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Magnesium in PDB 3ly2: Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor

Enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor

All present enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor:
3.1.4.17;

Protein crystallography data

The structure of Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor, PDB code: 3ly2 was solved by A.K.Shiau, A.R.Coyle, J.H.Hsien, L.M.Staszewski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.84 / 2.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 214.796, 233.964, 165.258, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 3ly2:

The structure of Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 16 atoms
Zinc (Zn) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor (pdb code 3ly2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor, PDB code: 3ly2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3ly2

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Magnesium binding site 1 out of 8 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor


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 A Coumarin-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:24.9
occ:1.00
 O A:HOH1004 2.1 27.0 1.0
OD1 A:ASP275 2.1 22.3 1.0
O A:HOH1007 2.1 23.8 1.0
O A:HOH1010 2.1 27.3 1.0
O A:HOH1005 2.1 21.7 1.0
O A:HOH1006 2.1 15.8 1.0
CG A:ASP275 3.0 23.6 1.0
OD2 A:ASP275 3.3 22.4 1.0
ZN A:ZN1001 3.9 27.9 1.0
N22 A:Z721000 4.0 70.3 1.0
NE2 A:HIS307 4.0 19.8 1.0
OE2 A:GLU304 4.0 34.3 1.0
O A:HOH1008 4.1 21.7 1.0
CD2 A:HIS274 4.1 21.0 1.0
O A:HOH2071 4.1 42.5 1.0
O A:HIS274 4.1 23.3 1.0
OG1 A:THR345 4.2 20.3 1.0
C21 A:Z721000 4.3 69.8 1.0
CD2 A:HIS307 4.3 20.2 1.0
CB A:ASP275 4.4 23.6 1.0
NE2 A:HIS274 4.5 25.8 1.0
OD1 A:ASP392 4.5 20.1 1.0
CD2 A:HIS278 4.6 21.4 1.0
C23 A:Z721000 4.6 69.6 1.0
O A:THR345 4.6 27.0 1.0
CB A:THR345 4.7 23.2 1.0
CD2 A:HIS234 4.8 26.3 1.0
CA A:ASP275 4.8 23.8 1.0
NE2 A:HIS234 4.8 27.9 1.0
NE2 A:HIS278 4.9 24.0 1.0
CD A:GLU304 5.0 30.9 1.0
C A:HIS274 5.0 23.3 1.0

Magnesium binding site 2 out of 8 in 3ly2

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Magnesium binding site 2 out of 8 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor


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 A Coumarin-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1002

b:20.8
occ:1.00
 O B:HOH1006 2.1 13.7 1.0
O B:HOH1005 2.1 17.9 1.0
OD1 B:ASP275 2.1 21.3 1.0
O B:HOH1004 2.1 19.2 1.0
O B:HOH1010 2.1 21.6 1.0
O B:HOH1007 2.1 21.1 1.0
CG B:ASP275 3.1 21.4 1.0
OD2 B:ASP275 3.5 18.9 1.0
N22 B:Z721000 3.9 58.5 1.0
OE2 B:GLU304 3.9 28.2 1.0
ZN B:ZN1001 4.0 27.4 1.0
NE2 B:HIS307 4.0 20.8 1.0
CD2 B:HIS274 4.1 20.4 1.0
OG1 B:THR345 4.2 23.4 1.0
O B:HIS274 4.2 20.5 1.0
O B:HOH2051 4.2 29.9 1.0
O B:HOH1008 4.2 21.6 1.0
C21 B:Z721000 4.3 59.1 1.0
CD2 B:HIS307 4.4 20.8 1.0
CB B:ASP275 4.5 19.7 1.0
O B:THR345 4.5 26.5 1.0
OD1 B:ASP392 4.5 20.9 1.0
O B:HOH2153 4.6 36.1 1.0
C23 B:Z721000 4.6 57.7 1.0
CD2 B:HIS278 4.6 21.3 1.0
NE2 B:HIS274 4.6 21.3 1.0
CB B:THR345 4.7 23.1 1.0
CA B:ASP275 4.8 19.4 1.0
CD B:GLU304 4.9 26.1 1.0
CG B:GLU304 4.9 23.2 1.0
NE2 B:HIS234 4.9 26.5 1.0
C B:HIS274 5.0 19.4 1.0

