Manganese 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:

Magnesium

(Mg)

2 atoms

The binding sites of Manganese atom in the Human Phosphdiesterase 9 Substrate Complex (Es Complex) (pdb code 3dyl). 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 Phosphdiesterase 9 Substrate Complex (Es Complex), PDB code: 3dyl:
Jump to Manganese binding site number: 1; 2;

Manganese 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 Manganese with other atoms in the Mn binding site number 1 of Human Phosphdiesterase 9 Substrate Complex (Es Complex) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn901 b:57.0 occ:1.00 O A:HOH1000 1.8 23.8 1.0 OD2 A:ASP293 2.1 50.5 1.0 NE2 A:HIS256 2.1 53.0 1.0 NE2 A:HIS292 2.2 48.2 1.0 OD1 A:ASP402 2.2 47.4 1.0 O1A A:PCG900 2.2 50.3 1.0 CD2 A:HIS256 2.9 51.6 1.0 CD2 A:HIS292 3.1 49.3 1.0 CG A:ASP293 3.1 46.8 1.0 CE1 A:HIS256 3.1 51.8 1.0 CG A:ASP402 3.2 47.8 1.0 CE1 A:HIS292 3.2 49.8 1.0 PA A:PCG900 3.4 66.1 1.0 OD2 A:ASP402 3.5 47.2 1.0 OD1 A:ASP293 3.7 45.0 1.0 MG A:MG902 3.7 39.1 1.0 O2A A:PCG900 3.9 58.4 1.0 O5' A:PCG900 4.0 58.9 1.0 CG A:HIS256 4.1 51.5 1.0 CB A:ASP293 4.1 47.6 1.0 O A:HOH131 4.1 50.8 1.0 ND1 A:HIS256 4.2 50.5 1.0 CG A:HIS292 4.2 48.9 1.0 ND1 A:HIS292 4.3 48.4 1.0 CD2 A:HIS252 4.3 50.5 1.0 CB A:ASP402 4.6 48.9 1.0 CG2 A:VAL260 4.6 44.4 1.0 O A:HOH1004 4.6 23.7 1.0 NE2 A:HIS252 4.7 50.8 1.0 O A:ASP402 5.0 47.5 1.0 C5' A:PCG900 5.0 58.5 1.0

Manganese 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 Manganese with other atoms in the Mn binding site number 2 of Human Phosphdiesterase 9 Substrate Complex (Es Complex) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn901 b:57.9 occ:1.00 OD1 B:ASP402 2.1 48.7 1.0 NE2 B:HIS292 2.2 48.7 1.0 OD2 B:ASP293 2.2 51.5 1.0 NE2 B:HIS256 2.2 53.4 1.0 O1 B:FMT1 2.5 69.4 1.0 O B:HOH0 2.5 20.1 1.0 CD2 B:HIS292 3.0 49.8 1.0 CG B:ASP402 3.1 48.4 1.0 CD2 B:HIS256 3.1 52.7 1.0 CG B:ASP293 3.2 46.8 1.0 OD2 B:ASP402 3.2 48.1 1.0 CE1 B:HIS292 3.3 50.6 1.0 CE1 B:HIS256 3.3 51.8 1.0 C B:FMT1 3.3 71.0 1.0 O2 B:FMT1 3.5 70.4 1.0 OD1 B:ASP293 3.6 45.1 1.0 O B:HOH2 3.9 23.4 1.0 MG B:MG902 4.1 46.8 1.0 CG B:HIS292 4.2 49.3 1.0 CB B:ASP293 4.2 47.3 1.0 CG B:HIS256 4.3 52.0 1.0 CD2 B:HIS252 4.3 50.7 1.0 ND1 B:HIS292 4.3 49.0 1.0 ND1 B:HIS256 4.4 50.6 1.0 CB B:ASP402 4.5 48.9 1.0 O B:HOH33 4.6 34.1 1.0 CG2 B:VAL260 4.7 44.1 1.0 NE2 B:HIS252 4.7 51.3 1.0 O B:ASP402 4.8 47.9 1.0 O B:HOH4 4.8 29.3 1.0 CA B:ASP402 5.0 48.4 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