Atomistry » Magnesium » PDB 5ser-5sfu » 5sfj
Atomistry »
  Magnesium »
    PDB 5ser-5sfu »
      5sfj »

Magnesium in PDB 5sfj: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)-4-N-(Pyridin-2- Ylmethyl)Pyrazole-3,4-Dicarboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)-4-N-(Pyridin-2- Ylmethyl)Pyrazole-3,4-Dicarboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)-4-N-(Pyridin-2- Ylmethyl)Pyrazole-3,4-Dicarboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)-4-N-(Pyridin-2- Ylmethyl)Pyrazole-3,4-Dicarboxamide, PDB code: 5sfj was solved by C.Joseph, J.U.Peters, J.Benz, D.Schlatter, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.65 / 2.41
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.771, 134.771, 235.33, 90, 90, 120
R / Rfree (%) 18.6 / 24.5

Other elements in 5sfj:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)-4-N-(Pyridin-2- Ylmethyl)Pyrazole-3,4-Dicarboxamide 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-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)-4-N-(Pyridin-2- Ylmethyl)Pyrazole-3,4-Dicarboxamide (pdb code 5sfj). 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-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)-4-N-(Pyridin-2- Ylmethyl)Pyrazole-3,4-Dicarboxamide, PDB code: 5sfj:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sfj

Go back to Magnesium Binding Sites List in 5sfj
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)-4-N-(Pyridin-2- Ylmethyl)Pyrazole-3,4-Dicarboxamide


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-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)-4-N-(Pyridin-2- Ylmethyl)Pyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:30.5
occ:1.00
 OD1 A:ASP564 1.9 30.0 1.0
O A:HOH956 1.9 27.1 1.0
O A:HOH936 2.0 34.9 1.0
O A:HOH912 2.0 25.1 1.0
O A:HOH915 2.3 32.8 1.0
O A:HOH925 2.3 24.9 1.0
CG A:ASP564 2.8 31.9 1.0
OD2 A:ASP564 3.1 34.0 1.0
O A:HOH948 3.7 42.6 1.0
ZN A:ZN801 3.7 42.1 1.0
NE2 A:HIS595 4.0 33.2 1.0
CD2 A:HIS563 4.1 35.1 1.0
CB A:ASP564 4.2 31.3 1.0
CD2 A:HIS567 4.2 36.7 1.0
OE2 A:GLU592 4.2 41.1 1.0
OG1 A:THR633 4.3 32.0 1.0
CD2 A:HIS595 4.3 35.7 1.0
O A:HIS563 4.3 31.9 1.0
NE2 A:HIS567 4.4 39.2 1.0
NE2 A:HIS563 4.5 32.6 1.0
O A:HOH951 4.5 31.8 1.0
OD2 A:ASP674 4.6 44.1 1.0
O A:THR633 4.6 35.2 1.0
CA A:ASP564 4.7 34.2 1.0
CD2 A:HIS525 4.7 39.8 1.0
NE2 A:HIS525 4.7 38.9 1.0
CG A:GLU592 4.8 36.3 1.0
CB A:THR633 4.8 29.1 1.0
CD A:GLU592 4.9 39.2 1.0

Magnesium binding site 2 out of 4 in 5sfj

Go back to Magnesium Binding Sites List in 5sfj
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)-4-N-(Pyridin-2- Ylmethyl)Pyrazole-3,4-Dicarboxamide


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-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)-4-N-(Pyridin-2- Ylmethyl)Pyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:30.7
occ:1.00
 O B:HOH923 1.8 30.3 1.0
O B:HOH949 2.0 29.6 1.0
O B:HOH927 2.0 22.9 1.0
OD1 B:ASP564 2.0 31.7 1.0
O B:HOH902 2.1 22.4 1.0
O B:HOH968 2.1 22.8 1.0
CG B:ASP564 3.0 31.0 1.0
OD2 B:ASP564 3.4 38.4 1.0
ZN B:ZN801 3.7 36.1 1.0
OE2 B:GLU592 3.9 33.8 1.0
NE2 B:HIS595 4.0 37.0 1.0
OG1 B:THR633 4.0 34.5 1.0
CD2 B:HIS563 4.1 31.3 1.0
O B:HIS563 4.2 33.9 1.0
O B:HOH963 4.2 35.6 1.0
O B:HOH936 4.3 28.8 1.0
CD2 B:HIS595 4.3 38.1 1.0
OD2 B:ASP674 4.4 37.6 1.0
CB B:ASP564 4.4 30.7 1.0
CD2 B:HIS567 4.4 29.6 1.0
NE2 B:HIS567 4.5 32.0 1.0
NE2 B:HIS563 4.5 30.7 1.0
CD2 B:HIS525 4.6 37.4 1.0
O B:THR633 4.6 30.1 1.0
CB B:THR633 4.7 34.9 1.0
CA B:ASP564 4.8 32.5 1.0
NE2 B:HIS525 4.8 29.1 1.0
CD B:GLU592 4.8 36.3 1.0
CG B:GLU592 4.9 35.8 1.0

