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Magnesium in PDB 5sfo: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-[2-(1-Methyl-4-Phenylimidazol-2- Yl)Ethyl]Pyrazole-3-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-[2-(1-Methyl-4-Phenylimidazol-2- Yl)Ethyl]Pyrazole-3-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-[2-(1-Methyl-4-Phenylimidazol-2- Yl)Ethyl]Pyrazole-3-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-[2-(1-Methyl-4-Phenylimidazol-2- Yl)Ethyl]Pyrazole-3-Carboxamide, PDB code: 5sfo was solved by C.Joseph, M.Koerner, 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) 43.58 / 1.96
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.004, 135.004, 234.814, 90, 90, 120
R / Rfree (%) 17.6 / 21.8

Other elements in 5sfo:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-N-[2-(1-Methyl-4-Phenylimidazol-2- Yl)Ethyl]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 4- (Azetidine-1-Carbonyl)-2-Methyl-N-[2-(1-Methyl-4-Phenylimidazol-2- Yl)Ethyl]Pyrazole-3-Carboxamide (pdb code 5sfo). 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- (Azetidine-1-Carbonyl)-2-Methyl-N-[2-(1-Methyl-4-Phenylimidazol-2- Yl)Ethyl]Pyrazole-3-Carboxamide, PDB code: 5sfo:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sfo

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

b:23.9
occ:1.00
 O A:HOH976 2.0 24.2 1.0
OD1 A:ASP564 2.0 22.4 1.0
O A:HOH995 2.0 23.3 1.0
O A:HOH933 2.0 21.9 1.0
O A:HOH936 2.1 20.7 1.0
O A:HOH957 2.2 21.4 1.0
CG A:ASP564 3.0 25.7 1.0
OD2 A:ASP564 3.4 24.2 1.0
ZN A:ZN801 3.7 27.9 1.0
O A:HOH1018 3.9 32.7 1.0
OE2 A:GLU592 4.1 30.5 1.0
NE2 A:HIS595 4.1 22.0 1.0
OG1 A:THR633 4.2 23.4 1.0
CD2 A:HIS567 4.3 21.9 1.0
O A:HOH1022 4.3 51.6 1.0
O A:HOH981 4.3 29.1 1.0
O A:HIS563 4.3 25.0 1.0
CD2 A:HIS563 4.3 21.7 1.0
CB A:ASP564 4.3 22.8 1.0
CD2 A:HIS595 4.4 20.3 1.0
NE2 A:HIS525 4.4 27.1 1.0
CD2 A:HIS525 4.5 25.9 1.0
NE2 A:HIS567 4.5 21.7 1.0
O A:THR633 4.5 26.1 1.0
OD2 A:ASP674 4.5 26.6 1.0
CB A:THR633 4.7 21.7 1.0
CA A:ASP564 4.7 23.0 1.0
NE2 A:HIS563 4.7 23.3 1.0
CG A:GLU592 4.8 24.9 1.0
CD A:GLU592 4.9 28.6 1.0

Magnesium binding site 2 out of 4 in 5sfo

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

b:20.9
occ:1.00
 O B:HOH955 1.9 21.9 1.0
O B:HOH939 2.0 19.5 1.0
O B:HOH999 2.1 17.5 1.0
OD1 B:ASP564 2.1 21.6 1.0
O B:HOH927 2.1 20.4 1.0
O B:HOH995 2.1 19.0 1.0
CG B:ASP564 3.1 20.4 1.0
OD2 B:ASP564 3.4 20.5 1.0
ZN B:ZN801 3.7 26.7 1.0
O B:HOH979 4.0 33.8 1.0
OE2 B:GLU592 4.1 23.8 1.0
NE2 B:HIS595 4.1 18.1 1.0
O B:HOH1051 4.1 47.5 1.0
OG1 B:THR633 4.2 22.8 1.0
CD2 B:HIS563 4.2 20.5 1.0
O B:HOH967 4.3 27.2 1.0
CD2 B:HIS567 4.3 25.3 1.0
OD2 B:ASP674 4.3 21.9 1.0
O B:HIS563 4.3 22.8 1.0
CD2 B:HIS595 4.4 20.1 1.0
NE2 B:HIS567 4.4 23.2 1.0
CB B:ASP564 4.5 18.8 1.0
CD2 B:HIS525 4.5 22.8 1.0
O B:THR633 4.5 22.1 1.0
NE2 B:HIS525 4.5 25.1 1.0
NE2 B:HIS563 4.5 20.9 1.0
CB B:THR633 4.6 20.8 1.0
CG B:GLU592 4.7 23.1 1.0
CA B:ASP564 4.7 19.4 1.0
CD B:GLU592 4.8 24.8 1.0

