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Zinc in PDB 5skq: Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Ethyl-6-(4-Fluorophenyl)Sulfanyl-N-Methyl-9H-Purin-2-Amine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Ethyl-6-(4-Fluorophenyl)Sulfanyl-N-Methyl-9H-Purin-2-Amine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Ethyl-6-(4-Fluorophenyl)Sulfanyl-N-Methyl-9H-Purin-2-Amine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Ethyl-6-(4-Fluorophenyl)Sulfanyl-N-Methyl-9H-Purin-2-Amine, PDB code: 5skq 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) 43.64 / 2.00
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.5, 135.5, 235.07, 90, 90, 120
R / Rfree (%) 16.9 / 23.5

Other elements in 5skq:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Ethyl-6-(4-Fluorophenyl)Sulfanyl-N-Methyl-9H-Purin-2-Amine also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Fluorine (F) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Ethyl-6-(4-Fluorophenyl)Sulfanyl-N-Methyl-9H-Purin-2-Amine (pdb code 5skq). 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 N- Ethyl-6-(4-Fluorophenyl)Sulfanyl-N-Methyl-9H-Purin-2-Amine, PDB code: 5skq:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5skq

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Ethyl-6-(4-Fluorophenyl)Sulfanyl-N-Methyl-9H-Purin-2-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 N- Ethyl-6-(4-Fluorophenyl)Sulfanyl-N-Methyl-9H-Purin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:28.1
occ:1.00
 O A:HOH978 2.1 29.1 1.0
NE2 A:HIS563 2.1 22.9 1.0
OD1 A:ASP674 2.2 25.4 1.0
NE2 A:HIS529 2.2 26.2 1.0
O A:HOH993 2.2 26.6 1.0
OD2 A:ASP564 2.2 26.5 1.0
CD2 A:HIS563 2.9 21.6 1.0
CD2 A:HIS529 3.0 30.0 1.0
CG A:ASP674 3.1 27.4 1.0
CG A:ASP564 3.1 24.5 1.0
CE1 A:HIS563 3.1 25.8 1.0
CE1 A:HIS529 3.3 27.2 1.0
OD2 A:ASP674 3.5 27.5 1.0
OD1 A:ASP564 3.6 21.6 1.0
MG A:MG802 3.8 20.9 1.0
CG A:HIS563 4.1 23.5 1.0
O A:HOH961 4.2 33.9 1.0
ND1 A:HIS563 4.2 24.6 1.0
CG A:HIS529 4.2 27.8 1.0
CD2 A:HIS525 4.2 27.4 1.0
CB A:ASP564 4.3 22.4 1.0
O A:HOH1028 4.3 22.9 1.0
ND1 A:HIS529 4.3 26.0 1.0
CB A:ASP674 4.4 24.0 1.0
O A:HOH912 4.5 22.7 1.0
NE2 A:HIS525 4.5 24.9 1.0
CG2 A:VAL533 4.6 20.8 1.0
O A:ASP674 4.8 23.5 1.0
CA A:ASP674 4.8 22.5 1.0

Zinc binding site 2 out of 4 in 5skq

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Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Ethyl-6-(4-Fluorophenyl)Sulfanyl-N-Methyl-9H-Purin-2-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 N- Ethyl-6-(4-Fluorophenyl)Sulfanyl-N-Methyl-9H-Purin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:26.6
occ:1.00
 OD2 B:ASP564 2.1 21.6 1.0
OD1 B:ASP674 2.1 16.8 1.0
O B:HOH937 2.2 14.3 1.0
NE2 B:HIS563 2.2 18.1 1.0
NE2 B:HIS529 2.2 20.4 1.0
O B:HOH966 2.7 36.4 1.0
CG B:ASP674 3.0 18.7 1.0
CD2 B:HIS563 3.0 19.7 1.0
CG B:ASP564 3.1 18.8 1.0
CD2 B:HIS529 3.1 22.0 1.0
OD2 B:ASP674 3.2 20.9 1.0
CE1 B:HIS529 3.2 21.6 1.0
CE1 B:HIS563 3.3 18.8 1.0
OD1 B:ASP564 3.6 21.5 1.0
MG B:MG802 3.7 16.0 1.0
O B:HOH1025 3.9 21.3 1.0
O B:HOH1004 4.0 26.9 1.0
CD2 B:HIS525 4.1 22.6 1.0
CG B:HIS563 4.2 20.6 1.0
CB B:ASP564 4.3 17.9 1.0
CG B:HIS529 4.3 19.4 1.0
ND1 B:HIS529 4.3 18.8 1.0
ND1 B:HIS563 4.3 19.6 1.0
NE2 B:HIS525 4.4 23.8 1.0
CB B:ASP674 4.4 19.5 1.0
O B:HOH956 4.5 15.6 1.0
O B:HOH1042 4.7 38.4 1.0
CG2 B:VAL533 4.7 21.1 1.0
CA B:ASP674 4.9 20.5 1.0
O B:ASP674 4.9 23.1 1.0

