Magnesium in PDB 7xw8: Crystal Structure of Lysine Specific Demethylase 1 (LSD1) with Tak-418 Distomer, Fad-Adduct

All present enzymatic activity of Crystal Structure of Lysine Specific Demethylase 1 (LSD1) with Tak-418 Distomer, Fad-Adduct:
1.14.99.66;

The structure of Crystal Structure of Lysine Specific Demethylase 1 (LSD1) with Tak-418 Distomer, Fad-Adduct, PDB code: 7xw8 was solved by H.Oki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.41 / 2.28
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	184.727, 184.727, 108.937, 90, 90, 120
R / Rfree (%)	19.8 / 23

The binding sites of Magnesium atom in the Crystal Structure of Lysine Specific Demethylase 1 (LSD1) with Tak-418 Distomer, Fad-Adduct (pdb code 7xw8). 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 Lysine Specific Demethylase 1 (LSD1) with Tak-418 Distomer, Fad-Adduct, PDB code: 7xw8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Lysine Specific Demethylase 1 (LSD1) with Tak-418 Distomer, Fad-Adduct


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 Lysine Specific Demethylase 1 (LSD1) with Tak-418 Distomer, Fad-Adduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:38.1 occ:1.00 OG A:SER687 2.9 49.2 1.0 OG1 A:THR684 3.1 43.4 1.0 CB A:ALA686 3.5 35.5 1.0 CB A:SER687 4.0 41.6 1.0 CB A:THR684 4.0 42.0 1.0 N A:SER687 4.0 35.8 1.0 CG2 A:THR684 4.2 38.6 1.0 C A:ALA686 4.4 40.1 1.0 CA A:ALA686 4.4 38.8 1.0 CA A:SER687 4.6 37.3 1.0 N A:ALA686 4.8 36.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Lysine Specific Demethylase 1 (LSD1) with Tak-418 Distomer, Fad-Adduct


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 Lysine Specific Demethylase 1 (LSD1) with Tak-418 Distomer, Fad-Adduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:57.8 occ:1.00 OE1 A:GLN419 3.3 54.3 1.0 CD A:GLN419 3.5 43.3 1.0 OE1 A:GLU381 3.5 60.3 1.0 CB A:ARG384 3.8 39.5 1.0 NE2 A:GLN419 3.9 46.4 1.0 CG A:GLN419 4.0 42.3 1.0 OE2 A:GLU381 4.1 79.6 1.0 CD A:ARG384 4.2 47.4 1.0 CD A:GLU381 4.2 59.9 1.0 CD2 A:LEU385 4.5 35.9 1.0 C A:ARG384 4.6 37.2 1.0 OH A:TYR520 4.6 48.2 1.0 O A:ARG384 4.6 36.6 1.0 CG A:ARG384 4.7 46.5 1.0 N A:LEU385 4.8 33.7 1.0 CA A:ARG384 4.8 45.4 1.0 O A:HOH1100 4.9 40.0 1.0 CG A:LEU385 5.0 32.9 1.0

Y.Hattori, S.Matsumoto, S.Morimoto, M.Daini, M.Toyofuku, S.Matsuda, R.Baba, K.Murakami, M.Iwatani, H.Oki, S.Iwasaki, K.Matsumiya, Y.Tominari, H.Kimura, M.Ito. Design, Synthesis, and Structure-Activity Relationship of Tak-418 and Its Derivatives As A Novel Series of LSD1 Inhibitors with Lowered Risk of Hematological Side Effects. Eur.J.Med.Chem. V. 239 14522 2022.
ISSN: ISSN 0223-5234
PubMed: 35749987
DOI: 10.1016/J.EJMECH.2022.114522