Magnesium binding site 3 out of 8 in 3ly2

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Magnesium binding site 3 out of 8 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1002

b:24.4
occ:1.00
 O C:HOH1006 2.1 22.7 1.0
O C:HOH1004 2.1 20.0 1.0
OD1 C:ASP275 2.1 20.8 1.0
O C:HOH1007 2.1 28.8 1.0
O C:HOH1010 2.1 25.2 1.0
O C:HOH1005 2.1 25.0 1.0
CG C:ASP275 3.1 23.0 1.0
OD2 C:ASP275 3.4 27.1 1.0
N22 C:Z721000 3.8 59.8 1.0
ZN C:ZN1001 3.9 33.1 1.0
O C:HIS274 4.0 22.9 1.0
OE2 C:GLU304 4.1 29.9 1.0
CD2 C:HIS274 4.1 27.0 1.0
O C:HOH1008 4.1 27.7 1.0
NE2 C:HIS307 4.2 20.6 1.0
OG1 C:THR345 4.2 29.1 1.0
O C:HOH2367 4.3 40.8 1.0
C21 C:Z721000 4.3 59.7 1.0
C23 C:Z721000 4.4 59.5 1.0
NE2 C:HIS274 4.4 30.4 1.0
CB C:ASP275 4.4 22.8 1.0
CD2 C:HIS307 4.5 22.1 1.0
OD1 C:ASP392 4.5 27.5 1.0
CD2 C:HIS278 4.6 26.2 1.0
O C:THR345 4.6 28.0 1.0
CD2 C:HIS234 4.7 28.6 1.0
NE2 C:HIS234 4.7 26.6 1.0
CB C:THR345 4.8 28.1 1.0
NE2 C:HIS278 4.8 25.1 1.0
CA C:ASP275 4.8 22.2 1.0
C C:HIS274 4.9 23.5 1.0

Magnesium binding site 4 out of 8 in 3ly2

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Magnesium binding site 4 out of 8 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1002

b:24.2
occ:1.00
 O D:HOH1004 2.1 21.5 1.0
O D:HOH1010 2.1 20.5 1.0
OD1 D:ASP275 2.1 25.1 1.0
O D:HOH1006 2.1 19.9 1.0
O D:HOH1007 2.1 26.5 1.0
O D:HOH1005 2.1 27.1 1.0
CG D:ASP275 3.1 27.0 1.0
OD2 D:ASP275 3.3 25.5 1.0
ZN D:ZN1001 3.8 28.0 1.0
N22 D:Z721000 3.8 65.8 1.0
O D:HOH1008 3.9 26.9 1.0
OE2 D:GLU304 4.1 28.4 1.0
OG1 D:THR345 4.1 32.1 1.0
O D:HIS274 4.2 22.7 1.0
O D:HOH2385 4.2 43.7 1.0
CD2 D:HIS274 4.2 23.3 1.0
C21 D:Z721000 4.3 65.3 1.0
NE2 D:HIS307 4.3 27.8 1.0
C23 D:Z721000 4.4 65.8 1.0
O D:THR345 4.4 30.5 1.0
CB D:ASP275 4.5 25.0 1.0
OD1 D:ASP392 4.5 26.3 1.0
CD2 D:HIS307 4.5 28.1 1.0
NE2 D:HIS274 4.6 26.2 1.0
CD2 D:HIS278 4.6 26.8 1.0
CB D:THR345 4.7 29.6 1.0
NE2 D:HIS234 4.8 31.2 1.0
CD2 D:HIS234 4.8 30.5 1.0
CA D:ASP275 4.9 24.2 1.0
O D:HOH2384 4.9 44.2 1.0
NE2 D:HIS278 5.0 26.0 1.0

