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Zinc in PDB 5shq: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Pyrrolidin-1-Yl-7H-Pyrrolo[2,3-D]Pyrimidine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Pyrrolidin-1-Yl-7H-Pyrrolo[2,3-D]Pyrimidine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Pyrrolidin-1-Yl-7H-Pyrrolo[2,3-D]Pyrimidine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Pyrrolidin-1-Yl-7H-Pyrrolo[2,3-D]Pyrimidine, PDB code: 5shq 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) 34.92 / 2.08
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.136, 135.136, 234.1, 90, 90, 120
R / Rfree (%) 18.2 / 22.2

Other elements in 5shq:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Pyrrolidin-1-Yl-7H-Pyrrolo[2,3-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 4- Pyrrolidin-1-Yl-7H-Pyrrolo[2,3-D]Pyrimidine (pdb code 5shq). 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 4- Pyrrolidin-1-Yl-7H-Pyrrolo[2,3-D]Pyrimidine, PDB code: 5shq:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5shq

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Pyrrolidin-1-Yl-7H-Pyrrolo[2,3-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 4- Pyrrolidin-1-Yl-7H-Pyrrolo[2,3-D]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:31.4
occ:1.00
 NE2 A:HIS529 2.1 30.2 1.0
OD2 A:ASP564 2.1 28.7 1.0
NE2 A:HIS563 2.1 26.5 1.0
OD1 A:ASP674 2.1 31.2 1.0
O A:HOH973 2.2 27.2 1.0
O A:HOH1005 2.3 32.9 1.0
CD2 A:HIS563 3.0 25.9 1.0
CD2 A:HIS529 3.1 30.1 1.0
CG A:ASP564 3.1 27.1 1.0
CG A:ASP674 3.1 31.3 1.0
CE1 A:HIS529 3.1 28.5 1.0
CE1 A:HIS563 3.1 28.0 1.0
OD2 A:ASP674 3.4 37.6 1.0
OD1 A:ASP564 3.6 26.1 1.0
MG A:MG802 3.8 26.2 1.0
O A:HOH1020 4.0 24.2 1.0
CD2 A:HIS525 4.1 29.9 1.0
CG A:HIS563 4.1 26.6 1.0
ND1 A:HIS563 4.2 26.6 1.0
ND1 A:HIS529 4.2 27.6 1.0
CG A:HIS529 4.2 27.9 1.0
CB A:ASP564 4.2 26.8 1.0
O A:HOH981 4.2 41.3 1.0
CB A:ASP674 4.4 28.9 1.0
NE2 A:HIS525 4.5 28.8 1.0
O A:HOH936 4.6 25.1 1.0
CG2 A:VAL533 4.7 26.7 1.0
O A:ASP674 4.8 28.4 1.0
CA A:ASP674 4.8 27.4 1.0

Zinc binding site 2 out of 4 in 5shq

Go back to Zinc Binding Sites List in 5shq
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Pyrrolidin-1-Yl-7H-Pyrrolo[2,3-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 4- Pyrrolidin-1-Yl-7H-Pyrrolo[2,3-D]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:30.3
occ:1.00
 NE2 B:HIS563 2.0 26.7 1.0
NE2 B:HIS529 2.2 24.4 1.0
OD2 B:ASP564 2.2 27.7 1.0
OD1 B:ASP674 2.2 28.1 1.0
O B:HOH937 2.2 22.2 1.0
O B:HOH966 2.4 37.1 1.0
CG B:ASP674 3.0 28.3 1.0
CD2 B:HIS563 3.0 25.5 1.0
CE1 B:HIS563 3.0 25.3 1.0
CD2 B:HIS529 3.1 26.3 1.0
CG B:ASP564 3.1 26.7 1.0
CE1 B:HIS529 3.2 26.7 1.0
OD2 B:ASP674 3.2 30.0 1.0
OD1 B:ASP564 3.6 27.1 1.0
MG B:MG802 3.8 26.8 1.0
O B:HOH1010 3.9 22.4 1.0
O B:HOH961 4.1 34.1 1.0
ND1 B:HIS563 4.1 26.8 1.0
CD2 B:HIS525 4.1 28.8 1.0
CG B:HIS563 4.1 25.8 1.0
CG B:HIS529 4.3 25.8 1.0
ND1 B:HIS529 4.3 25.6 1.0
CB B:ASP564 4.3 27.0 1.0
CB B:ASP674 4.4 28.0 1.0
O B:HOH1024 4.4 43.0 1.0
NE2 B:HIS525 4.5 31.0 1.0
O B:HOH945 4.5 25.7 1.0
CG2 B:VAL533 4.7 26.0 1.0
CA B:ASP674 4.8 26.3 1.0
O B:ASP674 4.8 27.6 1.0

