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Zinc in PDB 5skv: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[3-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]-1- Methylpyrazol-4-Yl]-3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[3-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]-1- Methylpyrazol-4-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-[3-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]-1- Methylpyrazol-4-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-[3-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]-1- Methylpyrazol-4-Yl]-3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide, PDB code: 5skv 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) 43.51 / 2.60
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.283, 135.283, 234.745, 90, 90, 120
R / Rfree (%) 19.9 / 25.5

Other elements in 5skv:

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

Zinc binding site 1 out of 4 in 5skv

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

b:42.4
occ:1.00
 OD2 A:ASP564 1.8 36.8 1.0
NE2 A:HIS563 2.0 35.3 1.0
O A:HOH973 2.0 40.8 1.0
OD1 A:ASP674 2.3 35.2 1.0
NE2 A:HIS529 2.3 30.7 1.0
CD2 A:HIS563 2.8 36.9 1.0
CG A:ASP564 2.9 38.1 1.0
CE1 A:HIS563 3.1 35.9 1.0
CD2 A:HIS529 3.2 31.9 1.0
CG A:ASP674 3.2 37.2 1.0
CE1 A:HIS529 3.4 33.9 1.0
OD1 A:ASP564 3.5 34.4 1.0
OD2 A:ASP674 3.5 37.8 1.0
O A:HOH947 3.8 36.1 1.0
MG A:MG802 3.9 40.7 1.0
CG A:HIS563 4.0 36.2 1.0
CD2 A:HIS525 4.1 32.9 1.0
ND1 A:HIS563 4.1 35.5 1.0
CB A:ASP564 4.1 33.6 1.0
NE2 A:HIS525 4.3 37.0 1.0
CG A:HIS529 4.4 31.1 1.0
CB A:ASP674 4.4 38.0 1.0
ND1 A:HIS529 4.5 31.4 1.0
O A:HOH941 4.6 28.9 1.0
O A:HOH944 4.7 25.3 1.0
CG2 A:VAL533 4.8 31.3 1.0
CA A:ASP674 4.9 35.6 1.0
O A:HOH938 5.0 29.7 1.0

Zinc binding site 2 out of 4 in 5skv

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

b:35.0
occ:1.00
 NE2 B:HIS563 2.0 31.7 1.0
OD2 B:ASP564 2.1 31.9 1.0
NE2 B:HIS529 2.1 27.9 1.0
O B:HOH980 2.2 29.9 1.0
OD1 B:ASP674 2.2 32.9 1.0
CD2 B:HIS563 3.0 31.6 1.0
CD2 B:HIS529 3.0 29.2 1.0
CE1 B:HIS563 3.1 34.3 1.0
CE1 B:HIS529 3.2 28.3 1.0
CG B:ASP564 3.2 32.8 1.0
CG B:ASP674 3.2 33.3 1.0
OD2 B:ASP674 3.6 35.1 1.0
OD1 B:ASP564 3.8 33.3 1.0
MG B:MG802 3.8 29.8 1.0
CD2 B:HIS525 4.1 29.0 1.0
CG B:HIS563 4.1 30.8 1.0
ND1 B:HIS563 4.1 31.3 1.0
O B:HOH960 4.2 27.9 1.0
CG B:HIS529 4.2 29.9 1.0
ND1 B:HIS529 4.2 30.0 1.0
O B:HOH916 4.3 35.0 1.0
CB B:ASP564 4.3 31.6 1.0
NE2 B:HIS525 4.4 29.5 1.0
CB B:ASP674 4.5 33.4 1.0
O B:HOH1000 4.6 35.9 1.0
O B:HOH965 4.8 25.4 1.0
O B:ASP674 4.8 32.6 1.0
CG2 B:VAL533 4.9 28.0 1.0
CA B:ASP674 4.9 32.4 1.0

Zinc binding site 3 out of 4 in 5skv

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

b:38.4
occ:1.00
 OD2 C:ASP564 2.0 28.5 1.0
NE2 C:HIS563 2.1 31.9 1.0
OD1 C:ASP674 2.1 33.6 1.0
NE2 C:HIS529 2.3 33.3 1.0
O C:HOH935 2.3 29.3 1.0
CD2 C:HIS563 3.0 34.0 1.0
CG C:ASP674 3.0 32.0 1.0
CG C:ASP564 3.1 27.8 1.0
CE1 C:HIS563 3.1 32.2 1.0
CD2 C:HIS529 3.1 33.3 1.0
OD2 C:ASP674 3.3 32.4 1.0
CE1 C:HIS529 3.3 36.5 1.0
OD1 C:ASP564 3.6 28.4 1.0
MG C:MG802 3.7 34.0 1.0
CD2 C:HIS525 4.0 36.4 1.0
O C:HOH954 4.1 28.9 1.0
CG C:HIS563 4.2 32.0 1.0
ND1 C:HIS563 4.2 30.0 1.0
O C:HOH1005 4.2 51.4 1.0
CB C:ASP564 4.3 28.6 1.0
CG C:HIS529 4.3 33.0 1.0
NE2 C:HIS525 4.4 34.9 1.0
ND1 C:HIS529 4.4 35.5 1.0
CB C:ASP674 4.4 34.7 1.0
O C:HOH906 4.5 40.9 1.0
O C:ASP674 4.7 37.1 1.0
CA C:ASP674 4.8 36.0 1.0
CG2 C:VAL533 4.9 29.4 1.0

Zinc binding site 4 out of 4 in 5skv

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

b:43.0
occ:1.00
 O D:HOH919 1.7 30.4 1.0
OD1 D:ASP674 2.1 38.7 1.0
NE2 D:HIS563 2.1 36.3 1.0
OD2 D:ASP564 2.2 39.4 1.0
NE2 D:HIS529 2.4 40.9 1.0
CD2 D:HIS563 2.9 37.4 1.0
CG D:ASP674 3.0 38.4 1.0
CG D:ASP564 3.2 38.9 1.0
CD2 D:HIS529 3.3 42.6 1.0
CE1 D:HIS563 3.3 38.0 1.0
OD2 D:ASP674 3.3 40.7 1.0
CE1 D:HIS529 3.4 44.0 1.0
O D:HOH904 3.8 39.0 1.0
MG D:MG802 3.8 50.6 1.0
OD1 D:ASP564 3.9 38.4 1.0
O D:HOH948 4.0 29.9 1.0
CG D:HIS563 4.1 38.3 1.0
CB D:ASP564 4.2 39.1 1.0
ND1 D:HIS563 4.3 36.8 1.0
CB D:ASP674 4.4 38.2 1.0
CD2 D:HIS525 4.4 42.2 1.0
O D:HOH924 4.4 37.6 1.0
CG D:HIS529 4.5 41.5 1.0
ND1 D:HIS529 4.5 42.6 1.0
O D:ASP674 4.7 32.8 1.0
NE2 D:HIS525 4.7 38.5 1.0
CG2 D:VAL533 4.8 38.8 1.0
CA D:ASP674 4.8 37.2 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 07:42:27 2024

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