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Arsenic in PDB 3gwt: 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: 3gwt 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 / 1.75
Space group I 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.706, 94.783, 105.995, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 25

Other elements in 3gwt:

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

Arsenic binding site 1 out of 5 in 3gwt

Go back to Arsenic Binding Sites List in 3gwt
Arsenic binding site 1 out of 5 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:26.5
occ:0.50
 AS A:ARS506 0.0 26.5 0.5
AS A:ARS506 1.5 27.7 0.5
SG A:CYS194 2.3 21.8 0.5
CB A:CYS194 3.1 25.0 0.5
CB A:CYS194 3.2 23.9 0.5
SG A:CYS194 3.4 30.9 0.5
CA A:CYS194 3.5 24.6 0.5
CA A:CYS194 3.5 23.4 0.5
O A:CYS194 3.6 25.4 1.0
C A:CYS194 4.0 24.0 1.0
CD2 A:TYR197 4.3 38.1 1.0
CD1 A:LEU170 4.5 31.3 1.0
O A:ILE153 4.5 50.4 1.0
CD2 A:LEU166 4.5 27.6 1.0
CB A:TYR197 4.6 23.7 1.0
N A:CYS194 4.8 24.5 1.0
CG A:TYR197 5.0 29.1 1.0
O A:HOH541 5.0 46.6 1.0

Arsenic binding site 2 out of 5 in 3gwt

Go back to Arsenic Binding Sites List in 3gwt
Arsenic binding site 2 out of 5 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:27.7
occ:0.50
 AS A:ARS506 0.0 27.7 0.5
AS A:ARS506 1.5 26.5 0.5
SG A:CYS194 2.3 30.9 0.5
SG A:CYS194 2.5 21.8 0.5
CB A:CYS194 2.9 25.0 0.5
CB A:CYS194 2.9 23.9 0.5
CA A:CYS194 3.4 24.6 0.5
CA A:CYS194 3.4 23.4 0.5
CE2 A:PHE156 3.8 33.7 1.0
CD2 A:PHE156 4.1 40.3 1.0
CD2 A:LEU166 4.2 27.6 1.0
C A:CYS194 4.4 24.0 1.0
N A:CYS194 4.4 24.5 1.0
O A:CYS194 4.5 25.4 1.0
O A:ILE153 4.6 50.4 1.0
CZ A:PHE156 4.9 43.5 1.0

Arsenic binding site 3 out of 5 in 3gwt

Go back to Arsenic Binding Sites List in 3gwt
Arsenic binding site 3 out of 5 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:56.6
occ:1.00
 SG A:CYS320 2.0 34.1 1.0
CB A:CYS320 2.9 32.8 1.0
CB A:GLU317 3.8 47.6 1.0
CG A:GLU317 3.8 53.1 1.0
N A:CYS320 4.0 36.1 1.0
CA A:CYS320 4.0 33.3 1.0
O A:LEU314 4.4 27.7 1.0
C A:HIS319 4.5 42.2 1.0
CB A:HIS319 4.6 50.1 1.0
O A:GLU317 4.6 47.1 1.0
OG1 A:THR222 5.0 26.3 1.0
CD A:GLU317 5.0 57.3 1.0
CG2 A:THR218 5.0 28.0 1.0
O A:HIS319 5.0 42.4 1.0
CA A:GLU317 5.0 45.7 1.0

Arsenic binding site 4 out of 5 in 3gwt

Go back to Arsenic Binding Sites List in 3gwt
Arsenic binding site 4 out of 5 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:46.4
occ:1.00
 SG A:CYS432 2.2 36.7 1.0
CB A:CYS432 3.3 34.5 1.0
N A:CYS432 3.5 35.1 1.0
CB A:SER429 3.6 41.0 1.0
CA A:CYS432 3.8 30.6 1.0
C A:MET431 3.9 39.2 1.0
C20 A:0661 4.1 52.1 0.7
CB A:MET431 4.2 42.6 1.0
O A:SER429 4.2 39.8 1.0
CA A:MET431 4.3 42.2 1.0
N A:MET431 4.4 41.4 1.0
O A:MET431 4.4 36.1 1.0
C19 A:0661 4.5 53.3 0.7
OG A:SER429 4.5 37.6 1.0
C A:SER429 4.5 39.7 1.0
O4 A:0661 4.6 53.6 0.7
NE2 A:GLN417 4.7 24.8 1.0
CA A:SER429 4.7 39.4 1.0
CG A:PHE414 4.8 31.7 1.0
C21 A:0661 4.9 52.1 0.7
CB A:PHE414 5.0 28.6 1.0
CD2 A:PHE414 5.0 36.3 1.0

Arsenic binding site 5 out of 5 in 3gwt

Go back to Arsenic Binding Sites List in 3gwt
Arsenic binding site 5 out of 5 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 5 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:As4

b:29.9
occ:0.33
 O A:HOH523 1.8 20.3 0.7
C2 A:0661 2.3 33.4 0.7
O A:HOH522 2.4 22.5 1.0
C27 A:0661 2.4 33.5 0.7
O1 A:0661 2.5 34.6 0.7
C1 A:0661 2.7 27.5 0.7
C3 A:0661 3.1 31.4 0.7
C6 A:0661 3.2 36.2 0.7
NE2 A:HIS234 3.3 22.3 1.0
O A:HOH74 3.5 26.2 1.0
O A:HOH78 3.5 26.3 1.0
C4 A:0661 3.8 30.0 0.7
C5 A:0661 3.8 36.2 0.7
ZN A:ZN504 3.9 22.0 1.0
OD1 A:ASP392 4.0 18.5 1.0
N1 A:0661 4.1 38.2 0.7
OD2 A:ASP392 4.1 25.4 1.0
CE1 A:HIS234 4.2 20.8 1.0
CD2 A:HIS234 4.2 21.2 1.0
CE2 A:TYR233 4.2 20.4 1.0
CG A:ASP392 4.3 24.5 1.0
NE2 A:HIS238 4.5 19.7 1.0
CE1 A:HIS238 4.7 15.5 1.0
MG A:MG505 4.7 27.1 1.0
OH A:TYR233 4.8 23.1 1.0
OD2 A:ASP275 4.8 19.6 1.0
O5 A:0661 4.9 27.7 0.7
O A:ASP392 4.9 21.8 1.0
CZ A:TYR233 5.0 20.3 1.0

Reference:

M.D.Woodrow, S.P.Ballantine, M.D.Barker, B.J.Clarke, J.Dawson, T.W.Dean, C.J.Delves, B.Evans, S.L.Gough, S.B.Guntrip, S.Holman, D.S.Holmes, M.Kranz, M.K.Lindvaal, F.S.Lucas, M.Neu, L.E.Ranshaw, Y.E.Solanke, D.O.Somers, P.Ward, J.O.Wiseman. Quinolines As A Novel Structural Class of Potent and Selective PDE4 Inhibitors. Optimisation For Inhaled Administration. Bioorg.Med.Chem.Lett. V. 19 5261 2009.
ISSN: ISSN 0960-894X
PubMed: 19656678
DOI: 10.1016/J.BMCL.2009.04.012
Page generated: Wed Jul 10 11:42:34 2024

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