Magnesium in PDB 7uj4: Inhibition of Human Menin By Sndx-5613

The structure of Inhibition of Human Menin By Sndx-5613, PDB code: 7uj4 was solved by B.M.Mckeever, S.Kulkarni, G.M.Mcgeehan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.91 / 1.96
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.536, 78.04, 92.859, 90, 101.36, 90
R / Rfree (%)	21.9 / 26.2

The structure of Inhibition of Human Menin By Sndx-5613 also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Magnesium atom in the Inhibition of Human Menin By Sndx-5613 (pdb code 7uj4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Inhibition of Human Menin By Sndx-5613, PDB code: 7uj4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Inhibition of Human Menin By Sndx-5613


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Inhibition of Human Menin By Sndx-5613 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:36.1 occ:1.00 O A:HOH708 2.0 39.0 1.0 O A:HOH703 2.0 31.7 1.0 OD1 A:ASP180 2.1 26.9 1.0 OE2 A:GLU359 2.1 38.3 1.0 O A:HOH767 2.2 28.3 1.0 O A:HOH715 2.3 31.7 1.0 CD A:GLU359 3.0 37.1 1.0 CG A:ASP180 3.2 28.1 1.0 OE1 A:GLU359 3.3 34.2 1.0 O1 A:OQ4601 4.0 24.4 1.0 CB A:ASP180 4.0 27.9 1.0 CA A:ASP180 4.1 28.8 1.0 OD2 A:ASP180 4.2 29.8 1.0 O A:HOH769 4.3 38.7 1.0 O A:GLU179 4.4 26.8 1.0 O A:HOH763 4.4 47.2 1.0 CG A:GLU359 4.4 34.3 1.0 O A:ASP180 4.8 28.5 1.0 C A:ASP180 4.9 24.7 1.0 C6 A:OQ4601 4.9 25.5 1.0

Magnesium binding site 2 out of 4 in the Inhibition of Human Menin By Sndx-5613


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Inhibition of Human Menin By Sndx-5613 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:38.5 occ:1.00 O A:HOH783 2.0 32.7 1.0 O A:HOH707 2.0 32.0 1.0 O A:HOH797 2.1 37.5 1.0 OD2 A:ASP350 2.1 39.9 1.0 O A:HOH718 2.4 35.9 1.0 CG A:ASP350 3.3 41.2 1.0 CB A:ASP350 3.9 36.0 1.0 O A:THR346 4.0 32.1 1.0 O A:VAL347 4.1 26.9 1.0 OE2 A:GLU316 4.4 47.1 1.0 CA A:VAL347 4.4 28.0 1.0 OD1 A:ASP350 4.4 36.3 1.0 OE1 A:GLU316 4.5 45.9 1.0 O A:ASP315 4.5 31.1 1.0 CD A:GLU316 4.7 43.0 1.0 C A:VAL347 4.8 27.3 1.0 C A:THR346 4.9 32.2 1.0

Magnesium binding site 3 out of 4 in the Inhibition of Human Menin By Sndx-5613


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Inhibition of Human Menin By Sndx-5613 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:33.0 occ:1.00 O B:HOH757 2.0 30.4 1.0 OE1 B:GLU359 2.1 41.3 1.0 OD1 B:ASP180 2.1 25.5 1.0 O B:HOH750 2.1 35.5 1.0 O B:HOH741 2.1 40.3 1.0 O B:HOH713 2.3 45.0 1.0 CD B:GLU359 3.0 39.1 1.0 CG B:ASP180 3.3 29.6 1.0 OE2 B:GLU359 3.3 41.2 1.0 O B:HOH749 4.0 40.6 1.0 O1 B:OQ4601 4.1 31.4 1.0 CB B:ASP180 4.1 34.8 1.0 OD2 B:ASP180 4.2 28.8 1.0 CA B:ASP180 4.3 30.3 1.0 O B:HOH767 4.4 35.3 1.0 CG B:GLU359 4.4 36.3 1.0 O B:GLU179 4.5 28.4 1.0 O B:ASP180 4.9 33.8 1.0

Magnesium binding site 4 out of 4 in the Inhibition of Human Menin By Sndx-5613


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Inhibition of Human Menin By Sndx-5613 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:38.6 occ:1.00 O B:HOH782 2.0 37.5 1.0 O B:HOH720 2.1 40.6 1.0 OD2 B:ASP350 2.1 45.6 1.0 O B:HOH800 2.1 38.7 1.0 O B:HOH746 2.1 33.9 1.0 O B:HOH709 2.2 33.7 1.0 CG B:ASP350 3.1 42.6 1.0 CB B:ASP350 3.5 41.5 1.0 OE1 B:GLU316 3.8 41.6 1.0 OE2 B:GLU316 4.1 41.1 1.0 O B:VAL347 4.2 28.1 1.0 CD B:GLU316 4.3 41.8 1.0 OD1 B:ASP350 4.3 42.1 1.0 O B:THR346 4.4 31.7 1.0 NZ B:LYS224 4.6 43.2 1.0 CA B:VAL347 4.8 24.5 1.0 O B:ASP315 4.8 25.2 1.0 CA B:ASP350 4.9 35.5 1.0 C B:VAL347 5.0 27.2 1.0

F.Perner, E.M.Stein, S.Singh, D.V.Wenge, A.Apazidis, H.Rahnamoun, D.Anand, C.Marinaccio, C.Hatton, Y.Wen, D.Schaller, S.Mowla, W.Xiao, H.A.Gamlen, A.J.Stonestrom, S.Persaud, J.G.Doench, G.M.Mcgeehan, A.Volkamer, J.D.Chodrra, R.L.Levine, S.A.Armstrong, S.F.Cai. MEN1 Mutations Mediate Clinical Resistance to Menin Inhibition Nature 2022.
ISSN: ESSN 1476-4687