Zinc binding site 3 out of 4 in 5skq

Go back to Zinc Binding Sites List in 5skq
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Ethyl-6-(4-Fluorophenyl)Sulfanyl-N-Methyl-9H-Purin-2-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 N- Ethyl-6-(4-Fluorophenyl)Sulfanyl-N-Methyl-9H-Purin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:28.1
occ:1.00
 NE2 C:HIS529 2.1 23.4 1.0
OD2 C:ASP564 2.1 21.3 1.0
NE2 C:HIS563 2.2 21.1 1.0
O C:HOH929 2.2 20.1 1.0
OD1 C:ASP674 2.2 19.7 1.0
O C:HOH999 2.3 36.5 1.0
CD2 C:HIS529 3.0 24.6 1.0
CD2 C:HIS563 3.0 21.4 1.0
CG C:ASP674 3.1 23.1 1.0
CE1 C:HIS529 3.1 24.1 1.0
CG C:ASP564 3.1 19.4 1.0
OD2 C:ASP674 3.3 25.7 1.0
CE1 C:HIS563 3.3 21.4 1.0
OD1 C:ASP564 3.5 18.6 1.0
MG C:MG802 3.8 22.0 1.0
CD2 C:HIS525 4.1 25.3 1.0
O C:HOH1036 4.1 23.7 1.0
CG C:HIS529 4.2 24.2 1.0
ND1 C:HIS529 4.2 22.6 1.0
CG C:HIS563 4.2 21.7 1.0
O C:HOH974 4.3 46.0 1.0
ND1 C:HIS563 4.3 20.5 1.0
O C:HOH1023 4.3 31.4 1.0
CB C:ASP564 4.4 19.3 1.0
NE2 C:HIS525 4.4 23.9 1.0
CB C:ASP674 4.4 21.6 1.0
O C:HOH979 4.6 16.3 1.0
CG2 C:VAL533 4.7 22.6 1.0
CA C:ASP674 4.8 22.4 1.0
O C:ASP674 4.8 26.4 1.0

Zinc binding site 4 out of 4 in 5skq

Go back to Zinc Binding Sites List in 5skq
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Ethyl-6-(4-Fluorophenyl)Sulfanyl-N-Methyl-9H-Purin-2-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 N- Ethyl-6-(4-Fluorophenyl)Sulfanyl-N-Methyl-9H-Purin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:33.3
occ:1.00
 O D:HOH940 1.9 33.7 1.0
NE2 D:HIS563 2.2 25.6 1.0
OD1 D:ASP674 2.2 27.1 1.0
NE2 D:HIS529 2.2 32.6 1.0
O D:HOH927 2.3 41.6 1.0
OD2 D:ASP564 2.3 28.1 1.0
CD2 D:HIS563 3.0 25.9 1.0
CG D:ASP674 3.0 29.9 1.0
CD2 D:HIS529 3.2 32.5 1.0
CG D:ASP564 3.2 29.5 1.0
CE1 D:HIS529 3.2 31.1 1.0
OD2 D:ASP674 3.3 32.7 1.0
CE1 D:HIS563 3.3 25.7 1.0
OD1 D:ASP564 3.6 30.1 1.0
MG D:MG802 3.9 26.8 1.0
CD2 D:HIS525 4.2 31.2 1.0
CG D:HIS563 4.2 25.8 1.0
ND1 D:HIS529 4.3 30.4 1.0
CG D:HIS529 4.3 28.6 1.0
O D:HOH908 4.3 39.4 1.0
O D:HOH998 4.3 23.4 1.0
ND1 D:HIS563 4.3 24.0 1.0
NE2 D:HIS525 4.4 33.3 1.0
CB D:ASP564 4.4 25.4 1.0
CB D:ASP674 4.4 28.1 1.0
O D:HOH923 4.6 28.0 1.0
O D:ASP674 4.7 29.6 1.0
CG2 D:VAL533 4.7 29.8 1.0
CA D:ASP674 4.8 27.8 1.0
O D:HOH973 5.0 23.2 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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