Magnesium binding site 3 out of 4 in 5sfj

Go back to Magnesium Binding Sites List in 5sfj
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)-4-N-(Pyridin-2- Ylmethyl)Pyrazole-3,4-Dicarboxamide


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-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)-4-N-(Pyridin-2- Ylmethyl)Pyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:30.0
occ:1.00
 O C:HOH907 1.9 29.1 1.0
O C:HOH931 2.0 37.1 1.0
OD1 C:ASP564 2.1 31.5 1.0
O C:HOH961 2.1 30.0 1.0
O C:HOH958 2.1 28.6 1.0
O C:HOH916 2.3 22.1 1.0
CG C:ASP564 3.0 31.7 1.0
OD2 C:ASP564 3.4 33.5 1.0
ZN C:ZN801 3.7 42.6 1.0
NE2 C:HIS595 4.1 41.5 1.0
CD2 C:HIS563 4.1 30.4 1.0
CD2 C:HIS567 4.2 36.2 1.0
OD2 C:ASP674 4.2 32.4 1.0
OE2 C:GLU592 4.2 34.9 1.0
O C:HOH938 4.4 37.6 1.0
CB C:ASP564 4.4 27.8 1.0
OG1 C:THR633 4.4 34.5 1.0
CD2 C:HIS595 4.4 40.1 1.0
NE2 C:HIS567 4.4 39.4 1.0
O C:HIS563 4.4 37.5 1.0
NE2 C:HIS563 4.4 31.9 1.0
O C:THR633 4.5 42.6 1.0
CB C:THR633 4.8 38.8 1.0
CA C:ASP564 4.8 29.0 1.0
CG C:GLU592 4.8 36.1 1.0
CD2 C:HIS525 4.8 47.1 1.0
NE2 C:HIS525 4.8 50.1 1.0
CD C:GLU592 4.9 36.6 1.0

Magnesium binding site 4 out of 4 in 5sfj

Go back to Magnesium Binding Sites List in 5sfj
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)-4-N-(Pyridin-2- Ylmethyl)Pyrazole-3,4-Dicarboxamide


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-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)-4-N-(Pyridin-2- Ylmethyl)Pyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:46.9
occ:1.00
 O D:HOH902 2.0 38.8 1.0
O D:HOH904 2.1 48.0 1.0
O D:HOH912 2.1 35.7 1.0
O D:HOH915 2.1 51.3 1.0
O D:HOH916 2.1 36.7 1.0
OD1 D:ASP564 2.3 50.4 1.0
CG D:ASP564 3.2 52.9 1.0
OD2 D:ASP564 3.4 58.2 1.0
O D:HOH914 3.5 41.2 1.0
ZN D:ZN801 3.6 56.4 1.0
OD2 D:ASP674 4.1 46.7 1.0
CD2 D:HIS563 4.2 42.4 1.0
OG1 D:THR633 4.2 45.7 1.0
OE2 D:GLU592 4.3 47.0 1.0
NE2 D:HIS595 4.4 53.1 1.0
CD2 D:HIS567 4.4 55.5 1.0
O D:THR633 4.5 51.0 1.0
CB D:ASP564 4.5 50.0 1.0
NE2 D:HIS563 4.6 41.3 1.0
O D:HIS563 4.6 43.0 1.0
NE2 D:HIS567 4.6 55.6 1.0
CD2 D:HIS595 4.7 57.3 1.0
CD2 D:HIS525 4.7 54.6 1.0
CB D:THR633 4.7 47.1 1.0
NE2 D:HIS525 4.8 53.5 1.0
CA D:ASP564 4.8 46.3 1.0
OD1 D:ASP674 4.9 45.0 1.0
CG D:ASP674 4.9 45.6 1.0

Reference:

A.Tosstorff, M.G.Rudolph, J.C.Cole, M.Reutlinger, C.Kramer, H.Schaffhauser, A.Nilly, A.Flohr, B.Kuhn. A High Quality, Industrial Data Set For Binding Affinity Prediction: Performance Comparison in Different Early Drug Discovery Scenarios. J.Comput.Aided Mol.Des. V. 36 753 2022.
ISSN: ESSN 1573-4951
PubMed: 36153472
DOI: 10.1007/S10822-022-00478-X
Page generated: Mon Sep 30 03:35:59 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy