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Zinc in PDB 5sk3: Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol, PDB code: 5sk3 was solved by C.Joseph, J.Benz, A.Flohr, K.Groebke-Zbinden, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.75 / 2.32
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.212, 135.212, 235.801, 90, 90, 120
R / Rfree (%) 16.9 / 22.6

Other elements in 5sk3:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol 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- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol (pdb code 5sk3). 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- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol, PDB code: 5sk3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sk3

Go back to Zinc Binding Sites List in 5sk3
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol


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- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn802

b:42.3
occ:1.00
 O A:HOH931 2.1 28.4 1.0
OD2 A:ASP564 2.1 41.6 1.0
OD1 A:ASP674 2.1 43.0 1.0
NE2 A:HIS563 2.1 30.7 1.0
NE2 A:HIS529 2.2 41.0 1.0
O A:HOH952 2.2 33.9 1.0
CD2 A:HIS563 3.0 34.6 1.0
CG A:ASP674 3.0 40.2 1.0
CD2 A:HIS529 3.1 38.2 1.0
CG A:ASP564 3.1 35.8 1.0
CE1 A:HIS529 3.2 41.9 1.0
CE1 A:HIS563 3.2 38.6 1.0
OD2 A:ASP674 3.3 45.3 1.0
OD1 A:ASP564 3.6 36.9 1.0
MG A:MG803 3.6 36.1 1.0
O A:HOH972 4.0 29.4 1.0
O A:HOH930 4.1 45.4 1.0
CD2 A:HIS525 4.1 45.5 1.0
CG A:HIS563 4.2 34.4 1.0
CG A:HIS529 4.3 36.8 1.0
ND1 A:HIS529 4.3 41.2 1.0
CB A:ASP564 4.3 32.8 1.0
ND1 A:HIS563 4.3 31.7 1.0
NE2 A:HIS525 4.3 42.5 1.0
CB A:ASP674 4.4 38.2 1.0
O A:HOH904 4.6 28.4 1.0
CG2 A:VAL533 4.8 27.9 1.0
CA A:ASP674 4.8 35.0 1.0
O A:ASP674 4.8 37.4 1.0
O A:HOH932 5.0 36.8 1.0

Zinc binding site 2 out of 4 in 5sk3

Go back to Zinc Binding Sites List in 5sk3
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol


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- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn802

b:39.9
occ:1.00
 O B:HOH952 2.1 27.8 1.0
NE2 B:HIS563 2.1 34.3 1.0
OD1 B:ASP674 2.1 36.5 1.0
NE2 B:HIS529 2.1 32.6 1.0
OD2 B:ASP564 2.2 36.9 1.0
O B:HOH961 2.4 36.0 1.0
CD2 B:HIS563 3.0 34.7 1.0
CG B:ASP674 3.1 34.5 1.0
CD2 B:HIS529 3.1 34.5 1.0
CE1 B:HIS529 3.1 31.1 1.0
CG B:ASP564 3.2 32.8 1.0
CE1 B:HIS563 3.2 36.3 1.0
OD2 B:ASP674 3.3 38.3 1.0
OD1 B:ASP564 3.6 37.4 1.0
MG B:MG803 3.8 37.6 1.0
O B:HOH974 3.9 25.0 1.0
CD2 B:HIS525 4.1 37.5 1.0
O B:HOH964 4.2 39.1 1.0
CG B:HIS563 4.2 32.7 1.0
ND1 B:HIS529 4.3 32.4 1.0
ND1 B:HIS563 4.3 32.5 1.0
CG B:HIS529 4.3 34.2 1.0
CB B:ASP564 4.3 34.6 1.0
CB B:ASP674 4.4 34.7 1.0
NE2 B:HIS525 4.5 38.7 1.0
O B:HOH934 4.6 33.8 1.0
CA B:ASP674 4.8 30.5 1.0
O B:ASP674 4.9 36.0 1.0
CG2 B:VAL533 4.9 28.2 1.0

Zinc binding site 3 out of 4 in 5sk3

Go back to Zinc Binding Sites List in 5sk3
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol


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- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn802

b:41.9
occ:1.00
 OD2 C:ASP564 2.1 39.4 1.0
O C:HOH933 2.1 29.3 1.0
NE2 C:HIS529 2.1 37.8 1.0
NE2 C:HIS563 2.2 34.8 1.0
OD1 C:ASP674 2.2 39.9 1.0
O C:HOH964 2.4 35.5 1.0
CG C:ASP674 3.0 34.1 1.0
CD2 C:HIS563 3.0 32.2 1.0
CD2 C:HIS529 3.1 36.9 1.0
CG C:ASP564 3.2 38.1 1.0
CE1 C:HIS529 3.2 36.6 1.0
OD2 C:ASP674 3.2 39.4 1.0
CE1 C:HIS563 3.2 36.4 1.0
OD1 C:ASP564 3.7 39.7 1.0
MG C:MG803 3.8 36.6 1.0
CD2 C:HIS525 4.1 40.3 1.0
O C:HOH977 4.2 31.4 1.0
O C:HOH963 4.2 44.6 1.0
CG C:HIS563 4.2 32.1 1.0
CG C:HIS529 4.3 31.7 1.0
ND1 C:HIS529 4.3 40.1 1.0
ND1 C:HIS563 4.3 35.0 1.0
NE2 C:HIS525 4.3 44.0 1.0
CB C:ASP564 4.3 35.6 1.0
O C:HOH989 4.4 51.5 1.0
CB C:ASP674 4.4 36.0 1.0
O C:HOH951 4.6 40.1 1.0
CA C:ASP674 4.8 35.4 1.0
CG2 C:VAL533 4.9 40.3 1.0
O C:ASP674 4.9 37.7 1.0
O C:HOH942 5.0 31.2 1.0

Zinc binding site 4 out of 4 in 5sk3

Go back to Zinc Binding Sites List in 5sk3
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol


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- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn802

b:57.9
occ:1.00
 OD2 D:ASP564 2.1 61.1 1.0
O D:HOH919 2.2 36.9 1.0
NE2 D:HIS563 2.2 44.5 1.0
OD1 D:ASP674 2.2 64.7 1.0
NE2 D:HIS529 2.3 48.2 1.0
O D:HOH908 2.3 46.8 1.0
CD2 D:HIS563 3.0 45.8 1.0
CD2 D:HIS529 3.1 53.4 1.0
CG D:ASP674 3.2 55.4 1.0
CG D:ASP564 3.2 56.9 1.0
CE1 D:HIS529 3.3 50.5 1.0
CE1 D:HIS563 3.4 49.0 1.0
OD2 D:ASP674 3.5 71.3 1.0
OD1 D:ASP564 3.8 54.3 1.0
MG D:MG803 3.8 50.5 1.0
O D:HOH911 3.9 57.4 1.0
O D:HOH927 3.9 44.6 1.0
CD2 D:HIS525 4.1 58.2 1.0
CG D:HIS563 4.2 49.7 1.0
CB D:ASP564 4.3 52.6 1.0
CG D:HIS529 4.3 49.5 1.0
ND1 D:HIS529 4.4 53.1 1.0
ND1 D:HIS563 4.4 45.2 1.0
NE2 D:HIS525 4.4 58.0 1.0
CB D:ASP674 4.5 54.2 1.0
O D:HOH904 4.6 45.7 1.0
CG2 D:VAL533 4.7 47.8 1.0
O D:ASP674 4.8 62.7 1.0
CA D:ASP674 4.8 54.5 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 06:10:02 2024

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