Magnesium in PDB 7e0g: Crystal Structure of Lysine Specific Demethylase 1 (LSD1) with Tak- 418, Fad-Adduct

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

The structure of Crystal Structure of Lysine Specific Demethylase 1 (LSD1) with Tak- 418, Fad-Adduct, PDB code: 7e0g was solved by H.Oki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.25
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	184.55, 184.55, 108.571, 90, 90, 120
R / Rfree (%)	19.4 / 23.8

The binding sites of Magnesium atom in the Crystal Structure of Lysine Specific Demethylase 1 (LSD1) with Tak- 418, Fad-Adduct (pdb code 7e0g). 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, Fad-Adduct, PDB code: 7e0g:
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, 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, Fad-Adduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1005 b:46.9 occ:1.00 OG A:SER687 3.1 55.3 1.0 OG1 A:THR684 3.1 50.4 1.0 CB A:ALA686 3.5 46.1 1.0 CB A:THR684 4.0 48.9 1.0 CB A:SER687 4.0 51.3 1.0 N A:SER687 4.1 46.4 1.0 CG2 A:THR684 4.2 44.1 1.0 C A:ALA686 4.5 44.4 1.0 CA A:ALA686 4.5 46.6 1.0 CA A:SER687 4.7 47.9 1.0 O A:HOH1216 4.8 51.8 1.0 N A:ALA686 4.9 45.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Lysine Specific Demethylase 1 (LSD1) with Tak- 418, 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, Fad-Adduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1006 b:63.5 occ:1.00 OE1 A:GLN419 3.2 57.9 1.0 CD A:GLN419 3.7 53.8 1.0 OE1 A:GLU381 3.8 61.7 1.0 CB A:ARG384 3.8 49.5 1.0 CG A:GLN419 4.1 46.3 1.0 CD A:ARG384 4.3 69.7 1.0 OE2 A:GLU381 4.4 69.5 1.0 NE2 A:GLN419 4.4 56.6 1.0 CD A:GLU381 4.5 63.4 1.0 C A:ARG384 4.6 40.7 1.0 CG A:ARG384 4.6 54.3 1.0 O A:ARG384 4.7 40.2 1.0 N A:LEU385 4.7 37.8 1.0 OH A:TYR520 4.8 59.0 1.0 CA A:ARG384 4.8 44.5 1.0 CD2 A:LEU385 4.8 42.0 1.0

R.Baba, S.Matsuda, Y.Arakawa, R.Yamada, N.Suzuki, T.Ando, H.Oki, S.Igaki, M.Daini, Y.Hattori, S.Matsumoto, M.Ito, A.Nakatani, H.Kimura. LSD1 Enzyme Inhibitor Tak-418 Unlocks Aberrant Epigenetic Machinery and Improves Autism Symptoms in Neurodevelopmental Disorder Models. Sci Adv V. 7 2021.
ISSN: ESSN 2375-2548
PubMed: 33712455
DOI: 10.1126/SCIADV.ABA1187