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Zinc 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:

Magnesium (Mg) 8 atoms
Chlorine (Cl) 16 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 8 binding sites of Zinc where determined in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with A Coumarin-Based Inhibitor, PDB code: 3ly2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3ly2

Go back to Zinc Binding Sites List in 3ly2
Zinc 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 Zinc with other atoms in the Zn 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:Zn1001

b:27.9
occ:1.00
OD2 A:ASP275 2.1 22.4 1.0
NE2 A:HIS238 2.1 21.7 1.0
O A:HOH1007 2.1 23.8 1.0
NE2 A:HIS274 2.1 25.8 1.0
OD2 A:ASP392 2.2 20.1 1.0
O A:HOH1008 2.2 21.7 1.0
CG A:ASP392 3.0 20.7 1.0
CE1 A:HIS238 3.0 19.9 1.0
OD1 A:ASP392 3.1 20.1 1.0
CE1 A:HIS274 3.1 23.4 1.0
CD2 A:HIS274 3.1 21.0 1.0
CD2 A:HIS238 3.2 22.2 1.0
CG A:ASP275 3.3 23.6 1.0
O A:HOH1006 3.8 15.8 1.0
MG A:MG1002 3.9 24.9 1.0
OD1 A:ASP275 3.9 22.3 1.0
O A:HOH1009 3.9 22.1 1.0
ND1 A:HIS238 4.2 21.5 1.0
ND1 A:HIS274 4.2 21.5 1.0
CD2 A:HIS234 4.2 26.3 1.0
CG A:HIS274 4.3 22.4 1.0
CG A:HIS238 4.3 21.6 1.0
CB A:ASP392 4.4 24.5 1.0
CB A:ASP275 4.4 23.6 1.0
NE2 A:HIS234 4.4 27.9 1.0
C19 A:Z721000 4.7 68.6 1.0
CG2 A:VAL242 4.8 21.0 1.0
O A:HOH1004 4.8 27.0 1.0
CL20 A:Z721000 4.8 71.4 1.0
CA A:ASP392 4.9 24.2 1.0
C21 A:Z721000 4.9 69.8 1.0

Zinc binding site 2 out of 8 in 3ly2

Go back to Zinc Binding Sites List in 3ly2
Zinc 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 Zinc with other atoms in the Zn 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:Zn1001

b:27.4
occ:1.00
NE2 B:HIS274 2.1 21.3 1.0
OD2 B:ASP275 2.1 18.9 1.0
NE2 B:HIS238 2.1 22.1 1.0
OD2 B:ASP392 2.1 20.6 1.0
O B:HOH1007 2.2 21.1 1.0
O B:HOH1008 2.2 21.6 1.0
CG B:ASP392 3.0 21.6 1.0
CD2 B:HIS274 3.0 20.4 1.0
CE1 B:HIS238 3.1 19.0 1.0
CE1 B:HIS274 3.1 17.8 1.0
OD1 B:ASP392 3.2 20.9 1.0
CD2 B:HIS238 3.2 21.2 1.0
CG B:ASP275 3.2 21.4 1.0
O B:HOH1006 3.7 13.7 1.0
OD1 B:ASP275 3.8 21.3 1.0
O B:HOH1009 3.9 15.5 1.0
MG B:MG1002 4.0 20.8 1.0
CG B:HIS274 4.2 20.0 1.0
ND1 B:HIS274 4.2 17.9 1.0
ND1 B:HIS238 4.2 19.7 1.0
CD2 B:HIS234 4.3 23.4 1.0
CG B:HIS238 4.3 21.7 1.0
CB B:ASP275 4.4 19.7 1.0
CB B:ASP392 4.4 21.7 1.0
NE2 B:HIS234 4.4 26.5 1.0
CG2 B:VAL242 4.8 18.2 1.0
O B:HOH1004 4.8 19.2 1.0
C19 B:Z721000 4.9 58.8 1.0
CA B:ASP392 4.9 23.7 1.0
CL20 B:Z721000 4.9 60.4 1.0

Zinc binding site 3 out of 8 in 3ly2

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Zinc 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 Zinc with other atoms in the Zn 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:Zn1001

b:33.1
occ:1.00
OD2 C:ASP392 2.1 29.7 1.0
NE2 C:HIS238 2.1 28.1 1.0
O C:HOH1007 2.1 28.8 1.0
NE2 C:HIS274 2.1 30.4 1.0
OD2 C:ASP275 2.1 27.1 1.0
O C:HOH1008 2.2 27.7 1.0
CG C:ASP392 3.0 29.4 1.0
CE1 C:HIS274 3.1 27.9 1.0
CD2 C:HIS238 3.1 27.9 1.0
CE1 C:HIS238 3.1 26.4 1.0
CD2 C:HIS274 3.1 27.0 1.0
OD1 C:ASP392 3.3 27.5 1.0
CG C:ASP275 3.3 23.0 1.0
OD1 C:ASP275 3.9 20.8 1.0
O C:HOH1009 3.9 26.0 1.0
MG C:MG1002 3.9 24.4 1.0
O C:HOH1006 4.1 22.7 1.0
ND1 C:HIS274 4.2 26.9 1.0
ND1 C:HIS238 4.2 25.4 1.0
CG C:HIS238 4.2 26.2 1.0
CG C:HIS274 4.3 27.3 1.0
CD2 C:HIS234 4.3 28.6 1.0
CB C:ASP392 4.4 29.6 1.0
CB C:ASP275 4.5 22.8 1.0
NE2 C:HIS234 4.5 26.6 1.0
C19 C:Z721000 4.8 59.3 1.0
CG2 C:VAL242 4.8 26.6 1.0
CA C:ASP392 4.9 29.9 1.0
C21 C:Z721000 4.9 59.7 1.0
O C:HOH1004 4.9 20.0 1.0
CL20 C:Z721000 5.0 61.4 1.0