Magnesium binding site 5 out of 8 in 3ly2

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Magnesium binding site 5 out of 8 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1002

b:28.7
occ:1.00
 O E:HOH1004 2.1 23.6 1.0
O E:HOH1006 2.1 25.4 1.0
OD1 E:ASP275 2.1 27.5 1.0
O E:HOH1007 2.1 31.2 1.0
O E:HOH1010 2.1 30.2 1.0
O E:HOH1005 2.1 24.6 1.0
CG E:ASP275 3.1 26.4 1.0
OD2 E:ASP275 3.4 26.1 1.0
N22 E:Z721000 3.8 60.5 1.0
ZN E:ZN1001 3.9 35.0 1.0
OE2 E:GLU304 4.0 33.0 1.0
O E:HIS274 4.1 25.1 1.0
CD2 E:HIS274 4.1 30.0 1.0
O E:HOH1008 4.2 30.0 1.0
NE2 E:HIS307 4.2 22.9 1.0
OG1 E:THR345 4.2 29.3 1.0
O E:HOH2096 4.3 35.0 1.0
C21 E:Z721000 4.3 59.4 1.0
C23 E:Z721000 4.4 60.5 1.0
NE2 E:HIS274 4.4 33.0 1.0
CB E:ASP275 4.4 24.0 1.0
CD2 E:HIS307 4.5 23.4 1.0
OD1 E:ASP392 4.5 29.3 1.0
CD2 E:HIS278 4.5 25.8 1.0
O E:THR345 4.6 26.7 1.0
CD2 E:HIS234 4.7 27.9 1.0
NE2 E:HIS234 4.7 27.4 1.0
NE2 E:HIS278 4.8 25.3 1.0
CB E:THR345 4.8 28.8 1.0
CA E:ASP275 4.8 22.5 1.0
C E:HIS274 5.0 23.6 1.0
CD E:GLU304 5.0 32.1 1.0

Magnesium binding site 6 out of 8 in 3ly2

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Magnesium binding site 6 out of 8 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1002

b:29.1
occ:1.00
 O F:HOH1004 2.1 29.1 1.0
OD1 F:ASP275 2.1 28.7 1.0
O F:HOH1010 2.1 25.9 1.0
O F:HOH1007 2.1 27.9 1.0
O F:HOH1005 2.1 27.7 1.0
O F:HOH1006 2.1 27.8 1.0
CG F:ASP275 3.1 29.6 1.0
OD2 F:ASP275 3.3 30.3 1.0
ZN F:ZN1001 3.8 36.2 1.0
N22 F:Z721000 3.8 69.1 1.0
O F:HOH1008 3.9 31.5 1.0
OE2 F:GLU304 4.1 32.6 1.0
OG1 F:THR345 4.1 32.3 1.0
O F:HIS274 4.2 27.4 1.0
CD2 F:HIS274 4.2 30.8 1.0
O F:HOH2121 4.2 38.0 1.0
C21 F:Z721000 4.3 68.3 1.0
NE2 F:HIS307 4.3 29.6 1.0
C23 F:Z721000 4.4 69.4 1.0
O F:THR345 4.4 33.6 1.0
CB F:ASP275 4.5 27.6 1.0
OD1 F:ASP392 4.5 26.5 1.0
CD2 F:HIS307 4.5 30.1 1.0
NE2 F:HIS274 4.6 35.6 1.0
CB F:THR345 4.6 33.2 1.0
CD2 F:HIS278 4.6 30.7 1.0
NE2 F:HIS234 4.8 34.8 1.0
CD2 F:HIS234 4.8 33.2 1.0
CA F:ASP275 4.9 26.7 1.0
NE2 F:HIS278 5.0 30.4 1.0

