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Zinc in PDB 5skj: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[2-[2-(Methylamino)-2-Oxoethyl]Phenyl]-3-(Pyrimidin-5- Ylamino)Pyridine-2-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[2-[2-(Methylamino)-2-Oxoethyl]Phenyl]-3-(Pyrimidin-5- Ylamino)Pyridine-2-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[2-[2-(Methylamino)-2-Oxoethyl]Phenyl]-3-(Pyrimidin-5- Ylamino)Pyridine-2-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[2-[2-(Methylamino)-2-Oxoethyl]Phenyl]-3-(Pyrimidin-5- Ylamino)Pyridine-2-Carboxamide, PDB code: 5skj was solved by C.Joseph, J.Benz, A.Flohr, K.Groebke-Zbinden, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.38 / 2.74
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.86, 134.86, 234.457, 90, 90, 120
R / Rfree (%) 16.6 / 24.9

Other elements in 5skj:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[2-[2-(Methylamino)-2-Oxoethyl]Phenyl]-3-(Pyrimidin-5- Ylamino)Pyridine-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 6- Cyclopropyl-N-[2-[2-(Methylamino)-2-Oxoethyl]Phenyl]-3-(Pyrimidin-5- Ylamino)Pyridine-2-Carboxamide (pdb code 5skj). 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- Cyclopropyl-N-[2-[2-(Methylamino)-2-Oxoethyl]Phenyl]-3-(Pyrimidin-5- Ylamino)Pyridine-2-Carboxamide, PDB code: 5skj:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5skj

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[2-[2-(Methylamino)-2-Oxoethyl]Phenyl]-3-(Pyrimidin-5- Ylamino)Pyridine-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 6- Cyclopropyl-N-[2-[2-(Methylamino)-2-Oxoethyl]Phenyl]-3-(Pyrimidin-5- Ylamino)Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:37.1
occ:1.00
 OD2 A:ASP564 2.0 30.9 1.0
NE2 A:HIS563 2.0 27.4 1.0
O A:HOH920 2.0 24.8 1.0
NE2 A:HIS529 2.1 30.5 1.0
OD1 A:ASP674 2.1 37.9 1.0
CD2 A:HIS563 2.9 29.9 1.0
CG A:ASP674 3.0 36.4 1.0
CD2 A:HIS529 3.0 32.2 1.0
CE1 A:HIS563 3.0 27.9 1.0
CE1 A:HIS529 3.1 32.0 1.0
CG A:ASP564 3.1 26.9 1.0
OD2 A:ASP674 3.3 37.5 1.0
MG A:MG802 3.7 40.1 1.0
OD1 A:ASP564 3.7 24.9 1.0
O A:HOH952 3.9 37.9 1.0
O A:HOH932 3.9 20.8 1.0
CG A:HIS563 4.1 27.7 1.0
ND1 A:HIS563 4.1 27.9 1.0
CD2 A:HIS525 4.1 30.7 1.0
CG A:HIS529 4.2 32.6 1.0
ND1 A:HIS529 4.2 33.0 1.0
CB A:ASP564 4.3 26.8 1.0
CB A:ASP674 4.3 35.5 1.0
NE2 A:HIS525 4.4 31.7 1.0
O A:HOH919 4.4 21.3 1.0
CG2 A:VAL533 4.7 31.4 1.0
O A:ASP674 4.7 35.5 1.0
O A:HOH910 4.8 32.1 1.0
CA A:ASP674 4.8 33.2 1.0

Zinc binding site 2 out of 4 in 5skj

Go back to Zinc Binding Sites List in 5skj
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[2-[2-(Methylamino)-2-Oxoethyl]Phenyl]-3-(Pyrimidin-5- Ylamino)Pyridine-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 6- Cyclopropyl-N-[2-[2-(Methylamino)-2-Oxoethyl]Phenyl]-3-(Pyrimidin-5- Ylamino)Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:35.1
occ:1.00
 NE2 B:HIS563 2.1 36.2 1.0
OD2 B:ASP564 2.1 31.3 1.0
NE2 B:HIS529 2.1 30.1 1.0
OD1 B:ASP674 2.2 29.3 1.0
O B:HOH937 2.3 20.5 1.0
CD2 B:HIS563 2.9 36.5 1.0
CG B:ASP674 2.9 29.1 1.0
CE1 B:HIS529 3.0 30.7 1.0
OD2 B:ASP674 3.1 32.8 1.0
CG B:ASP564 3.1 29.4 1.0
CD2 B:HIS529 3.2 29.2 1.0
CE1 B:HIS563 3.2 33.5 1.0
OD1 B:ASP564 3.7 30.9 1.0
O B:HOH955 3.8 22.9 1.0
MG B:MG802 3.9 33.8 1.0
CG B:HIS563 4.1 33.8 1.0
O B:HOH950 4.2 33.9 1.0
CD2 B:HIS525 4.2 39.3 1.0
ND1 B:HIS529 4.2 31.0 1.0
ND1 B:HIS563 4.2 33.5 1.0
CG B:HIS529 4.3 29.8 1.0
CB B:ASP564 4.3 26.6 1.0
CB B:ASP674 4.3 29.9 1.0
NE2 B:HIS525 4.4 37.1 1.0
O B:HOH912 4.5 20.3 1.0
CG2 B:VAL533 4.6 27.7 1.0
O B:ASP674 4.8 34.3 1.0
CA B:ASP674 4.8 31.2 1.0