Zinc binding site 4 out of 8 in 3ly2

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Zinc 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 Zinc with other atoms in the Zn 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:Zn1001

b:28.0
occ:1.00
OD2 D:ASP275 2.1 25.5 1.0
NE2 D:HIS274 2.1 26.2 1.0
NE2 D:HIS238 2.1 24.6 1.0
O D:HOH1007 2.1 26.5 1.0
OD2 D:ASP392 2.2 24.7 1.0
O D:HOH1008 2.2 26.9 1.0
CD2 D:HIS274 3.0 23.3 1.0
CG D:ASP392 3.0 25.6 1.0
CE1 D:HIS238 3.1 24.7 1.0
CE1 D:HIS274 3.1 25.6 1.0
CD2 D:HIS238 3.1 26.9 1.0
CG D:ASP275 3.2 27.0 1.0
OD1 D:ASP392 3.2 26.3 1.0
OD1 D:ASP275 3.8 25.1 1.0
MG D:MG1002 3.8 24.2 1.0
O D:HOH1009 3.9 29.6 1.0
O D:HOH1006 4.0 19.9 1.0
CG D:HIS274 4.2 24.4 1.0
ND1 D:HIS274 4.2 23.5 1.0
CD2 D:HIS234 4.2 30.5 1.0
ND1 D:HIS238 4.2 25.9 1.0
CG D:HIS238 4.3 25.8 1.0
CB D:ASP275 4.4 25.0 1.0
NE2 D:HIS234 4.5 31.2 1.0
CB D:ASP392 4.5 24.2 1.0
O D:HOH1004 4.6 21.5 1.0
CG2 D:VAL242 4.7 22.0 1.0
C19 D:Z721000 4.8 64.0 1.0
CA D:ASP392 5.0 25.0 1.0

Zinc binding site 5 out of 8 in 3ly2

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Zinc 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 Zinc with other atoms in the Zn 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:Zn1001

b:35.0
occ:1.00
OD2 E:ASP275 2.1 26.1 1.0
O E:HOH1007 2.1 31.2 1.0
NE2 E:HIS238 2.1 30.0 1.0
NE2 E:HIS274 2.1 33.0 1.0
OD2 E:ASP392 2.1 29.4 1.0
O E:HOH1008 2.2 30.0 1.0
CG E:ASP392 3.0 29.8 1.0
CE1 E:HIS274 3.1 31.2 1.0
CD2 E:HIS238 3.1 28.0 1.0
CE1 E:HIS238 3.1 26.9 1.0
CD2 E:HIS274 3.1 30.0 1.0
CG E:ASP275 3.3 26.4 1.0
OD1 E:ASP392 3.3 29.3 1.0
OD1 E:ASP275 3.8 27.5 1.0
MG E:MG1002 3.9 28.7 1.0
O E:HOH1009 3.9 30.4 1.0
O E:HOH1006 4.1 25.4 1.0
ND1 E:HIS274 4.2 28.8 1.0
ND1 E:HIS238 4.2 26.7 1.0
CG E:HIS238 4.2 26.3 1.0
CG E:HIS274 4.3 29.6 1.0
CD2 E:HIS234 4.3 27.9 1.0
CB E:ASP392 4.5 30.2 1.0
CB E:ASP275 4.5 24.0 1.0
NE2 E:HIS234 4.5 27.4 1.0
C19 E:Z721000 4.8 59.5 1.0
CG2 E:VAL242 4.8 27.2 1.0
C21 E:Z721000 4.9 59.4 1.0
CA E:ASP392 4.9 30.6 1.0
O E:HOH1004 4.9 23.6 1.0

