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Zinc in PDB 5sit: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(4-Methylphenyl)Pyrimidin-4-Amine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(4-Methylphenyl)Pyrimidin-4-Amine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(4-Methylphenyl)Pyrimidin-4-Amine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(4-Methylphenyl)Pyrimidin-4-Amine, PDB code: 5sit was solved by C.Joseph, J.Benz, A.Flohr, M.Beresini, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.05 / 1.99
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.161, 135.161, 234.715, 90, 90, 120
R / Rfree (%) 19.6 / 22.6

Other elements in 5sit:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(4-Methylphenyl)Pyrimidin-4-Amine 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 6- Methyl-N-(4-Methylphenyl)Pyrimidin-4-Amine (pdb code 5sit). 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- Methyl-N-(4-Methylphenyl)Pyrimidin-4-Amine, PDB code: 5sit:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sit

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

b:29.5
occ:1.00
 NE2 A:HIS563 2.1 24.8 1.0
OD2 A:ASP564 2.1 26.6 1.0
OD1 A:ASP674 2.1 29.0 1.0
NE2 A:HIS529 2.2 26.1 1.0
O A:HOH925 2.2 24.6 1.0
O A:HOH975 2.2 27.4 1.0
CD2 A:HIS563 2.9 24.0 1.0
CG A:ASP674 3.0 28.4 1.0
CG A:ASP564 3.1 25.3 1.0
CD2 A:HIS529 3.1 23.9 1.0
CE1 A:HIS563 3.2 27.0 1.0
CE1 A:HIS529 3.2 23.7 1.0
OD2 A:ASP674 3.3 32.9 1.0
OD1 A:ASP564 3.6 23.6 1.0
MG A:MG802 3.8 23.7 1.0
O A:HOH998 4.1 40.4 1.0
O A:HOH1001 4.1 23.9 1.0
CG A:HIS563 4.1 24.8 1.0
CD2 A:HIS525 4.1 26.9 1.0
ND1 A:HIS563 4.2 26.0 1.0
CB A:ASP564 4.2 24.5 1.0
CG A:HIS529 4.3 24.1 1.0
ND1 A:HIS529 4.3 22.5 1.0
CB A:ASP674 4.4 26.8 1.0
NE2 A:HIS525 4.5 29.2 1.0
O A:HOH938 4.6 22.8 1.0
CG2 A:VAL533 4.7 24.2 1.0
O A:ASP674 4.8 27.1 1.0
CA A:ASP674 4.9 25.4 1.0

Zinc binding site 2 out of 4 in 5sit

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

b:27.5
occ:1.00
 NE2 B:HIS529 2.1 21.4 1.0
OD2 B:ASP564 2.1 24.1 1.0
O B:HOH941 2.1 17.9 1.0
O B:HOH984 2.2 32.9 1.0
OD1 B:ASP674 2.2 25.4 1.0
NE2 B:HIS563 2.2 21.8 1.0
CD2 B:HIS529 3.0 22.5 1.0
CD2 B:HIS563 3.0 23.0 1.0
CG B:ASP564 3.1 24.8 1.0
CG B:ASP674 3.1 25.0 1.0
CE1 B:HIS529 3.2 23.3 1.0
CE1 B:HIS563 3.2 23.9 1.0
OD2 B:ASP674 3.3 27.4 1.0
OD1 B:ASP564 3.5 24.9 1.0
MG B:MG802 3.8 22.7 1.0
O B:HOH1010 4.0 21.4 1.0
O B:HOH1005 4.0 36.4 1.0
CD2 B:HIS525 4.1 25.2 1.0
CG B:HIS529 4.2 22.1 1.0
CG B:HIS563 4.2 22.5 1.0
CB B:ASP564 4.2 24.2 1.0
ND1 B:HIS529 4.3 20.5 1.0
ND1 B:HIS563 4.3 23.2 1.0
CB B:ASP674 4.4 24.2 1.0
NE2 B:HIS525 4.5 27.8 1.0
O B:HOH943 4.6 23.4 1.0
CG2 B:VAL533 4.7 23.7 1.0
O B:HOH1021 4.8 56.2 1.0
CA B:ASP674 4.8 23.9 1.0
O B:ASP674 4.8 24.6 1.0

