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Magnesium in PDB 1xlz: Catalytic Domain of Human Phosphodiesterase 4B in Complex with Filaminast

Enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4B in Complex with Filaminast

All present enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4B in Complex with Filaminast:
3.1.4.17;

Protein crystallography data

The structure of Catalytic Domain of Human Phosphodiesterase 4B in Complex with Filaminast, PDB code: 1xlz 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 / 2.06
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.539, 94.173, 106.303, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 23.7

Other elements in 1xlz:

The structure of Catalytic Domain of Human Phosphodiesterase 4B in Complex with Filaminast also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with Filaminast (pdb code 1xlz). 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 Filaminast, PDB code: 1xlz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1xlz

Go back to Magnesium Binding Sites List in 1xlz
Magnesium binding site 1 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with Filaminast


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 Filaminast within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:21.6
occ:1.00
O A:HOH1008 1.9 31.4 1.0
O A:HOH1007 2.0 26.2 1.0
OD1 A:ASP275 2.1 24.8 1.0
O A:HOH1005 2.1 26.9 1.0
O A:HOH1004 2.1 25.9 1.0
O A:HOH1006 2.3 27.1 1.0
CG A:ASP275 3.0 22.8 1.0
OD2 A:ASP275 3.2 23.4 1.0
ZN A:ZN1001 3.6 33.8 1.0
O A:HOH1009 4.1 25.4 1.0
OE2 A:GLU304 4.1 21.2 1.0
OG1 A:THR345 4.1 23.0 1.0
O A:HOH1013 4.2 35.1 1.0
CD2 A:HIS274 4.2 22.4 1.0
NE2 A:HIS307 4.2 17.0 1.0
O A:HIS274 4.3 21.2 1.0
CD2 A:HIS307 4.4 19.6 1.0
CB A:ASP275 4.4 22.0 1.0
NE2 A:HIS274 4.5 21.4 1.0
O A:THR345 4.5 24.6 1.0
CD2 A:HIS278 4.6 17.8 1.0
OD1 A:ASP392 4.6 23.3 1.0
CB A:THR345 4.6 22.8 1.0
O19 A:FIL1003 4.7 78.1 1.0
CD2 A:HIS234 4.8 23.3 1.0
CA A:ASP275 4.8 21.2 1.0
CG A:GLU304 4.9 22.6 1.0
NE2 A:HIS234 4.9 23.9 1.0
CD A:GLU304 4.9 24.2 1.0
NE2 A:HIS278 4.9 20.3 1.0
O A:HOH1033 4.9 42.3 1.0

Magnesium binding site 2 out of 2 in 1xlz

Go back to Magnesium Binding Sites List in 1xlz
Magnesium binding site 2 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with Filaminast


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 Filaminast within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1002

b:23.2
occ:1.00
O B:HOH2007 2.0 36.3 1.0
OD1 B:ASP275 2.1 22.8 1.0
O B:HOH2006 2.1 27.9 1.0
O B:HOH2004 2.1 27.9 1.0
O B:HOH2003 2.2 27.0 1.0
O B:HOH2005 2.2 28.0 1.0
CG B:ASP275 3.1 22.1 1.0
OD2 B:ASP275 3.4 24.5 1.0
ZN B:ZN1001 3.7 34.9 1.0
OE2 B:GLU304 4.0 25.9 1.0
O B:HOH2022 4.1 34.4 1.0
NE2 B:HIS307 4.2 19.0 1.0
O B:HOH2008 4.2 32.2 1.0
O B:HIS274 4.2 21.0 1.0
OG1 B:THR345 4.2 22.9 1.0
CD2 B:HIS274 4.2 20.3 1.0
CD2 B:HIS307 4.4 21.4 1.0
CB B:ASP275 4.5 21.8 1.0
CD2 B:HIS278 4.6 22.1 1.0
O B:THR345 4.6 24.7 1.0
NE2 B:HIS274 4.6 15.6 1.0
OD1 B:ASP392 4.7 26.0 1.0
CD2 B:HIS234 4.7 21.5 1.0
NE2 B:HIS234 4.7 20.5 1.0
CB B:THR345 4.7 22.4 1.0
NE2 B:HIS278 4.8 23.0 1.0
CA B:ASP275 4.8 21.2 1.0
CD B:GLU304 4.9 26.1 1.0
CG B:GLU304 4.9 23.1 1.0

Reference:

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
Page generated: Mon Dec 14 07:04:31 2020

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