Zinc binding site 6 out of 8 in 3ly2

Go back to Zinc Binding Sites List in 3ly2
Zinc 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 Zinc with other atoms in the Zn 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:Zn1001

b:36.2
occ:1.00
OD2 F:ASP275 2.1 30.3 1.0
O F:HOH1007 2.1 27.9 1.0
NE2 F:HIS274 2.1 35.6 1.0
OD2 F:ASP392 2.1 27.5 1.0
NE2 F:HIS238 2.1 28.1 1.0
O F:HOH1008 2.2 31.5 1.0
CG F:ASP392 3.0 26.1 1.0
CD2 F:HIS274 3.0 30.8 1.0
CE1 F:HIS238 3.1 28.6 1.0
OD1 F:ASP392 3.1 26.5 1.0
CE1 F:HIS274 3.2 34.0 1.0
CD2 F:HIS238 3.2 28.4 1.0
CG F:ASP275 3.2 29.6 1.0
OD1 F:ASP275 3.8 28.7 1.0
MG F:MG1002 3.8 29.1 1.0
O F:HOH1009 3.8 40.0 1.0
O F:HOH1006 4.0 27.8 1.0
CG F:HIS274 4.2 31.4 1.0
CD2 F:HIS234 4.2 33.2 1.0
ND1 F:HIS274 4.2 31.9 1.0
ND1 F:HIS238 4.2 28.4 1.0
CG F:HIS238 4.3 28.1 1.0
CB F:ASP275 4.4 27.6 1.0
CB F:ASP392 4.4 28.7 1.0
NE2 F:HIS234 4.5 34.8 1.0
O F:HOH1004 4.6 29.1 1.0
CG2 F:VAL242 4.7 25.7 1.0
C19 F:Z721000 4.8 67.5 1.0
CA F:ASP392 4.9 30.2 1.0
C21 F:Z721000 4.9 68.3 1.0

Zinc binding site 7 out of 8 in 3ly2

Go back to Zinc Binding Sites List in 3ly2
Zinc 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 Zinc with other atoms in the Zn 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:Zn1001

b:32.6
occ:1.00
OD2 G:ASP275 2.1 27.3 1.0
NE2 G:HIS274 2.1 25.9 1.0
O G:HOH1007 2.1 31.4 1.0
NE2 G:HIS238 2.1 27.5 1.0
OD2 G:ASP392 2.2 30.0 1.0
O G:HOH1008 2.2 19.9 1.0
CG G:ASP392 3.0 30.8 1.0
CD2 G:HIS274 3.1 22.7 1.0
CE1 G:HIS274 3.1 24.0 1.0
CE1 G:HIS238 3.1 25.5 1.0
CD2 G:HIS238 3.1 26.3 1.0
OD1 G:ASP392 3.1 31.8 1.0
CG G:ASP275 3.2 26.9 1.0
OD1 G:ASP275 3.7 25.0 1.0
MG G:MG1002 3.9 27.1 1.0
O G:HOH1009 3.9 37.5 1.0
O G:HOH1006 3.9 24.2 1.0
ND1 G:HIS274 4.2 22.3 1.0
CG G:HIS274 4.2 23.8 1.0
CD2 G:HIS234 4.2 28.1 1.0
ND1 G:HIS238 4.2 26.2 1.0
CG G:HIS238 4.2 25.7 1.0
CB G:ASP392 4.4 32.2 1.0
CB G:ASP275 4.4 24.6 1.0
NE2 G:HIS234 4.5 29.4 1.0
C19 G:Z721000 4.8 68.1 1.0
CG2 G:VAL242 4.8 28.7 1.0
O G:HOH1004 4.8 21.4 1.0
CL20 G:Z721000 4.8 69.7 1.0
C21 G:Z721000 4.9 69.3 1.0
CA G:ASP392 4.9 32.0 1.0

Zinc binding site 8 out of 8 in 3ly2

Go back to Zinc Binding Sites List in 3ly2
Zinc 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 Zinc with other atoms in the Zn 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:Zn1001

b:31.4
occ:1.00
OD2 H:ASP275 2.1 28.0 1.0
NE2 H:HIS274 2.1 23.9 1.0
NE2 H:HIS238 2.1 26.4 1.0
O H:HOH1007 2.1 27.2 1.0
OD2 H:ASP392 2.2 31.5 1.0
O H:HOH1008 2.2 24.7 1.0
CG H:ASP392 3.0 32.2 1.0
CD2 H:HIS274 3.1 21.6 1.0
CE1 H:HIS238 3.1 25.2 1.0
CE1 H:HIS274 3.1 21.7 1.0
CD2 H:HIS238 3.1 25.9 1.0
OD1 H:ASP392 3.1 34.5 1.0
CG H:ASP275 3.2 27.5 1.0
OD1 H:ASP275 3.7 26.6 1.0
O H:HOH1009 3.9 37.5 1.0
MG H:MG1002 3.9 26.6 1.0
O H:HOH1006 3.9 25.0 1.0
CD2 H:HIS234 4.2 28.6 1.0
ND1 H:HIS274 4.2 24.3 1.0
CG H:HIS274 4.2 24.1 1.0
ND1 H:HIS238 4.2 25.9 1.0
CG H:HIS238 4.2 25.6 1.0
CB H:ASP392 4.4 33.8 1.0
CB H:ASP275 4.4 25.6 1.0
NE2 H:HIS234 4.4 27.9 1.0
C19 H:Z721000 4.7 68.0 1.0
O H:HOH1004 4.7 18.4 1.0
CL20 H:Z721000 4.8 71.3 1.0
CG2 H:VAL242 4.8 28.4 1.0
C21 H:Z721000 4.9 69.1 1.0
CA H:ASP392 4.9 32.7 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: Wed Dec 16 04:33:31 2020

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