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Zinc in PDB 5sgw: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Phenyl-6-(2-Phenylpyrazol-3-Yl)-3,4-Dihydropyridazin-5-One

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Phenyl-6-(2-Phenylpyrazol-3-Yl)-3,4-Dihydropyridazin-5-One

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Phenyl-6-(2-Phenylpyrazol-3-Yl)-3,4-Dihydropyridazin-5-One:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Phenyl-6-(2-Phenylpyrazol-3-Yl)-3,4-Dihydropyridazin-5-One, PDB code: 5sgw was solved by C.Joseph, J.Benz, A.Flohr, M.Koerner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.56 / 1.90
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.589, 135.589, 235.349, 90, 90, 120
R / Rfree (%) 18.7 / 21.6

Other elements in 5sgw:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Phenyl-6-(2-Phenylpyrazol-3-Yl)-3,4-Dihydropyridazin-5-One also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Phenyl-6-(2-Phenylpyrazol-3-Yl)-3,4-Dihydropyridazin-5-One (pdb code 5sgw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Phenyl-6-(2-Phenylpyrazol-3-Yl)-3,4-Dihydropyridazin-5-One, PDB code: 5sgw:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sgw

Go back to Zinc Binding Sites List in 5sgw
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Phenyl-6-(2-Phenylpyrazol-3-Yl)-3,4-Dihydropyridazin-5-One


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Phenyl-6-(2-Phenylpyrazol-3-Yl)-3,4-Dihydropyridazin-5-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:25.6
occ:1.00
 OD2 A:ASP564 2.1 21.2 1.0
NE2 A:HIS563 2.1 21.1 1.0
NE2 A:HIS529 2.2 21.9 1.0
OD1 A:ASP674 2.2 22.9 1.0
O A:HOH926 2.2 20.3 1.0
O A:HOH1008 2.3 25.9 1.0
CD2 A:HIS563 3.0 19.6 1.0
CG A:ASP674 3.1 23.9 1.0
CG A:ASP564 3.1 21.4 1.0
CD2 A:HIS529 3.1 21.9 1.0
CE1 A:HIS529 3.2 21.5 1.0
CE1 A:HIS563 3.2 21.1 1.0
OD2 A:ASP674 3.3 28.4 1.0
OD1 A:ASP564 3.6 20.3 1.0
MG A:MG802 3.7 21.3 1.0
O A:HOH1039 4.1 22.5 1.0
CD2 A:HIS525 4.1 22.7 1.0
CG A:HIS563 4.2 20.7 1.0
O A:HOH964 4.2 27.1 1.0
ND1 A:HIS563 4.2 21.7 1.0
CB A:ASP564 4.2 21.2 1.0
CG A:HIS529 4.3 21.7 1.0
ND1 A:HIS529 4.3 21.0 1.0
NE2 A:HIS525 4.4 23.9 1.0
CB A:ASP674 4.4 22.9 1.0
O A:HOH1024 4.4 47.2 1.0
O A:HOH945 4.6 19.6 1.0
O A:ASP674 4.7 22.3 1.0
CG2 A:VAL533 4.8 21.4 1.0
CA A:ASP674 4.8 22.3 1.0

Zinc binding site 2 out of 4 in 5sgw

Go back to Zinc Binding Sites List in 5sgw
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Phenyl-6-(2-Phenylpyrazol-3-Yl)-3,4-Dihydropyridazin-5-One


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Phenyl-6-(2-Phenylpyrazol-3-Yl)-3,4-Dihydropyridazin-5-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:23.7
occ:1.00
 OD1 B:ASP674 2.1 19.4 1.0
O B:HOH914 2.1 16.3 1.0
OD2 B:ASP564 2.1 18.6 1.0
NE2 B:HIS563 2.1 18.4 1.0
NE2 B:HIS529 2.2 18.6 1.0
O B:HOH1017 2.3 25.5 1.0
CG B:ASP674 3.0 20.8 1.0
CD2 B:HIS563 3.1 18.5 1.0
CD2 B:HIS529 3.1 19.5 1.0
CG B:ASP564 3.1 19.4 1.0
CE1 B:HIS563 3.2 19.0 1.0
CE1 B:HIS529 3.2 20.2 1.0
OD2 B:ASP674 3.2 23.6 1.0
OD1 B:ASP564 3.6 20.0 1.0
MG B:MG802 3.7 17.3 1.0
O B:HOH1024 4.0 18.5 1.0
O B:HOH955 4.1 27.2 1.0
CD2 B:HIS525 4.1 22.6 1.0
CG B:HIS563 4.2 18.6 1.0
ND1 B:HIS563 4.3 18.7 1.0
CG B:HIS529 4.3 19.6 1.0
ND1 B:HIS529 4.3 19.7 1.0
CB B:ASP564 4.3 18.8 1.0
CB B:ASP674 4.4 19.7 1.0
NE2 B:HIS525 4.4 23.0 1.0
O B:HOH1048 4.5 41.1 1.0
O B:HOH956 4.7 18.1 1.0
CG2 B:VAL533 4.7 20.1 1.0
CA B:ASP674 4.8 19.3 1.0
O B:ASP674 4.8 19.0 1.0

