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Arsenic in PDB 3o56: Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A 5- Heterocycle Pyrazolopyridine Inhibitor

Enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A 5- Heterocycle Pyrazolopyridine Inhibitor

All present enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A 5- Heterocycle Pyrazolopyridine Inhibitor:
3.1.4.17;

Protein crystallography data

The structure of Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A 5- Heterocycle Pyrazolopyridine Inhibitor, PDB code: 3o56 was solved by D.O.Somers, M.Neu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.42
Space group I 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.531, 94.592, 105.089, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 26

Other elements in 3o56:

The structure of Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A 5- Heterocycle Pyrazolopyridine Inhibitor also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Zinc (Zn) 1 atom

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A 5- Heterocycle Pyrazolopyridine Inhibitor (pdb code 3o56). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 4 binding sites of Arsenic where determined in the Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A 5- Heterocycle Pyrazolopyridine Inhibitor, PDB code: 3o56:
Jump to Arsenic binding site number: 1; 2; 3; 4;

Arsenic binding site 1 out of 4 in 3o56

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Arsenic binding site 1 out of 4 in the Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A 5- Heterocycle Pyrazolopyridine Inhibitor


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A 5- Heterocycle Pyrazolopyridine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As505

b:59.0
occ:0.50
 AS A:ARS505 0.0 59.0 0.5
AS A:ARS505 1.7 62.1 0.5
SG A:CYS194 2.7 45.0 0.5
CA A:CYS194 3.5 47.5 0.5
CA A:CYS194 3.5 45.9 0.5
CB A:CYS194 3.6 48.4 0.5
CB A:CYS194 3.6 46.1 0.5
O A:CYS194 3.7 47.9 1.0
SG A:CYS194 3.7 54.3 0.5
C A:CYS194 4.0 45.4 1.0
O A:ILE153 4.2 94.1 1.0
CD2 A:TYR197 4.2 63.0 1.0
CD1 A:LEU170 4.2 55.4 1.0
CB A:TYR197 4.5 50.4 1.0
CE2 A:PHE156 4.8 81.0 1.0
N A:CYS194 4.8 47.6 1.0
CG A:TYR197 4.8 57.6 1.0
N A:ALA198 4.9 46.2 1.0

Arsenic binding site 2 out of 4 in 3o56

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Arsenic binding site 2 out of 4 in the Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A 5- Heterocycle Pyrazolopyridine Inhibitor


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A 5- Heterocycle Pyrazolopyridine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As505

b:62.1
occ:0.50
 AS A:ARS505 0.0 62.1 0.5
AS A:ARS505 1.7 59.0 0.5
SG A:CYS194 2.8 54.3 0.5
SG A:CYS194 3.1 45.0 0.5
CE2 A:PHE156 3.3 81.0 1.0
CB A:CYS194 3.4 48.4 0.5
CB A:CYS194 3.5 46.1 0.5
CA A:CYS194 3.6 47.5 0.5
CA A:CYS194 3.6 45.9 0.5
CD2 A:PHE156 3.8 80.9 1.0
O A:ILE153 4.0 94.1 1.0
CZ A:PHE156 4.3 82.2 1.0
N A:CYS194 4.6 47.6 1.0
CD2 A:LEU166 4.6 55.2 1.0
C A:CYS194 4.6 45.4 1.0
O A:CYS194 4.6 47.9 1.0
CG2 A:ILE153 4.7 94.6 1.0
CD2 A:TYR197 4.7 63.0 1.0
C A:ILE153 4.8 93.5 1.0
C A:SER154 5.0 92.5 1.0

Arsenic binding site 3 out of 4 in 3o56

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Arsenic binding site 3 out of 4 in the Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A 5- Heterocycle Pyrazolopyridine Inhibitor


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A 5- Heterocycle Pyrazolopyridine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As2

b:61.5
occ:0.50
 SG A:CYS320 1.8 58.7 1.0
CB A:CYS320 2.8 62.9 1.0
CB A:GLU317 3.9 76.2 1.0
CA A:CYS320 3.9 63.1 1.0
N A:CYS320 4.0 67.0 1.0
CG A:GLU317 4.1 78.5 1.0
O A:LEU314 4.5 49.0 1.0
O A:GLU317 4.7 76.9 1.0
C A:HIS319 4.7 73.0 1.0

Arsenic binding site 4 out of 4 in 3o56

Go back to Arsenic Binding Sites List in 3o56
Arsenic binding site 4 out of 4 in the Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A 5- Heterocycle Pyrazolopyridine Inhibitor


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A 5- Heterocycle Pyrazolopyridine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As3

b:71.8
occ:0.50
 C30 A:ZG1506 1.4 85.5 0.5
SG A:CYS432 2.1 63.7 1.0
C31 A:ZG1506 2.2 85.2 0.5
C27 A:ZG1506 2.8 85.4 0.5
O A:HOH124 2.9 55.7 0.5
O A:HOH104 3.3 61.9 1.0
O29 A:ZG1506 3.4 84.3 0.5
C28 A:ZG1506 3.5 84.4 0.5
CB A:CYS432 3.6 63.4 1.0
N A:CYS432 3.6 62.4 1.0
N25 A:ZG1506 3.7 85.4 0.5
CB A:SER429 3.8 72.2 1.0
C A:MET431 4.0 66.2 1.0
CB A:MET431 4.1 72.6 1.0
CA A:CYS432 4.1 61.9 1.0
O A:HOH62 4.3 65.6 1.0
CA A:MET431 4.4 70.0 1.0
N A:MET431 4.4 70.1 1.0
OG A:SER429 4.5 67.7 1.0
NE2 A:GLN417 4.5 44.2 1.0
C26 A:ZG1506 4.5 85.1 0.5
O A:MET431 4.6 66.2 1.0
O A:SER429 4.7 70.0 1.0
C A:SER429 4.8 70.4 1.0
CG A:PHE414 4.8 43.5 1.0
CD2 A:PHE414 4.9 47.3 1.0
CA A:SER429 5.0 71.7 1.0
C26 A:ZG1506 5.0 84.8 0.5

Reference:

C.J.Mitchell, S.P.Ballantine, D.M.Coe, C.M.Cook, C.J.Delves, M.D.Dowle, C.D.Edlin, J.N.Hamblin, S.Holman, M.R.Johnson, P.S.Jones, S.E.Keeling, M.Kranz, M.Lindvall, F.S.Lucas, M.Neu, Y.E.Solanke, D.O.Somers, N.A.Trivedi, J.O.Wiseman. Pyrazolopyridines As Potent PDE4B Inhibitors: 5-Heterocycle Sar. Bioorg.Med.Chem.Lett. V. 20 5803 2010.
ISSN: ISSN 0960-894X
PubMed: 20732811
DOI: 10.1016/J.BMCL.2010.07.136
Page generated: Wed Jul 10 11:50:56 2024

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