Magnesium binding site 3 out of 4 in 5sfo

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

b:22.9
occ:1.00
 OD1 C:ASP564 2.0 21.0 1.0
O C:HOH1033 2.0 20.9 1.0
O C:HOH998 2.1 22.7 1.0
O C:HOH982 2.1 21.3 1.0
O C:HOH961 2.1 24.7 1.0
O C:HOH930 2.2 20.1 1.0
CG C:ASP564 3.1 21.0 1.0
OD2 C:ASP564 3.5 20.7 1.0
ZN C:ZN801 3.8 27.6 1.0
NE2 C:HIS595 4.0 23.4 1.0
OE2 C:GLU592 4.0 26.2 1.0
O C:HOH1014 4.1 33.2 1.0
CD2 C:HIS567 4.2 25.8 1.0
OG1 C:THR633 4.2 22.4 1.0
CD2 C:HIS563 4.3 22.1 1.0
O C:HOH1007 4.3 29.5 1.0
O C:HIS563 4.3 23.7 1.0
CD2 C:HIS595 4.4 21.7 1.0
O C:HOH1052 4.4 47.7 1.0
CB C:ASP564 4.4 20.7 1.0
NE2 C:HIS567 4.4 24.5 1.0
O C:THR633 4.5 25.3 1.0
OD2 C:ASP674 4.5 26.9 1.0
CD2 C:HIS525 4.5 28.3 1.0
NE2 C:HIS525 4.6 25.8 1.0
NE2 C:HIS563 4.7 21.2 1.0
CB C:THR633 4.7 23.0 1.0
CA C:ASP564 4.8 22.4 1.0
CG C:GLU592 4.8 24.3 1.0
CD C:GLU592 4.8 24.4 1.0

Magnesium binding site 4 out of 4 in 5sfo

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

b:31.4
occ:1.00
 O D:HOH986 1.9 23.4 1.0
O D:HOH966 2.1 27.3 1.0
O D:HOH940 2.1 31.3 1.0
OD1 D:ASP564 2.1 26.9 1.0
O D:HOH949 2.1 26.4 1.0
O D:HOH928 2.2 24.2 1.0
CG D:ASP564 3.1 28.4 1.0
OD2 D:ASP564 3.4 30.9 1.0
ZN D:ZN801 3.7 32.8 1.0
O D:HOH946 3.9 45.7 1.0
NE2 D:HIS595 4.0 32.1 1.0
O D:HOH955 4.0 36.9 1.0
OE2 D:GLU592 4.1 31.9 1.0
CD2 D:HIS567 4.2 32.5 1.0
OG1 D:THR633 4.3 29.4 1.0
CD2 D:HIS595 4.3 31.7 1.0
NE2 D:HIS567 4.4 33.0 1.0
O D:HIS563 4.4 28.8 1.0
NE2 D:HIS525 4.4 34.3 1.0
CD2 D:HIS563 4.4 27.4 1.0
CD2 D:HIS525 4.5 32.7 1.0
CB D:ASP564 4.5 28.0 1.0
OD2 D:ASP674 4.5 34.1 1.0
O D:THR633 4.5 30.9 1.0
CB D:THR633 4.8 29.1 1.0
NE2 D:HIS563 4.8 26.0 1.0
CA D:ASP564 4.8 28.3 1.0
CG D:GLU592 4.8 34.8 1.0
CD D:GLU592 4.9 34.8 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 03:36:31 2024

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