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Zinc in PDB 5sg9: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- [(E)-2-(4-Methyl-6-Pyrrolidin-1-Ylpyrimidin-2-Yl)Ethenyl]Quinoline

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- [(E)-2-(4-Methyl-6-Pyrrolidin-1-Ylpyrimidin-2-Yl)Ethenyl]Quinoline

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- [(E)-2-(4-Methyl-6-Pyrrolidin-1-Ylpyrimidin-2-Yl)Ethenyl]Quinoline:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- [(E)-2-(4-Methyl-6-Pyrrolidin-1-Ylpyrimidin-2-Yl)Ethenyl]Quinoline, PDB code: 5sg9 was solved by C.Joseph, J.Benz, A.Flohr, W.Neidhart, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.58 / 2.13
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.064, 135.064, 234.822, 90, 90, 120
R / Rfree (%) 17.6 / 20.3

Other elements in 5sg9:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- [(E)-2-(4-Methyl-6-Pyrrolidin-1-Ylpyrimidin-2-Yl)Ethenyl]Quinoline 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 2- [(E)-2-(4-Methyl-6-Pyrrolidin-1-Ylpyrimidin-2-Yl)Ethenyl]Quinoline (pdb code 5sg9). 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 2- [(E)-2-(4-Methyl-6-Pyrrolidin-1-Ylpyrimidin-2-Yl)Ethenyl]Quinoline, PDB code: 5sg9:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sg9

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- [(E)-2-(4-Methyl-6-Pyrrolidin-1-Ylpyrimidin-2-Yl)Ethenyl]Quinoline


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 2- [(E)-2-(4-Methyl-6-Pyrrolidin-1-Ylpyrimidin-2-Yl)Ethenyl]Quinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:35.1
occ:1.00
 OD2 A:ASP564 2.1 31.8 1.0
OD1 A:ASP674 2.1 40.3 1.0
NE2 A:HIS563 2.1 31.6 1.0
O A:HOH907 2.1 31.6 1.0
NE2 A:HIS529 2.2 32.6 1.0
O A:HOH978 2.2 33.3 1.0
CD2 A:HIS563 2.9 31.7 1.0
CG A:ASP674 2.9 36.5 1.0
CG A:ASP564 3.1 30.4 1.0
CD2 A:HIS529 3.1 31.3 1.0
OD2 A:ASP674 3.2 43.1 1.0
CE1 A:HIS563 3.2 32.9 1.0
CE1 A:HIS529 3.2 32.8 1.0
OD1 A:ASP564 3.6 29.1 1.0
MG A:MG802 3.8 29.0 1.0
O A:HOH1004 4.1 26.6 1.0
CG A:HIS563 4.1 31.8 1.0
CD2 A:HIS525 4.2 34.4 1.0
O A:HOH998 4.2 37.6 1.0
ND1 A:HIS563 4.2 31.5 1.0
CB A:ASP564 4.2 31.0 1.0
CG A:HIS529 4.3 30.8 1.0
ND1 A:HIS529 4.3 30.5 1.0
CB A:ASP674 4.3 35.9 1.0
O A:HOH906 4.5 28.7 1.0
NE2 A:HIS525 4.5 36.0 1.0
CG2 A:VAL533 4.7 27.7 1.0
CA A:ASP674 4.8 32.3 1.0
O A:ASP674 4.8 30.4 1.0

Zinc binding site 2 out of 4 in 5sg9

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Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- [(E)-2-(4-Methyl-6-Pyrrolidin-1-Ylpyrimidin-2-Yl)Ethenyl]Quinoline


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 2- [(E)-2-(4-Methyl-6-Pyrrolidin-1-Ylpyrimidin-2-Yl)Ethenyl]Quinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:32.9
occ:1.00
 O B:HOH913 2.0 24.4 1.0
OD1 B:ASP674 2.1 31.0 1.0
NE2 B:HIS563 2.1 29.8 1.0
O B:HOH987 2.1 39.9 1.0
OD2 B:ASP564 2.1 25.0 1.0
NE2 B:HIS529 2.2 28.9 1.0
CD2 B:HIS563 3.0 28.6 1.0
CD2 B:HIS529 3.0 30.4 1.0
CG B:ASP674 3.0 33.2 1.0
CG B:ASP564 3.1 26.0 1.0
CE1 B:HIS563 3.1 30.0 1.0
CE1 B:HIS529 3.2 28.9 1.0
OD2 B:ASP674 3.3 32.1 1.0
OD1 B:ASP564 3.6 27.1 1.0
MG B:MG802 3.8 26.6 1.0
O B:HOH1004 4.1 30.0 1.0
CD2 B:HIS525 4.1 30.1 1.0
CG B:HIS563 4.2 28.4 1.0
ND1 B:HIS563 4.2 29.1 1.0
CG B:HIS529 4.2 29.3 1.0
ND1 B:HIS529 4.3 27.9 1.0
CB B:ASP564 4.3 27.3 1.0
O B:HOH980 4.4 40.1 1.0
O B:HOH1016 4.4 48.7 1.0
CB B:ASP674 4.4 32.7 1.0
NE2 B:HIS525 4.5 31.1 1.0
O B:HOH946 4.6 34.6 1.0
CG2 B:VAL533 4.7 28.3 1.0
CA B:ASP674 4.8 30.8 1.0
O B:ASP674 4.9 30.0 1.0

