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Zinc in PDB 5skr: Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Methyl-N-(2-Methyl-5-Pyridin-2-Ylpyrazol-3-Yl)-4-Pyridin-4- Ylpyrazole-3-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Methyl-N-(2-Methyl-5-Pyridin-2-Ylpyrazol-3-Yl)-4-Pyridin-4- Ylpyrazole-3-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Methyl-N-(2-Methyl-5-Pyridin-2-Ylpyrazol-3-Yl)-4-Pyridin-4- Ylpyrazole-3-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Methyl-N-(2-Methyl-5-Pyridin-2-Ylpyrazol-3-Yl)-4-Pyridin-4- Ylpyrazole-3-Carboxamide, PDB code: 5skr was solved by C.Joseph, J.Benz, A.Flohr, M.Koerner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.59 / 1.99
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.501, 135.501, 235.242, 90, 90, 120
R / Rfree (%) 17.9 / 21.9

Other elements in 5skr:

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

Zinc binding site 1 out of 4 in 5skr

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

b:30.8
occ:1.00
 NE2 A:HIS563 2.1 28.4 1.0
NE2 A:HIS529 2.1 26.3 1.0
OD2 A:ASP564 2.2 28.1 1.0
OD1 A:ASP674 2.2 29.9 1.0
O A:HOH1010 2.2 35.7 1.0
O A:HOH931 2.2 24.3 1.0
CD2 A:HIS563 3.0 24.6 1.0
CG A:ASP674 3.0 33.5 1.0
CG A:ASP564 3.1 27.9 1.0
CD2 A:HIS529 3.1 28.7 1.0
CE1 A:HIS529 3.2 26.1 1.0
CE1 A:HIS563 3.2 29.1 1.0
OD2 A:ASP674 3.2 36.5 1.0
OD1 A:ASP564 3.6 26.6 1.0
MG A:MG802 3.8 25.8 1.0
O A:HOH1019 4.0 25.5 1.0
O A:HOH949 4.1 36.1 1.0
CG A:HIS563 4.2 24.5 1.0
CD2 A:HIS525 4.2 32.0 1.0
ND1 A:HIS563 4.2 24.7 1.0
CG A:HIS529 4.3 27.2 1.0
ND1 A:HIS529 4.3 24.3 1.0
CB A:ASP564 4.3 28.3 1.0
CB A:ASP674 4.4 26.9 1.0
NE2 A:HIS525 4.4 30.4 1.0
O A:HOH922 4.6 22.7 1.0
CG2 A:VAL533 4.7 25.0 1.0
O A:ASP674 4.8 24.1 1.0
CA A:ASP674 4.9 23.1 1.0

Zinc binding site 2 out of 4 in 5skr

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

b:29.4
occ:1.00
 O B:HOH930 2.1 19.8 1.0
OD1 B:ASP674 2.1 24.5 1.0
NE2 B:HIS529 2.1 18.9 1.0
OD2 B:ASP564 2.2 24.1 1.0
NE2 B:HIS563 2.2 20.4 1.0
O B:HOH985 2.2 35.3 1.0
CD2 B:HIS563 3.0 22.5 1.0
CG B:ASP674 3.0 27.1 1.0
CD2 B:HIS529 3.0 22.3 1.0
CG B:ASP564 3.2 22.9 1.0
CE1 B:HIS529 3.2 24.6 1.0
CE1 B:HIS563 3.3 23.7 1.0
OD2 B:ASP674 3.3 28.7 1.0
OD1 B:ASP564 3.6 25.6 1.0
MG B:MG802 3.7 25.6 1.0
O B:HOH1011 4.1 26.9 1.0
CD2 B:HIS525 4.1 27.9 1.0
O B:HOH990 4.2 37.3 1.0
CG B:HIS563 4.2 23.6 1.0
CG B:HIS529 4.2 22.6 1.0
ND1 B:HIS529 4.3 20.1 1.0
ND1 B:HIS563 4.3 23.4 1.0
CB B:ASP564 4.4 25.9 1.0
NE2 B:HIS525 4.4 27.2 1.0
CB B:ASP674 4.4 25.4 1.0
O B:HOH937 4.6 24.3 1.0
O B:HOH1046 4.6 49.5 1.0
CG2 B:VAL533 4.7 20.4 1.0
CA B:ASP674 4.8 23.4 1.0
O B:ASP674 4.8 24.0 1.0

