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Zinc in PDB 5sfe: Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide, PDB code: 5sfe was solved by C.Joseph, L.Gobbi, J.Benz, D.Schlatter, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.75 / 1.86
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.85, 135.85, 235.666, 90, 90, 120
R / Rfree (%) 17.9 / 22.1

Other elements in 5sfe:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Fluorine (F) 7 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide (pdb code 5sfe). 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-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide, PDB code: 5sfe:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sfe

Go back to Zinc Binding Sites List in 5sfe
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide


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-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:29.4
occ:1.00
 NE2 A:HIS563 2.1 22.7 1.0
O A:HOH963 2.2 22.9 1.0
OD2 A:ASP564 2.2 25.2 1.0
OD1 A:ASP674 2.2 25.1 1.0
NE2 A:HIS529 2.2 25.2 1.0
O A:HOH1011 2.3 39.6 1.0
CD2 A:HIS563 3.0 23.9 1.0
CG A:ASP674 3.1 29.2 1.0
CG A:ASP564 3.1 26.0 1.0
CD2 A:HIS529 3.2 25.1 1.0
CE1 A:HIS563 3.2 24.4 1.0
CE1 A:HIS529 3.2 24.9 1.0
OD2 A:ASP674 3.4 33.0 1.0
OD1 A:ASP564 3.6 24.8 1.0
MG A:MG802 3.7 23.3 1.0
CD2 A:HIS525 4.1 29.0 1.0
O A:HOH1042 4.1 25.6 1.0
CG A:HIS563 4.2 22.4 1.0
ND1 A:HIS563 4.3 23.6 1.0
O A:HOH990 4.3 33.9 1.0
CB A:ASP564 4.3 23.2 1.0
CG A:HIS529 4.3 26.5 1.0
ND1 A:HIS529 4.4 22.6 1.0
NE2 A:HIS525 4.4 31.2 1.0
CB A:ASP674 4.4 22.5 1.0
O A:HOH922 4.5 24.0 1.0
O A:HOH1043 4.6 42.8 1.0
CG2 A:VAL533 4.7 25.2 1.0
CA A:ASP674 4.8 23.8 1.0
O A:ASP674 4.9 26.5 1.0

Zinc binding site 2 out of 4 in 5sfe

Go back to Zinc Binding Sites List in 5sfe
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide


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-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:27.7
occ:1.00
 O B:HOH938 2.1 19.8 1.0
OD1 B:ASP674 2.1 21.7 1.0
NE2 B:HIS563 2.1 22.5 1.0
NE2 B:HIS529 2.2 22.6 1.0
OD2 B:ASP564 2.2 21.5 1.0
O B:HOH990 2.2 35.0 1.0
CG B:ASP674 3.0 27.8 1.0
CD2 B:HIS563 3.0 22.0 1.0
CD2 B:HIS529 3.1 26.6 1.0
CG B:ASP564 3.2 23.0 1.0
CE1 B:HIS563 3.2 20.5 1.0
CE1 B:HIS529 3.2 25.1 1.0
OD2 B:ASP674 3.3 29.6 1.0
OD1 B:ASP564 3.6 23.2 1.0
MG B:MG802 3.7 22.0 1.0
O B:HOH1042 4.0 24.9 1.0
CD2 B:HIS525 4.1 28.5 1.0
CG B:HIS563 4.2 20.6 1.0
O B:HOH1019 4.2 38.8 1.0
ND1 B:HIS563 4.2 22.1 1.0
CG B:HIS529 4.3 25.4 1.0
ND1 B:HIS529 4.3 20.4 1.0
CB B:ASP674 4.4 24.7 1.0
NE2 B:HIS525 4.4 30.1 1.0
CB B:ASP564 4.4 20.4 1.0
O B:HOH1060 4.5 37.7 1.0
O B:HOH961 4.6 23.4 1.0
CG2 B:VAL533 4.7 20.7 1.0
CA B:ASP674 4.8 23.0 1.0
O B:ASP674 5.0 23.5 1.0

