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Zinc in PDB 5sjp: Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl N-[[4-[[4-(Azetidine-1-Carbonyl)-2-Methylpyrazole-3-Carbonyl]Amino]- 6-Methylpyridin-2-Yl]Carbamothioyl]Carbamate

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl N-[[4-[[4-(Azetidine-1-Carbonyl)-2-Methylpyrazole-3-Carbonyl]Amino]- 6-Methylpyridin-2-Yl]Carbamothioyl]Carbamate

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl N-[[4-[[4-(Azetidine-1-Carbonyl)-2-Methylpyrazole-3-Carbonyl]Amino]- 6-Methylpyridin-2-Yl]Carbamothioyl]Carbamate:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl N-[[4-[[4-(Azetidine-1-Carbonyl)-2-Methylpyrazole-3-Carbonyl]Amino]- 6-Methylpyridin-2-Yl]Carbamothioyl]Carbamate, PDB code: 5sjp was solved by C.Joseph, J.Benz, A.Flohr, C.Lerner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.52 / 2.25
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.3, 135.3, 234.703, 90, 90, 120
R / Rfree (%) 17.3 / 23.4

Other elements in 5sjp:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl N-[[4-[[4-(Azetidine-1-Carbonyl)-2-Methylpyrazole-3-Carbonyl]Amino]- 6-Methylpyridin-2-Yl]Carbamothioyl]Carbamate 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 Ethyl N-[[4-[[4-(Azetidine-1-Carbonyl)-2-Methylpyrazole-3-Carbonyl]Amino]- 6-Methylpyridin-2-Yl]Carbamothioyl]Carbamate (pdb code 5sjp). 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 Ethyl N-[[4-[[4-(Azetidine-1-Carbonyl)-2-Methylpyrazole-3-Carbonyl]Amino]- 6-Methylpyridin-2-Yl]Carbamothioyl]Carbamate, PDB code: 5sjp:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sjp

Go back to Zinc Binding Sites List in 5sjp
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl N-[[4-[[4-(Azetidine-1-Carbonyl)-2-Methylpyrazole-3-Carbonyl]Amino]- 6-Methylpyridin-2-Yl]Carbamothioyl]Carbamate


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 Ethyl N-[[4-[[4-(Azetidine-1-Carbonyl)-2-Methylpyrazole-3-Carbonyl]Amino]- 6-Methylpyridin-2-Yl]Carbamothioyl]Carbamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:38.8
occ:1.00
 NE2 A:HIS563 2.1 25.6 1.0
NE2 A:HIS529 2.1 38.0 1.0
OD2 A:ASP564 2.1 37.3 1.0
O A:HOH960 2.2 29.7 1.0
OD1 A:ASP674 2.2 44.9 1.0
O A:HOH957 2.5 38.6 1.0
CD2 A:HIS563 3.0 26.9 1.0
CD2 A:HIS529 3.1 35.4 1.0
CG A:ASP674 3.1 36.4 1.0
CE1 A:HIS529 3.1 35.3 1.0
CE1 A:HIS563 3.1 29.7 1.0
CG A:ASP564 3.1 33.1 1.0
OD2 A:ASP674 3.3 41.9 1.0
MG A:MG802 3.6 31.4 1.0
OD1 A:ASP564 3.7 30.3 1.0
O A:HOH986 4.1 32.6 1.0
CG A:HIS563 4.1 27.9 1.0
O A:HOH964 4.2 48.7 1.0
ND1 A:HIS529 4.2 38.0 1.0
CD2 A:HIS525 4.2 35.1 1.0
ND1 A:HIS563 4.2 27.8 1.0
CG A:HIS529 4.2 35.5 1.0
CB A:ASP564 4.3 30.1 1.0
CB A:ASP674 4.4 36.7 1.0
O A:HOH919 4.5 26.2 1.0
NE2 A:HIS525 4.5 34.6 1.0
O A:HOH988 4.6 56.4 1.0
CG2 A:VAL533 4.8 27.5 1.0
O A:ASP674 4.9 38.6 1.0
CA A:ASP674 4.9 33.4 1.0
O A:HOH946 4.9 30.8 1.0

Zinc binding site 2 out of 4 in 5sjp

Go back to Zinc Binding Sites List in 5sjp
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl N-[[4-[[4-(Azetidine-1-Carbonyl)-2-Methylpyrazole-3-Carbonyl]Amino]- 6-Methylpyridin-2-Yl]Carbamothioyl]Carbamate


