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Magnesium in PDB 5axp: Crystal Structure of the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(2-Oxo-1,3-Oxazolidin-3-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl- 1H-Pyrazol-5-Yl)Pyridazin-4(1H)-One

Enzymatic activity of Crystal Structure of the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(2-Oxo-1,3-Oxazolidin-3-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl- 1H-Pyrazol-5-Yl)Pyridazin-4(1H)-One

All present enzymatic activity of Crystal Structure of the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(2-Oxo-1,3-Oxazolidin-3-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl- 1H-Pyrazol-5-Yl)Pyridazin-4(1H)-One:
3.1.4.17; 3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(2-Oxo-1,3-Oxazolidin-3-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl- 1H-Pyrazol-5-Yl)Pyridazin-4(1H)-One, PDB code: 5axp was solved by H.Oki, Y.Zama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.753, 81.849, 159.684, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 23.4

Other elements in 5axp:

The structure of Crystal Structure of the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(2-Oxo-1,3-Oxazolidin-3-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl- 1H-Pyrazol-5-Yl)Pyridazin-4(1H)-One also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(2-Oxo-1,3-Oxazolidin-3-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl- 1H-Pyrazol-5-Yl)Pyridazin-4(1H)-One (pdb code 5axp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(2-Oxo-1,3-Oxazolidin-3-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl- 1H-Pyrazol-5-Yl)Pyridazin-4(1H)-One, PDB code: 5axp:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5axp

Go back to Magnesium Binding Sites List in 5axp
Magnesium binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(2-Oxo-1,3-Oxazolidin-3-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl- 1H-Pyrazol-5-Yl)Pyridazin-4(1H)-One


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 the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(2-Oxo-1,3-Oxazolidin-3-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl- 1H-Pyrazol-5-Yl)Pyridazin-4(1H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:28.5
occ:1.00
 O A:HOH1172 2.0 25.2 1.0
O A:HOH1159 2.1 25.3 1.0
OD1 A:ASP554 2.1 24.3 1.0
O A:HOH1108 2.1 23.8 1.0
O A:HOH1178 2.2 27.2 1.0
O A:HOH1104 2.3 26.9 1.0
CG A:ASP554 3.1 26.0 1.0
OD2 A:ASP554 3.4 24.8 1.0
ZN A:ZN1002 3.8 32.8 1.0
NE2 A:HIS585 3.9 28.2 1.0
O A:HOH1155 4.0 27.1 1.0
O A:HOH1228 4.1 53.1 1.0
O A:HOH1229 4.1 27.8 1.0
OE2 A:GLU582 4.2 33.9 1.0
OG1 A:THR623 4.2 25.4 1.0
CD2 A:HIS585 4.3 26.7 1.0
O A:HIS553 4.3 28.0 1.0
CD2 A:HIS553 4.4 23.4 1.0
O A:HOH1110 4.4 46.2 1.0
CD2 A:HIS557 4.4 25.1 1.0
CB A:ASP554 4.5 25.2 1.0
OD2 A:ASP664 4.5 35.6 1.0
O A:THR623 4.6 27.9 1.0
NE2 A:HIS515 4.6 30.7 1.0
CD2 A:HIS515 4.6 29.2 1.0
NE2 A:HIS557 4.6 32.2 1.0
NE2 A:HIS553 4.7 26.8 1.0
CB A:THR623 4.8 24.1 1.0
CG A:GLU582 4.8 29.6 1.0
CA A:ASP554 4.8 28.0 1.0
CD A:GLU582 4.9 34.1 1.0

Magnesium binding site 2 out of 2 in 5axp

Go back to Magnesium Binding Sites List in 5axp
Magnesium binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(2-Oxo-1,3-Oxazolidin-3-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl- 1H-Pyrazol-5-Yl)Pyridazin-4(1H)-One


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 the Catalytic Domain of PDE10A Complexed with 1- (2-Fluoro-4-(2-Oxo-1,3-Oxazolidin-3-Yl)Phenyl)-5-Methoxy-3-(1-Phenyl- 1H-Pyrazol-5-Yl)Pyridazin-4(1H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1001

b:28.3
occ:1.00
 O B:HOH1124 2.0 22.1 1.0
OD1 B:ASP554 2.0 25.1 1.0
O B:HOH1149 2.1 29.1 1.0
O B:HOH1154 2.1 27.0 1.0
O B:HOH1171 2.1 28.1 1.0
O B:HOH1109 2.1 27.2 1.0
CG B:ASP554 3.1 27.5 1.0
OD2 B:ASP554 3.5 27.0 1.0
ZN B:ZN1002 3.8 31.0 1.0
NE2 B:HIS585 4.1 28.0 1.0
OE2 B:GLU582 4.1 33.2 1.0
OG1 B:THR623 4.1 26.7 1.0
CD2 B:HIS553 4.2 24.0 1.0
O B:HOH1214 4.2 34.7 1.0
O B:HOH1138 4.3 30.3 1.0
CD2 B:HIS585 4.3 26.9 1.0
O B:HIS553 4.4 26.1 1.0
OD2 B:ASP664 4.4 39.0 1.0
CB B:ASP554 4.4 24.7 1.0
O B:THR623 4.4 29.7 1.0
CD2 B:HIS557 4.5 27.3 1.0
NE2 B:HIS515 4.6 30.4 1.0
NE2 B:HIS553 4.6 23.4 1.0
CD2 B:HIS515 4.7 30.4 1.0
O B:HOH1159 4.7 53.9 1.0
CG B:GLU582 4.7 27.8 1.0
CB B:THR623 4.7 24.5 1.0
NE2 B:HIS557 4.8 27.2 1.0
CA B:ASP554 4.8 27.3 1.0
CD B:GLU582 4.8 30.4 1.0

Reference:

M.Yoshikawa, H.Kamisaki, J.Kunitomo, H.Oki, H.Kokubo, A.Suzuki, T.Ikemoto, K.Nakashima, N.Kamiguchi, A.Harada, H.Kimura, T.Taniguchi. Design and Synthesis of A Novel 2-Oxindole Scaffold As A Highly Potent and Brain-Penetrant Phosphodiesterase 10A Inhibitor Bioorg.Med.Chem. V. 23 7138 2015.
ISSN: ESSN 1464-3391
PubMed: 26494583
DOI: 10.1016/J.BMC.2015.10.002
Page generated: Tue Aug 12 05:30:44 2025

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