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Magnesium in PDB 5sdw: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N,4- N,2-Trimethyl-3-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole-3,4- Dicarboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N,4- N,2-Trimethyl-3-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole-3,4- Dicarboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N,4- N,2-Trimethyl-3-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole-3,4- Dicarboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N,4- N,2-Trimethyl-3-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole-3,4- Dicarboxamide, PDB code: 5sdw 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) 41.79 / 2.35
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 136.75, 136.75, 235.59, 90, 90, 120
R / Rfree (%) 18 / 24.3

Other elements in 5sdw:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N,4- N,2-Trimethyl-3-N-(2-Phenyl-1H-Benzimidazol-5-Yl)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 4-N,4- N,2-Trimethyl-3-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole-3,4- Dicarboxamide (pdb code 5sdw). 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 4-N,4- N,2-Trimethyl-3-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole-3,4- Dicarboxamide, PDB code: 5sdw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sdw

Go back to Magnesium Binding Sites List in 5sdw
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N,4- N,2-Trimethyl-3-N-(2-Phenyl-1H-Benzimidazol-5-Yl)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 4-N,4- N,2-Trimethyl-3-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole-3,4- Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:39.0
occ:1.00
O A:HOH903 1.8 42.6 1.0
O A:HOH954 1.9 44.6 1.0
OD1 A:ASP564 2.1 47.3 1.0
O A:HOH939 2.1 47.3 1.0
O A:HOH918 2.2 35.4 1.0
O A:HOH931 2.2 51.1 1.0
CG A:ASP564 3.0 44.2 1.0
OD2 A:ASP564 3.2 50.7 1.0
ZN A:ZN801 3.9 49.5 1.0
O A:HOH932 4.0 52.5 1.0
NE2 A:HIS595 4.1 46.8 1.0
CD2 A:HIS567 4.1 44.6 1.0
CD2 A:HIS563 4.3 37.2 1.0
OE2 A:GLU592 4.3 46.8 1.0
NE2 A:HIS567 4.3 49.5 1.0
CB A:ASP564 4.4 40.0 1.0
OG1 A:THR633 4.4 44.4 1.0
O A:HIS563 4.4 40.2 1.0
CD2 A:HIS525 4.5 49.6 1.0
NE2 A:HIS525 4.5 46.8 1.0
OD2 A:ASP674 4.5 55.3 1.0
CD2 A:HIS595 4.5 46.3 1.0
NE2 A:HIS563 4.6 34.1 1.0
O A:THR633 4.8 47.5 1.0
CB A:THR633 4.8 44.1 1.0
CA A:ASP564 4.8 38.8 1.0
CG A:GLU592 4.9 48.6 1.0

Magnesium binding site 2 out of 4 in 5sdw

Go back to Magnesium Binding Sites List in 5sdw
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N,4- N,2-Trimethyl-3-N-(2-Phenyl-1H-Benzimidazol-5-Yl)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 4-N,4- N,2-Trimethyl-3-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole-3,4- Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:32.9
occ:1.00
O B:HOH920 2.0 40.1 1.0
O B:HOH910 2.0 40.4 1.0
O B:HOH930 2.1 31.0 1.0
O B:HOH927 2.1 34.9 1.0
O B:HOH957 2.2 40.5 1.0
OD1 B:ASP564 2.3 46.2 1.0
CG B:ASP564 3.3 40.3 1.0
OD2 B:ASP564 3.7 46.2 1.0
OE2 B:GLU592 3.9 52.7 1.0
ZN B:ZN801 4.0 46.5 1.0
NE2 B:HIS595 4.0 45.0 1.0
OG1 B:THR633 4.1 36.8 1.0
O B:HOH948 4.1 49.6 1.0
CD2 B:HIS595 4.3 43.2 1.0
O B:THR633 4.4 39.8 1.0
CD2 B:HIS563 4.4 36.1 1.0
CD2 B:HIS567 4.4 45.8 1.0
NE2 B:HIS567 4.4 48.3 1.0
O B:HOH945 4.4 50.1 1.0
OD2 B:ASP674 4.4 46.2 1.0
O B:HIS563 4.5 42.2 1.0
CG B:GLU592 4.5 47.5 1.0
CB B:THR633 4.6 42.1 1.0
CB B:ASP564 4.6 36.5 1.0
CD B:GLU592 4.6 50.9 1.0
CD2 B:HIS525 4.7 50.5 1.0
NE2 B:HIS563 4.8 37.4 1.0
CA B:ASP564 4.9 41.2 1.0
NE2 B:HIS525 4.9 47.4 1.0
C B:THR633 5.0 38.7 1.0

