Magnesium in PDB 1xmy: Catalytic Domain of Human Phosphodiesterase 4B in Complex with (R)- Rolipram

All present enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4B in Complex with (R)- Rolipram:
3.1.4.17;

The structure of Catalytic Domain of Human Phosphodiesterase 4B in Complex with (R)- Rolipram, PDB code: 1xmy was solved by G.L.Card, B.P.England, Y.Suzuki, D.Fong, B.Powell, B.Lee, C.Luu, M.Tabrizizad, S.Gillette, P.N.Ibrahim, D.R.Artis, G.Bollag, M.V.Milburn, S.-H.Kim, J.Schlessinger, K.Y.J.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.71 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.670, 94.633, 106.432, 90.00, 90.00, 90.00
R / Rfree (%)	24.3 / 29.8

The structure of Catalytic Domain of Human Phosphodiesterase 4B in Complex with (R)- Rolipram also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with (R)- Rolipram (pdb code 1xmy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with (R)- Rolipram, PDB code: 1xmy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with (R)- Rolipram


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Catalytic Domain of Human Phosphodiesterase 4B in Complex with (R)- Rolipram within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:30.8 occ:1.00 O A:HOH1003 1.7 39.7 1.0 OD1 A:ASP275 2.0 19.8 1.0 O A:HOH1007 2.0 26.9 1.0 O A:HOH1004 2.1 52.0 1.0 O A:HOH1006 2.1 37.6 1.0 O A:HOH1005 2.5 27.7 1.0 CG A:ASP275 2.8 25.0 1.0 OD2 A:ASP275 3.0 29.7 1.0 ZN A:ZN1001 3.6 39.1 1.0 OG1 A:THR345 3.9 29.2 1.0 O A:HIS274 4.0 22.4 1.0 O A:HOH1008 4.0 18.4 1.0 OE2 A:GLU304 4.2 17.0 1.0 NE2 A:HIS307 4.2 16.7 1.0 CD2 A:HIS274 4.2 7.6 1.0 CB A:ASP275 4.3 20.8 1.0 CD2 A:HIS307 4.4 14.7 1.0 NE2 A:HIS274 4.4 9.2 1.0 O A:THR345 4.5 25.3 1.0 OD1 A:ASP392 4.6 23.8 1.0 O A:HOH4 4.6 28.8 1.0 CB A:THR345 4.6 25.1 1.0 O A:HOH20 4.6 38.4 1.0 CA A:ASP275 4.7 20.7 1.0 OD2 A:ASP392 4.8 30.1 1.0 CD2 A:HIS278 4.8 21.0 1.0 CD2 A:HIS234 4.8 20.2 1.0 O A:HOH29 4.9 37.5 1.0 C A:HIS274 4.9 21.0 1.0 CG A:GLU304 5.0 22.9 1.0 NE2 A:HIS234 5.0 19.6 1.0

Magnesium binding site 2 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with (R)- Rolipram


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Catalytic Domain of Human Phosphodiesterase 4B in Complex with (R)- Rolipram within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:26.8 occ:1.00 O B:HOH2003 2.0 34.6 1.0 OD1 B:ASP275 2.1 21.5 1.0 O B:HOH2006 2.1 48.1 1.0 O B:HOH2005 2.1 31.8 1.0 O B:HOH2007 2.3 32.8 1.0 O B:HOH2004 2.3 28.0 1.0 CG B:ASP275 3.1 24.5 1.0 OD2 B:ASP275 3.5 27.1 1.0 ZN B:ZN1001 3.8 41.7 1.0 O B:HIS274 4.0 22.7 1.0 OE2 B:GLU304 4.1 27.0 1.0 NE2 B:HIS307 4.1 15.2 1.0 OG1 B:THR345 4.2 17.0 1.0 O B:HOH2008 4.2 36.4 1.0 CD2 B:HIS274 4.2 14.7 1.0 O B:HOH33 4.3 52.2 1.0 CD2 B:HIS278 4.4 19.7 1.0 CB B:ASP275 4.5 21.7 1.0 CD2 B:HIS307 4.5 16.3 1.0 OD1 B:ASP392 4.5 24.6 1.0 NE2 B:HIS234 4.6 25.3 1.0 CD2 B:HIS234 4.6 24.0 1.0 NE2 B:HIS278 4.6 24.1 1.0 O B:THR345 4.7 19.7 1.0 NE2 B:HIS274 4.7 12.1 1.0 CA B:ASP275 4.8 21.5 1.0 CB B:THR345 4.9 18.9 1.0 C B:HIS274 4.9 21.3 1.0

G.L.Card, B.P.England, Y.Suzuki, D.Fong, B.Powell, B.Lee, C.Luu, M.Tabrizizad, S.Gillette, P.N.Ibrahim, D.R.Artis, G.Bollag, M.V.Milburn, S.-H.Kim, J.Schlessinger, K.Y.J.Zhang. Structural Basis For the Activity of Drugs That Inhibit Phosphodiesterases. Structure V. 12 2233 2004.
ISSN: ISSN 0969-2126
PubMed: 15576036
DOI: 10.1016/J.STR.2004.10.004