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Magnesium in PDB 5b4k: Crystal Structure of the Catalytic Domain of Human PDE10A Complexed with N-(4-((5-Methyl-5H-Pyrrolo[3,2-D]Pyrimidin-4-Yl)Oxy)Phenyl)-1H- Benzimidazol-2-Amine

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human PDE10A Complexed with N-(4-((5-Methyl-5H-Pyrrolo[3,2-D]Pyrimidin-4-Yl)Oxy)Phenyl)-1H- Benzimidazol-2-Amine

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human PDE10A Complexed with N-(4-((5-Methyl-5H-Pyrrolo[3,2-D]Pyrimidin-4-Yl)Oxy)Phenyl)-1H- Benzimidazol-2-Amine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human PDE10A Complexed with N-(4-((5-Methyl-5H-Pyrrolo[3,2-D]Pyrimidin-4-Yl)Oxy)Phenyl)-1H- Benzimidazol-2-Amine, PDB code: 5b4k 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) 80.83 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.734, 81.683, 161.654, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 26.1

Other elements in 5b4k:

The structure of Crystal Structure of the Catalytic Domain of Human PDE10A Complexed with N-(4-((5-Methyl-5H-Pyrrolo[3,2-D]Pyrimidin-4-Yl)Oxy)Phenyl)-1H- Benzimidazol-2-Amine also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Catalytic Domain of Human PDE10A Complexed with N-(4-((5-Methyl-5H-Pyrrolo[3,2-D]Pyrimidin-4-Yl)Oxy)Phenyl)-1H- Benzimidazol-2-Amine (pdb code 5b4k). 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 Human PDE10A Complexed with N-(4-((5-Methyl-5H-Pyrrolo[3,2-D]Pyrimidin-4-Yl)Oxy)Phenyl)-1H- Benzimidazol-2-Amine, PDB code: 5b4k:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5b4k

Go back to Magnesium Binding Sites List in 5b4k
Magnesium binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Human PDE10A Complexed with N-(4-((5-Methyl-5H-Pyrrolo[3,2-D]Pyrimidin-4-Yl)Oxy)Phenyl)-1H- Benzimidazol-2-Amine


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 Human PDE10A Complexed with N-(4-((5-Methyl-5H-Pyrrolo[3,2-D]Pyrimidin-4-Yl)Oxy)Phenyl)-1H- Benzimidazol-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:30.1
occ:1.00
 O A:HOH1112 2.0 24.1 1.0
O A:HOH1103 2.0 28.1 1.0
O A:HOH1137 2.0 43.5 1.0
O A:HOH1127 2.1 41.8 1.0
OD1 A:ASP554 2.1 38.1 1.0
O A:HOH1102 2.5 21.3 1.0
CG A:ASP554 3.2 38.9 1.0
OD2 A:ASP554 3.5 40.9 1.0
NE2 A:HIS585 3.8 33.4 1.0
ZN A:ZN1002 3.9 64.5 1.0
O A:HOH1117 3.9 60.2 1.0
CD2 A:HIS585 4.1 33.6 1.0
O A:HIS553 4.1 47.6 1.0
O A:HOH1126 4.1 34.5 1.0
OE2 A:GLU582 4.2 42.6 1.0
CD2 A:HIS557 4.3 39.0 1.0
OG1 A:THR623 4.4 47.0 1.0
CD2 A:HIS553 4.4 43.3 1.0
CB A:ASP554 4.5 36.9 1.0
O A:THR623 4.5 46.4 1.0
NE2 A:HIS557 4.5 36.8 1.0
CD2 A:HIS515 4.5 48.4 1.0
NE2 A:HIS515 4.7 46.3 1.0
NE2 A:HIS553 4.8 43.7 1.0
CA A:ASP554 4.8 40.2 1.0
CG A:GLU582 4.8 41.8 1.0
CD A:GLU582 4.8 46.3 1.0
OD2 A:ASP664 4.8 50.8 1.0
CB A:THR623 4.9 46.5 1.0
CE1 A:HIS585 4.9 35.8 1.0
C A:HIS553 5.0 45.6 1.0

Magnesium binding site 2 out of 2 in 5b4k

Go back to Magnesium Binding Sites List in 5b4k
Magnesium binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Human PDE10A Complexed with N-(4-((5-Methyl-5H-Pyrrolo[3,2-D]Pyrimidin-4-Yl)Oxy)Phenyl)-1H- Benzimidazol-2-Amine


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 Human PDE10A Complexed with N-(4-((5-Methyl-5H-Pyrrolo[3,2-D]Pyrimidin-4-Yl)Oxy)Phenyl)-1H- Benzimidazol-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1001

b:55.2
occ:1.00
 O B:HOH1136 2.0 30.7 1.0
O B:HOH1106 2.1 38.5 1.0
O B:HOH1117 2.2 30.6 1.0
O B:HOH1141 2.2 42.4 1.0
OD1 B:ASP554 2.3 37.4 1.0
O B:HOH1102 2.4 42.7 1.0
CG B:ASP554 3.2 37.5 1.0
OD2 B:ASP554 3.5 40.2 1.0
O B:HOH1101 3.7 31.3 1.0
ZN B:ZN1002 3.8 59.1 1.0
OE2 B:GLU582 4.0 50.9 1.0
NE2 B:HIS585 4.0 47.5 1.0
CD2 B:HIS515 4.3 61.5 1.0
O B:HIS553 4.3 44.6 1.0
CD2 B:HIS585 4.4 46.2 1.0
NE2 B:HIS515 4.4 63.5 1.0
CD2 B:HIS557 4.4 48.3 1.0
NE2 B:HIS557 4.4 46.1 1.0
CD2 B:HIS553 4.4 40.2 1.0
OG1 B:THR623 4.5 37.8 1.0
CB B:ASP554 4.6 37.4 1.0
OD2 B:ASP664 4.6 43.8 1.0
NE2 B:HIS553 4.8 38.5 1.0
CG B:GLU582 4.8 53.0 1.0
O B:THR623 4.8 46.4 1.0
CD B:GLU582 4.9 55.9 1.0
CA B:ASP554 5.0 42.0 1.0
CB B:THR623 5.0 38.7 1.0

Reference:

M.Yoshikawa, T.Hitaka, T.Hasui, M.Fushimi, J.Kunitomo, H.Kokubo, H.Oki, K.Nakashima, T.Taniguchi. Design and Synthesis of Potent and Selective Pyridazin-4(1H)-One-Based PDE10A Inhibitors Interacting with TYR683 in the PDE10A Selectivity Pocket Bioorg.Med.Chem. V. 24 3447 2016.
ISSN: ESSN 1464-3391
PubMed: 27301679
DOI: 10.1016/J.BMC.2016.05.049
Page generated: Sun Sep 29 01:01:11 2024

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