Magnesium binding site 3 out of 4 in 5sdw

Go back to Magnesium Binding Sites List in 5sdw
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N,4- N,2-Trimethyl-3-N-(2-Phenyl-1H-Benzimidazol-5-Yl)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 4-N,4- N,2-Trimethyl-3-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole-3,4- Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:42.7
occ:1.00
O C:HOH920 1.8 37.4 1.0
O C:HOH936 1.9 34.0 1.0
OD1 C:ASP564 2.1 36.5 1.0
O C:HOH919 2.1 47.4 1.0
O C:HOH950 2.2 40.4 1.0
O C:HOH947 2.3 43.0 1.0
CG C:ASP564 3.1 36.6 1.0
OD2 C:ASP564 3.5 43.4 1.0
ZN C:ZN801 3.8 45.2 1.0
OG1 C:THR633 4.0 36.0 1.0
OE2 C:GLU592 4.0 47.3 1.0
CD2 C:HIS563 4.1 34.2 1.0
OD2 C:ASP674 4.2 46.4 1.0
CD2 C:HIS567 4.2 44.3 1.0
NE2 C:HIS595 4.3 45.6 1.0
O C:HIS563 4.3 37.0 1.0
NE2 C:HIS563 4.4 35.2 1.0
O C:THR633 4.4 40.3 1.0
NE2 C:HIS567 4.4 48.2 1.0
CB C:ASP564 4.5 34.1 1.0
CD2 C:HIS595 4.5 45.6 1.0
O C:HOH951 4.6 53.9 1.0
CD2 C:HIS525 4.6 43.8 1.0
NE2 C:HIS525 4.6 49.3 1.0
CB C:THR633 4.7 38.3 1.0
CA C:ASP564 4.9 36.1 1.0
O C:HOH962 4.9 52.4 1.0
CD C:GLU592 4.9 52.5 1.0
CG C:GLU592 4.9 48.7 1.0

Magnesium binding site 4 out of 4 in 5sdw

Go back to Magnesium Binding Sites List in 5sdw
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N,4- N,2-Trimethyl-3-N-(2-Phenyl-1H-Benzimidazol-5-Yl)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 4-N,4- N,2-Trimethyl-3-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole-3,4- Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:65.2
occ:1.00
O D:HOH911 1.9 57.0 1.0
OD1 D:ASP564 2.1 52.5 1.0
O D:HOH912 2.1 49.1 1.0
O D:HOH915 2.1 55.0 1.0
O D:HOH901 2.3 56.0 1.0
CG D:ASP564 3.1 62.1 1.0
OD2 D:ASP564 3.5 69.0 1.0
OE2 D:GLU592 3.8 71.1 1.0
NE2 D:HIS595 3.9 65.9 1.0
OG1 D:THR633 4.0 52.9 1.0
ZN D:ZN801 4.0 62.5 1.0
CD2 D:HIS595 4.2 61.0 1.0
CD2 D:HIS567 4.3 59.2 1.0
CD2 D:HIS563 4.3 54.2 1.0
O D:HIS563 4.3 54.1 1.0
CB D:ASP564 4.4 58.3 1.0
NE2 D:HIS567 4.4 58.5 1.0
OD2 D:ASP674 4.6 65.8 1.0
CB D:THR633 4.6 59.7 1.0
CA D:ASP564 4.6 58.8 1.0
O D:THR633 4.7 69.5 1.0
CD2 D:HIS525 4.7 73.6 1.0
NE2 D:HIS525 4.7 72.8 1.0
CD D:GLU592 4.8 67.3 1.0
NE2 D:HIS563 4.8 48.7 1.0
CG D:GLU592 4.9 62.4 1.0
CE1 D:HIS595 5.0 62.6 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: Tue Aug 12 19:13:41 2025

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