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Zinc in PDB 5shs: Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- (Naphthalen-1-Ylmethyl)-7-Piperidin-1-Yltriazolo[4,5-D]Pyrimidine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- (Naphthalen-1-Ylmethyl)-7-Piperidin-1-Yltriazolo[4,5-D]Pyrimidine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- (Naphthalen-1-Ylmethyl)-7-Piperidin-1-Yltriazolo[4,5-D]Pyrimidine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- (Naphthalen-1-Ylmethyl)-7-Piperidin-1-Yltriazolo[4,5-D]Pyrimidine, PDB code: 5shs was solved by C.Joseph, J.Benz, A.Flohr, M.Brunner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.77 / 2.30
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.35, 135.35, 235.8, 90, 90, 120
R / Rfree (%) 16.3 / 23.3

Other elements in 5shs:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- (Naphthalen-1-Ylmethyl)-7-Piperidin-1-Yltriazolo[4,5-D]Pyrimidine 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 3- (Naphthalen-1-Ylmethyl)-7-Piperidin-1-Yltriazolo[4,5-D]Pyrimidine (pdb code 5shs). 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 3- (Naphthalen-1-Ylmethyl)-7-Piperidin-1-Yltriazolo[4,5-D]Pyrimidine, PDB code: 5shs:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5shs

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- (Naphthalen-1-Ylmethyl)-7-Piperidin-1-Yltriazolo[4,5-D]Pyrimidine


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 3- (Naphthalen-1-Ylmethyl)-7-Piperidin-1-Yltriazolo[4,5-D]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:35.1
occ:1.00
 NE2 A:HIS563 2.0 30.3 1.0
NE2 A:HIS529 2.0 37.9 1.0
O A:HOH986 2.1 31.2 1.0
OD2 A:ASP564 2.2 34.3 1.0
OD1 A:ASP674 2.2 39.0 1.0
O A:HOH958 2.2 27.8 1.0
CD2 A:HIS529 3.0 34.7 1.0
CD2 A:HIS563 3.0 28.9 1.0
CE1 A:HIS529 3.1 34.9 1.0
CE1 A:HIS563 3.1 27.1 1.0
CG A:ASP564 3.2 27.6 1.0
CG A:ASP674 3.2 35.4 1.0
OD2 A:ASP674 3.6 38.2 1.0
OD1 A:ASP564 3.8 24.0 1.0
MG A:MG802 3.9 27.7 1.0
O A:HOH924 4.0 34.5 1.0
CG A:HIS529 4.1 32.6 1.0
CG A:HIS563 4.1 26.1 1.0
ND1 A:HIS529 4.1 40.1 1.0
ND1 A:HIS563 4.2 22.4 1.0
CB A:ASP564 4.2 23.4 1.0
CD2 A:HIS525 4.3 31.1 1.0
O A:HOH1001 4.4 30.6 1.0
CB A:ASP674 4.5 34.9 1.0
CG2 A:VAL533 4.6 26.0 1.0
NE2 A:HIS525 4.6 28.3 1.0
O A:HOH906 4.7 23.0 1.0
O A:ASP674 4.8 39.3 1.0
CA A:ASP674 4.8 31.2 1.0

Zinc binding site 2 out of 4 in 5shs

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Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- (Naphthalen-1-Ylmethyl)-7-Piperidin-1-Yltriazolo[4,5-D]Pyrimidine


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 3- (Naphthalen-1-Ylmethyl)-7-Piperidin-1-Yltriazolo[4,5-D]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:32.4
occ:1.00
 NE2 B:HIS563 2.1 25.3 1.0
O B:HOH954 2.2 18.6 1.0
NE2 B:HIS529 2.2 26.2 1.0
OD2 B:ASP564 2.2 27.7 1.0
OD1 B:ASP674 2.3 29.9 1.0
O B:HOH971 2.5 35.8 1.0
CD2 B:HIS563 2.9 26.5 1.0
CG B:ASP564 3.1 29.4 1.0
CG B:ASP674 3.1 28.0 1.0
CE1 B:HIS563 3.2 28.1 1.0
CD2 B:HIS529 3.2 26.6 1.0
CE1 B:HIS529 3.2 25.9 1.0
OD2 B:ASP674 3.3 26.8 1.0
OD1 B:ASP564 3.6 25.5 1.0
MG B:MG802 3.8 19.4 1.0
O B:HOH965 4.0 16.7 1.0
O B:HOH968 4.1 33.8 1.0
CG B:HIS563 4.1 25.2 1.0
ND1 B:HIS563 4.2 29.4 1.0
CD2 B:HIS525 4.2 28.1 1.0
CB B:ASP564 4.2 25.1 1.0
ND1 B:HIS529 4.3 23.5 1.0
CG B:HIS529 4.3 25.1 1.0
CB B:ASP674 4.5 27.0 1.0
O B:HOH931 4.5 17.2 1.0
NE2 B:HIS525 4.7 31.4 1.0
CG2 B:VAL533 4.8 21.6 1.0
O B:ASP674 4.8 31.9 1.0
CA B:ASP674 4.9 25.9 1.0