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 Ethyl N-[[4-[[4-(Azetidine-1-Carbonyl)-2-Methylpyrazole-3-Carbonyl]Amino]- 6-Methylpyridin-2-Yl]Carbamothioyl]Carbamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:38.5
occ:1.00
 O B:HOH942 2.1 27.1 1.0
OD2 B:ASP564 2.1 32.4 1.0
NE2 B:HIS563 2.1 31.8 1.0
NE2 B:HIS529 2.2 34.1 1.0
OD1 B:ASP674 2.2 36.0 1.0
O B:HOH940 2.5 41.0 1.0
CD2 B:HIS563 3.1 32.6 1.0
CG B:ASP674 3.1 31.8 1.0
CE1 B:HIS529 3.1 33.3 1.0
CG B:ASP564 3.2 27.4 1.0
CE1 B:HIS563 3.2 34.5 1.0
CD2 B:HIS529 3.2 34.6 1.0
OD2 B:ASP674 3.3 34.2 1.0
OD1 B:ASP564 3.7 33.9 1.0
MG B:MG802 3.7 26.5 1.0
O B:HOH984 3.9 26.6 1.0
CD2 B:HIS525 4.1 34.8 1.0
CG B:HIS563 4.2 30.8 1.0
ND1 B:HIS529 4.3 30.3 1.0
ND1 B:HIS563 4.3 32.7 1.0
CB B:ASP564 4.3 27.2 1.0
CG B:HIS529 4.3 32.1 1.0
O B:HOH960 4.3 44.6 1.0
CB B:ASP674 4.4 32.4 1.0
NE2 B:HIS525 4.4 37.8 1.0
O B:HOH1002 4.6 53.0 1.0
O B:HOH925 4.6 32.1 1.0
CG2 B:VAL533 4.8 25.5 1.0
O B:ASP674 4.8 34.2 1.0
CA B:ASP674 4.9 30.6 1.0

Zinc binding site 3 out of 4 in 5sjp

Go back to Zinc Binding Sites List in 5sjp
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl N-[[4-[[4-(Azetidine-1-Carbonyl)-2-Methylpyrazole-3-Carbonyl]Amino]- 6-Methylpyridin-2-Yl]Carbamothioyl]Carbamate


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 Ethyl N-[[4-[[4-(Azetidine-1-Carbonyl)-2-Methylpyrazole-3-Carbonyl]Amino]- 6-Methylpyridin-2-Yl]Carbamothioyl]Carbamate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:40.1
occ:1.00
 O C:HOH964 2.0 25.7 1.0
OD2 C:ASP564 2.1 35.7 1.0
NE2 C:HIS529 2.2 32.4 1.0
NE2 C:HIS563 2.2 33.1 1.0
OD1 C:ASP674 2.2 32.6 1.0
O C:HOH938 2.3 36.6 1.0
CD2 C:HIS563 3.0 27.6 1.0
CG C:ASP674 3.1 32.3 1.0
CG C:ASP564 3.1 34.2 1.0
CD2 C:HIS529 3.1 34.3 1.0
CE1 C:HIS529 3.2 36.0 1.0
CE1 C:HIS563 3.3 30.4 1.0
OD2 C:ASP674 3.4 35.9 1.0
OD1 C:ASP564 3.6 33.3 1.0
MG C:MG802 3.7 31.6 1.0
CD2 C:HIS525 4.0 40.2 1.0
O C:HOH987 4.1 34.5 1.0
O C:HOH994 4.2 41.9 1.0
CG C:HIS563 4.2 27.8 1.0
ND1 C:HIS529 4.3 32.8 1.0
NE2 C:HIS525 4.3 35.8 1.0
CG C:HIS529 4.3 31.5 1.0
O C:HOH1005 4.3 44.9 1.0
ND1 C:HIS563 4.3 26.7 1.0
CB C:ASP564 4.3 30.6 1.0
CB C:ASP674 4.4 32.3 1.0
O C:HOH935 4.5 32.8 1.0
CA C:ASP674 4.8 31.9 1.0
CG2 C:VAL533 5.0 30.5 1.0
O C:ASP674 5.0 35.6 1.0

Zinc binding site 4 out of 4 in 5sjp

Go back to Zinc Binding Sites List in 5sjp
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl N-[[4-[[4-(Azetidine-1-Carbonyl)-2-Methylpyrazole-3-Carbonyl]Amino]- 6-Methylpyridin-2-Yl]Carbamothioyl]Carbamate


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 Ethyl N-[[4-[[4-(Azetidine-1-Carbonyl)-2-Methylpyrazole-3-Carbonyl]Amino]- 6-Methylpyridin-2-Yl]Carbamothioyl]Carbamate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:52.3
occ:1.00
 O D:HOH926 2.0 33.8 1.0
OD1 D:ASP674 2.1 55.4 1.0
NE2 D:HIS563 2.2 38.0 1.0
OD2 D:ASP564 2.2 48.2 1.0
NE2 D:HIS529 2.2 53.4 1.0
O D:HOH911 2.5 49.1 1.0
CD2 D:HIS563 3.0 47.7 1.0
CG D:ASP674 3.1 47.0 1.0
CD2 D:HIS529 3.2 53.4 1.0
CG D:ASP564 3.2 47.7 1.0
CE1 D:HIS563 3.2 48.4 1.0
CE1 D:HIS529 3.3 52.3 1.0
OD2 D:ASP674 3.4 46.4 1.0
MG D:MG802 3.8 44.4 1.0
OD1 D:ASP564 3.8 46.6 1.0
O D:HOH937 4.1 40.7 1.0
CD2 D:HIS525 4.1 54.3 1.0
O D:HOH916 4.2 52.6 1.0
CG D:HIS563 4.2 46.2 1.0
ND1 D:HIS563 4.3 43.1 1.0
CB D:ASP564 4.3 46.3 1.0
CG D:HIS529 4.3 50.7 1.0
ND1 D:HIS529 4.4 52.2 1.0
NE2 D:HIS525 4.4 59.7 1.0
CB D:ASP674 4.4 50.4 1.0
O D:ASP674 4.7 66.4 1.0
CG2 D:VAL533 4.8 53.1 1.0
CA D:ASP674 4.9 48.4 1.0
O D:HOH905 4.9 40.8 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 06:06:32 2024

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