Magnesium in PDB 1xm6: Catalytic Domain of Human Phosphodiesterase 4B in Complex with (R)- Mesopram

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

The structure of Catalytic Domain of Human Phosphodiesterase 4B in Complex with (R)- Mesopram, PDB code: 1xm6 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 / 1.92
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.221, 94.062, 105.236, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 22.7

The structure of Catalytic Domain of Human Phosphodiesterase 4B in Complex with (R)- Mesopram 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)- Mesopram (pdb code 1xm6). 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)- Mesopram, PDB code: 1xm6:
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)- Mesopram


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)- Mesopram within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:21.3 occ:1.00 O A:HOH1008 2.0 28.2 1.0 OD1 A:ASP275 2.1 22.8 1.0 O A:HOH1004 2.1 25.5 1.0 O A:HOH1007 2.1 24.0 1.0 O A:HOH1005 2.2 24.8 1.0 O A:HOH1006 2.2 27.2 1.0 CG A:ASP275 3.1 21.4 1.0 OD2 A:ASP275 3.4 21.1 1.0 ZN A:ZN1001 3.7 31.1 1.0 O A:HOH1028 3.9 30.1 1.0 OE2 A:GLU304 4.0 20.3 1.0 CD2 A:HIS274 4.1 22.2 1.0 NE2 A:HIS307 4.1 18.9 1.0 O A:HOH1009 4.1 24.9 1.0 OG1 A:THR345 4.2 21.6 1.0 O A:HOH1015 4.2 31.6 1.0 O A:HIS274 4.2 22.3 1.0 CD2 A:HIS307 4.3 19.6 1.0 CB A:ASP275 4.5 21.9 1.0 NE2 A:HIS274 4.5 20.9 1.0 O A:THR345 4.6 23.7 1.0 CD2 A:HIS278 4.6 21.3 1.0 CB A:THR345 4.7 22.6 1.0 OD1 A:ASP392 4.7 23.9 1.0 O A:HOH1029 4.8 37.5 1.0 NE2 A:HIS234 4.8 23.2 1.0 CA A:ASP275 4.8 20.9 1.0 CD2 A:HIS234 4.8 23.6 1.0 CD A:GLU304 4.9 22.1 1.0 CG A:GLU304 4.9 21.6 1.0 NE2 A:HIS278 5.0 22.4 1.0

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


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)- Mesopram within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:22.7 occ:1.00 O B:HOH2007 2.1 25.5 1.0 OD1 B:ASP275 2.1 22.2 1.0 O B:HOH2006 2.2 28.5 1.0 O B:HOH2004 2.2 26.9 1.0 O B:HOH2005 2.2 22.9 1.0 O B:HOH2003 2.2 26.6 1.0 CG B:ASP275 3.2 20.5 1.0 OD2 B:ASP275 3.4 20.1 1.0 ZN B:ZN1001 3.6 31.2 1.0 O B:HOH2049 3.8 32.8 1.0 OE2 B:GLU304 4.0 24.3 1.0 CD2 B:HIS274 4.0 23.2 1.0 O B:HOH2008 4.1 28.8 1.0 OG1 B:THR345 4.1 22.1 1.0 NE2 B:HIS307 4.2 22.7 1.0 O B:HIS274 4.3 22.1 1.0 O B:HOH2011 4.3 27.4 1.0 CD2 B:HIS307 4.3 21.4 1.0 NE2 B:HIS274 4.5 20.3 1.0 CB B:ASP275 4.6 21.1 1.0 O B:THR345 4.6 25.6 1.0 CD2 B:HIS278 4.6 20.7 1.0 OD1 B:ASP392 4.6 25.6 1.0 CB B:THR345 4.7 23.4 1.0 CD2 B:HIS234 4.8 20.7 1.0 NE2 B:HIS234 4.8 22.3 1.0 O B:HOH2083 4.8 40.8 1.0 NE2 B:HIS278 4.9 21.4 1.0 CD B:GLU304 4.9 23.9 1.0 CG B:GLU304 4.9 22.0 1.0 CA B:ASP275 4.9 20.8 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