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Zinc in PDB 5sk0: Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-1-Methyl-4-Pyridin-4- Ylpyrazole-3-Carboxamide

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

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-1-Methyl-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 N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-1-Methyl-4-Pyridin-4- Ylpyrazole-3-Carboxamide, PDB code: 5sk0 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) 43.91 / 2.02
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 136.679, 136.679, 236.402, 90, 90, 120
R / Rfree (%) 16.2 / 18.7

Other elements in 5sk0:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-1-Methyl-4-Pyridin-4- Ylpyrazole-3-Carboxamide also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-1-Methyl-4-Pyridin-4- Ylpyrazole-3-Carboxamide (pdb code 5sk0). 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 N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-1-Methyl-4-Pyridin-4- Ylpyrazole-3-Carboxamide, PDB code: 5sk0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sk0

Go back to Zinc Binding Sites List in 5sk0
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-1-Methyl-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 N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-1-Methyl-4-Pyridin-4- Ylpyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:31.7
occ:1.00
 O A:HOH927 1.9 35.4 1.0
NE2 A:HIS563 2.1 29.9 1.0
OD2 A:ASP564 2.2 33.6 1.0
O A:HOH987 2.2 30.4 1.0
OD1 A:ASP674 2.2 33.1 1.0
NE2 A:HIS529 2.2 29.0 1.0
CD2 A:HIS563 3.0 27.1 1.0
CD2 A:HIS529 3.1 33.8 1.0
CE1 A:HIS563 3.1 32.4 1.0
CG A:ASP674 3.1 31.9 1.0
CG A:ASP564 3.2 28.8 1.0
CE1 A:HIS529 3.2 33.1 1.0
OD2 A:ASP674 3.5 35.3 1.0
OD1 A:ASP564 3.7 28.8 1.0
MG A:MG802 3.8 29.4 1.0
O A:HOH969 4.0 32.7 1.0
CG A:HIS563 4.2 24.8 1.0
O A:HOH1028 4.2 27.3 1.0
CD2 A:HIS525 4.2 35.4 1.0
ND1 A:HIS563 4.2 29.0 1.0
CG A:HIS529 4.3 31.6 1.0
ND1 A:HIS529 4.3 33.5 1.0
CB A:ASP564 4.4 34.6 1.0
CB A:ASP674 4.5 27.2 1.0
NE2 A:HIS525 4.5 33.7 1.0
O A:HOH917 4.5 31.1 1.0
CG2 A:VAL533 4.8 26.1 1.0
CA A:ASP674 4.9 25.6 1.0
O A:ASP674 4.9 27.5 1.0

Zinc binding site 2 out of 4 in 5sk0

Go back to Zinc Binding Sites List in 5sk0
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-1-Methyl-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 N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-1-Methyl-4-Pyridin-4- Ylpyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:31.8
occ:1.00
 O B:HOH949 1.9 42.2 1.0
NE2 B:HIS563 2.0 28.1 1.0
O B:HOH957 2.1 23.3 1.0
OD2 B:ASP564 2.1 24.9 1.0
OD1 B:ASP674 2.1 28.4 1.0
NE2 B:HIS529 2.2 24.6 1.0
CD2 B:HIS563 3.0 26.0 1.0
CG B:ASP674 3.0 28.7 1.0
CG B:ASP564 3.1 24.6 1.0
CD2 B:HIS529 3.1 27.9 1.0
CE1 B:HIS563 3.2 28.9 1.0
CE1 B:HIS529 3.2 25.3 1.0
OD2 B:ASP674 3.3 30.5 1.0
OD1 B:ASP564 3.6 25.0 1.0
MG B:MG802 3.7 27.6 1.0
O B:HOH1027 4.0 28.3 1.0
CD2 B:HIS525 4.1 30.0 1.0
CG B:HIS563 4.1 26.0 1.0
ND1 B:HIS563 4.2 28.4 1.0
CB B:ASP564 4.3 25.6 1.0
O B:HOH935 4.3 37.5 1.0
ND1 B:HIS529 4.3 23.9 1.0
CG B:HIS529 4.3 24.9 1.0
NE2 B:HIS525 4.3 30.9 1.0
CB B:ASP674 4.4 26.8 1.0
O B:HOH1052 4.6 40.4 1.0
O B:HOH959 4.7 26.7 1.0
CG2 B:VAL533 4.8 23.6 1.0
CA B:ASP674 4.8 28.2 1.0
O B:ASP674 5.0 30.5 1.0

