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Zinc in PDB 5shd: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-(Methylcarbamoyl)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-(Methylcarbamoyl)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-(Methylcarbamoyl)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-(Methylcarbamoyl)Pyridin-3-Yl]-3-(Pyrimidin-5- Ylamino)Pyridine-2-Carboxamide, PDB code: 5shd 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) 43.58 / 2.60
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.486, 135.486, 234.991, 90, 90, 120
R / Rfree (%) 17.9 / 26.6

Other elements in 5shd:

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

Zinc binding site 1 out of 4 in 5shd

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

b:47.1
occ:1.00
 NE2 A:HIS563 2.0 31.4 1.0
OD2 A:ASP564 2.0 44.5 1.0
NE2 A:HIS529 2.1 34.6 1.0
OD1 A:ASP674 2.1 52.8 1.0
O A:HOH927 2.2 33.9 1.0
CE1 A:HIS563 2.9 33.4 1.0
CD2 A:HIS563 3.0 33.9 1.0
CG A:ASP674 3.1 42.7 1.0
CD2 A:HIS529 3.1 37.3 1.0
CG A:ASP564 3.1 38.4 1.0
CE1 A:HIS529 3.1 40.0 1.0
OD2 A:ASP674 3.3 50.2 1.0
OD1 A:ASP564 3.7 33.8 1.0
MG A:MG802 3.7 32.5 1.0
O A:HOH925 4.0 46.2 1.0
ND1 A:HIS563 4.0 30.3 1.0
CG A:HIS563 4.1 34.2 1.0
CD2 A:HIS525 4.1 41.2 1.0
CB A:ASP564 4.2 34.9 1.0
CG A:HIS529 4.2 36.4 1.0
ND1 A:HIS529 4.2 39.1 1.0
O A:HOH954 4.3 37.9 1.0
NE2 A:HIS525 4.4 45.5 1.0
CB A:ASP674 4.4 41.0 1.0
O A:ASP674 4.6 45.3 1.0
O A:HOH912 4.6 22.5 1.0
CG2 A:VAL533 4.8 36.9 1.0
CA A:ASP674 4.8 37.8 1.0

Zinc binding site 2 out of 4 in 5shd

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

b:41.3
occ:1.00
 NE2 B:HIS563 2.1 41.4 1.0
NE2 B:HIS529 2.1 35.7 1.0
OD2 B:ASP564 2.2 36.7 1.0
O B:HOH909 2.2 30.4 1.0
OD1 B:ASP674 2.3 42.0 1.0
CD2 B:HIS563 2.9 35.7 1.0
CG B:ASP674 3.1 45.4 1.0
CD2 B:HIS529 3.1 37.5 1.0
CE1 B:HIS529 3.1 34.2 1.0
CG B:ASP564 3.2 36.0 1.0
CE1 B:HIS563 3.2 37.3 1.0
OD2 B:ASP674 3.2 45.6 1.0
OD1 B:ASP564 3.7 30.9 1.0
MG B:MG802 3.9 36.0 1.0
CG B:HIS563 4.1 35.1 1.0
O B:HOH957 4.1 26.4 1.0
ND1 B:HIS563 4.2 36.5 1.0
O B:HOH946 4.2 38.3 1.0
ND1 B:HIS529 4.2 36.3 1.0
CG B:HIS529 4.2 38.0 1.0
CB B:ASP564 4.3 34.1 1.0
CD2 B:HIS525 4.4 42.3 1.0
CB B:ASP674 4.4 41.7 1.0
O B:HOH910 4.6 36.4 1.0
NE2 B:HIS525 4.6 39.7 1.0
CA B:ASP674 4.8 42.5 1.0
CG2 B:VAL533 4.8 30.1 1.0
O B:ASP674 4.9 46.5 1.0

Zinc binding site 3 out of 4 in 5shd

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

b:44.3
occ:1.00
 O C:HOH932 2.0 26.5 1.0
NE2 C:HIS529 2.1 33.5 1.0
OD1 C:ASP674 2.1 37.9 1.0
OD2 C:ASP564 2.1 36.7 1.0
NE2 C:HIS563 2.2 37.5 1.0
CG C:ASP674 2.9 35.6 1.0
CE1 C:HIS529 3.0 35.0 1.0
O C:HOH959 3.0 49.2 1.0
CD2 C:HIS563 3.1 38.6 1.0
OD2 C:ASP674 3.1 40.0 1.0
CD2 C:HIS529 3.1 34.5 1.0
CG C:ASP564 3.2 34.9 1.0
CE1 C:HIS563 3.3 40.1 1.0
MG C:MG802 3.7 35.2 1.0
OD1 C:ASP564 3.7 40.6 1.0
CD2 C:HIS525 4.0 46.9 1.0
ND1 C:HIS529 4.1 32.4 1.0
CG C:HIS529 4.2 35.4 1.0
CG C:HIS563 4.3 37.0 1.0
O C:HOH933 4.3 23.6 1.0
NE2 C:HIS525 4.3 48.2 1.0
CB C:ASP674 4.3 37.0 1.0
ND1 C:HIS563 4.4 33.8 1.0
O C:HOH914 4.4 31.2 1.0
CB C:ASP564 4.4 35.0 1.0
O C:HOH955 4.4 32.6 1.0
CA C:ASP674 4.8 38.7 1.0
O C:ASP674 4.8 39.4 1.0
O C:HOH925 4.8 18.5 1.0
CG2 C:VAL533 5.0 30.8 1.0

Zinc binding site 4 out of 4 in 5shd

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

b:71.3
occ:1.00
 NE2 D:HIS563 2.0 52.0 1.0
OD1 D:ASP674 2.2 77.5 1.0
OD2 D:ASP564 2.2 81.3 1.0
O D:HOH919 2.3 38.0 1.0
NE2 D:HIS529 2.3 69.5 1.0
O D:HOH912 2.8 49.8 1.0
CE1 D:HIS563 3.0 52.9 1.0
CD2 D:HIS563 3.0 53.8 1.0
CG D:ASP674 3.2 68.3 1.0
CG D:ASP564 3.2 59.5 1.0
CE1 D:HIS529 3.2 67.1 1.0
CD2 D:HIS529 3.4 64.2 1.0
OD2 D:ASP674 3.7 66.6 1.0
OD1 D:ASP564 3.9 61.3 1.0
ND1 D:HIS563 4.1 52.9 1.0
CG D:HIS563 4.1 52.0 1.0
CD2 D:HIS525 4.1 64.1 1.0
O D:HOH921 4.1 44.5 1.0
CB D:ASP564 4.2 60.6 1.0
MG D:MG802 4.2 65.7 1.0
CB D:ASP674 4.3 72.3 1.0
O D:HOH907 4.4 57.0 1.0
ND1 D:HIS529 4.4 64.5 1.0
CG D:HIS529 4.5 64.3 1.0
O D:ASP674 4.6 77.2 1.0
NE2 D:HIS525 4.6 60.8 1.0
CA D:ASP674 4.8 64.2 1.0
CG2 D:VAL533 4.8 61.3 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 05:27:06 2024

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