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Zinc in PDB 5sh8: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(5-Methyl-2-Phenylpyrazol-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- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide, PDB code: 5sh8 was solved by C.Joseph, J.Benz, A.Flohr, E.Vieira, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.54 / 2.00
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.51, 135.51, 235.29, 90, 90, 120
R / Rfree (%) 16 / 18.6

Other elements in 5sh8:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide also contains other interesting chemical elements:

Praseodymium (Pr) 3 atoms
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- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide (pdb code 5sh8). 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- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide, PDB code: 5sh8:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sh8

Go back to Zinc Binding Sites List in 5sh8
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(5-Methyl-2-Phenylpyrazol-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- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn802

b:30.2
occ:1.00
 O A:HOH958 2.0 35.6 1.0
OD2 A:ASP564 2.0 26.7 1.0
NE2 A:HIS563 2.1 22.5 1.0
NE2 A:HIS529 2.1 27.5 1.0
OD1 A:ASP674 2.2 30.2 1.0
O A:HOH986 2.4 29.0 1.0
CG A:ASP564 3.0 24.6 1.0
CD2 A:HIS563 3.0 23.7 1.0
CG A:ASP674 3.1 29.6 1.0
CD2 A:HIS529 3.1 24.0 1.0
CE1 A:HIS563 3.1 25.3 1.0
CE1 A:HIS529 3.2 22.6 1.0
OD2 A:ASP674 3.3 31.4 1.0
OD1 A:ASP564 3.5 24.8 1.0
MG A:MG803 3.9 24.0 1.0
O A:HOH1013 4.1 27.1 1.0
O A:HOH1008 4.1 26.7 1.0
CG A:HIS563 4.2 24.6 1.0
CD2 A:HIS525 4.2 27.8 1.0
ND1 A:HIS563 4.2 27.6 1.0
CB A:ASP564 4.2 24.3 1.0
CG A:HIS529 4.2 24.1 1.0
ND1 A:HIS529 4.3 23.2 1.0
CB A:ASP674 4.4 27.0 1.0
O A:HOH944 4.6 22.4 1.0
NE2 A:HIS525 4.7 29.2 1.0
CG2 A:VAL533 4.8 25.7 1.0
CA A:ASP674 4.8 26.2 1.0
O A:ASP674 4.8 31.9 1.0
O A:HOH959 5.0 27.0 1.0

Zinc binding site 2 out of 4 in 5sh8

Go back to Zinc Binding Sites List in 5sh8
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(5-Methyl-2-Phenylpyrazol-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- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn802

b:28.2
occ:1.00
 O B:HOH1006 1.9 44.7 1.0
O B:HOH965 2.2 19.4 1.0
OD1 B:ASP674 2.2 27.2 1.0
OD2 B:ASP564 2.2 23.7 1.0
NE2 B:HIS529 2.2 16.4 1.0
NE2 B:HIS563 2.3 22.6 1.0
CD2 B:HIS563 3.1 16.4 1.0
CG B:ASP674 3.1 27.0 1.0
CG B:ASP564 3.1 22.7 1.0
CD2 B:HIS529 3.2 22.1 1.0
CE1 B:HIS529 3.3 24.2 1.0
OD2 B:ASP674 3.3 25.6 1.0
CE1 B:HIS563 3.4 21.3 1.0
OD1 B:ASP564 3.4 23.4 1.0
MG B:MG803 3.8 24.6 1.0
O B:HOH1016 4.0 21.1 1.0
CD2 B:HIS525 4.1 26.1 1.0
CG B:HIS563 4.3 20.7 1.0
O B:HOH987 4.3 26.9 1.0
CG B:HIS529 4.4 20.2 1.0
ND1 B:HIS529 4.4 16.1 1.0
CB B:ASP674 4.4 26.1 1.0
NE2 B:HIS525 4.4 29.1 1.0
CB B:ASP564 4.4 24.4 1.0
O B:HOH1025 4.4 38.7 1.0
ND1 B:HIS563 4.4 20.6 1.0
O B:HOH952 4.5 26.2 1.0
O B:ASP674 4.8 26.1 1.0
CG2 B:VAL533 4.8 23.5 1.0
CA B:ASP674 4.8 27.1 1.0

