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Zinc in PDB 5skk: Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[1- Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-6-[(3S)-Oxolan-3-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[1- Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-6-[(3S)-Oxolan-3-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[1- Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-6-[(3S)-Oxolan-3-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[1- Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-6-[(3S)-Oxolan-3-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide, PDB code: 5skk was solved by C.Joseph, J.Benz, A.Flohr, M.Koerner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.62 / 2.15
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.136, 135.136, 235.033, 90, 90, 120
R / Rfree (%) 19 / 24.2

Other elements in 5skk:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[1- Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-6-[(3S)-Oxolan-3-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide 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 N-[1- Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-6-[(3S)-Oxolan-3-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide (pdb code 5skk). 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-[1- Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-6-[(3S)-Oxolan-3-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide, PDB code: 5skk:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5skk

Go back to Zinc Binding Sites List in 5skk
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[1- Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-6-[(3S)-Oxolan-3-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide


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-[1- Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-6-[(3S)-Oxolan-3-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:37.3
occ:1.00
 OD2 A:ASP564 2.1 35.4 1.0
OD1 A:ASP674 2.1 39.3 1.0
NE2 A:HIS529 2.1 33.9 1.0
O A:HOH957 2.2 27.9 1.0
NE2 A:HIS563 2.2 31.7 1.0
O A:HOH973 2.5 40.6 1.0
CD2 A:HIS563 3.0 31.1 1.0
CG A:ASP674 3.0 35.8 1.0
CE1 A:HIS529 3.1 31.4 1.0
CG A:ASP564 3.1 35.4 1.0
CD2 A:HIS529 3.2 32.2 1.0
OD2 A:ASP674 3.3 43.2 1.0
CE1 A:HIS563 3.3 37.0 1.0
OD1 A:ASP564 3.7 34.8 1.0
MG A:MG802 3.7 35.9 1.0
O A:HOH934 4.1 39.6 1.0
O A:HOH976 4.1 30.2 1.0
CD2 A:HIS525 4.2 37.3 1.0
CG A:HIS563 4.2 31.1 1.0
ND1 A:HIS529 4.2 32.1 1.0
CB A:ASP564 4.3 35.3 1.0
CG A:HIS529 4.3 32.8 1.0
ND1 A:HIS563 4.3 32.3 1.0
CB A:ASP674 4.4 32.1 1.0
NE2 A:HIS525 4.5 36.0 1.0
O A:HOH927 4.6 30.1 1.0
O A:ASP674 4.7 36.9 1.0
CG2 A:VAL533 4.7 25.6 1.0
CA A:ASP674 4.9 29.5 1.0

Zinc binding site 2 out of 4 in 5skk

Go back to Zinc Binding Sites List in 5skk
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[1- Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-6-[(3S)-Oxolan-3-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide


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-[1- Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-6-[(3S)-Oxolan-3-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:35.5
occ:1.00
 NE2 B:HIS563 2.0 28.7 1.0
OD2 B:ASP564 2.1 34.7 1.0
O B:HOH950 2.2 23.4 1.0
OD1 B:ASP674 2.2 33.6 1.0
NE2 B:HIS529 2.3 29.7 1.0
O B:HOH933 2.5 47.6 1.0
CD2 B:HIS563 3.0 30.6 1.0
CG B:ASP564 3.1 30.9 1.0
CD2 B:HIS529 3.1 28.3 1.0
CE1 B:HIS563 3.1 34.0 1.0
CG B:ASP674 3.1 35.3 1.0
OD2 B:ASP674 3.3 34.7 1.0
CE1 B:HIS529 3.3 32.9 1.0
OD1 B:ASP564 3.5 30.6 1.0
MG B:MG802 3.7 30.6 1.0
O B:HOH993 4.0 24.2 1.0
CD2 B:HIS525 4.0 30.7 1.0
O B:HOH963 4.0 38.7 1.0
CG B:HIS563 4.1 28.9 1.0
ND1 B:HIS563 4.2 29.2 1.0
CB B:ASP564 4.3 31.4 1.0
CG B:HIS529 4.3 30.4 1.0
NE2 B:HIS525 4.4 29.2 1.0
ND1 B:HIS529 4.4 29.1 1.0
CB B:ASP674 4.5 31.0 1.0
O B:HOH941 4.7 33.4 1.0
O B:HOH999 4.7 48.2 1.0
CG2 B:VAL533 4.7 30.1 1.0
O B:ASP674 4.8 34.1 1.0
CA B:ASP674 4.9 30.1 1.0

