Magnesium in PDB 3dy8: Human Phosphodiesterase 9 in Complex with Product 5'-Gmp (E+P Complex)

All present enzymatic activity of Human Phosphodiesterase 9 in Complex with Product 5'-Gmp (E+P Complex):
3.1.4.35;

The structure of Human Phosphodiesterase 9 in Complex with Product 5'-Gmp (E+P Complex), PDB code: 3dy8 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)	10.00 / 2.15
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	103.394, 103.394, 269.429, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 19.9

The structure of Human Phosphodiesterase 9 in Complex with Product 5'-Gmp (E+P Complex) also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Magnesium atom in the Human Phosphodiesterase 9 in Complex with Product 5'-Gmp (E+P Complex) (pdb code 3dy8). 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 Phosphodiesterase 9 in Complex with Product 5'-Gmp (E+P Complex), PDB code: 3dy8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Phosphodiesterase 9 in Complex with Product 5'-Gmp (E+P Complex)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Phosphodiesterase 9 in Complex with Product 5'-Gmp (E+P Complex) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:39.8 occ:1.00 O A:HOH1140 2.1 28.4 0.5 O A:HOH1136 2.2 32.6 1.0 OD1 A:ASP293 2.2 39.0 1.0 O2P A:5GP900 2.2 51.9 0.5 O A:HOH1137 2.3 27.1 1.0 O A:HOH1138 2.4 24.0 0.5 O A:HOH1135 2.5 30.4 1.0 P A:5GP900 3.1 48.0 0.5 O1P A:5GP900 3.2 47.6 0.5 CG A:ASP293 3.2 35.8 1.0 OD2 A:ASP293 3.6 38.8 1.0 O5' A:5GP900 3.8 50.5 0.5 NE2 A:HIS325 3.9 35.5 1.0 OE2 A:GLU322 4.0 42.0 1.0 O A:HOH917 4.0 35.7 1.0 MN A:MN901 4.1 36.9 1.0 CD2 A:HIS325 4.1 34.4 1.0 O A:HOH1139 4.1 25.2 0.5 O A:HIS292 4.2 36.1 1.0 OG1 A:THR363 4.4 37.6 1.0 CD2 A:HIS292 4.4 35.6 1.0 CD2 A:HIS296 4.4 33.5 1.0 O3P A:5GP900 4.4 49.4 0.5 CB A:ASP293 4.6 36.3 1.0 OD2 A:ASP402 4.7 37.2 1.0 NE2 A:HIS296 4.7 35.6 1.0 CG A:GLU322 4.7 35.5 1.0 CD2 A:HIS252 4.8 32.7 1.0 CA A:ASP293 4.8 36.0 1.0 CD A:GLU322 4.8 39.1 1.0 NE2 A:HIS292 4.9 36.4 1.0 CB A:THR363 4.9 37.2 1.0 O A:THR363 4.9 36.9 1.0 NE2 A:HIS252 4.9 37.7 1.0

Magnesium binding site 2 out of 2 in the Human Phosphodiesterase 9 in Complex with Product 5'-Gmp (E+P Complex)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Phosphodiesterase 9 in Complex with Product 5'-Gmp (E+P Complex) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg902 b:39.7 occ:1.00 O B:HOH1269 2.2 32.4 1.0 OD1 B:ASP293 2.2 38.9 1.0 O B:HOH1268 2.2 30.0 1.0 O B:HOH1265 2.3 32.9 1.0 O B:HOH1266 2.3 34.4 1.0 O B:HOH1267 2.3 31.5 1.0 CG B:ASP293 3.2 36.8 1.0 OD2 B:ASP293 3.4 40.1 1.0 OE2 B:GLU322 3.9 42.0 1.0 NE2 B:HIS325 3.9 31.9 1.0 MN B:MN901 4.0 36.1 1.0 O B:HOH1051 4.1 30.6 1.0 CD2 B:HIS325 4.2 33.7 1.0 CD2 B:HIS296 4.3 32.8 1.0 O B:HIS292 4.3 36.4 1.0 CD2 B:HIS292 4.4 38.9 1.0 OG1 B:THR363 4.4 37.3 1.0 O1 B:FMT1 4.4 37.9 1.0 O B:HOH1191 4.5 52.0 1.0 CB B:ASP293 4.5 36.3 1.0 O B:HOH1134 4.6 48.5 1.0 CD2 B:HIS252 4.6 38.6 1.0 OD2 B:ASP402 4.6 40.4 1.0 NE2 B:HIS296 4.7 35.4 1.0 NE2 B:HIS252 4.7 37.9 1.0 CG B:GLU322 4.8 36.0 1.0 CD B:GLU322 4.8 41.8 1.0 CA B:ASP293 4.8 36.2 1.0 O B:THR363 4.9 36.2 1.0 NE2 B:HIS292 4.9 34.5 1.0 CB B:THR363 4.9 36.9 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