Zinc binding site 3 out of 4 in 5skr

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

b:32.6
occ:1.00
 O C:HOH938 2.0 24.5 1.0
NE2 C:HIS563 2.1 26.0 1.0
OD1 C:ASP674 2.2 27.7 1.0
OD2 C:ASP564 2.2 28.5 1.0
NE2 C:HIS529 2.2 25.1 1.0
O C:HOH1021 2.3 38.0 1.0
CD2 C:HIS563 3.0 24.6 1.0
CG C:ASP674 3.0 30.7 1.0
CD2 C:HIS529 3.1 27.7 1.0
CG C:ASP564 3.1 28.6 1.0
CE1 C:HIS563 3.2 26.5 1.0
CE1 C:HIS529 3.2 30.2 1.0
OD2 C:ASP674 3.3 34.5 1.0
OD1 C:ASP564 3.6 25.8 1.0
MG C:MG802 3.8 25.9 1.0
O C:HOH1025 4.1 23.5 1.0
CD2 C:HIS525 4.1 36.6 1.0
CG C:HIS563 4.1 26.3 1.0
ND1 C:HIS563 4.2 26.1 1.0
CG C:HIS529 4.3 27.1 1.0
CB C:ASP564 4.3 25.3 1.0
ND1 C:HIS529 4.3 26.1 1.0
O C:HOH1020 4.4 41.9 1.0
CB C:ASP674 4.4 32.1 1.0
O C:HOH933 4.5 29.4 1.0
NE2 C:HIS525 4.5 34.8 1.0
CG2 C:VAL533 4.8 24.1 1.0
CA C:ASP674 4.8 29.8 1.0
O C:ASP674 4.8 28.2 1.0

Zinc binding site 4 out of 4 in 5skr

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

b:35.4
occ:1.00
 O D:HOH921 2.0 27.8 1.0
NE2 D:HIS563 2.1 28.1 1.0
NE2 D:HIS529 2.1 36.4 1.0
OD1 D:ASP674 2.2 35.2 1.0
O D:HOH968 2.2 35.8 1.0
OD2 D:ASP564 2.2 28.8 1.0
CD2 D:HIS563 2.9 32.3 1.0
CD2 D:HIS529 3.1 36.3 1.0
CG D:ASP674 3.1 35.4 1.0
CG D:ASP564 3.1 30.2 1.0
CE1 D:HIS563 3.2 33.3 1.0
CE1 D:HIS529 3.2 34.7 1.0
OD2 D:ASP674 3.3 33.4 1.0
OD1 D:ASP564 3.7 29.9 1.0
MG D:MG802 3.8 31.7 1.0
CD2 D:HIS525 4.1 40.2 1.0
CG D:HIS563 4.1 28.5 1.0
O D:HOH992 4.2 31.1 1.0
ND1 D:HIS563 4.2 30.9 1.0
O D:HOH946 4.2 42.0 1.0
CG D:HIS529 4.2 33.9 1.0
CB D:ASP564 4.3 30.3 1.0
ND1 D:HIS529 4.3 33.5 1.0
NE2 D:HIS525 4.4 37.4 1.0
CB D:ASP674 4.4 32.8 1.0
CG2 D:VAL533 4.7 35.8 1.0
O D:HOH922 4.7 26.4 1.0
O D:ASP674 4.7 31.1 1.0
CA D:ASP674 4.9 31.2 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 07:38:47 2024

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