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Zinc in PDB 5sgf: Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl 1-Methyl-5-(Propylcarbamoyl)Pyrazole-4-Carboxylate

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl 1-Methyl-5-(Propylcarbamoyl)Pyrazole-4-Carboxylate

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl 1-Methyl-5-(Propylcarbamoyl)Pyrazole-4-Carboxylate:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl 1-Methyl-5-(Propylcarbamoyl)Pyrazole-4-Carboxylate, PDB code: 5sgf was solved by C.Joseph, J.Benz, A.Flohr, J.Peters, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.34 / 2.30
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.027, 135.027, 234.883, 90, 90, 120
R / Rfree (%) 19.9 / 25.7

Other elements in 5sgf:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl 1-Methyl-5-(Propylcarbamoyl)Pyrazole-4-Carboxylate 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 Ethyl 1-Methyl-5-(Propylcarbamoyl)Pyrazole-4-Carboxylate (pdb code 5sgf). 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 Ethyl 1-Methyl-5-(Propylcarbamoyl)Pyrazole-4-Carboxylate, PDB code: 5sgf:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sgf

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl 1-Methyl-5-(Propylcarbamoyl)Pyrazole-4-Carboxylate


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 Ethyl 1-Methyl-5-(Propylcarbamoyl)Pyrazole-4-Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:42.4
occ:1.00
 NE2 A:HIS563 2.0 31.1 1.0
OD2 A:ASP564 2.1 38.2 1.0
NE2 A:HIS529 2.1 37.4 1.0
OD1 A:ASP674 2.2 39.9 1.0
O A:HOH927 2.3 27.8 1.0
O A:HOH967 2.4 38.7 1.0
CD2 A:HIS563 2.9 35.7 1.0
CD2 A:HIS529 3.0 34.6 1.0
CG A:ASP674 3.0 39.1 1.0
CE1 A:HIS563 3.1 34.4 1.0
CE1 A:HIS529 3.1 38.5 1.0
CG A:ASP564 3.2 35.0 1.0
OD2 A:ASP674 3.3 46.9 1.0
OD1 A:ASP564 3.8 34.9 1.0
MG A:MG802 3.8 35.4 1.0
CG A:HIS563 4.1 36.0 1.0
ND1 A:HIS563 4.1 30.2 1.0
O A:HOH971 4.1 30.1 1.0
ND1 A:HIS529 4.2 38.1 1.0
CG A:HIS529 4.2 35.0 1.0
CB A:ASP564 4.3 30.4 1.0
CD2 A:HIS525 4.3 38.0 1.0
CB A:ASP674 4.4 39.4 1.0
O A:HOH917 4.4 42.6 1.0
O A:HOH925 4.6 32.8 1.0
CG2 A:VAL533 4.7 30.5 1.0
NE2 A:HIS525 4.7 39.4 1.0
O A:ASP674 4.8 36.6 1.0
CA A:ASP674 4.9 36.9 1.0

Zinc binding site 2 out of 4 in 5sgf

Go back to Zinc Binding Sites List in 5sgf
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl 1-Methyl-5-(Propylcarbamoyl)Pyrazole-4-Carboxylate


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 Ethyl 1-Methyl-5-(Propylcarbamoyl)Pyrazole-4-Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:41.8
occ:1.00
 OD2 B:ASP564 2.0 37.6 1.0
O B:HOH930 2.1 27.2 1.0
OD1 B:ASP674 2.2 42.1 1.0
NE2 B:HIS563 2.2 32.4 1.0
NE2 B:HIS529 2.2 32.6 1.0
O B:HOH936 2.5 36.2 1.0
CG B:ASP674 3.0 37.1 1.0
CG B:ASP564 3.1 31.6 1.0
CD2 B:HIS563 3.1 32.9 1.0
CD2 B:HIS529 3.2 35.3 1.0
OD2 B:ASP674 3.2 43.1 1.0
CE1 B:HIS563 3.2 35.3 1.0
CE1 B:HIS529 3.3 37.4 1.0
OD1 B:ASP564 3.6 31.1 1.0
MG B:MG802 3.8 36.6 1.0
O B:HOH957 3.9 27.2 1.0
CD2 B:HIS525 4.1 40.3 1.0
O B:HOH954 4.2 34.4 1.0
CB B:ASP564 4.2 29.8 1.0
CG B:HIS563 4.3 32.5 1.0
ND1 B:HIS563 4.3 36.6 1.0
CG B:HIS529 4.3 34.2 1.0
ND1 B:HIS529 4.4 36.8 1.0
NE2 B:HIS525 4.4 41.4 1.0
CB B:ASP674 4.4 37.0 1.0
O B:HOH932 4.7 34.6 1.0
O B:ASP674 4.8 45.9 1.0
CA B:ASP674 4.8 36.3 1.0
CG2 B:VAL533 4.9 33.3 1.0

