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Zinc in PDB 5skm: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-N,N-Dimethyl-2-[2-(1-Pyridin-2-Ylpyrrolidin-3-Yl) Ethyl]Quinazolin-4-Amine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-N,N-Dimethyl-2-[2-(1-Pyridin-2-Ylpyrrolidin-3-Yl) Ethyl]Quinazolin-4-Amine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-N,N-Dimethyl-2-[2-(1-Pyridin-2-Ylpyrrolidin-3-Yl) Ethyl]Quinazolin-4-Amine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-N,N-Dimethyl-2-[2-(1-Pyridin-2-Ylpyrrolidin-3-Yl) Ethyl]Quinazolin-4-Amine, PDB code: 5skm was solved by C.Joseph, J.Benz, A.Flohr, K.Groebke-Zbinden, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.75 / 1.91
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 136.021, 136.021, 236.102, 90, 90, 120
R / Rfree (%) 18 / 22.1

Other elements in 5skm:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-N,N-Dimethyl-2-[2-(1-Pyridin-2-Ylpyrrolidin-3-Yl) Ethyl]Quinazolin-4-Amine also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
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- Chloro-N,N-Dimethyl-2-[2-(1-Pyridin-2-Ylpyrrolidin-3-Yl) Ethyl]Quinazolin-4-Amine (pdb code 5skm). 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- Chloro-N,N-Dimethyl-2-[2-(1-Pyridin-2-Ylpyrrolidin-3-Yl) Ethyl]Quinazolin-4-Amine, PDB code: 5skm:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5skm

Go back to Zinc Binding Sites List in 5skm
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-N,N-Dimethyl-2-[2-(1-Pyridin-2-Ylpyrrolidin-3-Yl) Ethyl]Quinazolin-4-Amine


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- Chloro-N,N-Dimethyl-2-[2-(1-Pyridin-2-Ylpyrrolidin-3-Yl) Ethyl]Quinazolin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:30.8
occ:1.00
 O A:HOH952 2.0 34.0 1.0
O A:HOH989 2.1 25.9 1.0
NE2 A:HIS563 2.1 26.8 1.0
NE2 A:HIS529 2.2 28.4 1.0
OD1 A:ASP674 2.2 26.3 1.0
OD2 A:ASP564 2.2 25.6 1.0
CD2 A:HIS563 3.0 25.1 1.0
CG A:ASP674 3.1 28.5 1.0
CD2 A:HIS529 3.1 25.8 1.0
CG A:ASP564 3.1 28.0 1.0
CE1 A:HIS563 3.2 25.9 1.0
CE1 A:HIS529 3.2 27.1 1.0
OD2 A:ASP674 3.4 32.3 1.0
OD1 A:ASP564 3.6 24.4 1.0
MG A:MG802 3.7 23.7 1.0
O A:HOH901 3.8 46.3 1.0
O A:HOH1027 4.1 27.8 1.0
CG A:HIS563 4.2 22.2 1.0
CD2 A:HIS525 4.2 28.8 1.0
ND1 A:HIS563 4.2 27.2 1.0
O A:HOH957 4.3 46.8 1.0
CG A:HIS529 4.3 27.4 1.0
ND1 A:HIS529 4.3 23.5 1.0
CB A:ASP564 4.4 24.8 1.0
O A:HOH993 4.4 35.4 1.0
CB A:ASP674 4.4 27.0 1.0
O A:HOH919 4.5 22.8 1.0
NE2 A:HIS525 4.5 31.0 1.0
CG2 A:VAL533 4.8 23.5 1.0
CA A:ASP674 4.9 27.6 1.0
O A:ASP674 4.9 26.6 1.0

Zinc binding site 2 out of 4 in 5skm

Go back to Zinc Binding Sites List in 5skm
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-N,N-Dimethyl-2-[2-(1-Pyridin-2-Ylpyrrolidin-3-Yl) Ethyl]Quinazolin-4-Amine


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- Chloro-N,N-Dimethyl-2-[2-(1-Pyridin-2-Ylpyrrolidin-3-Yl) Ethyl]Quinazolin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:28.6
occ:1.00
 O B:HOH965 2.1 22.2 1.0
OD1 B:ASP674 2.1 22.3 1.0
NE2 B:HIS529 2.1 22.9 1.0
O B:HOH1004 2.2 30.5 1.0
NE2 B:HIS563 2.2 22.5 1.0
OD2 B:ASP564 2.2 22.0 1.0
CG B:ASP674 3.0 26.4 1.0
CD2 B:HIS529 3.1 28.8 1.0
CD2 B:HIS563 3.1 22.8 1.0
CG B:ASP564 3.2 23.8 1.0
CE1 B:HIS563 3.2 22.1 1.0
CE1 B:HIS529 3.2 25.9 1.0
OD2 B:ASP674 3.3 26.0 1.0
OD1 B:ASP564 3.6 23.9 1.0
MG B:MG802 3.7 23.8 1.0
O B:HOH901 3.8 40.5 1.0
O B:HOH1036 4.0 23.2 1.0
CD2 B:HIS525 4.1 28.2 1.0
O B:HOH988 4.3 33.9 1.0
CG B:HIS563 4.3 23.0 1.0
CG B:HIS529 4.3 25.3 1.0
ND1 B:HIS529 4.3 22.2 1.0
ND1 B:HIS563 4.3 20.3 1.0
CB B:ASP674 4.4 24.9 1.0
CB B:ASP564 4.4 21.8 1.0
O B:HOH1040 4.4 33.3 1.0
NE2 B:HIS525 4.5 30.7 1.0
O B:HOH953 4.7 22.2 1.0
CG2 B:VAL533 4.8 20.6 1.0
CA B:ASP674 4.8 25.0 1.0
O B:ASP674 5.0 25.9 1.0

