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

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 2 in 3qi3

Go back to Magnesium Binding Sites List in 3qi3
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg535

b:42.5
occ:1.00
OD1 A:ASP293 2.1 34.6 1.0
O A:HOH537 2.3 39.0 1.0
O A:HOH541 2.3 31.7 1.0
O A:HOH540 2.4 46.2 1.0
O A:HOH538 2.6 36.7 1.0
O A:HOH539 2.6 42.8 1.0
CG A:ASP293 3.1 34.9 1.0
OD2 A:ASP293 3.4 37.6 1.0
NE2 A:HIS325 3.8 33.3 1.0
ZN A:ZN534 3.9 54.9 1.0
OE2 A:GLU322 4.1 35.5 1.0
O A:HIS292 4.1 35.9 1.0
CD2 A:HIS325 4.1 34.2 1.0
CD2 A:HIS296 4.2 37.6 1.0
CD2 A:HIS292 4.2 38.4 1.0
O A:HOH542 4.3 38.3 1.0
O A:HOH536 4.4 39.7 1.0
OG1 A:THR363 4.4 32.5 1.0
CB A:ASP293 4.4 34.5 1.0
CD2 A:HIS252 4.5 39.1 1.0
NE2 A:HIS296 4.6 37.9 1.0
NE2 A:HIS292 4.6 43.0 1.0
NE2 A:HIS252 4.6 38.6 1.0
CA A:ASP293 4.7 35.4 1.0
O A:HOH548 4.7 52.1 1.0
CE1 A:HIS325 4.8 33.4 1.0
OD2 A:ASP402 4.9 43.9 1.0
CD A:GLU322 5.0 34.6 1.0
CB A:THR363 5.0 30.1 1.0
C A:HIS292 5.0 36.0 1.0

Magnesium binding site 2 out of 2 in 3qi3

Go back to Magnesium Binding Sites List in 3qi3
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg535

b:49.9
occ:1.00
OD1 B:ASP293 2.1 46.4 1.0
O B:HOH538 2.3 38.1 1.0
O B:HOH541 2.3 51.3 1.0
O B:HOH540 2.4 40.8 1.0
O B:HOH539 2.5 46.3 1.0
O B:HOH537 2.6 50.0 1.0
CG B:ASP293 3.1 44.0 1.0
OD2 B:ASP293 3.4 51.5 1.0
ZN B:ZN534 3.9 67.1 1.0
NE2 B:HIS325 3.9 35.9 1.0
CD2 B:HIS292 4.0 46.2 1.0
OE2 B:GLU322 4.0 43.0 1.0
O B:HIS292 4.1 36.5 1.0
CD2 B:HIS325 4.1 33.6 1.0
OG1 B:THR363 4.2 38.1 1.0
CB B:ASP293 4.4 40.1 1.0
NE2 B:HIS292 4.4 52.5 1.0
CD2 B:HIS296 4.5 37.2 1.0
OD2 B:ASP402 4.6 48.3 1.0
CA B:ASP293 4.6 37.5 1.0
O B:HOH536 4.7 49.4 1.0
O B:THR363 4.8 38.9 1.0
CB B:THR363 4.8 36.9 1.0
C B:HIS292 4.8 37.7 1.0
CD2 B:HIS252 4.8 40.3 1.0
NE2 B:HIS252 4.9 41.7 1.0
CD B:GLU322 4.9 40.9 1.0
CE1 B:HIS325 4.9 33.9 1.0
OD1 B:ASP402 5.0 52.2 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: Mon Dec 14 08:42:31 2020

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