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Magnesium in PDB 4gh6: Crystal Structure of the PDE9A Catalytic Domain in Complex with Inhibitor 28

Enzymatic activity of Crystal Structure of the PDE9A Catalytic Domain in Complex with Inhibitor 28

All present enzymatic activity of Crystal Structure of the PDE9A Catalytic Domain in Complex with Inhibitor 28:
3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of the PDE9A Catalytic Domain in Complex with Inhibitor 28, PDB code: 4gh6 was solved by J.Hou, H.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.70
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 104.276, 104.276, 270.073, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 24.5

Other elements in 4gh6:

The structure of Crystal Structure of the PDE9A Catalytic Domain in Complex with Inhibitor 28 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the PDE9A Catalytic Domain in Complex with Inhibitor 28 (pdb code 4gh6). 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 the PDE9A Catalytic Domain in Complex with Inhibitor 28, PDB code: 4gh6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4gh6

Go back to Magnesium Binding Sites List in 4gh6
Magnesium binding site 1 out of 2 in the Crystal Structure of the PDE9A Catalytic Domain in Complex with Inhibitor 28


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 the PDE9A Catalytic Domain in Complex with Inhibitor 28 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:43.2
occ:1.00
OD1 A:ASP293 2.1 42.0 1.0
O A:HOH705 2.3 30.7 1.0
O A:HOH706 2.3 29.7 1.0
O A:HOH704 2.4 33.1 1.0
O A:HOH702 2.4 34.2 1.0
O A:HOH703 2.5 41.2 1.0
CG A:ASP293 3.1 36.3 1.0
OD2 A:ASP293 3.5 42.8 1.0
NE2 A:HIS325 3.8 32.1 1.0
ZN A:ZN602 4.0 60.4 1.0
CD2 A:HIS296 4.0 35.5 1.0
OE2 A:GLU322 4.1 44.0 1.0
O A:HOH701 4.1 37.8 1.0
O A:HOH707 4.1 35.0 1.0
CD2 A:HIS325 4.1 33.1 1.0
O A:HOH709 4.2 40.7 1.0
CD2 A:HIS252 4.3 37.8 1.0
O A:HIS292 4.3 33.9 1.0
NE2 A:HIS252 4.4 36.9 1.0
CD2 A:HIS292 4.4 34.6 1.0
CB A:ASP293 4.4 36.3 1.0
NE2 A:HIS296 4.5 34.7 1.0
OG1 A:THR363 4.5 31.3 1.0
CA A:ASP293 4.7 34.4 1.0
NE2 A:HIS292 4.8 40.5 1.0
CE1 A:HIS325 4.9 34.5 1.0
CD A:GLU322 4.9 42.6 1.0
OD2 A:ASP402 5.0 43.6 1.0
CG A:GLU322 5.0 38.9 1.0

Magnesium binding site 2 out of 2 in 4gh6

Go back to Magnesium Binding Sites List in 4gh6
Magnesium binding site 2 out of 2 in the Crystal Structure of the PDE9A Catalytic Domain in Complex with Inhibitor 28


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 the PDE9A Catalytic Domain in Complex with Inhibitor 28 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg604

b:36.6
occ:1.00
OD1 B:ASP293 2.1 43.3 1.0
O B:HOH701 2.4 27.0 1.0
O B:HOH706 2.4 40.7 1.0
O B:HOH705 2.4 32.0 1.0
O B:HOH703 2.5 35.9 1.0
O B:HOH704 2.5 51.3 1.0
CG B:ASP293 3.2 42.2 1.0
NE2 B:HIS325 3.5 33.8 1.0
OD2 B:ASP293 3.6 48.5 1.0
CD2 B:HIS325 3.8 34.3 1.0
OE2 B:GLU322 3.8 39.9 1.0
CD2 B:HIS296 4.0 36.7 1.0
O B:HIS292 4.1 43.4 1.0
ZN B:ZN603 4.3 61.7 1.0
NE2 B:HIS296 4.4 35.6 1.0
CB B:ASP293 4.5 41.8 1.0
CD2 B:HIS292 4.5 41.4 1.0
O B:HOH702 4.5 48.3 1.0
OG1 B:THR363 4.6 37.3 1.0
CE1 B:HIS325 4.6 34.2 1.0
NE2 B:HIS252 4.7 34.6 1.0
CA B:ASP293 4.7 40.8 1.0
CD2 B:HIS252 4.7 35.9 1.0
CD B:GLU322 4.7 41.2 1.0
CG B:GLU322 4.9 38.5 1.0
C B:HIS292 5.0 42.7 1.0
NE2 B:HIS292 5.0 46.8 1.0

Reference:

F.Meng, J.Hou, Y.X.Shao, P.Y.Wu, M.Huang, X.Zhu, Y.Cai, Z.Li, J.Xu, P.Liu, H.B.Luo, Y.Wan, H.Ke. Structure-Based Discovery of Highly Selective Phosphodiesterase-9A Inhibitors and Implications For Inhibitor Design. J.Med.Chem. V. 55 8549 2012.
ISSN: ISSN 0022-2623
PubMed: 22985069
DOI: 10.1021/JM301189C
Page generated: Mon Dec 14 16:20:58 2020

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