Zinc binding site 3 out of 4 in 5sit

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Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(4-Methylphenyl)Pyrimidin-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- Methyl-N-(4-Methylphenyl)Pyrimidin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:28.5
occ:1.00
 O C:HOH935 2.0 22.1 1.0
NE2 C:HIS563 2.1 28.1 1.0
OD2 C:ASP564 2.1 23.1 1.0
OD1 C:ASP674 2.2 24.9 1.0
NE2 C:HIS529 2.2 27.8 1.0
O C:HOH995 2.2 31.3 1.0
CD2 C:HIS563 3.0 24.3 1.0
CG C:ASP674 3.1 26.1 1.0
CG C:ASP564 3.1 22.3 1.0
CD2 C:HIS529 3.1 25.9 1.0
CE1 C:HIS563 3.2 25.2 1.0
CE1 C:HIS529 3.2 27.8 1.0
OD2 C:ASP674 3.3 31.7 1.0
OD1 C:ASP564 3.6 21.6 1.0
MG C:MG802 3.8 24.8 1.0
O C:HOH1011 4.1 23.3 1.0
CD2 C:HIS525 4.1 27.1 1.0
O C:HOH999 4.1 38.9 1.0
CG C:HIS563 4.2 24.8 1.0
ND1 C:HIS563 4.3 24.1 1.0
CG C:HIS529 4.3 25.6 1.0
CB C:ASP564 4.3 22.6 1.0
ND1 C:HIS529 4.3 26.0 1.0
CB C:ASP674 4.4 25.2 1.0
NE2 C:HIS525 4.5 27.4 1.0
O C:HOH947 4.6 26.4 1.0
CG2 C:VAL533 4.8 24.8 1.0
CA C:ASP674 4.8 26.2 1.0
O C:ASP674 4.8 26.3 1.0

Zinc binding site 4 out of 4 in 5sit

Go back to Zinc Binding Sites List in 5sit
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(4-Methylphenyl)Pyrimidin-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- Methyl-N-(4-Methylphenyl)Pyrimidin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:36.1
occ:1.00
 O D:HOH926 2.0 28.6 1.0
NE2 D:HIS563 2.1 26.9 1.0
O D:HOH972 2.1 34.3 1.0
NE2 D:HIS529 2.2 33.6 1.0
OD2 D:ASP564 2.2 32.1 1.0
OD1 D:ASP674 2.2 33.3 1.0
CD2 D:HIS563 3.0 28.4 1.0
CG D:ASP564 3.1 31.9 1.0
CD2 D:HIS529 3.1 34.8 1.0
CG D:ASP674 3.1 33.4 1.0
CE1 D:HIS563 3.2 28.6 1.0
CE1 D:HIS529 3.3 34.4 1.0
OD2 D:ASP674 3.4 33.5 1.0
OD1 D:ASP564 3.6 32.0 1.0
MG D:MG802 3.8 33.6 1.0
O D:HOH974 4.0 45.1 1.0
O D:HOH975 4.1 32.5 1.0
CD2 D:HIS525 4.2 40.4 1.0
CG D:HIS563 4.2 27.7 1.0
CB D:ASP564 4.2 31.2 1.0
ND1 D:HIS563 4.2 27.5 1.0
CG D:HIS529 4.3 32.0 1.0
ND1 D:HIS529 4.3 32.9 1.0
CB D:ASP674 4.5 32.1 1.0
NE2 D:HIS525 4.6 42.5 1.0
O D:HOH924 4.6 30.4 1.0
CG2 D:VAL533 4.8 32.9 1.0
O D:ASP674 4.9 34.3 1.0
CA D:ASP674 4.9 32.3 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 05:49:46 2024

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