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Magnesium in PDB 5sjz: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-(Morpholine-4-Carbonyl)-N-(2-Pyrrolidin-1-Yl-[1,2, 4]Triazolo[1,5-A]Pyridin-7-Yl)Pyrazole-3-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-(Morpholine-4-Carbonyl)-N-(2-Pyrrolidin-1-Yl-[1,2, 4]Triazolo[1,5-A]Pyridin-7-Yl)Pyrazole-3-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-(Morpholine-4-Carbonyl)-N-(2-Pyrrolidin-1-Yl-[1,2, 4]Triazolo[1,5-A]Pyridin-7-Yl)Pyrazole-3-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-(Morpholine-4-Carbonyl)-N-(2-Pyrrolidin-1-Yl-[1,2, 4]Triazolo[1,5-A]Pyridin-7-Yl)Pyrazole-3-Carboxamide, PDB code: 5sjz was solved by C.Joseph, J.Benz, A.Flohr, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.48 / 2.19
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.161, 135.161, 235.97, 90, 90, 120
R / Rfree (%) 17 / 22.6

Other elements in 5sjz:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-(Morpholine-4-Carbonyl)-N-(2-Pyrrolidin-1-Yl-[1,2, 4]Triazolo[1,5-A]Pyridin-7-Yl)Pyrazole-3-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 2- Methyl-4-(Morpholine-4-Carbonyl)-N-(2-Pyrrolidin-1-Yl-[1,2, 4]Triazolo[1,5-A]Pyridin-7-Yl)Pyrazole-3-Carboxamide (pdb code 5sjz). 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 2- Methyl-4-(Morpholine-4-Carbonyl)-N-(2-Pyrrolidin-1-Yl-[1,2, 4]Triazolo[1,5-A]Pyridin-7-Yl)Pyrazole-3-Carboxamide, PDB code: 5sjz:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sjz

Go back to Magnesium Binding Sites List in 5sjz
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-(Morpholine-4-Carbonyl)-N-(2-Pyrrolidin-1-Yl-[1,2, 4]Triazolo[1,5-A]Pyridin-7-Yl)Pyrazole-3-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 2- Methyl-4-(Morpholine-4-Carbonyl)-N-(2-Pyrrolidin-1-Yl-[1,2, 4]Triazolo[1,5-A]Pyridin-7-Yl)Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:35.6
occ:1.00
 O A:HOH983 2.0 32.7 1.0
OD1 A:ASP564 2.0 37.2 1.0
O A:HOH970 2.0 31.1 1.0
O A:HOH942 2.1 30.8 1.0
O A:HOH931 2.1 36.5 1.0
O A:HOH940 2.2 31.6 1.0
CG A:ASP564 3.0 39.1 1.0
OD2 A:ASP564 3.4 46.3 1.0
ZN A:ZN801 3.8 39.4 1.0
NE2 A:HIS595 3.9 34.4 1.0
O A:HOH965 4.0 38.5 1.0
OE2 A:GLU592 4.1 36.9 1.0
O A:HOH971 4.1 41.8 1.0
CD2 A:HIS567 4.3 36.8 1.0
O A:HIS563 4.3 36.6 1.0
CD2 A:HIS595 4.3 34.5 1.0
CD2 A:HIS563 4.3 30.4 1.0
CB A:ASP564 4.3 37.0 1.0
OG1 A:THR633 4.4 38.2 1.0
O A:HOH949 4.4 50.6 1.0
CD2 A:HIS525 4.5 43.4 1.0
NE2 A:HIS567 4.5 33.7 1.0
NE2 A:HIS525 4.5 36.2 1.0
O A:THR633 4.6 41.3 1.0
NE2 A:HIS563 4.7 29.8 1.0
OD2 A:ASP674 4.7 44.2 1.0
CA A:ASP564 4.7 34.3 1.0
CG A:GLU592 4.8 35.7 1.0
CB A:THR633 4.8 34.6 1.0
CD A:GLU592 4.9 40.6 1.0

Magnesium binding site 2 out of 4 in 5sjz

Go back to Magnesium Binding Sites List in 5sjz
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-(Morpholine-4-Carbonyl)-N-(2-Pyrrolidin-1-Yl-[1,2, 4]Triazolo[1,5-A]Pyridin-7-Yl)Pyrazole-3-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 2- Methyl-4-(Morpholine-4-Carbonyl)-N-(2-Pyrrolidin-1-Yl-[1,2, 4]Triazolo[1,5-A]Pyridin-7-Yl)Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:32.3
occ:1.00
 O B:HOH947 1.9 28.5 1.0
O B:HOH944 2.0 35.0 1.0
O B:HOH996 2.0 29.8 1.0
OD1 B:ASP564 2.1 37.2 1.0
O B:HOH929 2.1 31.3 1.0
O B:HOH945 2.2 29.9 1.0
CG B:ASP564 3.1 32.0 1.0
OD2 B:ASP564 3.4 36.8 1.0
ZN B:ZN801 3.7 38.6 1.0
O B:HOH989 4.0 41.8 1.0
OE2 B:GLU592 4.0 35.2 1.0
NE2 B:HIS595 4.2 33.7 1.0
O B:HOH1006 4.2 47.1 1.0
CD2 B:HIS563 4.2 32.0 1.0
O B:HOH972 4.2 37.1 1.0
OG1 B:THR633 4.2 31.5 1.0
CD2 B:HIS567 4.3 34.4 1.0
O B:HIS563 4.4 35.5 1.0
OD2 B:ASP674 4.4 35.2 1.0
NE2 B:HIS567 4.4 33.1 1.0
CB B:ASP564 4.5 30.6 1.0
NE2 B:HIS563 4.5 29.9 1.0
CD2 B:HIS595 4.5 39.6 1.0
CD2 B:HIS525 4.5 37.2 1.0
O B:THR633 4.6 33.2 1.0
NE2 B:HIS525 4.7 35.9 1.0
CG B:GLU592 4.7 35.0 1.0
CB B:THR633 4.8 33.0 1.0
CA B:ASP564 4.8 33.7 1.0
CD B:GLU592 4.8 38.6 1.0

