Magnesium in PDB 8ql1: Crystal Structure of the Human MDN1-Midas/NLE1-Ubl Complex

The structure of Crystal Structure of the Human MDN1-Midas/NLE1-Ubl Complex, PDB code: 8ql1 was solved by K.Wild, F.Fiorentino, E.Hurt, I.Sinning, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	118.52 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	237.16, 69.818, 103.183, 90, 91.79, 90
R / Rfree (%)	21.4 / 24.8

The binding sites of Magnesium atom in the Crystal Structure of the Human MDN1-Midas/NLE1-Ubl Complex (pdb code 8ql1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Human MDN1-Midas/NLE1-Ubl Complex, PDB code: 8ql1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the Human MDN1-Midas/NLE1-Ubl Complex


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 Human MDN1-Midas/NLE1-Ubl Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg5701 b:29.1 occ:1.00 OE2 B:GLU85 1.9 46.9 1.0 OG A:SER5394 2.0 34.3 1.0 OG A:SER5392 2.1 35.7 1.0 O B:HOH205 2.1 30.8 1.0 OG1 A:THR5461 2.3 29.0 1.0 O A:HOH5803 2.3 29.4 1.0 CB A:SER5392 3.1 41.2 1.0 CD B:GLU85 3.2 41.5 1.0 CB A:SER5394 3.3 37.8 1.0 CB A:THR5461 3.4 36.1 1.0 CG2 A:THR5461 3.5 29.6 1.0 OD2 A:ASP5390 3.9 29.0 1.0 O A:ARG5499 3.9 32.0 1.0 OE1 B:GLU85 4.0 43.2 1.0 OD1 A:ASP5390 4.1 34.4 1.0 CG B:GLU85 4.1 48.0 1.0 OD2 A:ASP5497 4.2 37.4 1.0 OD1 A:ASP5497 4.2 34.0 1.0 N A:SER5394 4.2 37.4 1.0 CA A:SER5394 4.3 44.9 1.0 CG A:ASP5390 4.4 41.8 1.0 CA A:SER5392 4.4 35.8 1.0 CG A:ASP5497 4.6 37.1 1.0 C A:SER5392 4.6 41.4 1.0 CA A:THR5461 4.6 29.1 1.0 O A:SER5392 4.9 35.8 1.0 N A:MET5395 4.9 35.0 1.0 C A:SER5394 4.9 37.0 1.0 N A:SER5393 5.0 38.5 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the Human MDN1-Midas/NLE1-Ubl Complex


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 Human MDN1-Midas/NLE1-Ubl Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg5701 b:45.2 occ:1.00 OE2 D:GLU85 2.0 67.4 1.0 OG C:SER5394 2.0 61.7 1.0 O D:HOH205 2.0 34.9 1.0 OG C:SER5392 2.0 49.1 1.0 O C:HOH5808 2.1 38.2 1.0 OG1 C:THR5461 2.3 50.6 1.0 CB C:SER5392 3.1 43.9 1.0 CD D:GLU85 3.2 71.9 1.0 CB C:SER5394 3.3 49.3 1.0 CB C:THR5461 3.4 43.5 1.0 CG2 C:THR5461 3.5 48.3 1.0 OD2 C:ASP5390 3.8 40.2 1.0 O C:ARG5499 4.0 44.0 1.0 OE1 D:GLU85 4.0 69.1 1.0 OD1 C:ASP5390 4.1 41.9 1.0 OD2 C:ASP5497 4.1 39.3 1.0 CG D:GLU85 4.1 74.7 1.0 N C:SER5394 4.2 56.4 1.0 OD1 C:ASP5497 4.2 38.2 1.0 CA C:SER5394 4.3 48.1 1.0 CG C:ASP5390 4.4 45.4 1.0 CA C:SER5392 4.4 51.5 1.0 C C:SER5392 4.6 54.0 1.0 CA C:THR5461 4.6 44.4 1.0 CG C:ASP5497 4.6 44.5 1.0 O C:SER5392 4.9 44.7 1.0 N C:MET5395 4.9 46.2 1.0 C C:SER5394 4.9 50.6 1.0 N C:SER5393 5.0 55.8 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the Human MDN1-Midas/NLE1-Ubl Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Human MDN1-Midas/NLE1-Ubl Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg5701 b:35.6 occ:1.00 OE2 F:GLU85 1.9 45.9 1.0 OG E:SER5394 2.0 38.2 1.0 OG E:SER5392 2.0 37.9 1.0 O E:HOH5823 2.0 27.8 1.0 O E:HOH5827 2.1 31.9 1.0 OG1 E:THR5461 2.3 48.8 1.0 CB E:SER5392 3.2 35.3 1.0 CD F:GLU85 3.2 50.7 1.0 CB E:SER5394 3.3 37.6 1.0 CB E:THR5461 3.5 43.2 1.0 CG2 E:THR5461 3.6 40.7 1.0 OD2 E:ASP5390 3.9 31.4 1.0 O E:ARG5499 4.0 37.6 1.0 OD1 E:ASP5390 4.0 34.1 1.0 CG F:GLU85 4.0 52.3 1.0 OE1 F:GLU85 4.1 45.6 1.0 OD2 E:ASP5497 4.1 37.0 1.0 N E:SER5394 4.1 41.3 1.0 CA E:SER5394 4.3 38.4 1.0 OD1 E:ASP5497 4.3 34.9 1.0 CG E:ASP5390 4.4 36.5 1.0 CA E:SER5392 4.4 36.5 1.0 C E:SER5392 4.5 38.5 1.0 CG E:ASP5497 4.6 43.1 1.0 CA E:THR5461 4.7 37.9 1.0 O E:SER5392 4.8 39.4 1.0 N E:MET5395 4.9 41.4 1.0 C E:SER5394 4.9 43.4 1.0 N E:SER5393 4.9 43.4 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the Human MDN1-Midas/NLE1-Ubl Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Human MDN1-Midas/NLE1-Ubl Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg5701 b:26.9 occ:1.00 OE2 H:GLU85 2.0 49.0 1.0 OG G:SER5394 2.1 37.6 1.0 O H:HOH206 2.2 37.3 1.0 OG G:SER5392 2.2 35.0 1.0 OG1 G:THR5461 2.3 37.4 1.0 O G:HOH5802 2.3 28.2 1.0 CD H:GLU85 3.2 42.6 1.0 CB G:SER5392 3.3 34.3 1.0 CB G:THR5461 3.4 33.6 1.0 CB G:SER5394 3.4 38.9 1.0 CG2 G:THR5461 3.5 30.2 1.0 OD2 G:ASP5390 3.8 32.8 1.0 O G:ARG5499 3.9 37.5 1.0 OE1 H:GLU85 4.0 45.6 1.0 OD2 G:ASP5497 4.1 40.4 1.0 OD1 G:ASP5390 4.1 40.8 1.0 CG H:GLU85 4.2 51.2 1.0 OD1 G:ASP5497 4.2 32.5 1.0 N G:SER5394 4.3 36.7 1.0 CG G:ASP5390 4.4 38.9 1.0 CA G:SER5394 4.4 43.7 1.0 CA G:SER5392 4.5 35.4 1.0 CG G:ASP5497 4.6 34.7 1.0 CA G:THR5461 4.6 34.3 1.0 C G:SER5392 4.7 40.9 1.0 O G:HOH5820 4.7 43.7 1.0 N G:MET5395 5.0 34.9 1.0 O G:SER5392 5.0 39.5 1.0 C G:SER5394 5.0 35.9 1.0

F.Fiorentina, I.Sinning. NDE1-Midas/NLE1-Ubl To Be Published.