Zinc binding site 3 out of 4 in 5sfe

Go back to Zinc Binding Sites List in 5sfe
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide


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-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:28.8
occ:1.00
 O C:HOH945 2.0 20.5 1.0
NE2 C:HIS563 2.2 23.8 1.0
OD2 C:ASP564 2.2 24.2 1.0
OD1 C:ASP674 2.2 23.1 1.0
NE2 C:HIS529 2.2 24.8 1.0
O C:HOH991 2.4 39.1 1.0
CD2 C:HIS563 3.0 20.1 1.0
CG C:ASP674 3.0 28.0 1.0
CG C:ASP564 3.1 26.5 1.0
CE1 C:HIS563 3.2 20.7 1.0
CD2 C:HIS529 3.2 27.2 1.0
CE1 C:HIS529 3.3 25.4 1.0
OD2 C:ASP674 3.3 33.7 1.0
OD1 C:ASP564 3.6 22.8 1.0
MG C:MG802 3.7 22.9 1.0
O C:HOH1050 4.0 25.3 1.0
CD2 C:HIS525 4.0 31.6 1.0
CG C:HIS563 4.2 22.3 1.0
ND1 C:HIS563 4.3 23.8 1.0
O C:HOH1037 4.3 37.6 1.0
NE2 C:HIS525 4.4 28.6 1.0
CB C:ASP564 4.4 23.0 1.0
CB C:ASP674 4.4 21.6 1.0
CG C:HIS529 4.4 23.5 1.0
ND1 C:HIS529 4.4 23.2 1.0
O C:HOH1046 4.4 39.1 1.0
O C:HOH963 4.6 24.5 1.0
CG2 C:VAL533 4.8 26.1 1.0
CA C:ASP674 4.8 24.6 1.0
O C:ASP674 4.9 24.4 1.0

Zinc binding site 4 out of 4 in 5sfe

Go back to Zinc Binding Sites List in 5sfe
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide


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-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:35.6
occ:1.00
 O D:HOH949 2.0 27.7 1.0
NE2 D:HIS529 2.2 34.1 1.0
NE2 D:HIS563 2.2 26.4 1.0
O D:HOH987 2.2 38.4 1.0
OD1 D:ASP674 2.2 28.5 1.0
OD2 D:ASP564 2.2 32.5 1.0
CD2 D:HIS563 3.0 30.4 1.0
CD2 D:HIS529 3.1 38.2 1.0
CG D:ASP674 3.1 33.0 1.0
CG D:ASP564 3.1 33.2 1.0
CE1 D:HIS529 3.2 32.0 1.0
CE1 D:HIS563 3.3 27.7 1.0
OD2 D:ASP674 3.4 38.5 1.0
OD1 D:ASP564 3.6 34.6 1.0
MG D:MG802 3.7 33.2 1.0
O D:HOH989 4.0 31.7 1.0
CD2 D:HIS525 4.1 40.8 1.0
O D:HOH971 4.2 42.9 1.0
CG D:HIS563 4.2 25.9 1.0
CG D:HIS529 4.3 34.0 1.0
ND1 D:HIS529 4.3 32.8 1.0
ND1 D:HIS563 4.3 28.7 1.0
CB D:ASP564 4.3 29.1 1.0
CB D:ASP674 4.4 31.9 1.0
NE2 D:HIS525 4.4 44.9 1.0
O D:HOH921 4.6 32.4 1.0
CG2 D:VAL533 4.8 33.1 1.0
CA D:ASP674 4.8 29.9 1.0
O D:ASP674 4.9 31.8 1.0

Reference:

L.Gobbi, J.Benz, D.Schlatter, M.G.Rudolph. Crystal Structure of A Human Phosphodiesterase 10 Complex To Be Published.
Page generated: Mon Oct 28 04:55:14 2024

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