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Zinc in PDB 5sjl: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]Pyridin-3-Yl]- 3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]Pyridin-3-Yl]- 3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]Pyridin-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- Cyclopropyl-N-[4-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]Pyridin-3-Yl]- 3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide, PDB code: 5sjl 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) 43.76 / 2.64
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.938, 135.938, 235.673, 90, 90, 120
R / Rfree (%) 20.2 / 24.4

Other elements in 5sjl:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]Pyridin-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- Cyclopropyl-N-[4-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]Pyridin-3-Yl]- 3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide (pdb code 5sjl). 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- Cyclopropyl-N-[4-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]Pyridin-3-Yl]- 3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide, PDB code: 5sjl:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sjl

Go back to Zinc Binding Sites List in 5sjl
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]Pyridin-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- Cyclopropyl-N-[4-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]Pyridin-3-Yl]- 3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:38.0
occ:1.00
 OD2 A:ASP564 1.9 40.1 1.0
NE2 A:HIS563 2.1 31.6 1.0
OD1 A:ASP674 2.2 33.5 1.0
NE2 A:HIS529 2.2 32.2 1.0
O A:HOH926 2.4 28.4 1.0
CG A:ASP564 3.0 36.7 1.0
CD2 A:HIS563 3.0 31.8 1.0
CG A:ASP674 3.0 33.8 1.0
CE1 A:HIS563 3.1 32.6 1.0
CD2 A:HIS529 3.1 36.0 1.0
CE1 A:HIS529 3.2 36.2 1.0
OD2 A:ASP674 3.3 32.6 1.0
OD1 A:ASP564 3.5 35.7 1.0
MG A:MG802 3.9 29.0 1.0
CD2 A:HIS525 4.0 40.1 1.0
O A:HOH945 4.0 33.8 1.0
ND1 A:HIS563 4.2 31.6 1.0
CG A:HIS563 4.2 31.4 1.0
CB A:ASP564 4.2 32.4 1.0
CG A:HIS529 4.2 33.4 1.0
ND1 A:HIS529 4.3 34.9 1.0
NE2 A:HIS525 4.4 38.4 1.0
CB A:ASP674 4.4 33.2 1.0
O A:HOH969 4.5 31.5 1.0
O A:ASP674 4.8 30.8 1.0
CA A:ASP674 4.9 31.5 1.0
CG2 A:VAL533 4.9 27.2 1.0
O A:HOH948 4.9 24.3 1.0
O A:HOH960 4.9 37.3 1.0

Zinc binding site 2 out of 4 in 5sjl

Go back to Zinc Binding Sites List in 5sjl
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]Pyridin-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- Cyclopropyl-N-[4-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]Pyridin-3-Yl]- 3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:32.8
occ:1.00
 OD2 B:ASP564 2.1 29.3 1.0
NE2 B:HIS563 2.2 26.3 1.0
NE2 B:HIS529 2.2 23.1 1.0
O B:HOH934 2.3 23.3 1.0
OD1 B:ASP674 2.3 31.8 1.0
CD2 B:HIS563 3.0 27.4 1.0
CD2 B:HIS529 3.1 25.4 1.0
CG B:ASP674 3.1 31.2 1.0
CG B:ASP564 3.1 27.0 1.0
OD2 B:ASP674 3.2 35.6 1.0
CE1 B:HIS529 3.3 25.2 1.0
CE1 B:HIS563 3.3 28.6 1.0
OD1 B:ASP564 3.6 25.7 1.0
MG B:MG802 3.8 26.0 1.0
CD2 B:HIS525 4.2 32.3 1.0
CG B:HIS563 4.2 26.6 1.0
O B:HOH980 4.2 24.9 1.0
CG B:HIS529 4.2 27.6 1.0
CB B:ASP564 4.3 27.1 1.0
ND1 B:HIS529 4.3 26.5 1.0
ND1 B:HIS563 4.3 27.0 1.0
CB B:ASP674 4.5 30.5 1.0
NE2 B:HIS525 4.6 29.4 1.0
O B:HOH943 4.7 36.2 1.0
O B:HOH936 4.7 24.4 1.0
CG2 B:VAL533 4.8 31.0 1.0
O B:ASP674 4.9 25.9 1.0
CA B:ASP674 4.9 29.4 1.0

