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Arsenic in PDB 1f0j: Catalytic Domain of Human Phosphodiesterase 4B2B

Enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4B2B

All present enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4B2B:
3.1.4.17;

Protein crystallography data

The structure of Catalytic Domain of Human Phosphodiesterase 4B2B, PDB code: 1f0j was solved by R.X.Xu, A.M.Hassell, D.Vanderwall, M.H.Lambert, W.D.Holmes, M.A.Luther, W.J.Rocque, M.V.Milburn, Y.Zhao, H.Ke, R.T.Nolte, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.00 / 1.77
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 104.540, 159.580, 109.040, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 22.3

Other elements in 1f0j:

The structure of Catalytic Domain of Human Phosphodiesterase 4B2B also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Zinc (Zn) 2 atoms

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Catalytic Domain of Human Phosphodiesterase 4B2B (pdb code 1f0j). 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, PDB code: 1f0j:
Jump to Arsenic binding site number: 1; 2; 3; 4; 5;

Arsenic binding site 1 out of 5 in 1f0j

Go back to Arsenic Binding Sites List in 1f0j
Arsenic binding site 1 out of 5 in the Catalytic Domain of Human Phosphodiesterase 4B2B


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As1103

b:40.5
occ:1.00
O A:HOH1330 2.5 28.8 1.0
O A:HOH1624 2.6 25.5 1.0
NE2 A:HIS234 3.2 17.4 1.0
OD2 A:ASP392 3.5 19.8 1.0
ZN A:ZN1101 3.6 21.5 1.0
AS A:ARS1212 3.7 67.6 1.0
OD1 A:ASP392 3.8 18.4 1.0
CG A:ASP392 4.0 19.0 1.0
CD2 A:HIS234 4.1 16.8 1.0
MG A:MG1102 4.2 52.3 1.0
CE1 A:HIS234 4.3 16.9 1.0
NE2 A:HIS238 4.3 13.8 1.0
CE2 A:TYR233 4.4 15.6 1.0
CE1 A:HIS238 4.6 13.1 1.0
OD2 A:ASP275 4.7 13.7 1.0
O A:ASP392 4.8 18.2 1.0
OH A:TYR233 4.9 16.3 1.0

Arsenic binding site 2 out of 5 in 1f0j

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Arsenic binding site 2 out of 5 in the Catalytic Domain of Human Phosphodiesterase 4B2B


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As1111

b:39.3
occ:1.00
SG A:CYS194 2.3 18.6 1.0
CB A:CYS194 3.2 17.5 1.0
CA A:CYS194 3.5 17.0 1.0
O A:CYS194 3.8 16.6 1.0
C A:CYS194 4.0 17.1 1.0
CZ A:PHE156 4.1 20.9 1.0
CE1 A:PHE156 4.3 20.7 1.0
CE2 A:PHE156 4.3 21.0 1.0
CD1 A:PHE156 4.5 20.9 1.0
CD2 A:PHE156 4.5 20.9 1.0
CD1 A:LEU166 4.6 21.4 1.0
CG A:PHE156 4.6 21.1 1.0
O A:HOH1539 4.7 43.2 1.0
N A:CYS194 4.8 16.2 1.0
CD1 A:LEU170 5.0 22.4 1.0

Arsenic binding site 3 out of 5 in 1f0j

Go back to Arsenic Binding Sites List in 1f0j
Arsenic binding site 3 out of 5 in the Catalytic Domain of Human Phosphodiesterase 4B2B


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As1212

b:67.6
occ:1.00
SG A:CYS499 2.4 47.7 1.0
CB A:CYS499 3.0 47.3 1.0
AS A:ARS1103 3.7 40.5 1.0
CG A:MET347 4.2 25.3 1.0
CA A:CYS499 4.4 47.1 1.0
O A:HOH1330 4.4 28.8 1.0
CE A:MET503 4.6 43.9 1.0
CZ A:PHE446 4.8 26.1 1.0
SD A:MET347 4.9 26.7 1.0

Arsenic binding site 4 out of 5 in 1f0j

Go back to Arsenic Binding Sites List in 1f0j
Arsenic binding site 4 out of 5 in the Catalytic Domain of Human Phosphodiesterase 4B2B


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As1203

b:43.3
occ:1.00
O B:HOH1250 2.4 25.1 1.0
O B:HOH1541 2.6 29.3 1.0
NE2 B:HIS234 3.4 18.7 1.0
O B:HOH1543 3.5 34.7 1.0
ZN B:ZN1201 3.7 22.1 1.0
OD2 B:ASP392 3.7 19.6 1.0
OD1 B:ASP392 3.9 18.2 1.0
CG B:ASP392 4.1 19.1 1.0
CD2 B:HIS234 4.2 18.9 1.0
CE2 B:TYR233 4.3 17.9 1.0
NE2 B:HIS238 4.4 17.3 1.0
MG B:MG1202 4.4 45.9 1.0
CE1 B:HIS234 4.5 19.1 1.0
CE1 B:HIS238 4.7 17.0 1.0
OD2 B:ASP275 4.8 14.6 1.0
O B:ASP392 4.8 19.9 1.0
O B:HOH1426 4.8 42.7 1.0
OH B:TYR233 4.9 17.6 1.0
CD2 B:LEU393 5.0 22.1 1.0

Arsenic binding site 5 out of 5 in 1f0j

Go back to Arsenic Binding Sites List in 1f0j
Arsenic binding site 5 out of 5 in the Catalytic Domain of Human Phosphodiesterase 4B2B


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As1211

b:44.8
occ:1.00
SG B:CYS194 2.4 26.6 1.0
CB B:CYS194 3.2 25.4 1.0
CA B:CYS194 3.4 24.9 1.0
O B:CYS194 3.8 25.0 1.0
CE2 B:PHE156 3.9 38.7 1.0
CZ B:PHE156 3.9 38.7 1.0
C B:CYS194 4.0 24.9 1.0
CD2 B:PHE156 4.0 38.7 1.0
CE1 B:PHE156 4.0 38.6 1.0
CD1 B:PHE156 4.1 38.8 1.0
CG B:PHE156 4.1 39.0 1.0
CD2 B:LEU166 4.5 45.9 1.0
CD2 B:TYR197 4.6 29.3 1.0
CD1 B:ILE153 4.6 43.3 1.0
N B:CYS194 4.7 24.2 1.0
CB B:TYR197 5.0 27.1 1.0
CB B:PHE156 5.0 39.3 1.0

Reference:

R.X.Xu, A.M.Hassell, D.Vanderwall, M.H.Lambert, W.D.Holmes, M.A.Luther, W.J.Rocque, M.V.Milburn, Y.Zhao, H.Ke, R.T.Nolte. Atomic Structure of PDE4: Insights Into Phosphodiesterase Mechanism and Specificity. Science V. 288 1822 2000.
ISSN: ISSN 0036-8075
PubMed: 10846163
DOI: 10.1126/SCIENCE.288.5472.1822
Page generated: Tue Oct 27 16:46:27 2020

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