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Iodine in PDB 1so2: Catalytic Domain of Human Phosphodiesterase 3B in Complex with A Dihydropyridazine Inhibitor

Enzymatic activity of Catalytic Domain of Human Phosphodiesterase 3B in Complex with A Dihydropyridazine Inhibitor

All present enzymatic activity of Catalytic Domain of Human Phosphodiesterase 3B in Complex with A Dihydropyridazine Inhibitor:
3.1.4.17;

Protein crystallography data

The structure of Catalytic Domain of Human Phosphodiesterase 3B in Complex with A Dihydropyridazine Inhibitor, PDB code: 1so2 was solved by G.Scapin, S.B.Patel, C.Chung, J.P.Varnerin, S.D.Edmondson, A.Mastracchio, E.R.Parmee, J.W.Becker, S.B.Singh, L.H.Van Derploeg, M.R.Tota, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 147.482, 121.772, 126.671, 90.00, 100.74, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1so2:

The structure of Catalytic Domain of Human Phosphodiesterase 3B in Complex with A Dihydropyridazine Inhibitor also contains other interesting chemical elements:

Magnesium (Mg) 9 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Catalytic Domain of Human Phosphodiesterase 3B in Complex with A Dihydropyridazine Inhibitor (pdb code 1so2). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the Catalytic Domain of Human Phosphodiesterase 3B in Complex with A Dihydropyridazine Inhibitor, PDB code: 1so2:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 1so2

Go back to Iodine Binding Sites List in 1so2
Iodine binding site 1 out of 4 in the Catalytic Domain of Human Phosphodiesterase 3B in Complex with A Dihydropyridazine Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Catalytic Domain of Human Phosphodiesterase 3B in Complex with A Dihydropyridazine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I461

b:73.0
occ:1.00
 I54 A:666461 0.0 73.0 1.0
C5 A:666461 2.2 60.9 1.0
C6 A:666461 3.1 59.9 1.0
C4 A:666461 3.2 57.5 1.0
OG A:SER990 3.3 44.5 1.0
N A:PHE991 3.6 37.6 1.0
CA A:PHE991 3.7 38.4 1.0
CB A:SER990 3.9 40.6 1.0
CD1 A:PHE991 4.0 36.8 1.0
CB A:PHE991 4.1 37.4 1.0
CD1 A:ILE995 4.1 46.0 1.0
C A:SER990 4.1 38.4 1.0
C1 A:666461 4.5 55.2 1.0
CG A:PHE991 4.6 37.5 1.0
C3 A:666461 4.6 53.1 1.0
O A:SER990 4.6 39.5 1.0
CA A:SER990 4.7 40.2 1.0
O A:LEU987 4.8 42.5 1.0
CD1 A:LEU987 5.0 38.6 1.0

Iodine binding site 2 out of 4 in 1so2

Go back to Iodine Binding Sites List in 1so2
Iodine binding site 2 out of 4 in the Catalytic Domain of Human Phosphodiesterase 3B in Complex with A Dihydropyridazine Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Catalytic Domain of Human Phosphodiesterase 3B in Complex with A Dihydropyridazine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I462

b:68.2
occ:1.00
 I54 B:666462 0.0 68.2 1.0
C5 B:666462 2.1 62.4 1.0
C6 B:666462 3.1 60.1 1.0
C4 B:666462 3.2 58.6 1.0
OG B:SER990 3.5 47.7 1.0
N B:PHE991 3.8 38.5 1.0
CA B:PHE991 3.8 36.9 1.0
CD1 B:ILE995 3.9 45.6 1.0
CB B:SER990 4.0 42.6 1.0
CB B:PHE991 4.1 34.8 1.0
C B:SER990 4.2 39.4 1.0
CD1 B:PHE991 4.2 35.1 1.0
C1 B:666462 4.5 50.8 1.0
C3 B:666462 4.5 53.0 1.0
O B:SER990 4.6 40.3 1.0
CG B:PHE991 4.7 34.3 1.0
O B:LEU987 4.8 36.9 1.0
CA B:SER990 4.8 41.1 1.0
CD1 B:LEU987 4.8 28.9 1.0

Iodine binding site 3 out of 4 in 1so2

Go back to Iodine Binding Sites List in 1so2
Iodine binding site 3 out of 4 in the Catalytic Domain of Human Phosphodiesterase 3B in Complex with A Dihydropyridazine Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Catalytic Domain of Human Phosphodiesterase 3B in Complex with A Dihydropyridazine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I463

b:85.5
occ:1.00
 I54 C:666463 0.0 85.5 1.0
C5 C:666463 2.1 74.1 1.0
C6 C:666463 3.1 72.6 1.0
C4 C:666463 3.2 71.0 1.0
OG C:SER990 3.6 52.5 1.0
N C:PHE991 3.9 49.3 1.0
CA C:PHE991 4.0 49.9 1.0
CB C:SER990 4.1 49.4 1.0
C C:SER990 4.2 49.6 1.0
CD1 C:PHE991 4.2 55.5 1.0
O C:SER990 4.4 49.9 1.0
CB C:PHE991 4.4 51.5 1.0
C1 C:666463 4.5 68.6 1.0
C3 C:666463 4.6 65.8 1.0
CG C:PHE991 4.8 54.4 1.0
O C:LEU987 4.8 47.2 1.0
CA C:SER990 4.8 50.0 1.0
CG1 C:ILE995 5.0 49.2 1.0

Iodine binding site 4 out of 4 in 1so2

Go back to Iodine Binding Sites List in 1so2
Iodine binding site 4 out of 4 in the Catalytic Domain of Human Phosphodiesterase 3B in Complex with A Dihydropyridazine Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Catalytic Domain of Human Phosphodiesterase 3B in Complex with A Dihydropyridazine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I464

b:82.7
occ:1.00
 I54 D:666464 0.0 82.7 1.0
C5 D:666464 2.1 65.5 1.0
C6 D:666464 3.1 65.8 1.0
C4 D:666464 3.2 64.2 1.0
CB D:SER990 3.8 48.4 1.0
N D:PHE991 3.9 46.0 1.0
CA D:PHE991 4.1 46.6 1.0
OG D:SER990 4.1 52.1 1.0
C D:SER990 4.2 47.1 1.0
CD1 D:PHE991 4.3 45.8 1.0
C1 D:666464 4.5 62.0 1.0
CB D:PHE991 4.5 45.6 1.0
CD1 D:ILE995 4.5 52.9 1.0
O D:LEU987 4.5 44.9 1.0
C3 D:666464 4.5 61.3 1.0
O D:SER990 4.6 45.5 1.0
CA D:SER990 4.7 48.2 1.0
CD1 D:LEU987 4.8 39.0 1.0
CG D:PHE991 4.9 46.1 1.0

Reference:

G.Scapin, S.B.Patel, C.Chung, J.P.Varnerin, S.D.Edmondson, A.Mastracchio, E.R.Parmee, S.B.Singh, J.W.Becker, L.H.Van Der Ploeg, M.R.Tota. Crystal Structure of Human Phosphodiesterase 3B: Atomic Basis For Substrate and Inhibitor Specificity Biochemistry V. 43 6091 2004.
ISSN: ISSN 0006-2960
PubMed: 15147193
DOI: 10.1021/BI049868I
Page generated: Sun Aug 11 12:48:24 2024

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