Zinc binding site 3 out of 4 in 5sjl

Go back to Zinc Binding Sites List in 5sjl
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]Pyridin-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- Cyclopropyl-N-[4-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]Pyridin-3-Yl]- 3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:38.2
occ:1.00
 NE2 C:HIS529 2.0 31.5 1.0
OD2 C:ASP564 2.1 33.8 1.0
O C:HOH923 2.1 23.8 1.0
OD1 C:ASP674 2.1 30.9 1.0
NE2 C:HIS563 2.1 31.0 1.0
CD2 C:HIS529 3.0 31.0 1.0
CD2 C:HIS563 3.0 31.6 1.0
CE1 C:HIS529 3.0 30.2 1.0
CG C:ASP674 3.1 30.1 1.0
CG C:ASP564 3.1 32.3 1.0
CE1 C:HIS563 3.2 30.0 1.0
OD2 C:ASP674 3.3 30.6 1.0
OD1 C:ASP564 3.7 33.7 1.0
MG C:MG802 3.9 31.8 1.0
CD2 C:HIS525 4.0 32.6 1.0
ND1 C:HIS529 4.1 28.3 1.0
CG C:HIS529 4.1 28.7 1.0
CG C:HIS563 4.2 29.9 1.0
ND1 C:HIS563 4.3 27.6 1.0
CB C:ASP564 4.3 26.9 1.0
O C:HOH957 4.3 34.8 1.0
NE2 C:HIS525 4.4 31.7 1.0
CB C:ASP674 4.4 32.1 1.0
O C:HOH908 4.4 35.0 1.0
O C:HOH936 4.7 45.4 1.0
O C:ASP674 4.7 33.5 1.0
CA C:ASP674 4.8 32.5 1.0
CG2 C:VAL533 4.9 30.1 1.0
O C:HOH906 5.0 28.5 1.0

Zinc binding site 4 out of 4 in 5sjl

Go back to Zinc Binding Sites List in 5sjl
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]Pyridin-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- Cyclopropyl-N-[4-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]Pyridin-3-Yl]- 3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:39.8
occ:1.00
 NE2 D:HIS563 2.0 37.5 1.0
OD2 D:ASP564 2.1 37.6 1.0
NE2 D:HIS529 2.1 41.3 1.0
O D:HOH902 2.2 35.0 1.0
OD1 D:ASP674 2.3 41.9 1.0
O D:HOH946 2.5 37.1 1.0
CD2 D:HIS563 2.8 39.1 1.0
CE1 D:HIS529 3.1 43.8 1.0
CG D:ASP674 3.1 36.8 1.0
CD2 D:HIS529 3.2 44.1 1.0
CE1 D:HIS563 3.2 39.0 1.0
CG D:ASP564 3.2 33.9 1.0
OD2 D:ASP674 3.3 39.8 1.0
MG D:MG802 3.7 36.3 1.0
O D:HOH912 3.7 40.2 1.0
OD1 D:ASP564 3.8 37.7 1.0
CG D:HIS563 4.0 35.9 1.0
CD2 D:HIS525 4.1 40.7 1.0
O D:HOH927 4.1 36.6 1.0
ND1 D:HIS563 4.2 37.3 1.0
ND1 D:HIS529 4.2 41.9 1.0
CG D:HIS529 4.3 43.1 1.0
CB D:ASP564 4.3 33.0 1.0
CB D:ASP674 4.5 35.1 1.0
O D:HOH932 4.5 28.8 1.0
NE2 D:HIS525 4.6 42.5 1.0
O D:ASP674 4.7 35.8 1.0
CG2 D:VAL533 4.8 37.6 1.0
CA D:ASP674 4.9 36.5 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 06:02:37 2024

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