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Zinc in PDB 1xm4: Catalytic Domain of Human Phosphodiesterase 4B in Complex with Piclamilast

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

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

Protein crystallography data

The structure of Catalytic Domain of Human Phosphodiesterase 4B in Complex with Piclamilast, PDB code: 1xm4 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 / 2.31
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.573, 94.317, 106.681, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 26.3

Other elements in 1xm4:

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

Magnesium (Mg) 2 atoms
Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with Piclamilast (pdb code 1xm4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with Piclamilast, PDB code: 1xm4:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1xm4

Go back to Zinc Binding Sites List in 1xm4
Zinc binding site 1 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with Piclamilast


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Catalytic Domain of Human Phosphodiesterase 4B in Complex with Piclamilast within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:35.9
occ:1.00
O A:HOH1008 2.1 34.1 1.0
NE2 A:HIS238 2.2 14.6 1.0
OD2 A:ASP392 2.2 19.9 1.0
NE2 A:HIS274 2.2 18.7 1.0
OD2 A:ASP275 2.2 21.4 1.0
O A:HOH1009 2.4 31.3 1.0
CG A:ASP392 3.0 17.8 1.0
OD1 A:ASP392 3.1 15.2 1.0
CE1 A:HIS274 3.1 21.1 1.0
CE1 A:HIS238 3.2 19.4 1.0
CD2 A:HIS238 3.2 17.3 1.0
CD2 A:HIS274 3.2 18.3 1.0
CG A:ASP275 3.2 21.9 1.0
OD1 A:ASP275 3.7 24.0 1.0
MG A:MG1002 3.8 26.2 1.0
O A:HOH1013 4.1 29.2 1.0
O A:HOH1007 4.2 27.8 1.0
ND1 A:HIS274 4.3 21.9 1.0
ND1 A:HIS238 4.3 15.0 1.0
CD2 A:HIS234 4.3 20.1 1.0
CG A:HIS274 4.3 20.6 1.0
CG A:HIS238 4.3 17.1 1.0
CB A:ASP275 4.4 21.1 1.0
CB A:ASP392 4.5 20.8 1.0
NE2 A:HIS234 4.6 17.5 1.0
CG2 A:VAL242 4.7 18.4 1.0
O A:HOH1005 4.7 30.0 1.0
CA A:ASP392 5.0 20.2 1.0
C19 A:PIL1003 5.0 39.0 1.0

Zinc binding site 2 out of 2 in 1xm4

Go back to Zinc Binding Sites List in 1xm4
Zinc binding site 2 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with Piclamilast


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Catalytic Domain of Human Phosphodiesterase 4B in Complex with Piclamilast within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:38.4
occ:1.00
O B:HOH2007 2.1 32.5 1.0
OD1 B:ASP275 2.1 15.5 1.0
NE2 B:HIS238 2.2 16.5 1.0
OD2 B:ASP392 2.2 18.3 1.0
NE2 B:HIS274 2.3 20.6 1.0
O B:HOH2008 2.5 31.1 1.0
CG B:ASP392 3.1 19.3 1.0
CG B:ASP275 3.1 22.2 1.0
CD2 B:HIS238 3.2 19.5 1.0
CE1 B:HIS238 3.2 17.2 1.0
CE1 B:HIS274 3.2 22.8 1.0
OD1 B:ASP392 3.2 15.9 1.0
CD2 B:HIS274 3.3 21.1 1.0
OD2 B:ASP275 3.5 20.3 1.0
MG B:MG1002 3.8 30.1 1.0
O B:HOH2006 4.0 38.7 1.0
O B:HOH76 4.2 40.3 1.0
CD2 B:HIS234 4.2 20.2 1.0
ND1 B:HIS238 4.3 17.4 1.0
CG B:HIS238 4.3 17.4 1.0
ND1 B:HIS274 4.3 22.0 1.0
NE2 B:HIS234 4.3 22.4 1.0
CB B:ASP275 4.4 21.3 1.0
CG B:HIS274 4.4 19.6 1.0
CB B:ASP392 4.6 20.4 1.0
CG2 B:VAL242 4.7 21.1 1.0
O B:HOH2004 4.8 32.7 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: Wed Dec 16 03:12:29 2020

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