Zinc binding site 3 out of 4 in 5sg9

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Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- [(E)-2-(4-Methyl-6-Pyrrolidin-1-Ylpyrimidin-2-Yl)Ethenyl]Quinoline


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 2- [(E)-2-(4-Methyl-6-Pyrrolidin-1-Ylpyrimidin-2-Yl)Ethenyl]Quinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:35.2
occ:1.00
 O C:HOH981 1.9 47.5 1.0
OD2 C:ASP564 2.0 30.2 1.0
NE2 C:HIS563 2.0 29.9 1.0
O C:HOH965 2.1 27.1 1.0
OD1 C:ASP674 2.2 31.2 1.0
NE2 C:HIS529 2.2 30.2 1.0
CD2 C:HIS563 2.9 27.5 1.0
CD2 C:HIS529 3.1 30.1 1.0
CG C:ASP674 3.1 34.5 1.0
CG C:ASP564 3.1 30.6 1.0
CE1 C:HIS563 3.1 29.2 1.0
CE1 C:HIS529 3.2 31.6 1.0
OD2 C:ASP674 3.4 38.5 1.0
OD1 C:ASP564 3.7 31.1 1.0
MG C:MG802 3.9 33.1 1.0
CD2 C:HIS525 4.1 33.0 1.0
CG C:HIS563 4.1 27.6 1.0
ND1 C:HIS563 4.2 27.9 1.0
O C:HOH1003 4.2 36.6 1.0
CG C:HIS529 4.3 30.7 1.0
O C:HOH997 4.3 45.9 1.0
CB C:ASP564 4.3 29.8 1.0
ND1 C:HIS529 4.3 31.2 1.0
CB C:ASP674 4.4 35.5 1.0
O C:HOH1018 4.4 49.9 1.0
NE2 C:HIS525 4.4 32.6 1.0
O C:HOH948 4.6 37.0 1.0
CG2 C:VAL533 4.7 27.9 1.0
O C:ASP674 4.8 34.4 1.0
CA C:ASP674 4.8 34.2 1.0

Zinc binding site 4 out of 4 in 5sg9

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Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- [(E)-2-(4-Methyl-6-Pyrrolidin-1-Ylpyrimidin-2-Yl)Ethenyl]Quinoline


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 2- [(E)-2-(4-Methyl-6-Pyrrolidin-1-Ylpyrimidin-2-Yl)Ethenyl]Quinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:42.1
occ:1.00
 O D:HOH925 1.9 28.8 1.0
NE2 D:HIS563 2.1 33.0 1.0
OD1 D:ASP674 2.1 39.7 1.0
NE2 D:HIS529 2.2 43.2 1.0
OD2 D:ASP564 2.2 36.4 1.0
O D:HOH964 2.2 42.1 1.0
CD2 D:HIS563 2.9 35.8 1.0
CG D:ASP674 3.0 38.5 1.0
CG D:ASP564 3.2 34.5 1.0
CD2 D:HIS529 3.2 44.5 1.0
CE1 D:HIS563 3.2 34.2 1.0
CE1 D:HIS529 3.2 44.8 1.0
OD2 D:ASP674 3.3 41.8 1.0
OD1 D:ASP564 3.6 37.2 1.0
MG D:MG802 3.8 39.1 1.0
O D:HOH911 3.9 45.2 1.0
O D:HOH971 4.0 36.1 1.0
CG D:HIS563 4.1 34.7 1.0
ND1 D:HIS563 4.2 35.8 1.0
CD2 D:HIS525 4.2 39.2 1.0
ND1 D:HIS529 4.3 41.8 1.0
CB D:ASP564 4.3 34.7 1.0
CG D:HIS529 4.3 41.9 1.0
CB D:ASP674 4.4 39.1 1.0
O D:HOH916 4.5 39.4 1.0
NE2 D:HIS525 4.6 44.4 1.0
CG2 D:VAL533 4.7 38.6 1.0
CA D:ASP674 4.8 38.8 1.0
O D:ASP674 4.8 38.4 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 05:09:09 2024

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