Sodium in PDB 3dyq: Human Phosphodiestrase 9 (Inhibited By Omitting Divalent Cation) in Complex with Cgmp

All present enzymatic activity of Human Phosphodiestrase 9 (Inhibited By Omitting Divalent Cation) in Complex with Cgmp:
3.1.4.35;

The structure of Human Phosphodiestrase 9 (Inhibited By Omitting Divalent Cation) in Complex with Cgmp, PDB code: 3dyq 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)	50.00 / 2.50
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	103.650, 103.650, 270.041, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 22.6

The binding sites of Sodium atom in the Human Phosphodiestrase 9 (Inhibited By Omitting Divalent Cation) in Complex with Cgmp (pdb code 3dyq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Human Phosphodiestrase 9 (Inhibited By Omitting Divalent Cation) in Complex with Cgmp, PDB code: 3dyq:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Human Phosphodiestrase 9 (Inhibited By Omitting Divalent Cation) in Complex with Cgmp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Phosphodiestrase 9 (Inhibited By Omitting Divalent Cation) in Complex with Cgmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na901 b:34.8 occ:1.00 OD1 A:ASP402 2.1 48.4 1.0 OD2 A:ASP293 2.1 47.9 1.0 NE2 A:HIS292 2.4 55.8 1.0 NE2 A:HIS256 2.5 50.3 1.0 O1A A:PCG900 2.6 80.8 1.0 CG A:ASP402 3.0 46.1 1.0 NA A:NA902 3.1 57.6 1.0 OD2 A:ASP402 3.1 48.0 1.0 CG A:ASP293 3.1 47.2 1.0 CD2 A:HIS292 3.2 54.2 1.0 CE1 A:HIS256 3.4 51.8 1.0 CD2 A:HIS256 3.5 52.4 1.0 OD1 A:ASP293 3.5 48.1 1.0 CE1 A:HIS292 3.6 57.5 1.0 CD2 A:HIS252 4.0 47.6 1.0 PA A:PCG900 4.1 85.5 1.0 NE2 A:HIS252 4.1 48.6 1.0 O5' A:PCG900 4.4 80.0 1.0 CG A:HIS292 4.4 49.9 1.0 CB A:ASP293 4.4 46.1 1.0 CB A:ASP402 4.4 47.1 1.0 ND1 A:HIS256 4.5 48.2 1.0 O A:HOH93 4.5 35.1 1.0 CG A:HIS256 4.6 50.1 1.0 ND1 A:HIS292 4.6 53.2 1.0 O A:ASP402 4.8 46.8 1.0 O A:HOH95 4.9 37.4 1.0 CA A:ASP402 5.0 46.3 1.0

Sodium binding site 2 out of 4 in the Human Phosphodiestrase 9 (Inhibited By Omitting Divalent Cation) in Complex with Cgmp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Phosphodiestrase 9 (Inhibited By Omitting Divalent Cation) in Complex with Cgmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na902 b:57.6 occ:1.00 O A:HOH93 2.2 35.1 1.0 O A:HOH95 2.3 37.4 1.0 OD1 A:ASP293 2.3 48.1 1.0 O1A A:PCG900 2.9 80.8 1.0 NA A:NA901 3.1 34.8 1.0 CG A:ASP293 3.2 47.2 1.0 OD2 A:ASP293 3.3 47.9 1.0 PA A:PCG900 3.5 85.5 1.0 O2A A:PCG900 3.5 82.1 1.0 O5' A:PCG900 3.9 80.0 1.0 CD2 A:HIS292 3.9 54.2 1.0 OD2 A:ASP402 3.9 48.0 1.0 OG1 A:THR363 4.1 40.9 1.0 NE2 A:HIS292 4.2 55.8 1.0 O A:HIS292 4.4 47.5 1.0 NE2 A:HIS325 4.5 47.4 1.0 OE2 A:GLU322 4.5 45.7 1.0 OD1 A:ASP402 4.5 48.4 1.0 NE2 A:HIS252 4.5 48.6 1.0 CD2 A:HIS252 4.6 47.6 1.0 CB A:ASP293 4.6 46.1 1.0 CB A:THR363 4.6 44.0 1.0 CG A:ASP402 4.6 46.1 1.0 O A:THR363 4.7 45.6 1.0 O A:HOH92 4.7 47.4 1.0 CD2 A:HIS325 4.7 45.0 1.0 CD2 A:HIS296 4.8 44.9 1.0