Zinc binding site 3 out of 4 in 5skk

Go back to Zinc Binding Sites List in 5skk
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[1- Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-6-[(3S)-Oxolan-3-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide


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-[1- Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-6-[(3S)-Oxolan-3-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:40.7
occ:1.00
 O C:HOH921 2.0 28.8 1.0
NE2 C:HIS563 2.1 34.1 1.0
OD2 C:ASP564 2.1 32.3 1.0
NE2 C:HIS529 2.2 32.8 1.0
OD1 C:ASP674 2.2 36.7 1.0
O C:HOH946 2.5 47.8 1.0
CD2 C:HIS563 2.9 31.2 1.0
CG C:ASP674 3.0 34.7 1.0
CD2 C:HIS529 3.1 34.6 1.0
CG C:ASP564 3.1 31.5 1.0
OD2 C:ASP674 3.2 28.8 1.0
CE1 C:HIS563 3.2 30.8 1.0
CE1 C:HIS529 3.3 34.7 1.0
OD1 C:ASP564 3.6 31.3 1.0
MG C:MG802 3.7 30.9 1.0
O C:HOH971 4.0 33.9 1.0
CD2 C:HIS525 4.1 41.8 1.0
CG C:HIS563 4.1 34.7 1.0
ND1 C:HIS563 4.2 30.4 1.0
O C:HOH966 4.3 38.7 1.0
CG C:HIS529 4.3 34.6 1.0
CB C:ASP564 4.3 29.9 1.0
ND1 C:HIS529 4.3 32.8 1.0
CB C:ASP674 4.4 36.7 1.0
NE2 C:HIS525 4.5 45.0 1.0
O C:HOH916 4.6 36.9 1.0
O C:ASP674 4.7 38.9 1.0
CG2 C:VAL533 4.7 33.8 1.0
O C:HOH982 4.8 46.2 1.0
CA C:ASP674 4.8 38.1 1.0

Zinc binding site 4 out of 4 in 5skk

Go back to Zinc Binding Sites List in 5skk
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[1- Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-6-[(3S)-Oxolan-3-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide


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-[1- Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-6-[(3S)-Oxolan-3-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:46.7
occ:1.00
 O D:HOH924 2.0 33.9 1.0
NE2 D:HIS563 2.1 34.0 1.0
OD2 D:ASP564 2.2 46.8 1.0
NE2 D:HIS529 2.2 42.5 1.0
OD1 D:ASP674 2.2 39.1 1.0
O D:HOH926 2.6 41.4 1.0
CD2 D:HIS563 3.1 35.9 1.0
CG D:ASP564 3.1 38.0 1.0
CD2 D:HIS529 3.1 39.0 1.0
CG D:ASP674 3.1 38.8 1.0
CE1 D:HIS563 3.2 37.0 1.0
CE1 D:HIS529 3.2 43.3 1.0
OD2 D:ASP674 3.4 40.5 1.0
MG D:MG802 3.6 40.8 1.0
OD1 D:ASP564 3.7 42.0 1.0
O D:HOH917 4.0 40.4 1.0
O D:HOH956 4.1 36.4 1.0
CD2 D:HIS525 4.1 49.7 1.0
CB D:ASP564 4.2 38.4 1.0
CG D:HIS563 4.2 36.6 1.0
ND1 D:HIS563 4.3 34.9 1.0
CG D:HIS529 4.3 38.3 1.0
ND1 D:HIS529 4.3 39.4 1.0
CB D:ASP674 4.5 40.4 1.0
O D:HOH922 4.6 39.6 1.0
NE2 D:HIS525 4.6 53.8 1.0
O D:ASP674 4.7 45.7 1.0
CG2 D:VAL533 4.8 40.7 1.0
CA D:ASP674 4.8 38.0 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 07:37:52 2024

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