Zinc binding site 3 out of 4 in 5skj

Go back to Zinc Binding Sites List in 5skj
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[2-[2-(Methylamino)-2-Oxoethyl]Phenyl]-3-(Pyrimidin-5- Ylamino)Pyridine-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 6- Cyclopropyl-N-[2-[2-(Methylamino)-2-Oxoethyl]Phenyl]-3-(Pyrimidin-5- Ylamino)Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:36.7
occ:1.00
 OD1 C:ASP674 1.9 35.2 1.0
OD2 C:ASP564 2.1 36.2 1.0
NE2 C:HIS563 2.1 28.9 1.0
O C:HOH928 2.1 21.8 1.0
NE2 C:HIS529 2.1 31.2 1.0
CG C:ASP674 2.9 31.5 1.0
CD2 C:HIS563 3.0 27.8 1.0
CE1 C:HIS529 3.1 33.1 1.0
CD2 C:HIS529 3.1 31.8 1.0
CG C:ASP564 3.2 32.4 1.0
CE1 C:HIS563 3.2 27.1 1.0
OD2 C:ASP674 3.3 33.8 1.0
OD1 C:ASP564 3.8 31.3 1.0
MG C:MG802 3.8 34.2 1.0
O C:HOH957 3.9 28.8 1.0
CD2 C:HIS525 4.1 37.9 1.0
CG C:HIS563 4.1 27.9 1.0
CB C:ASP674 4.2 32.6 1.0
ND1 C:HIS529 4.2 30.2 1.0
ND1 C:HIS563 4.2 24.8 1.0
CG C:HIS529 4.3 32.3 1.0
CB C:ASP564 4.3 30.9 1.0
NE2 C:HIS525 4.4 40.1 1.0
O C:HOH915 4.5 26.4 1.0
O C:ASP674 4.6 39.7 1.0
CA C:ASP674 4.7 31.3 1.0
CG2 C:VAL533 4.7 29.8 1.0

Zinc binding site 4 out of 4 in 5skj

Go back to Zinc Binding Sites List in 5skj
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[2-[2-(Methylamino)-2-Oxoethyl]Phenyl]-3-(Pyrimidin-5- Ylamino)Pyridine-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 6- Cyclopropyl-N-[2-[2-(Methylamino)-2-Oxoethyl]Phenyl]-3-(Pyrimidin-5- Ylamino)Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:51.2
occ:1.00
 OD1 D:ASP674 2.0 55.1 1.0
O D:HOH915 2.1 35.7 1.0
NE2 D:HIS563 2.1 40.3 1.0
OD2 D:ASP564 2.2 51.3 1.0
NE2 D:HIS529 2.4 47.5 1.0
CE1 D:HIS563 3.0 40.2 1.0
CG D:ASP674 3.1 51.6 1.0
CD2 D:HIS563 3.1 38.3 1.0
CG D:ASP564 3.1 45.5 1.0
CE1 D:HIS529 3.3 47.0 1.0
OD1 D:ASP564 3.5 40.5 1.0
OD2 D:ASP674 3.5 60.0 1.0
CD2 D:HIS529 3.5 48.9 1.0
O D:HOH919 3.6 39.4 1.0
ND1 D:HIS563 4.1 38.9 1.0
CG D:HIS563 4.2 36.0 1.0
O D:HOH907 4.2 33.5 1.0
CD2 D:HIS525 4.2 49.5 1.0
MG D:MG802 4.3 45.8 1.0
CB D:ASP674 4.3 56.6 1.0
CB D:ASP564 4.4 45.9 1.0
ND1 D:HIS529 4.5 46.3 1.0
O D:ASP674 4.5 48.7 1.0
CG D:HIS529 4.6 46.5 1.0
NE2 D:HIS525 4.7 50.5 1.0
O D:HOH913 4.7 42.8 1.0
CA D:ASP674 4.8 50.4 1.0
CG2 D:VAL533 4.8 50.6 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 07:35:36 2024

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