Zinc binding site 3 out of 4 in 5sh8

Go back to Zinc Binding Sites List in 5sh8
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(5-Methyl-2-Phenylpyrazol-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- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn802

b:31.8
occ:1.00
 O C:HOH952 2.1 31.9 1.0
OD1 C:ASP674 2.1 26.4 1.0
NE2 C:HIS529 2.1 19.0 1.0
NE2 C:HIS563 2.1 25.3 1.0
OD2 C:ASP564 2.3 21.4 1.0
O C:HOH979 2.4 41.1 1.0
CG C:ASP674 3.0 28.7 1.0
CD2 C:HIS563 3.0 26.7 1.0
CD2 C:HIS529 3.0 25.5 1.0
OD2 C:ASP674 3.1 29.4 1.0
CG C:ASP564 3.2 23.5 1.0
CE1 C:HIS563 3.2 21.5 1.0
CE1 C:HIS529 3.2 24.6 1.0
OD1 C:ASP564 3.6 22.3 1.0
MG C:MG803 3.8 21.7 1.0
CD2 C:HIS525 3.9 27.2 1.0
O C:HOH1008 4.0 20.7 1.0
CG C:HIS563 4.2 27.1 1.0
O C:HOH976 4.2 27.6 1.0
CG C:HIS529 4.2 23.3 1.0
ND1 C:HIS563 4.2 23.5 1.0
ND1 C:HIS529 4.3 24.1 1.0
CB C:ASP564 4.3 27.6 1.0
NE2 C:HIS525 4.4 32.2 1.0
CB C:ASP674 4.4 26.2 1.0
O C:HOH1025 4.4 42.8 1.0
O C:HOH908 4.6 26.1 1.0
CG2 C:VAL533 4.7 21.7 1.0
CA C:ASP674 4.8 26.7 1.0
O C:ASP674 4.9 26.1 1.0

Zinc binding site 4 out of 4 in 5sh8

Go back to Zinc Binding Sites List in 5sh8
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(5-Methyl-2-Phenylpyrazol-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- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn802

b:33.2
occ:1.00
 O D:HOH971 1.9 20.9 1.0
OD2 D:ASP564 2.1 34.0 1.0
O D:HOH946 2.1 31.4 1.0
NE2 D:HIS529 2.1 30.2 1.0
NE2 D:HIS563 2.2 27.4 1.0
OD1 D:ASP674 2.3 34.9 1.0
CD2 D:HIS529 3.0 32.3 1.0
CD2 D:HIS563 3.0 32.3 1.0
CG D:ASP564 3.0 29.2 1.0
CG D:ASP674 3.2 33.1 1.0
CE1 D:HIS563 3.3 29.9 1.0
CE1 D:HIS529 3.3 33.0 1.0
OD2 D:ASP674 3.4 30.3 1.0
OD1 D:ASP564 3.6 25.4 1.0
O D:HOH1003 3.7 22.6 1.0
MG D:MG803 3.8 26.6 1.0
CB D:ASP564 4.2 28.9 1.0
CG D:HIS529 4.2 28.0 1.0
CG D:HIS563 4.2 29.4 1.0
O D:HOH988 4.2 27.8 1.0
CD2 D:HIS525 4.3 42.5 1.0
ND1 D:HIS563 4.3 26.6 1.0
ND1 D:HIS529 4.3 32.8 1.0
CB D:ASP674 4.5 32.0 1.0
O D:HOH918 4.6 34.4 1.0
CG2 D:VAL533 4.7 30.5 1.0
NE2 D:HIS525 4.8 36.2 1.0
O D:ASP674 4.8 31.5 1.0
CA D:ASP674 4.9 28.9 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: Thu Aug 21 07:59:05 2025

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