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Magnesium 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:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5skj

Go back to Magnesium Binding Sites List in 5skj
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg802

b:40.1
occ:1.00
 O A:HOH932 1.6 20.8 1.0
O A:HOH910 1.9 32.1 1.0
O A:HOH920 1.9 24.8 1.0
O A:HOH925 2.0 24.5 1.0
O A:HOH919 2.1 21.3 1.0
OD1 A:ASP564 2.2 24.9 1.0
CG A:ASP564 3.1 26.9 1.0
OD2 A:ASP564 3.2 30.9 1.0
ZN A:ZN801 3.7 37.1 1.0
O A:HOH912 4.1 28.4 1.0
OE2 A:GLU592 4.1 49.6 1.0
CD2 A:HIS563 4.2 29.9 1.0
O A:THR633 4.2 31.5 1.0
OG1 A:THR633 4.2 29.0 1.0
CD2 A:HIS567 4.3 32.8 1.0
NE2 A:HIS595 4.3 28.1 1.0
NE2 A:HIS567 4.5 34.3 1.0
OD2 A:ASP674 4.5 37.5 1.0
CB A:ASP564 4.5 26.8 1.0
NE2 A:HIS563 4.5 27.4 1.0
NE2 A:HIS525 4.5 31.7 1.0
CD2 A:HIS595 4.6 26.4 1.0
CD2 A:HIS525 4.6 30.7 1.0
CG A:GLU592 4.7 40.0 1.0
CB A:THR633 4.7 30.3 1.0
O A:HIS563 4.7 32.6 1.0
O A:HOH964 4.7 27.8 1.0
CD A:GLU592 4.7 42.7 1.0
CA A:ASP564 5.0 28.9 1.0

Magnesium binding site 2 out of 4 in 5skj

Go back to Magnesium Binding Sites List in 5skj
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg802

b:33.8
occ:1.00
 O B:HOH937 1.6 20.5 1.0
O B:HOH912 1.8 20.3 1.0
O B:HOH935 1.9 23.7 1.0
O B:HOH955 1.9 22.9 1.0
O B:HOH905 2.2 22.4 1.0
OD1 B:ASP564 2.5 30.9 1.0
CG B:ASP564 3.4 29.4 1.0
OE2 B:GLU592 3.7 27.8 1.0
OD2 B:ASP564 3.7 31.3 1.0
ZN B:ZN801 3.9 35.1 1.0
OG1 B:THR633 4.0 33.9 1.0
O B:HOH914 4.1 24.8 1.0
NE2 B:HIS595 4.2 39.9 1.0
CD2 B:HIS563 4.2 36.5 1.0
OD2 B:ASP674 4.3 32.8 1.0
O B:THR633 4.3 28.7 1.0
CD2 B:HIS595 4.4 42.6 1.0
CD2 B:HIS567 4.5 32.8 1.0
CB B:THR633 4.6 33.8 1.0
CD B:GLU592 4.6 27.8 1.0
CG B:GLU592 4.6 30.8 1.0
O B:HIS563 4.6 34.2 1.0
NE2 B:HIS567 4.6 33.0 1.0
CD2 B:HIS525 4.7 39.3 1.0
NE2 B:HIS563 4.7 36.2 1.0
CB B:ASP564 4.8 26.6 1.0
NE2 B:HIS525 4.8 37.1 1.0
C B:THR633 4.9 27.7 1.0
CA B:ASP564 5.0 27.7 1.0

Magnesium binding site 3 out of 4 in 5skj

Go back to Magnesium Binding Sites List in 5skj
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg802

b:34.2
occ:1.00
 O C:HOH957 1.8 28.8 1.0
O C:HOH926 1.8 27.0 1.0
O C:HOH915 1.9 26.4 1.0
O C:HOH928 2.0 21.8 1.0
O C:HOH922 2.1 21.9 1.0
OD1 C:ASP564 2.3 31.3 1.0
CG C:ASP564 3.2 32.4 1.0
OD2 C:ASP564 3.4 36.2 1.0
ZN C:ZN801 3.8 36.7 1.0
OE2 C:GLU592 3.9 35.8 1.0
O C:HOH907 4.0 25.4 1.0
NE2 C:HIS595 4.2 38.3 1.0
CD2 C:HIS563 4.3 27.8 1.0
OD2 C:ASP674 4.3 33.8 1.0
CD2 C:HIS567 4.3 33.6 1.0
O C:HIS563 4.4 27.9 1.0
NE2 C:HIS567 4.4 33.5 1.0
OG1 C:THR633 4.4 31.6 1.0
O C:THR633 4.5 35.8 1.0
CD2 C:HIS595 4.5 33.1 1.0
CB C:THR633 4.6 32.7 1.0
CB C:ASP564 4.6 30.9 1.0
NE2 C:HIS563 4.7 28.9 1.0
CG C:GLU592 4.7 30.9 1.0
CD C:GLU592 4.7 32.6 1.0
O C:HOH961 4.8 35.1 1.0
NE2 C:HIS525 4.8 40.1 1.0
CD2 C:HIS525 4.9 37.9 1.0
OD1 C:ASP674 4.9 35.2 1.0
CG C:ASP674 5.0 31.5 1.0

Magnesium binding site 4 out of 4 in 5skj

Go back to Magnesium Binding Sites List in 5skj
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg802

b:45.8
occ:1.00
 O D:HOH913 1.7 42.8 1.0
OD1 D:ASP564 2.0 40.5 1.0
O D:HOH907 2.3 33.5 1.0
O D:HOH919 2.4 39.4 1.0
O D:HOH915 2.6 35.7 1.0
O D:HOH918 3.1 37.6 1.0
CG D:ASP564 3.2 45.5 1.0
NE2 D:HIS595 3.4 48.8 1.0
CD2 D:HIS567 3.6 44.2 1.0
OE2 D:GLU592 3.6 54.5 1.0
NE2 D:HIS567 3.8 46.6 1.0
CD2 D:HIS595 3.8 53.1 1.0
OD2 D:ASP564 3.9 51.3 1.0
O D:HIS563 4.3 42.7 1.0
ZN D:ZN801 4.3 51.2 1.0
CB D:ASP564 4.4 45.9 1.0
CE1 D:HIS595 4.5 47.0 1.0
CA D:ASP564 4.6 46.2 1.0
CD D:GLU592 4.6 52.1 1.0
CD2 D:HIS525 4.7 49.5 1.0
OG1 D:THR633 4.7 41.9 1.0
CD2 D:HIS563 4.8 38.3 1.0
NE2 D:HIS525 4.9 50.5 1.0
CG D:HIS567 4.9 46.0 1.0
O D:THR633 4.9 50.0 1.0
CG D:GLU592 5.0 47.3 1.0
CG D:HIS595 5.0 47.0 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 Sep 30 04:35:11 2024

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