Q453E) in Complex with Inhibitor BAY73-6691 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn534

b:54.9
occ:1.00
OD2 A:ASP293 2.1 37.6 1.0
OD1 A:ASP402 2.1 47.7 1.0
NE2 A:HIS292 2.1 43.0 1.0
NE2 A:HIS256 2.1 46.4 1.0
O A:HOH537 2.4 39.0 1.0
O A:HOH536 2.6 39.7 1.0
CD2 A:HIS292 3.0 38.4 1.0
CD2 A:HIS256 3.1 40.7 1.0
CE1 A:HIS292 3.1 39.1 1.0
CE1 A:HIS256 3.1 42.0 1.0
CG A:ASP402 3.2 42.8 1.0
CG A:ASP293 3.2 34.9 1.0
OD2 A:ASP402 3.6 43.9 1.0
OD1 A:ASP293 3.7 34.6 1.0
MG A:MG535 3.9 42.5 1.0
CG A:HIS292 4.2 38.5 1.0
ND1 A:HIS292 4.2 39.7 1.0
ND1 A:HIS256 4.2 41.9 1.0
CG A:HIS256 4.2 40.9 1.0
CD2 A:HIS252 4.3 39.1 1.0
CB A:ASP293 4.4 34.5 1.0
CB A:ASP402 4.5 40.4 1.0
O A:HOH539 4.5 42.8 1.0
O A:ASP402 4.5 41.1 1.0
NE2 A:HIS252 4.6 38.6 1.0
O A:HOH540 4.7 46.2 1.0
CG2 A:VAL260 4.7 32.0 1.0
CA A:ASP402 4.8 40.5 1.0
O A:HOH548 4.9 52.1 1.0

Zinc binding site 2 out of 2 in 3qi3

Go back to Zinc Binding Sites List in 3qi3
Zinc binding site 2 out of 2 in the Crystal Structure of PDE9A(Q453E) in Complex with Inhibitor BAY73-6691


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(Q453E) in Complex with Inhibitor BAY73-6691 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn534

b:67.1
occ:1.00
OD2 B:ASP293 2.1 51.5 1.0
OD1 B:ASP402 2.1 52.2 1.0
NE2 B:HIS292 2.1 52.5 1.0
NE2 B:HIS256 2.1 57.7 1.0
O B:HOH541 2.5 51.3 1.0
O B:HOH536 3.0 49.4 1.0
CD2 B:HIS292 3.0 46.2 1.0
CD2 B:HIS256 3.1 50.9 1.0
CG B:ASP402 3.1 46.5 1.0
CG B:ASP293 3.2 44.0 1.0
CE1 B:HIS292 3.2 48.1 1.0
CE1 B:HIS256 3.2 51.7 1.0
OD2 B:ASP402 3.5 48.3 1.0
OD1 B:ASP293 3.7 46.4 1.0
MG B:MG535 3.9 49.9 1.0
CD2 B:HIS252 4.1 40.3 1.0
CG B:HIS292 4.2 44.7 1.0
ND1 B:HIS292 4.2 47.1 1.0
CG B:HIS256 4.2 49.6 1.0
ND1 B:HIS256 4.2 50.2 1.0
CB B:ASP293 4.3 40.1 1.0
NE2 B:HIS252 4.5 41.7 1.0
CB B:ASP402 4.5 44.9 1.0
O B:HOH537 4.5 50.0 1.0
O B:ASP402 4.5 44.9 1.0
CG2 B:VAL260 4.7 27.2 1.0
CA B:ASP402 4.8 43.1 1.0
O B:HOH544 4.9 63.6 1.0
O B:HOH538 5.0 38.1 1.0

Reference:

J.Hou, J.Xu, M.Liu, R.Zhao, H.B.Luo, H.Ke. Structural Asymmetry of Phosphodiesterase-9, Potential Protonation of A Glutamic Acid, and Role of the Invariant Glutamine. Plos One V. 6 18092 2011.
ISSN: ESSN 1932-6203
PubMed: 21483814
DOI: 10.1371/JOURNAL.PONE.0018092
Page generated: Wed Dec 16 04:45:14 2020

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