Zinc binding site 3 out of 4 in 5shq

Go back to Zinc Binding Sites List in 5shq
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Pyrrolidin-1-Yl-7H-Pyrrolo[2,3-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 4- Pyrrolidin-1-Yl-7H-Pyrrolo[2,3-D]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:32.0
occ:1.00
 O C:HOH926 2.0 23.6 1.0
NE2 C:HIS529 2.1 29.4 1.0
OD2 C:ASP564 2.2 26.5 1.0
O C:HOH992 2.2 35.3 1.0
OD1 C:ASP674 2.2 27.4 1.0
NE2 C:HIS563 2.2 27.9 1.0
CG C:ASP674 3.0 30.4 1.0
CD2 C:HIS563 3.1 27.0 1.0
CD2 C:HIS529 3.1 28.1 1.0
CE1 C:HIS529 3.1 29.7 1.0
CG C:ASP564 3.1 25.9 1.0
OD2 C:ASP674 3.2 34.1 1.0
CE1 C:HIS563 3.3 28.1 1.0
OD1 C:ASP564 3.6 25.8 1.0
MG C:MG802 3.8 26.2 1.0
O C:HOH1022 4.1 26.0 1.0
CD2 C:HIS525 4.1 32.6 1.0
O C:HOH1015 4.2 41.7 1.0
ND1 C:HIS529 4.2 28.2 1.0
CG C:HIS529 4.2 27.6 1.0
CG C:HIS563 4.3 27.6 1.0
ND1 C:HIS563 4.3 26.8 1.0
CB C:ASP564 4.3 26.4 1.0
NE2 C:HIS525 4.4 33.4 1.0
CB C:ASP674 4.4 31.0 1.0
O C:HOH950 4.6 28.3 1.0
CG2 C:VAL533 4.8 26.8 1.0
CA C:ASP674 4.8 29.8 1.0
O C:ASP674 4.8 31.4 1.0

Zinc binding site 4 out of 4 in 5shq

Go back to Zinc Binding Sites List in 5shq
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Pyrrolidin-1-Yl-7H-Pyrrolo[2,3-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 4- Pyrrolidin-1-Yl-7H-Pyrrolo[2,3-D]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:40.5
occ:1.00
 NE2 D:HIS563 2.0 32.1 1.0
O D:HOH934 2.1 28.9 1.0
OD2 D:ASP564 2.2 39.2 1.0
O D:HOH970 2.2 40.5 1.0
NE2 D:HIS529 2.2 40.0 1.0
OD1 D:ASP674 2.3 37.1 1.0
CD2 D:HIS563 2.8 33.7 1.0
CG D:ASP564 3.1 35.2 1.0
CG D:ASP674 3.1 39.5 1.0
CD2 D:HIS529 3.1 42.9 1.0
CE1 D:HIS563 3.2 34.7 1.0
CE1 D:HIS529 3.3 41.8 1.0
OD2 D:ASP674 3.4 41.0 1.0
OD1 D:ASP564 3.6 36.8 1.0
MG D:MG802 3.9 39.4 1.0
CG D:HIS563 4.1 31.6 1.0
O D:HOH943 4.1 51.1 1.0
O D:HOH977 4.1 34.3 1.0
ND1 D:HIS563 4.2 32.7 1.0
CD2 D:HIS525 4.2 43.7 1.0
CB D:ASP564 4.2 35.7 1.0
CG D:HIS529 4.3 38.8 1.0
ND1 D:HIS529 4.4 41.3 1.0
CB D:ASP674 4.5 40.0 1.0
O D:HOH931 4.5 39.8 1.0
NE2 D:HIS525 4.6 45.8 1.0
CG2 D:VAL533 4.7 37.9 1.0
O D:ASP674 4.8 37.6 1.0
CA D:ASP674 4.9 38.6 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 05:34:35 2024

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