Zinc binding site 3 out of 4 in 5sgf

Go back to Zinc Binding Sites List in 5sgf
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl 1-Methyl-5-(Propylcarbamoyl)Pyrazole-4-Carboxylate


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 Ethyl 1-Methyl-5-(Propylcarbamoyl)Pyrazole-4-Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:39.9
occ:1.00
 O C:HOH925 2.0 24.7 1.0
NE2 C:HIS563 2.1 33.7 1.0
OD1 C:ASP674 2.1 37.1 1.0
OD2 C:ASP564 2.1 35.4 1.0
O C:HOH962 2.1 40.5 1.0
NE2 C:HIS529 2.1 35.8 1.0
CG C:ASP674 3.0 31.5 1.0
CE1 C:HIS563 3.0 32.1 1.0
CE1 C:HIS529 3.1 39.8 1.0
CD2 C:HIS563 3.1 32.6 1.0
CG C:ASP564 3.1 31.5 1.0
CD2 C:HIS529 3.2 37.8 1.0
OD2 C:ASP674 3.3 35.4 1.0
OD1 C:ASP564 3.7 38.0 1.0
MG C:MG802 3.9 31.1 1.0
ND1 C:HIS563 4.2 29.3 1.0
CB C:ASP564 4.2 29.4 1.0
CD2 C:HIS525 4.2 45.0 1.0
CG C:HIS563 4.2 30.7 1.0
ND1 C:HIS529 4.2 34.9 1.0
CG C:HIS529 4.3 33.9 1.0
O C:HOH976 4.4 36.3 1.0
CB C:ASP674 4.4 34.1 1.0
O C:HOH940 4.4 53.0 1.0
NE2 C:HIS525 4.5 46.8 1.0
O C:HOH934 4.5 34.9 1.0
CA C:ASP674 4.7 32.1 1.0
CG2 C:VAL533 4.8 32.3 1.0
O C:ASP674 4.8 38.1 1.0

Zinc binding site 4 out of 4 in 5sgf

Go back to Zinc Binding Sites List in 5sgf
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl 1-Methyl-5-(Propylcarbamoyl)Pyrazole-4-Carboxylate


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 Ethyl 1-Methyl-5-(Propylcarbamoyl)Pyrazole-4-Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:63.3
occ:1.00
 NE2 D:HIS563 2.2 54.7 1.0
OD1 D:ASP674 2.2 61.9 1.0
NE2 D:HIS529 2.3 61.9 1.0
O D:HOH908 2.3 29.0 1.0
OD2 D:ASP564 2.4 66.4 1.0
O D:HOH913 2.4 40.3 1.0
CD2 D:HIS563 3.1 56.0 1.0
CG D:ASP674 3.2 61.2 1.0
CG D:ASP564 3.2 56.6 1.0
CD2 D:HIS529 3.2 64.5 1.0
CE1 D:HIS529 3.3 59.1 1.0
CE1 D:HIS563 3.3 59.8 1.0
OD2 D:ASP674 3.6 80.2 1.0
OD1 D:ASP564 3.7 52.4 1.0
MG D:MG802 3.9 59.2 1.0
CB D:ASP564 4.2 55.7 1.0
CD2 D:HIS525 4.3 74.2 1.0
O D:HOH917 4.3 43.3 1.0
CG D:HIS563 4.3 56.0 1.0
O D:HOH903 4.3 48.2 1.0
ND1 D:HIS563 4.3 59.0 1.0
ND1 D:HIS529 4.4 59.4 1.0
CG D:HIS529 4.4 60.3 1.0
CB D:ASP674 4.4 64.0 1.0
O D:ASP674 4.6 76.9 1.0
NE2 D:HIS525 4.6 75.0 1.0
CG2 D:VAL533 4.7 63.3 1.0
CA D:ASP674 4.8 62.6 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 05:11:59 2024

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