Sodium binding site 3 out of 4 in the Human Phosphodiestrase 9 (Inhibited By Omitting Divalent Cation) in Complex with Cgmp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Human Phosphodiestrase 9 (Inhibited By Omitting Divalent Cation) in Complex with Cgmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na901 b:43.3 occ:1.00 OD1 B:ASP402 2.1 46.4 1.0 OD2 B:ASP293 2.1 52.7 1.0 NE2 B:HIS292 2.4 53.3 1.0 NE2 B:HIS256 2.7 56.4 1.0 CG B:ASP402 3.0 45.6 1.0 OD2 B:ASP402 3.1 51.2 1.0 CG B:ASP293 3.1 47.8 1.0 CD2 B:HIS292 3.2 52.6 1.0 O B:HOH1 3.2 44.2 1.0 OD1 B:ASP293 3.4 51.6 1.0 CE1 B:HIS292 3.5 57.6 1.0 CD2 B:HIS256 3.5 54.7 1.0 NA B:NA902 3.6 55.4 1.0 CE1 B:HIS256 3.7 56.3 1.0 CD2 B:HIS252 4.0 48.1 1.0 NE2 B:HIS252 4.2 48.5 1.0 O B:HOH77 4.3 54.5 1.0 CG B:HIS292 4.4 50.1 1.0 CB B:ASP402 4.4 45.3 1.0 CB B:ASP293 4.4 46.5 1.0 ND1 B:HIS292 4.5 54.4 1.0 CG B:HIS256 4.7 51.8 1.0 O B:ASP402 4.7 45.6 1.0 ND1 B:HIS256 4.8 51.1 1.0 CA B:ASP402 4.9 45.7 1.0 CG2 B:VAL260 4.9 41.6 1.0

Sodium binding site 4 out of 4 in the Human Phosphodiestrase 9 (Inhibited By Omitting Divalent Cation) in Complex with Cgmp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Human Phosphodiestrase 9 (Inhibited By Omitting Divalent Cation) in Complex with Cgmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na902 b:55.4 occ:1.00 OD1 B:ASP293 2.3 51.6 1.0 CG B:ASP293 3.3 47.8 1.0 O B:HOH1142 3.4 47.7 1.0 NA B:NA901 3.6 43.3 1.0 OD2 B:ASP293 3.7 52.7 1.0 OE2 B:GLU322 3.8 51.6 1.0 NE2 B:HIS325 4.1 42.8 1.0 CD2 B:HIS292 4.3 52.6 1.0 CD2 B:HIS296 4.3 43.7 1.0 OG1 B:THR363 4.3 44.1 1.0 CD2 B:HIS325 4.4 42.1 1.0 O B:HOH77 4.4 54.5 1.0 OD2 B:ASP402 4.4 51.2 1.0 O B:HIS292 4.5 48.2 1.0 NE2 B:HIS252 4.5 48.5 1.0 NE2 B:HIS296 4.5 44.8 1.0 CD2 B:HIS252 4.6 48.1 1.0 NE2 B:HIS292 4.7 53.3 1.0 CB B:ASP293 4.7 46.5 1.0 CD B:GLU322 4.7 45.4 1.0 CB B:THR363 4.9 44.5 1.0 CG B:GLU322 4.9 43.6 1.0 O B:THR363 4.9 46.0 1.0 CA B:ASP293 5.0 46.1 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