Zinc binding site 3 out of 4 in 5skm

Go back to Zinc Binding Sites List in 5skm
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-N,N-Dimethyl-2-[2-(1-Pyridin-2-Ylpyrrolidin-3-Yl) Ethyl]Quinazolin-4-Amine


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- Chloro-N,N-Dimethyl-2-[2-(1-Pyridin-2-Ylpyrrolidin-3-Yl) Ethyl]Quinazolin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:29.7
occ:1.00
 O C:HOH931 2.0 22.0 1.0
NE2 C:HIS563 2.1 26.3 1.0
NE2 C:HIS529 2.2 25.7 1.0
OD1 C:ASP674 2.2 22.7 1.0
OD2 C:ASP564 2.2 22.5 1.0
O C:HOH1013 2.2 30.7 1.0
CD2 C:HIS563 3.0 22.9 1.0
CG C:ASP674 3.0 25.7 1.0
CD2 C:HIS529 3.1 26.8 1.0
CG C:ASP564 3.2 26.6 1.0
CE1 C:HIS563 3.2 22.1 1.0
CE1 C:HIS529 3.2 27.9 1.0
OD2 C:ASP674 3.3 34.2 1.0
OD1 C:ASP564 3.6 23.7 1.0
MG C:MG802 3.7 24.6 1.0
O C:HOH902 3.9 40.1 1.0
O C:HOH1040 4.0 23.7 1.0
CD2 C:HIS525 4.1 29.6 1.0
CG C:HIS563 4.2 23.4 1.0
ND1 C:HIS563 4.3 24.7 1.0
O C:HOH1016 4.3 36.9 1.0
CG C:HIS529 4.3 25.3 1.0
ND1 C:HIS529 4.3 23.5 1.0
O C:HOH1000 4.4 32.0 1.0
CB C:ASP564 4.4 25.0 1.0
CB C:ASP674 4.4 22.7 1.0
NE2 C:HIS525 4.4 28.2 1.0
O C:HOH956 4.6 24.4 1.0
CG2 C:VAL533 4.8 26.6 1.0
CA C:ASP674 4.8 26.4 1.0
O C:ASP674 4.9 25.9 1.0

Zinc binding site 4 out of 4 in 5skm

Go back to Zinc Binding Sites List in 5skm
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-N,N-Dimethyl-2-[2-(1-Pyridin-2-Ylpyrrolidin-3-Yl) Ethyl]Quinazolin-4-Amine


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- Chloro-N,N-Dimethyl-2-[2-(1-Pyridin-2-Ylpyrrolidin-3-Yl) Ethyl]Quinazolin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:36.7
occ:1.00
 O D:HOH960 2.0 29.6 1.0
NE2 D:HIS563 2.1 27.4 1.0
O D:HOH974 2.2 40.1 1.0
NE2 D:HIS529 2.2 35.2 1.0
OD1 D:ASP674 2.2 29.4 1.0
OD2 D:ASP564 2.2 33.5 1.0
CD2 D:HIS563 2.9 34.1 1.0
CG D:ASP674 3.1 33.3 1.0
CD2 D:HIS529 3.1 39.5 1.0
CG D:ASP564 3.2 34.2 1.0
CE1 D:HIS529 3.2 33.3 1.0
CE1 D:HIS563 3.3 32.0 1.0
OD2 D:ASP674 3.3 39.1 1.0
OD1 D:ASP564 3.6 36.4 1.0
MG D:MG802 3.7 34.7 1.0
O D:HOH965 4.1 31.3 1.0
CD2 D:HIS525 4.1 38.5 1.0
CG D:HIS563 4.2 28.3 1.0
O D:HOH978 4.3 43.2 1.0
CG D:HIS529 4.3 35.4 1.0
ND1 D:HIS529 4.3 36.2 1.0
ND1 D:HIS563 4.3 28.3 1.0
CB D:ASP564 4.4 30.3 1.0
CB D:ASP674 4.4 32.5 1.0
NE2 D:HIS525 4.5 43.4 1.0
O D:HOH938 4.6 30.9 1.0
CG2 D:VAL533 4.8 35.4 1.0
O D:ASP674 4.9 31.1 1.0
CA D:ASP674 4.9 29.8 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 07:38:47 2024

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