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Zinc in PDB 5si2: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-(1-Pyridin-2-Ylpyrrolidin-3-Yl)-3-(Pyrimidin-5- Ylamino)Pyridine-2-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-(1-Pyridin-2-Ylpyrrolidin-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-(1-Pyridin-2-Ylpyrrolidin-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-(1-Pyridin-2-Ylpyrrolidin-3-Yl)-3-(Pyrimidin-5- Ylamino)Pyridine-2-Carboxamide, PDB code: 5si2 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) 41.26 / 2.40
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.679, 134.679, 234.138, 90, 90, 120
R / Rfree (%) 21 / 27.9

Other elements in 5si2:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-(1-Pyridin-2-Ylpyrrolidin-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-(1-Pyridin-2-Ylpyrrolidin-3-Yl)-3-(Pyrimidin-5- Ylamino)Pyridine-2-Carboxamide (pdb code 5si2). 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-(1-Pyridin-2-Ylpyrrolidin-3-Yl)-3-(Pyrimidin-5- Ylamino)Pyridine-2-Carboxamide, PDB code: 5si2:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5si2

Go back to Zinc Binding Sites List in 5si2
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-(1-Pyridin-2-Ylpyrrolidin-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-(1-Pyridin-2-Ylpyrrolidin-3-Yl)-3-(Pyrimidin-5- Ylamino)Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:41.0
occ:1.00
 OD2 A:ASP564 1.9 38.9 1.0
NE2 A:HIS563 2.1 28.0 1.0
OD1 A:ASP674 2.2 42.5 1.0
NE2 A:HIS529 2.2 32.4 1.0
O A:HOH933 2.4 28.7 1.0
O A:HOH956 2.5 39.7 1.0
CG A:ASP674 3.0 42.3 1.0
CG A:ASP564 3.0 32.2 1.0
CD2 A:HIS563 3.0 31.3 1.0
CE1 A:HIS529 3.1 33.3 1.0
CE1 A:HIS563 3.1 31.7 1.0
CD2 A:HIS529 3.2 32.7 1.0
OD2 A:ASP674 3.2 44.1 1.0
OD1 A:ASP564 3.5 29.9 1.0
MG A:MG802 3.9 38.3 1.0
O A:HOH920 3.9 27.4 1.0
CG A:HIS563 4.2 32.3 1.0
ND1 A:HIS563 4.2 30.2 1.0
CD2 A:HIS525 4.2 44.3 1.0
ND1 A:HIS529 4.2 35.3 1.0
CB A:ASP564 4.3 28.6 1.0
CG A:HIS529 4.3 30.5 1.0
O A:HOH910 4.4 31.0 1.0
CB A:ASP674 4.4 35.8 1.0
NE2 A:HIS525 4.7 42.9 1.0
CG2 A:VAL533 4.8 37.0 1.0
O A:ASP674 4.8 36.8 1.0
CA A:ASP674 4.9 35.7 1.0
O A:HOH927 4.9 32.6 1.0

Zinc binding site 2 out of 4 in 5si2

Go back to Zinc Binding Sites List in 5si2
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-(1-Pyridin-2-Ylpyrrolidin-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-(1-Pyridin-2-Ylpyrrolidin-3-Yl)-3-(Pyrimidin-5- Ylamino)Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:43.0
occ:1.00
 O B:HOH925 1.9 34.8 1.0
NE2 B:HIS529 2.1 30.8 1.0
NE2 B:HIS563 2.2 31.8 1.0
OD2 B:ASP564 2.2 30.8 1.0
OD1 B:ASP674 2.3 36.5 1.0
CD2 B:HIS563 3.1 29.6 1.0
CG B:ASP674 3.1 35.6 1.0
CG B:ASP564 3.1 31.7 1.0
CD2 B:HIS529 3.1 31.9 1.0
CE1 B:HIS529 3.1 32.4 1.0
CE1 B:HIS563 3.2 31.9 1.0
OD2 B:ASP674 3.3 40.3 1.0
OD1 B:ASP564 3.6 34.0 1.0
MG B:MG802 3.6 30.2 1.0
CD2 B:HIS525 4.0 37.1 1.0
O B:HOH947 4.1 27.6 1.0
CG B:HIS563 4.2 30.1 1.0
NE2 B:HIS525 4.2 39.5 1.0
ND1 B:HIS529 4.2 34.7 1.0
CG B:HIS529 4.3 36.4 1.0
ND1 B:HIS563 4.3 27.1 1.0
CB B:ASP564 4.3 30.6 1.0
O B:HOH941 4.4 41.3 1.0
CB B:ASP674 4.5 33.3 1.0
CG2 B:VAL533 4.7 36.5 1.0
O B:ASP674 4.7 33.3 1.0
CA B:ASP674 4.9 31.7 1.0
O B:HOH931 4.9 34.2 1.0