Zinc binding site 3 out of 4 in 5sgw

Go back to Zinc Binding Sites List in 5sgw
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Phenyl-6-(2-Phenylpyrazol-3-Yl)-3,4-Dihydropyridazin-5-One


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Phenyl-6-(2-Phenylpyrazol-3-Yl)-3,4-Dihydropyridazin-5-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:24.8
occ:1.00
 O C:HOH914 2.1 18.7 1.0
OD2 C:ASP564 2.1 20.8 1.0
NE2 C:HIS563 2.1 21.1 1.0
OD1 C:ASP674 2.1 21.2 1.0
NE2 C:HIS529 2.1 20.6 1.0
O C:HOH1018 2.3 26.1 1.0
CG C:ASP674 3.0 23.8 1.0
CD2 C:HIS563 3.0 21.1 1.0
CD2 C:HIS529 3.1 20.9 1.0
CG C:ASP564 3.1 20.9 1.0
CE1 C:HIS563 3.2 20.3 1.0
CE1 C:HIS529 3.2 20.6 1.0
OD2 C:ASP674 3.2 28.2 1.0
OD1 C:ASP564 3.6 20.6 1.0
MG C:MG802 3.8 23.4 1.0
O C:HOH1041 4.1 19.7 1.0
CD2 C:HIS525 4.1 24.8 1.0
CG C:HIS563 4.2 19.9 1.0
O C:HOH987 4.2 29.5 1.0
ND1 C:HIS563 4.2 19.9 1.0
CG C:HIS529 4.2 20.7 1.0
ND1 C:HIS529 4.3 20.4 1.0
CB C:ASP564 4.3 20.6 1.0
CB C:ASP674 4.4 22.8 1.0
NE2 C:HIS525 4.4 24.8 1.0
O C:HOH1048 4.5 45.4 1.0
O C:HOH954 4.7 20.7 1.0
O C:ASP674 4.8 21.5 1.0
CG2 C:VAL533 4.8 21.8 1.0
CA C:ASP674 4.8 22.6 1.0

Zinc binding site 4 out of 4 in 5sgw

Go back to Zinc Binding Sites List in 5sgw
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Phenyl-6-(2-Phenylpyrazol-3-Yl)-3,4-Dihydropyridazin-5-One


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Phenyl-6-(2-Phenylpyrazol-3-Yl)-3,4-Dihydropyridazin-5-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:28.9
occ:1.00
 O D:HOH908 2.1 21.6 1.0
OD1 D:ASP674 2.2 23.8 1.0
NE2 D:HIS563 2.2 22.8 1.0
NE2 D:HIS529 2.2 28.1 1.0
O D:HOH990 2.2 26.7 1.0
OD2 D:ASP564 2.2 23.9 1.0
CD2 D:HIS563 3.0 23.9 1.0
CG D:ASP674 3.0 27.1 1.0
CD2 D:HIS529 3.1 27.3 1.0
CG D:ASP564 3.1 25.0 1.0
CE1 D:HIS529 3.2 27.4 1.0
CE1 D:HIS563 3.2 23.9 1.0
OD2 D:ASP674 3.3 28.9 1.0
OD1 D:ASP564 3.6 25.6 1.0
MG D:MG802 3.8 27.8 1.0
O D:HOH984 4.1 25.6 1.0
CD2 D:HIS525 4.1 30.7 1.0
O D:HOH958 4.1 35.1 1.0
CG D:HIS563 4.2 22.9 1.0
ND1 D:HIS529 4.3 26.6 1.0
CG D:HIS529 4.3 26.1 1.0
ND1 D:HIS563 4.3 23.4 1.0
CB D:ASP564 4.4 24.1 1.0
NE2 D:HIS525 4.4 32.8 1.0
CB D:ASP674 4.4 26.6 1.0
O D:HOH930 4.7 24.6 1.0
O D:ASP674 4.7 25.7 1.0
CG2 D:VAL533 4.7 26.8 1.0
CA D:ASP674 4.8 26.5 1.0

Reference:

A.Flohr, D.Schlatter, B.Kuhn, M.G.Rudolph. Crystal Structure of A Human Phosphodiesterase 10 Complex To Be Published.
Page generated: Mon Oct 28 05:20:15 2024

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