Manganese 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:

Magnesium

(Mg)

2 atoms

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

Manganese 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 Manganese with other atoms in the Mn 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:Mn901 b:36.9 occ:1.00 O A:HOH1139 2.0 25.2 0.5 OD2 A:ASP293 2.1 38.8 1.0 OD1 A:ASP402 2.2 38.1 1.0 NE2 A:HIS256 2.2 33.1 1.0 NE2 A:HIS292 2.2 36.4 1.0 O A:HOH1138 2.4 24.0 0.5 O2P A:5GP900 2.5 51.9 0.5 O3P A:5GP900 2.7 49.4 0.5 CD2 A:HIS292 3.1 35.6 1.0 P A:5GP900 3.1 48.0 0.5 CG A:ASP293 3.1 35.8 1.0 CD2 A:HIS256 3.1 34.9 1.0 CG A:ASP402 3.2 37.3 1.0 CE1 A:HIS256 3.2 36.1 1.0 CE1 A:HIS292 3.3 36.9 1.0 OD2 A:ASP402 3.5 37.2 1.0 OD1 A:ASP293 3.6 39.0 1.0 O A:HOH914 3.9 38.7 1.0 MG A:MG902 4.1 39.8 1.0 O1P A:5GP900 4.2 47.6 0.5 O A:HOH1140 4.2 28.4 0.5 CB A:ASP293 4.2 36.3 1.0 CG A:HIS292 4.3 35.9 1.0 O5' A:5GP900 4.3 50.5 0.5 CG A:HIS256 4.3 36.5 1.0 ND1 A:HIS256 4.3 35.9 1.0 ND1 A:HIS292 4.4 33.9 1.0 CD2 A:HIS252 4.4 32.7 1.0 CB A:ASP402 4.5 36.7 1.0 CG2 A:VAL260 4.6 33.8 1.0 O A:ASP402 4.7 37.9 1.0 O A:HOH1136 4.8 32.6 1.0 NE2 A:HIS252 4.8 37.7 1.0 CA A:ASP402 4.9 36.8 1.0 C5' A:5GP900 4.9 47.6 0.5

Manganese 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 Manganese with other atoms in the Mn 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:Mn901 b:36.1 occ:1.00 OD2 B:ASP293 2.1 40.1 1.0 OD1 B:ASP402 2.1 39.7 1.0 NE2 B:HIS256 2.2 33.6 1.0 O1 B:FMT1 2.2 37.9 1.0 NE2 B:HIS292 2.3 34.5 1.0 O B:HOH1265 2.4 32.9 1.0 C B:FMT1 3.0 38.7 1.0 CD2 B:HIS292 3.0 38.9 1.0 CD2 B:HIS256 3.1 34.3 1.0 CG B:ASP402 3.1 38.0 1.0 CG B:ASP293 3.2 36.8 1.0 CE1 B:HIS256 3.2 34.7 1.0 CE1 B:HIS292 3.4 38.3 1.0 OD2 B:ASP402 3.4 40.4 1.0 OD1 B:ASP293 3.8 38.9 1.0 MG B:MG902 4.0 39.7 1.0 O2 B:FMT1 4.1 37.4 1.0 O B:HOH1266 4.2 34.4 1.0 CB B:ASP293 4.2 36.3 1.0 CD2 B:HIS252 4.3 38.6 1.0 CG B:HIS292 4.3 36.9 1.0 CG B:HIS256 4.3 38.2 1.0 ND1 B:HIS256 4.3 34.7 1.0 ND1 B:HIS292 4.4 33.6 1.0 CB B:ASP402 4.5 36.3 1.0 NE2 B:HIS252 4.6 37.9 1.0 CG2 B:VAL260 4.7 32.7 1.0 O B:ASP402 4.7 37.9 1.0 O B:HOH1269 4.8 32.4 1.0 CA B:ASP402 4.9 37.0 1.0 O B:HOH1134 4.9 48.5 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