Zinc binding site 3 out of 4 in 5si2

Go back to Zinc Binding Sites List in 5si2
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-(1-Pyridin-2-Ylpyrrolidin-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-(1-Pyridin-2-Ylpyrrolidin-3-Yl)-3-(Pyrimidin-5- Ylamino)Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:39.7
occ:1.00
 NE2 C:HIS563 2.0 34.4 1.0
OD2 C:ASP564 2.1 44.0 1.0
NE2 C:HIS529 2.1 35.1 1.0
O C:HOH905 2.2 20.1 1.0
OD1 C:ASP674 2.2 36.2 1.0
O C:HOH950 2.4 30.9 1.0
CD2 C:HIS563 3.0 32.3 1.0
CD2 C:HIS529 3.0 33.0 1.0
CG C:ASP674 3.0 34.3 1.0
CE1 C:HIS563 3.1 36.5 1.0
CG C:ASP564 3.1 37.6 1.0
CE1 C:HIS529 3.1 35.4 1.0
OD2 C:ASP674 3.2 36.5 1.0
OD1 C:ASP564 3.6 43.9 1.0
MG C:MG802 3.7 32.4 1.0
O C:HOH976 3.9 45.4 1.0
CD2 C:HIS525 4.1 47.5 1.0
CG C:HIS563 4.2 31.2 1.0
ND1 C:HIS563 4.2 30.8 1.0
CG C:HIS529 4.2 30.8 1.0
ND1 C:HIS529 4.2 31.6 1.0
CB C:ASP564 4.3 34.1 1.0
CB C:ASP674 4.4 35.6 1.0
O C:HOH921 4.5 39.0 1.0
NE2 C:HIS525 4.6 48.9 1.0
CA C:ASP674 4.8 37.5 1.0
O C:ASP674 4.8 49.2 1.0
O C:HOH943 4.8 24.9 1.0
CG2 C:VAL533 4.9 31.1 1.0

Zinc binding site 4 out of 4 in 5si2

Go back to Zinc Binding Sites List in 5si2
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-(1-Pyridin-2-Ylpyrrolidin-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-(1-Pyridin-2-Ylpyrrolidin-3-Yl)-3-(Pyrimidin-5- Ylamino)Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:56.8
occ:1.00
 OD2 D:ASP564 2.0 65.5 1.0
NE2 D:HIS563 2.0 45.8 1.0
O D:HOH918 2.2 36.1 1.0
OD1 D:ASP674 2.3 60.1 1.0
NE2 D:HIS529 2.3 46.1 1.0
O D:HOH926 2.5 38.5 1.0
CD2 D:HIS563 2.9 47.7 1.0
CG D:ASP564 3.0 56.7 1.0
CE1 D:HIS563 3.1 47.0 1.0
CE1 D:HIS529 3.2 47.5 1.0
CG D:ASP674 3.2 59.7 1.0
CD2 D:HIS529 3.3 51.6 1.0
OD2 D:ASP674 3.5 62.3 1.0
OD1 D:ASP564 3.6 56.0 1.0
MG D:MG802 3.9 62.0 1.0
CG D:HIS563 4.0 50.0 1.0
ND1 D:HIS563 4.1 44.9 1.0
O D:HOH920 4.2 46.4 1.0
CB D:ASP564 4.2 51.8 1.0
CD2 D:HIS525 4.3 58.5 1.0
ND1 D:HIS529 4.3 47.6 1.0
CG D:HIS529 4.4 47.4 1.0
CB D:ASP674 4.6 57.9 1.0
O D:HOH905 4.7 45.2 1.0
NE2 D:HIS525 4.7 59.0 1.0
CG2 D:VAL533 4.8 64.3 1.0
O D:ASP674 4.8 62.5 1.0
CA D:ASP674 4.9 57.0 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 05:39:26 2024

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