Magnesium binding site 7 out of 8 in 3ly2

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Magnesium binding site 7 out of 8 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1002

b:27.1
occ:1.00
 O G:HOH1004 2.1 21.4 1.0
O G:HOH1006 2.1 24.2 1.0
O G:HOH1010 2.1 26.3 1.0
OD1 G:ASP275 2.1 25.0 1.0
O G:HOH1007 2.1 31.4 1.0
O G:HOH1005 2.1 28.5 1.0
CG G:ASP275 3.1 26.9 1.0
OD2 G:ASP275 3.5 27.3 1.0
N22 G:Z721000 3.9 70.4 1.0
ZN G:ZN1001 3.9 32.6 1.0
O G:HIS274 4.0 25.6 1.0
OE2 G:GLU304 4.0 29.0 1.0
O G:HOH1008 4.1 19.9 1.0
C21 G:Z721000 4.2 69.3 1.0
O G:HOH2126 4.2 28.4 1.0
CD2 G:HIS274 4.2 22.7 1.0
NE2 G:HIS307 4.2 21.9 1.0
OG1 G:THR345 4.2 29.4 1.0
OD1 G:ASP392 4.5 31.8 1.0
CB G:ASP275 4.5 24.6 1.0
CD2 G:HIS307 4.5 23.8 1.0
C23 G:Z721000 4.5 69.7 1.0
NE2 G:HIS274 4.6 25.9 1.0
CB G:THR345 4.6 30.9 1.0
CD2 G:HIS278 4.6 23.8 1.0
O G:THR345 4.7 32.4 1.0
CD2 G:HIS234 4.8 28.1 1.0
NE2 G:HIS234 4.8 29.4 1.0
O G:HOH2268 4.8 33.4 1.0
CA G:ASP275 4.8 23.2 1.0
C G:HIS274 4.9 25.6 1.0
CD G:GLU304 5.0 29.5 1.0
NE2 G:HIS278 5.0 23.2 1.0

Magnesium binding site 8 out of 8 in 3ly2

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Magnesium binding site 8 out of 8 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg1002

b:26.6
occ:1.00
 O H:HOH1004 2.1 18.4 1.0
OD1 H:ASP275 2.1 26.6 1.0
O H:HOH1006 2.1 25.0 1.0
O H:HOH1010 2.1 28.4 1.0
O H:HOH1007 2.1 27.2 1.0
O H:HOH1005 2.1 23.3 1.0
CG H:ASP275 3.1 27.5 1.0
OD2 H:ASP275 3.4 28.0 1.0
N22 H:Z721000 3.9 69.9 1.0
ZN H:ZN1001 3.9 31.4 1.0
O H:HIS274 4.0 27.9 1.0
OE2 H:GLU304 4.0 32.4 1.0
O H:HOH1008 4.1 24.7 1.0
NE2 H:HIS307 4.2 20.4 1.0
C21 H:Z721000 4.2 69.1 1.0
CD2 H:HIS274 4.2 21.6 1.0
OG1 H:THR345 4.2 30.9 1.0
OD1 H:ASP392 4.5 34.5 1.0
CD2 H:HIS307 4.5 21.1 1.0
CB H:ASP275 4.5 25.6 1.0
C23 H:Z721000 4.5 68.8 1.0
NE2 H:HIS274 4.5 23.9 1.0
CB H:THR345 4.6 31.1 1.0
CD2 H:HIS278 4.6 26.9 1.0
O H:THR345 4.7 31.5 1.0
CD2 H:HIS234 4.8 28.6 1.0
NE2 H:HIS234 4.8 27.9 1.0
CA H:ASP275 4.8 24.4 1.0
C H:HIS274 4.9 26.1 1.0
CD H:GLU304 5.0 32.0 1.0
NE2 H:HIS278 5.0 27.0 1.0

Reference:

S.P.Govek, G.Oshiro, J.V.Anzola, C.Beauregard, J.Chen, A.R.Coyle, D.A.Gamache, M.R.Hellberg, J.N.Hsien, J.M.Lerch, J.C.Liao, J.W.Malecha, L.M.Staszewski, D.J.Thomas, J.M.Yanni, S.A.Noble, A.K.Shiau. Water-Soluble PDE4 Inhibitors For the Treatment of Dry Eye. Bioorg.Med.Chem.Lett. V. 20 2928 2010.
ISSN: ISSN 0960-894X
PubMed: 20378348
DOI: 10.1016/J.BMCL.2010.03.023
Page generated: Mon Dec 14 08:25:02 2020

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