Zinc binding site 3 out of 4 in 5sk0

Go back to Zinc Binding Sites List in 5sk0
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-1-Methyl-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 N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-1-Methyl-4-Pyridin-4- Ylpyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:31.1
occ:1.00
 O C:HOH947 1.8 43.8 1.0
O C:HOH936 2.0 23.9 1.0
OD1 C:ASP674 2.1 26.8 1.0
NE2 C:HIS563 2.1 27.6 1.0
OD2 C:ASP564 2.1 26.2 1.0
NE2 C:HIS529 2.2 27.1 1.0
CD2 C:HIS563 3.0 26.3 1.0
CG C:ASP674 3.0 28.7 1.0
CG C:ASP564 3.1 23.3 1.0
CD2 C:HIS529 3.1 26.7 1.0
CE1 C:HIS563 3.2 21.0 1.0
OD2 C:ASP674 3.2 40.7 1.0
CE1 C:HIS529 3.3 28.1 1.0
OD1 C:ASP564 3.6 24.2 1.0
MG C:MG802 3.8 25.4 1.0
CD2 C:HIS525 4.1 29.6 1.0
O C:HOH1003 4.1 25.7 1.0
CG C:HIS563 4.1 24.7 1.0
ND1 C:HIS563 4.2 25.6 1.0
CB C:ASP564 4.3 23.1 1.0
CG C:HIS529 4.3 24.6 1.0
CB C:ASP674 4.4 28.3 1.0
O C:HOH1006 4.4 45.3 1.0
ND1 C:HIS529 4.4 28.8 1.0
NE2 C:HIS525 4.4 33.1 1.0
O C:HOH1029 4.4 34.9 1.0
O C:HOH944 4.5 28.3 1.0
CG2 C:VAL533 4.7 32.2 1.0
CA C:ASP674 4.8 26.4 1.0
O C:ASP674 5.0 27.0 1.0

Zinc binding site 4 out of 4 in 5sk0

Go back to Zinc Binding Sites List in 5sk0
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-1-Methyl-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 N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-1-Methyl-4-Pyridin-4- Ylpyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:35.1
occ:1.00
 O D:HOH928 1.9 29.8 1.0
O D:HOH982 2.1 34.4 1.0
OD2 D:ASP564 2.1 35.5 1.0
NE2 D:HIS563 2.1 23.9 1.0
NE2 D:HIS529 2.2 33.1 1.0
OD1 D:ASP674 2.3 35.7 1.0
CD2 D:HIS563 3.0 32.5 1.0
CG D:ASP674 3.1 37.4 1.0
CD2 D:HIS529 3.1 33.2 1.0
CG D:ASP564 3.1 30.7 1.0
CE1 D:HIS563 3.2 32.8 1.0
CE1 D:HIS529 3.2 30.0 1.0
OD2 D:ASP674 3.3 37.4 1.0
OD1 D:ASP564 3.6 30.5 1.0
MG D:MG802 3.7 36.0 1.0
CD2 D:HIS525 4.1 32.6 1.0
O D:HOH985 4.2 31.8 1.0
CG D:HIS563 4.2 30.1 1.0
O D:HOH939 4.3 43.1 1.0
ND1 D:HIS563 4.3 27.7 1.0
CG D:HIS529 4.3 30.2 1.0
ND1 D:HIS529 4.3 30.4 1.0
CB D:ASP564 4.4 30.0 1.0
NE2 D:HIS525 4.5 50.9 1.0
CB D:ASP674 4.5 35.1 1.0
CG2 D:VAL533 4.6 32.0 1.0
O D:ASP674 4.6 31.4 1.0
O D:HOH905 4.7 35.5 1.0
CA D:ASP674 4.9 28.8 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 06:10:02 2024

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