Magnesium in PDB 3dyl: Human Phosphdiesterase 9 Substrate Complex (Es Complex)

All present enzymatic activity of Human Phosphdiesterase 9 Substrate Complex (Es Complex):
3.1.4.35;

The structure of Human Phosphdiesterase 9 Substrate Complex (Es Complex), PDB code: 3dyl was solved by S.Liu, M.N.Mansour, K.Dillman, J.Perez, D.Danley, F.Menniti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	96.67 / 2.70
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	103.787, 103.787, 269.799, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 21.9

The structure of Human Phosphdiesterase 9 Substrate Complex (Es Complex) also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Magnesium atom in the Human Phosphdiesterase 9 Substrate Complex (Es Complex) (pdb code 3dyl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Phosphdiesterase 9 Substrate Complex (Es Complex), PDB code: 3dyl:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Phosphdiesterase 9 Substrate Complex (Es Complex)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Phosphdiesterase 9 Substrate Complex (Es Complex) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:39.1 occ:1.00 O2A A:PCG900 1.8 58.4 1.0 O A:HOH1004 1.9 23.7 1.0 O A:HOH1005 2.2 21.9 1.0 OD1 A:ASP293 2.2 45.0 1.0 O A:HOH1000 2.2 23.8 1.0 O A:HOH1003 2.3 24.2 1.0 PA A:PCG900 3.0 66.1 1.0 CG A:ASP293 3.1 46.8 1.0 O5' A:PCG900 3.4 58.9 1.0 OD2 A:ASP293 3.4 50.5 1.0 O1A A:PCG900 3.7 50.3 1.0 MN A:MN901 3.7 57.0 1.0 O A:HOH25 4.0 41.0 1.0 CD2 A:HIS292 4.0 49.3 1.0 NE2 A:HIS325 4.1 49.1 1.0 O A:HIS292 4.2 48.8 1.0 OE2 A:GLU322 4.2 47.0 1.0 OG1 A:THR363 4.2 44.4 1.0 OD2 A:ASP402 4.3 47.2 1.0 CD2 A:HIS325 4.4 46.8 1.0 NE2 A:HIS292 4.5 48.2 1.0 CB A:ASP293 4.5 47.6 1.0 CD2 A:HIS296 4.5 47.2 1.0 O3' A:PCG900 4.7 62.6 1.0 CD2 A:HIS252 4.7 50.5 1.0 CB A:THR363 4.8 46.3 1.0 O A:THR363 4.8 47.3 1.0 NE2 A:HIS252 4.8 50.8 1.0 C5' A:PCG900 4.8 58.5 1.0 CA A:ASP293 4.9 47.3 1.0 NE2 A:HIS296 4.9 44.9 1.0 OD1 A:ASP402 4.9 47.4 1.0 CG A:GLU322 5.0 47.5 1.0

Magnesium binding site 2 out of 2 in the Human Phosphdiesterase 9 Substrate Complex (Es Complex)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Phosphdiesterase 9 Substrate Complex (Es Complex) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg902 b:46.8 occ:1.00 O B:HOH5 1.8 44.2 1.0 O B:HOH0 2.0 20.1 1.0 O B:HOH3 2.1 28.6 1.0 OD1 B:ASP293 2.1 45.1 1.0 O B:HOH2 2.3 23.4 1.0 O B:HOH4 2.4 29.3 1.0 CG B:ASP293 3.2 46.8 1.0 OD2 B:ASP293 3.5 51.5 1.0 NE2 B:HIS325 3.7 48.8 1.0 O B:HOH27 3.8 28.5 1.0 OE2 B:GLU322 3.8 47.4 1.0 O1 B:FMT1 3.9 69.4 1.0 MN B:MN901 4.1 57.9 1.0 CD2 B:HIS296 4.1 47.8 1.0 CD2 B:HIS325 4.1 47.2 1.0 O B:HIS292 4.2 49.2 1.0 NE2 B:HIS296 4.4 45.2 1.0 CD2 B:HIS292 4.4 49.8 1.0 O B:HOH33 4.5 34.1 1.0 CB B:ASP293 4.5 47.3 1.0 CD2 B:HIS252 4.6 50.7 1.0 OG1 B:THR363 4.6 45.7 1.0 NE2 B:HIS252 4.7 51.3 1.0 OD2 B:ASP402 4.7 48.1 1.0 CD B:GLU322 4.7 50.3 1.0 CG B:GLU322 4.8 47.5 1.0 CE1 B:HIS325 4.8 49.0 1.0 CA B:ASP293 4.9 47.5 1.0 NE2 B:HIS292 4.9 48.7 1.0

S.Liu, M.N.Mansour, K.S.Dillman, J.R.Perez, D.E.Danley, P.A.Aeed, S.P.Simons, P.K.Lemotte, F.S.Menniti. Structural Basis For the Catalytic Mechanism of Human Phosphodiesterase 9. Proc.Natl.Acad.Sci.Usa V. 105 13309 2008.
ISSN: ISSN 0027-8424
PubMed: 18757755
DOI: 10.1073/PNAS.0708850105