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Arsenic in PDB 3o57: 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: 3o57 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 / 2.00
Space group I 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.622, 94.907, 105.853, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 24

Other elements in 3o57:

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 3o57). 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: 3o57:
Jump to Arsenic binding site number: 1; 2; 3; 4;

Arsenic binding site 1 out of 4 in 3o57

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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:36.5
occ:0.50
 AS A:ARS505 0.0 36.5 0.5
AS A:ARS505 1.5 35.7 0.5
SG A:CYS194 2.5 27.0 0.5
CB A:CYS194 3.1 27.8 0.5
CB A:CYS194 3.1 25.8 0.5
SG A:CYS194 3.3 34.5 0.5
CA A:CYS194 3.4 25.6 0.5
CA A:CYS194 3.4 26.9 0.5
O A:CYS194 3.6 28.3 1.0
C A:CYS194 3.9 28.1 1.0
CD2 A:TYR197 4.4 42.0 1.0
CD2 A:LEU166 4.5 37.2 1.0
CD1 A:LEU170 4.5 29.2 1.0
O A:ILE153 4.6 56.2 1.0
CB A:TYR197 4.6 30.8 1.0
N A:CYS194 4.7 28.2 1.0
CE2 A:PHE156 4.9 55.1 1.0

Arsenic binding site 2 out of 4 in 3o57

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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:35.7
occ:0.50
 AS A:ARS505 0.0 35.7 0.5
AS A:ARS505 1.5 36.5 0.5
SG A:CYS194 2.3 34.5 0.5
SG A:CYS194 2.9 27.0 0.5
CB A:CYS194 2.9 25.8 0.5
CB A:CYS194 3.0 27.8 0.5
CA A:CYS194 3.5 25.6 0.5
CE2 A:PHE156 3.5 55.1 1.0
CA A:CYS194 3.5 26.9 0.5
CD2 A:PHE156 3.9 52.0 1.0
CD2 A:LEU166 4.2 37.2 1.0
C A:CYS194 4.5 28.1 1.0
N A:CYS194 4.5 28.2 1.0
O A:CYS194 4.6 28.3 1.0
O A:ILE153 4.6 56.2 1.0
CZ A:PHE156 4.6 59.8 1.0

Arsenic binding site 3 out of 4 in 3o57

Go back to Arsenic Binding Sites List in 3o57
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:52.0
occ:0.70
 SG A:CYS320 2.0 41.4 1.0
CB A:CYS320 2.8 42.3 1.0
CB A:GLU317 3.7 52.4 1.0
CG A:GLU317 3.7 54.8 1.0
N A:CYS320 4.0 43.2 1.0
CA A:CYS320 4.0 41.3 1.0
O A:LEU314 4.5 31.1 1.0
C A:HIS319 4.5 48.7 1.0
CB A:HIS319 4.7 57.4 1.0
O A:GLU317 4.8 52.1 1.0
CD A:GLU317 4.9 58.0 1.0
CG2 A:THR218 4.9 30.6 1.0
CA A:GLU317 5.0 49.9 1.0
OG1 A:THR222 5.0 25.6 1.0

Arsenic binding site 4 out of 4 in 3o57

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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:43.8
occ:0.70
 SG A:CYS432 1.9 39.7 1.0
CB A:CYS432 3.3 39.5 1.0
N A:CYS432 3.5 40.3 1.0
O41 A:ZG2506 3.5 40.0 0.3
CB A:SER429 3.6 44.7 1.0
O A:HOH655 3.8 66.0 1.0
CA A:CYS432 3.8 36.6 1.0
C A:MET431 4.0 45.6 1.0
CB A:MET431 4.0 51.3 1.0
CA A:MET431 4.4 49.7 1.0
OG A:SER429 4.4 40.3 1.0
O A:SER429 4.4 42.1 1.0
N A:MET431 4.5 49.1 1.0
O A:MET431 4.6 42.2 1.0
C A:SER429 4.6 44.4 1.0
C26 A:ZG2506 4.7 40.9 0.3
CA A:SER429 4.8 44.4 1.0
NE2 A:GLN417 4.8 28.4 1.0
CG A:PHE414 4.8 34.3 1.0
O A:HOH552 4.9 47.8 1.0

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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