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Arsenic in PDB 3frg: Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A Quinoline Inhibitor

Enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A Quinoline Inhibitor

All present enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A Quinoline Inhibitor:
3.1.4.17;

Protein crystallography data

The structure of Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A Quinoline Inhibitor, PDB code: 3frg 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 / 1.70
Space group I 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.485, 94.831, 105.320, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 24.2

Other elements in 3frg:

The structure of Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A Quinoline 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 Quinoline Inhibitor (pdb code 3frg). 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 Quinoline Inhibitor, PDB code: 3frg:
Jump to Arsenic binding site number: 1; 2; 3; 4;

Arsenic binding site 1 out of 4 in 3frg

Go back to Arsenic Binding Sites List in 3frg
Arsenic binding site 1 out of 4 in the Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A Quinoline 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 Quinoline Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As506

b:26.7
occ:0.50
 AS A:ARS506 0.0 26.7 0.5
AS A:ARS506 1.6 30.8 0.5
SG A:CYS194 2.4 25.4 0.5
CB A:CYS194 3.2 26.1 0.5
SG A:CYS194 3.3 29.3 0.5
CB A:CYS194 3.3 25.2 0.5
CA A:CYS194 3.5 22.6 0.5
CA A:CYS194 3.5 22.1 0.5
O A:CYS194 3.7 23.2 1.0
C A:CYS194 4.0 23.4 1.0
CD2 A:TYR197 4.3 35.8 1.0
CD1 A:LEU170 4.5 30.2 1.0
O A:ILE153 4.5 47.3 1.0
CD2 A:LEU166 4.5 27.0 1.0
CB A:TYR197 4.6 25.5 1.0
N A:CYS194 4.7 23.0 1.0
CE2 A:PHE156 4.9 44.0 1.0
O A:HOH687 4.9 44.4 1.0
CG A:TYR197 5.0 29.2 1.0

Arsenic binding site 2 out of 4 in 3frg

Go back to Arsenic Binding Sites List in 3frg
Arsenic binding site 2 out of 4 in the Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A Quinoline 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 Quinoline Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As506

b:30.8
occ:0.50
 AS A:ARS506 0.0 30.8 0.5
AS A:ARS506 1.6 26.7 0.5
SG A:CYS194 2.3 29.3 0.5
SG A:CYS194 2.8 25.4 0.5
CB A:CYS194 3.0 26.1 0.5
CB A:CYS194 3.1 25.2 0.5
CE2 A:PHE156 3.5 44.0 1.0
CA A:CYS194 3.5 22.1 0.5
CA A:CYS194 3.5 22.6 0.5
CD2 A:PHE156 3.9 44.3 1.0
CD2 A:LEU166 4.1 27.0 1.0
N A:CYS194 4.5 23.0 1.0
CZ A:PHE156 4.5 45.9 1.0
C A:CYS194 4.5 23.4 1.0
O A:ILE153 4.6 47.3 1.0
O A:CYS194 4.6 23.2 1.0

Arsenic binding site 3 out of 4 in 3frg

Go back to Arsenic Binding Sites List in 3frg
Arsenic binding site 3 out of 4 in the Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A Quinoline 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 Quinoline Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As2

b:53.1
occ:1.00
 SG A:CYS320 2.1 38.1 1.0
CB A:CYS320 2.9 34.6 1.0
CB A:GLU317 3.7 47.1 1.0
CG A:GLU317 3.7 50.4 1.0
CA A:CYS320 4.0 34.0 1.0
N A:CYS320 4.0 37.1 1.0
O A:LEU314 4.4 29.3 1.0
C A:HIS319 4.4 41.6 1.0
O A:HIS319 4.8 39.4 1.0
O A:GLU317 4.8 44.8 1.0
CD A:GLU317 4.9 58.1 1.0
CA A:GLU317 4.9 44.6 1.0
OG1 A:THR222 5.0 26.3 1.0

Arsenic binding site 4 out of 4 in 3frg

Go back to Arsenic Binding Sites List in 3frg
Arsenic binding site 4 out of 4 in the Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with A Quinoline 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 Quinoline Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As3

b:37.3
occ:1.00
 SG A:CYS432 2.1 32.7 1.0
CB A:CYS432 3.2 30.9 1.0
N A:CYS432 3.4 32.1 1.0
CB A:SER429 3.5 34.9 1.0
O A:HOH698 3.8 34.1 1.0
CA A:CYS432 3.8 27.7 1.0
O A:HOH715 3.8 45.6 1.0
C A:MET431 3.9 34.1 1.0
CB A:MET431 3.9 38.0 1.0
CA A:MET431 4.3 36.7 1.0
N A:MET431 4.4 35.1 1.0
OG A:SER429 4.4 31.8 1.0
O A:SER429 4.4 30.5 1.0
O A:MET431 4.5 34.7 1.0
C A:SER429 4.6 31.0 1.0
CA A:SER429 4.7 32.6 1.0
NE2 A:GLN417 4.7 24.6 1.0
CG A:PHE414 4.9 29.6 1.0
CD A:GLN417 5.0 23.3 1.0
CD1 A:PHE414 5.0 28.9 1.0

Reference:

C.J.Lunniss, A.W.Cooper, C.D.Eldred, M.Kranz, M.Lindvall, F.S.Lucas, M.Neu, A.G.Preston, L.E.Ranshaw, A.J.Redgrave, J.Ed Robinson, T.J.Shipley, Y.E.Solanke, D.O.Somers, J.O.Wiseman. Quinolines As A Novel Structural Class of Potent and Selective PDE4 Inhibitors: Optimisation For Oral Administration. Bioorg.Med.Chem.Lett. V. 19 1380 2009.
ISSN: ISSN 0960-894X
PubMed: 19195882
DOI: 10.1016/J.BMCL.2009.01.045
Page generated: Wed Jul 10 11:41:15 2024

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