Magnesium binding site 3 out of 4 in 5sjz

Go back to Magnesium Binding Sites List in 5sjz
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-(Morpholine-4-Carbonyl)-N-(2-Pyrrolidin-1-Yl-[1,2, 4]Triazolo[1,5-A]Pyridin-7-Yl)Pyrazole-3-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 2- Methyl-4-(Morpholine-4-Carbonyl)-N-(2-Pyrrolidin-1-Yl-[1,2, 4]Triazolo[1,5-A]Pyridin-7-Yl)Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:31.6
occ:1.00
 O C:HOH951 2.0 26.0 1.0
O C:HOH952 2.0 31.4 1.0
OD1 C:ASP564 2.0 35.4 1.0
O C:HOH954 2.0 29.6 1.0
O C:HOH927 2.1 33.7 1.0
O C:HOH968 2.2 28.6 1.0
CG C:ASP564 3.1 34.8 1.0
OD2 C:ASP564 3.6 37.4 1.0
OE2 C:GLU592 3.9 39.3 1.0
ZN C:ZN801 3.9 40.9 1.0
NE2 C:HIS595 4.0 40.6 1.0
O C:HOH978 4.1 41.6 1.0
OG1 C:THR633 4.2 32.4 1.0
CD2 C:HIS567 4.2 38.5 1.0
O C:HIS563 4.3 31.0 1.0
O C:HOH991 4.3 45.9 1.0
O C:HOH938 4.3 41.9 1.0
CD2 C:HIS595 4.3 36.6 1.0
CD2 C:HIS563 4.3 33.1 1.0
NE2 C:HIS567 4.4 38.8 1.0
CB C:ASP564 4.4 28.0 1.0
OD2 C:ASP674 4.4 37.1 1.0
O C:THR633 4.5 34.8 1.0
CB C:THR633 4.6 35.3 1.0
NE2 C:HIS525 4.7 40.6 1.0
CD2 C:HIS525 4.7 38.1 1.0
CD C:GLU592 4.7 40.7 1.0
CG C:GLU592 4.7 38.5 1.0
CA C:ASP564 4.8 30.7 1.0
NE2 C:HIS563 4.8 35.3 1.0

Magnesium binding site 4 out of 4 in 5sjz

Go back to Magnesium Binding Sites List in 5sjz
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-(Morpholine-4-Carbonyl)-N-(2-Pyrrolidin-1-Yl-[1,2, 4]Triazolo[1,5-A]Pyridin-7-Yl)Pyrazole-3-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 2- Methyl-4-(Morpholine-4-Carbonyl)-N-(2-Pyrrolidin-1-Yl-[1,2, 4]Triazolo[1,5-A]Pyridin-7-Yl)Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:41.8
occ:1.00
 O D:HOH952 1.9 48.0 1.0
O D:HOH927 2.0 40.2 1.0
OD1 D:ASP564 2.1 44.1 1.0
O D:HOH907 2.1 44.2 1.0
O D:HOH942 2.1 34.2 1.0
O D:HOH906 2.3 38.6 1.0
CG D:ASP564 3.1 42.8 1.0
OD2 D:ASP564 3.4 55.1 1.0
ZN D:ZN801 3.8 48.4 1.0
NE2 D:HIS595 3.9 44.5 1.0
OE2 D:GLU592 4.0 48.8 1.0
O D:HOH941 4.1 43.2 1.0
CD2 D:HIS567 4.1 47.3 1.0
O D:HOH943 4.1 44.3 1.0
OG1 D:THR633 4.2 39.9 1.0
CD2 D:HIS595 4.2 40.7 1.0
O D:HIS563 4.3 45.8 1.0
CD2 D:HIS563 4.4 38.8 1.0
NE2 D:HIS567 4.4 43.2 1.0
CB D:ASP564 4.4 43.2 1.0
CD2 D:HIS525 4.6 46.4 1.0
NE2 D:HIS525 4.6 50.2 1.0
OD2 D:ASP674 4.6 48.2 1.0
NE2 D:HIS563 4.7 36.6 1.0
CA D:ASP564 4.7 44.1 1.0
O D:THR633 4.8 49.9 1.0
CB D:THR633 4.8 45.8 1.0
CD D:GLU592 4.9 49.8 1.0
CE1 D:HIS595 4.9 44.0 1.0
CG D:GLU592 5.0 52.1 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 04:29:42 2024

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