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Zinc in PDB 5skc: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(1-Propan-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino)Pyridine- 2-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(1-Propan-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino)Pyridine- 2-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(1-Propan-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino)Pyridine- 2-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(1-Propan-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino)Pyridine- 2-Carboxamide, PDB code: 5skc was solved by C.Joseph, J.Benz, A.Flohr, E.Vieira, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.87 / 2.60
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 136.69, 136.69, 236.14, 90, 90, 120
R / Rfree (%) 21.6 / 24.2

Other elements in 5skc:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(1-Propan-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino)Pyridine- 2-Carboxamide 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 6- Methyl-N-(1-Propan-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino)Pyridine- 2-Carboxamide (pdb code 5skc). 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 6- Methyl-N-(1-Propan-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino)Pyridine- 2-Carboxamide, PDB code: 5skc:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5skc

Go back to Zinc Binding Sites List in 5skc
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(1-Propan-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino)Pyridine- 2-Carboxamide


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 6- Methyl-N-(1-Propan-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino)Pyridine- 2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:59.4
occ:1.00
 O A:HOH908 1.9 64.7 1.0
NE2 A:HIS563 2.0 50.4 1.0
NE2 A:HIS529 2.1 47.0 1.0
OD2 A:ASP564 2.3 61.4 1.0
OD1 A:ASP674 2.4 63.9 1.0
CD2 A:HIS563 2.9 49.5 1.0
CE1 A:HIS563 3.1 49.8 1.0
CE1 A:HIS529 3.1 46.9 1.0
CG A:ASP564 3.1 56.7 1.0
CD2 A:HIS529 3.2 46.4 1.0
CG A:ASP674 3.2 63.4 1.0
OD1 A:ASP564 3.6 56.3 1.0
MG A:MG802 3.6 47.7 1.0
OD2 A:ASP674 3.6 66.4 1.0
CG A:HIS563 4.0 48.4 1.0
CD2 A:HIS525 4.0 51.0 1.0
ND1 A:HIS563 4.1 49.1 1.0
ND1 A:HIS529 4.2 46.8 1.0
O A:HOH909 4.2 60.8 1.0
CB A:ASP564 4.3 50.8 1.0
O A:HOH929 4.3 61.0 1.0
CG A:HIS529 4.3 45.7 1.0
NE2 A:HIS525 4.4 51.8 1.0
CB A:ASP674 4.4 58.6 1.0
O A:HOH925 4.4 61.3 1.0
CG2 A:VAL533 4.7 45.9 1.0
O A:HOH907 4.8 43.1 1.0
CA A:ASP674 4.9 55.0 1.0
O A:ASP674 4.9 55.4 1.0

Zinc binding site 2 out of 4 in 5skc

Go back to Zinc Binding Sites List in 5skc
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(1-Propan-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino)Pyridine- 2-Carboxamide


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 6- Methyl-N-(1-Propan-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino)Pyridine- 2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:54.5
occ:1.00
 O B:HOH916 1.9 54.1 1.0
NE2 B:HIS529 2.0 48.0 1.0
NE2 B:HIS563 2.2 48.5 1.0
OD1 B:ASP674 2.3 56.8 1.0
OD2 B:ASP564 2.4 46.8 1.0
CD2 B:HIS563 2.9 46.9 1.0
CD2 B:HIS529 3.0 47.0 1.0
CE1 B:HIS529 3.0 48.1 1.0
CG B:ASP674 3.2 56.5 1.0
CG B:ASP564 3.2 46.8 1.0
CE1 B:HIS563 3.3 48.2 1.0
MG B:MG802 3.5 41.4 1.0
OD2 B:ASP674 3.6 60.4 1.0
OD1 B:ASP564 3.6 47.9 1.0
O B:HOH935 4.0 56.8 1.0
CD2 B:HIS525 4.1 53.0 1.0
CG B:HIS563 4.2 45.5 1.0
O B:HOH919 4.2 55.2 1.0
CG B:HIS529 4.2 46.6 1.0
ND1 B:HIS529 4.2 48.3 1.0
ND1 B:HIS563 4.3 47.0 1.0
NE2 B:HIS525 4.4 53.8 1.0
CB B:ASP564 4.4 45.3 1.0
CB B:ASP674 4.4 52.4 1.0
O B:HOH933 4.6 53.5 1.0
CG2 B:VAL533 4.6 43.0 1.0
O B:HOH920 4.8 52.9 1.0
O B:ASP674 4.8 51.3 1.0
CA B:ASP674 4.8 50.3 1.0

