Magnesium in PDB 5it3: Swirm Domain of Human LSD1

The structure of Swirm Domain of Human LSD1, PDB code: 5it3 was solved by P.D.Jeffrey, P.Yuan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.85 / 1.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	57.170, 49.970, 48.850, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 19.4

The binding sites of Magnesium atom in the Swirm Domain of Human LSD1 (pdb code 5it3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Swirm Domain of Human LSD1, PDB code: 5it3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Swirm Domain of Human LSD1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Swirm Domain of Human LSD1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:25.9 occ:1.00 O B:LEU183 2.0 23.6 1.0 O B:HOH478 2.0 29.9 1.0 O B:HOH489 2.0 35.0 1.0 O B:HOH444 2.1 30.1 1.0 O B:HOH455 2.2 22.4 1.0 N B:LEU183 2.7 27.7 1.0 C B:LEU183 3.0 21.8 1.0 CA B:LEU183 3.3 21.2 1.0 O B:HOH402 4.0 33.7 1.0 CB B:LEU183 4.1 22.6 1.0 N B:PRO184 4.2 20.7 1.0 O B:HOH413 4.3 24.4 1.0 CD2 B:LEU218 4.4 21.4 1.0 N B:HIS185 4.5 20.4 1.0 O B:HOH488 4.5 46.6 1.0 C B:PRO184 4.7 19.5 1.0 CA B:PRO184 4.7 22.6 1.0 OD1 B:ASN215 4.9 14.9 1.0 CA B:HIS185 4.9 21.7 1.0

Magnesium binding site 2 out of 2 in the Swirm Domain of Human LSD1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Swirm Domain of Human LSD1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:21.0 occ:0.50 O B:HOH412 1.8 22.0 1.0 O B:HOH426 1.9 21.7 1.0 O B:HOH424 2.0 23.6 1.0 OE1 B:GLU239 3.9 22.5 1.0 OE2 B:GLU239 3.9 22.7 1.0 O B:GLN236 4.0 26.2 1.0 O B:HOH415 4.0 20.6 1.0 O B:HOH438 4.2 25.9 1.0 CD B:GLU239 4.2 19.1 1.0 O B:LEU238 4.3 17.8 1.0 C B:GLN236 4.5 20.0 1.0 CA B:GLN236 4.8 17.6 1.0

R.Hu, X.Sun, U.F.S.Hameed, B.S.Moorthy, P.D.Jeffrey, L.Zhou, X.Ma, F.Chen, Q.Mu, J.Pei, K.Swaminathan, P.Yuan. A Tlx-Interacting Peptide of LSD1 Inhibits the Proliferation of Brain Tumor Stem Cells To Be Published.