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Zinc in PDB 5sgq: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxylic Acid

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxylic Acid

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxylic Acid:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxylic Acid, PDB code: 5sgq 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 / 2.04
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.496, 135.496, 235.736, 90, 90, 120
R / Rfree (%) 17.7 / 22.4

Other elements in 5sgq:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxylic Acid 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-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxylic Acid (pdb code 5sgq). 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-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxylic Acid, PDB code: 5sgq:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sgq

Go back to Zinc Binding Sites List in 5sgq
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxylic Acid


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-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:30.0
occ:1.00
 NE2 A:HIS529 2.1 26.9 1.0
OD2 A:ASP564 2.1 27.9 1.0
NE2 A:HIS563 2.1 23.9 1.0
O A:HOH960 2.2 21.6 1.0
OD1 A:ASP674 2.2 27.9 1.0
O A:HOH995 2.4 36.2 1.0
CD2 A:HIS563 3.0 20.5 1.0
CD2 A:HIS529 3.1 28.2 1.0
CG A:ASP674 3.1 27.6 1.0
CG A:ASP564 3.1 27.5 1.0
CE1 A:HIS529 3.1 29.4 1.0
CE1 A:HIS563 3.2 23.3 1.0
OD2 A:ASP674 3.3 32.5 1.0
OD1 A:ASP564 3.6 24.7 1.0
MG A:MG802 3.8 25.1 1.0
CD2 A:HIS525 4.2 29.4 1.0
O A:HOH964 4.2 30.8 1.0
O A:HOH1014 4.2 24.5 1.0
CG A:HIS563 4.2 23.1 1.0
CG A:HIS529 4.2 25.7 1.0
ND1 A:HIS563 4.2 21.9 1.0
ND1 A:HIS529 4.3 22.6 1.0
CB A:ASP564 4.3 23.0 1.0
CB A:ASP674 4.4 25.5 1.0
NE2 A:HIS525 4.5 30.2 1.0
O A:HOH921 4.6 27.2 1.0
O A:ASP674 4.8 28.9 1.0
CG2 A:VAL533 4.8 24.3 1.0
CA A:ASP674 4.9 24.1 1.0

Zinc binding site 2 out of 4 in 5sgq

Go back to Zinc Binding Sites List in 5sgq
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxylic Acid


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-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:29.4
occ:1.00
 NE2 B:HIS563 2.1 19.7 1.0
OD1 B:ASP674 2.2 27.1 1.0
O B:HOH942 2.2 20.1 1.0
O B:HOH968 2.2 33.5 1.0
OD2 B:ASP564 2.2 26.9 1.0
NE2 B:HIS529 2.2 21.5 1.0
CD2 B:HIS563 3.0 23.8 1.0
CG B:ASP674 3.0 29.0 1.0
CG B:ASP564 3.1 23.8 1.0
CD2 B:HIS529 3.2 24.3 1.0
CE1 B:HIS563 3.2 23.7 1.0
CE1 B:HIS529 3.3 26.9 1.0
OD2 B:ASP674 3.3 27.6 1.0
OD1 B:ASP564 3.5 25.2 1.0
MG B:MG802 3.8 25.9 1.0
O B:HOH992 4.1 26.2 1.0
O B:HOH956 4.2 33.8 1.0
CD2 B:HIS525 4.2 30.3 1.0
CG B:HIS563 4.2 22.2 1.0
ND1 B:HIS563 4.3 23.6 1.0
CB B:ASP564 4.3 25.3 1.0
CG B:HIS529 4.3 27.0 1.0
ND1 B:HIS529 4.4 22.0 1.0
CB B:ASP674 4.4 26.0 1.0
NE2 B:HIS525 4.4 26.9 1.0
O B:HOH944 4.6 22.0 1.0
CG2 B:VAL533 4.7 23.8 1.0
O B:ASP674 4.8 26.1 1.0
CA B:ASP674 4.8 24.8 1.0

Zinc binding site 3 out of 4 in 5sgq

Go back to Zinc Binding Sites List in 5sgq
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxylic Acid


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-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:31.7
occ:1.00
 O C:HOH957 2.1 26.2 1.0
NE2 C:HIS563 2.1 26.1 1.0
NE2 C:HIS529 2.1 27.4 1.0
OD1 C:ASP674 2.2 27.3 1.0
O C:HOH1000 2.2 30.8 1.0
OD2 C:ASP564 2.2 26.5 1.0
CD2 C:HIS563 3.0 23.8 1.0
CD2 C:HIS529 3.0 29.3 1.0
CG C:ASP674 3.1 32.0 1.0
CG C:ASP564 3.2 27.9 1.0
CE1 C:HIS529 3.2 32.8 1.0
CE1 C:HIS563 3.2 26.4 1.0
OD2 C:ASP674 3.3 33.1 1.0
OD1 C:ASP564 3.7 28.8 1.0
MG C:MG802 3.8 25.5 1.0
CD2 C:HIS525 4.1 34.5 1.0
O C:HOH1022 4.2 25.8 1.0
CG C:HIS563 4.2 25.3 1.0
CG C:HIS529 4.2 28.8 1.0
O C:HOH998 4.2 42.2 1.0
ND1 C:HIS563 4.3 24.1 1.0
ND1 C:HIS529 4.3 28.3 1.0
CB C:ASP564 4.3 24.9 1.0
NE2 C:HIS525 4.4 35.7 1.0
CB C:ASP674 4.4 29.4 1.0
O C:HOH939 4.6 25.4 1.0
CG2 C:VAL533 4.8 26.7 1.0
CA C:ASP674 4.8 27.3 1.0
O C:ASP674 4.8 29.1 1.0

Zinc binding site 4 out of 4 in 5sgq

Go back to Zinc Binding Sites List in 5sgq
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxylic Acid


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-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:36.2
occ:1.00
 O D:HOH914 2.1 24.3 1.0
NE2 D:HIS563 2.2 29.5 1.0
NE2 D:HIS529 2.2 36.5 1.0
OD2 D:ASP564 2.2 38.6 1.0
OD1 D:ASP674 2.2 32.5 1.0
O D:HOH964 2.3 30.5 1.0
CD2 D:HIS563 3.0 34.0 1.0
CG D:ASP674 3.1 33.1 1.0
CD2 D:HIS529 3.1 35.0 1.0
CG D:ASP564 3.1 26.2 1.0
CE1 D:HIS529 3.2 35.8 1.0
OD2 D:ASP674 3.3 34.6 1.0
CE1 D:HIS563 3.3 30.1 1.0
OD1 D:ASP564 3.6 30.3 1.0
MG D:MG802 3.8 30.6 1.0
O D:HOH978 4.0 33.3 1.0
O D:HOH950 4.2 41.8 1.0
CD2 D:HIS525 4.2 40.1 1.0
CG D:HIS563 4.2 30.1 1.0
CB D:ASP564 4.2 30.0 1.0
CG D:HIS529 4.3 33.4 1.0
ND1 D:HIS563 4.3 29.9 1.0
ND1 D:HIS529 4.3 34.2 1.0
CB D:ASP674 4.4 29.9 1.0
NE2 D:HIS525 4.6 39.0 1.0
O D:HOH932 4.6 36.0 1.0
O D:ASP674 4.7 31.1 1.0
CG2 D:VAL533 4.8 35.7 1.0
CA D:ASP674 4.8 29.9 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: Mon Oct 28 05:16:30 2024

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