Zinc binding site 3 out of 4 in 5skc

Go back to Zinc Binding Sites List in 5skc
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(1-Propan-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino)Pyridine- 2-Carboxamide


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 6- Methyl-N-(1-Propan-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino)Pyridine- 2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:57.6
occ:1.00
 O C:HOH906 1.9 44.4 1.0
NE2 C:HIS529 2.0 52.4 1.0
NE2 C:HIS563 2.1 42.9 1.0
OD1 C:ASP674 2.2 54.6 1.0
OD2 C:ASP564 2.2 56.1 1.0
CE1 C:HIS529 3.0 52.2 1.0
CD2 C:HIS529 3.1 51.2 1.0
CD2 C:HIS563 3.1 41.3 1.0
CE1 C:HIS563 3.1 42.2 1.0
CG C:ASP674 3.2 54.6 1.0
CG C:ASP564 3.3 53.2 1.0
O C:HOH921 3.4 90.1 1.0
OD2 C:ASP674 3.6 57.2 1.0
MG C:MG802 3.8 40.6 1.0
OD1 C:ASP564 3.9 53.9 1.0
O C:HOH922 4.0 46.9 1.0
CD2 C:HIS525 4.0 53.3 1.0
ND1 C:HIS529 4.1 51.4 1.0
CG C:HIS529 4.2 49.7 1.0
CG C:HIS563 4.2 41.1 1.0
ND1 C:HIS563 4.3 41.5 1.0
NE2 C:HIS525 4.3 54.2 1.0
CB C:ASP564 4.3 48.2 1.0
CB C:ASP674 4.4 51.4 1.0
O C:HOH926 4.4 44.5 1.0
CG2 C:VAL533 4.5 44.2 1.0
O C:ASP674 4.7 50.0 1.0
CA C:ASP674 4.7 49.5 1.0
O C:HOH910 4.8 48.7 1.0

Zinc binding site 4 out of 4 in 5skc

Go back to Zinc Binding Sites List in 5skc
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(1-Propan-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino)Pyridine- 2-Carboxamide


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 6- Methyl-N-(1-Propan-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino)Pyridine- 2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:75.8
occ:1.00
 NE2 D:HIS563 2.1 68.4 1.0
NE2 D:HIS529 2.2 78.0 1.0
OD1 D:ASP674 2.3 82.0 1.0
OD2 D:ASP564 2.4 78.4 1.0
O D:HOH902 2.7 51.2 1.0
CD2 D:HIS563 3.0 68.2 1.0
CD2 D:HIS529 3.2 76.6 1.0
CG D:ASP674 3.2 81.4 1.0
O D:HOH910 3.2 80.4 1.0
CE1 D:HIS529 3.2 78.5 1.0
CE1 D:HIS563 3.3 68.4 1.0
CG D:ASP564 3.3 75.6 1.0
OD2 D:ASP674 3.6 84.3 1.0
OD1 D:ASP564 3.8 74.8 1.0
O D:HOH908 3.9 57.3 1.0
CD2 D:HIS525 4.0 82.8 1.0
O D:HOH907 4.0 61.0 1.0
CG D:HIS563 4.2 67.8 1.0
NE2 D:HIS525 4.3 83.8 1.0
ND1 D:HIS563 4.3 68.4 1.0
CG D:HIS529 4.3 75.3 1.0
CB D:ASP564 4.4 72.3 1.0
ND1 D:HIS529 4.4 78.1 1.0
CB D:ASP674 4.4 77.4 1.0
O D:ASP674 4.7 76.7 1.0
CG2 D:VAL533 4.7 72.7 1.0
CA D:ASP674 4.8 75.7 1.0
O D:HOH905 4.9 64.0 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 07:35:36 2024

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