Zinc binding site 3 out of 4 in 5shs

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Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- (Naphthalen-1-Ylmethyl)-7-Piperidin-1-Yltriazolo[4,5-D]Pyrimidine


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 3- (Naphthalen-1-Ylmethyl)-7-Piperidin-1-Yltriazolo[4,5-D]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:33.3
occ:1.00
 NE2 C:HIS529 2.0 32.9 1.0
OD2 C:ASP564 2.1 31.4 1.0
NE2 C:HIS563 2.2 25.5 1.0
O C:HOH955 2.2 24.3 1.0
OD1 C:ASP674 2.3 33.4 1.0
O C:HOH923 2.6 34.4 1.0
CD2 C:HIS529 3.0 25.1 1.0
CD2 C:HIS563 3.0 20.2 1.0
CE1 C:HIS529 3.1 33.3 1.0
CG C:ASP564 3.1 27.8 1.0
CG C:ASP674 3.1 31.5 1.0
CE1 C:HIS563 3.3 26.4 1.0
OD2 C:ASP674 3.4 35.5 1.0
OD1 C:ASP564 3.6 28.1 1.0
MG C:MG802 3.8 26.5 1.0
CD2 C:HIS525 4.1 33.6 1.0
CG C:HIS529 4.2 22.7 1.0
ND1 C:HIS529 4.2 27.0 1.0
O C:HOH995 4.2 25.4 1.0
CG C:HIS563 4.2 24.4 1.0
O C:HOH991 4.3 30.6 1.0
CB C:ASP564 4.3 26.1 1.0
ND1 C:HIS563 4.4 27.1 1.0
O C:HOH950 4.5 24.1 1.0
CB C:ASP674 4.5 30.9 1.0
NE2 C:HIS525 4.5 35.4 1.0
CG2 C:VAL533 4.8 22.1 1.0
CA C:ASP674 4.9 27.7 1.0
O C:ASP674 4.9 29.9 1.0

Zinc binding site 4 out of 4 in 5shs

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Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- (Naphthalen-1-Ylmethyl)-7-Piperidin-1-Yltriazolo[4,5-D]Pyrimidine


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 3- (Naphthalen-1-Ylmethyl)-7-Piperidin-1-Yltriazolo[4,5-D]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:43.4
occ:1.00
 O D:HOH934 2.1 30.1 1.0
NE2 D:HIS563 2.2 29.3 1.0
NE2 D:HIS529 2.2 34.8 1.0
OD1 D:ASP674 2.3 38.8 1.0
OD2 D:ASP564 2.3 41.0 1.0
O D:HOH926 2.4 44.6 1.0
CD2 D:HIS563 3.0 30.5 1.0
CD2 D:HIS529 3.1 37.6 1.0
CG D:ASP674 3.1 42.6 1.0
CE1 D:HIS529 3.2 31.3 1.0
CE1 D:HIS563 3.3 34.8 1.0
CG D:ASP564 3.3 35.2 1.0
OD2 D:ASP674 3.3 35.6 1.0
O D:HOH917 3.8 48.2 1.0
OD1 D:ASP564 3.9 44.2 1.0
MG D:MG802 3.9 37.9 1.0
O D:HOH931 4.1 32.2 1.0
CD2 D:HIS525 4.1 48.6 1.0
CG D:HIS563 4.2 35.1 1.0
CG D:HIS529 4.3 38.7 1.0
ND1 D:HIS529 4.3 36.5 1.0
ND1 D:HIS563 4.3 28.6 1.0
CB D:ASP564 4.3 35.6 1.0
NE2 D:HIS525 4.4 41.8 1.0
CB D:ASP674 4.5 39.0 1.0
O D:HOH901 4.6 41.3 1.0
O D:ASP674 4.8 51.6 1.0
CG2 D:VAL533 4.8 41.1 1.0
CA D:ASP674 4.9 37.6 1.0
O D:HOH944 4.9 31.1 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 05:34:35 2024

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