Magnesium in PDB 5m0i: Crystal Structure of the Nuclear Complex with SHE2P and the ASH1 Mrna E3-Localization Element

The structure of Crystal Structure of the Nuclear Complex with SHE2P and the ASH1 Mrna E3-Localization Element, PDB code: 5m0i was solved by F.T.Edelmann, R.Janowski, D.Niessing, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.01 / 2.41
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	220.520, 58.340, 146.010, 90.00, 126.98, 90.00
R / Rfree (%)	18.9 / 23.5

The binding sites of Magnesium atom in the Crystal Structure of the Nuclear Complex with SHE2P and the ASH1 Mrna E3-Localization Element (pdb code 5m0i). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of the Nuclear Complex with SHE2P and the ASH1 Mrna E3-Localization Element, PDB code: 5m0i:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of the Nuclear Complex with SHE2P and the ASH1 Mrna E3-Localization Element


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 Nuclear Complex with SHE2P and the ASH1 Mrna E3-Localization Element within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg303 b:60.5 occ:1.00 OE1 D:GLU124 3.5 37.6 1.0 CB D:GLU124 3.7 35.5 1.0 O D:SER120 3.8 38.0 1.0 CB C:PHE50 4.0 32.9 1.0 CB D:SER120 4.0 39.1 1.0 CG D:GLU124 4.0 34.9 1.0 C C:PHE50 4.1 31.7 1.0 C D:SER120 4.1 37.2 1.0 O C:PHE50 4.2 32.3 1.0 CD D:GLU124 4.2 35.7 1.0 N C:GLU51 4.3 31.5 1.0 CG C:GLU51 4.3 33.7 1.0 CE1 D:TYR116 4.3 36.2 1.0 OE2 C:GLU51 4.4 39.8 1.0 CD C:GLU51 4.4 34.7 1.0 CA C:GLU51 4.5 32.5 1.0 OG1 C:THR54 4.5 33.8 1.0 N D:LEU121 4.5 36.0 1.0 CA C:PHE50 4.6 32.7 1.0 CA D:LEU121 4.6 38.2 1.0 OH C:TYR116 4.7 40.7 1.0 CA D:SER120 4.8 37.4 1.0 OH D:TYR116 4.9 40.5 1.0 CZ D:TYR116 5.0 35.7 1.0 OG D:SER120 5.0 42.8 1.0 CB C:GLU51 5.0 33.3 1.0 OE1 C:GLU51 5.0 36.1 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of the Nuclear Complex with SHE2P and the ASH1 Mrna E3-Localization Element


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 Nuclear Complex with SHE2P and the ASH1 Mrna E3-Localization Element within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg307 b:62.5 occ:1.00 CE1 C:TYR116 3.6 37.0 1.0 OH C:TYR116 4.1 40.7 1.0 CB C:GLU124 4.1 38.9 1.0 O C:SER120 4.2 36.6 1.0 CB C:SER120 4.2 41.4 1.0 CZ C:TYR116 4.2 38.5 1.0 OE1 C:GLU124 4.2 46.5 1.0 OG1 D:THR54 4.4 36.3 1.0 C C:SER120 4.4 37.2 1.0 CG C:GLU124 4.4 41.4 1.0 OH D:TYR116 4.5 40.5 1.0 CD1 C:TYR116 4.5 37.3 1.0 CG D:GLU51 4.5 39.1 1.0 CA C:LEU121 4.6 35.0 1.0 N C:LEU121 4.6 35.3 1.0 C D:PHE50 4.6 32.9 1.0 O D:PHE50 4.6 31.4 1.0 CG C:GLU51 4.7 33.7 1.0 CB D:PHE50 4.7 35.0 1.0 OE2 D:GLU51 4.7 43.0 1.0 N D:GLU51 4.7 33.8 1.0 CD D:GLU51 4.8 41.5 1.0 CA D:GLU51 4.8 35.0 1.0 CD C:GLU124 4.8 44.0 1.0 CD1 C:LEU121 4.9 35.2 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of the Nuclear Complex with SHE2P and the ASH1 Mrna E3-Localization Element


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 Nuclear Complex with SHE2P and the ASH1 Mrna E3-Localization Element within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:80.2 occ:1.00 O B:HOH410 3.3 41.6 1.0 OE1 B:GLU124 3.8 45.6 1.0 CB B:GLU124 3.8 40.8 1.0 O B:SER120 4.0 40.4 1.0 CE1 B:TYR116 4.1 39.9 1.0 CG B:GLU124 4.1 42.0 1.0 CB B:SER120 4.2 43.7 1.0 C A:PHE50 4.2 37.3 1.0 CB A:PHE50 4.3 38.2 1.0 C B:SER120 4.3 40.8 1.0 N A:GLU51 4.4 37.7 1.0 CG A:GLU51 4.4 39.6 1.0 OE2 A:GLU51 4.4 41.5 1.0 O A:PHE50 4.4 37.3 1.0 CD B:GLU124 4.4 43.4 1.0 CD A:GLU51 4.5 41.7 1.0 OG1 A:THR54 4.5 40.2 1.0 OH B:TYR116 4.6 45.6 1.0 N B:LEU121 4.6 39.3 1.0 CA B:LEU121 4.6 37.3 1.0 OH A:TYR116 4.6 45.7 1.0 CA A:GLU51 4.6 38.1 1.0 CZ B:TYR116 4.7 40.4 1.0 CA A:PHE50 4.8 38.2 1.0 CG B:GLU51 4.9 38.2 1.0 CD1 B:TYR116 4.9 39.9 1.0 CA B:SER120 4.9 41.7 1.0 OE2 B:GLU51 5.0 39.0 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of the Nuclear Complex with SHE2P and the ASH1 Mrna E3-Localization Element


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 Nuclear Complex with SHE2P and the ASH1 Mrna E3-Localization Element within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:71.1 occ:1.00 O B:HOH410 3.3 41.6 1.0 CB A:SER120 3.9 41.0 1.0 C B:PHE50 3.9 35.6 1.0 O B:PHE50 4.0 36.7 1.0 OE1 A:GLU124 4.0 43.5 1.0 OG1 B:THR54 4.1 37.6 1.0 N B:GLU51 4.1 35.5 1.0 CE1 A:TYR116 4.1 41.5 1.0 O A:SER120 4.1 37.2 1.0 CB B:PHE50 4.1 37.5 1.0 CG B:GLU51 4.1 38.2 1.0 CB A:GLU124 4.2 39.7 1.0 CA B:GLU51 4.3 36.2 1.0 OH B:TYR116 4.3 45.6 1.0 C A:SER120 4.3 37.9 1.0 CD B:GLU51 4.4 39.5 1.0 CG A:GLU124 4.4 39.8 1.0 OE2 B:GLU51 4.5 39.0 1.0 CA B:PHE50 4.6 37.1 1.0 N A:LEU121 4.7 36.4 1.0 CD A:GLU124 4.7 42.0 1.0 OG A:SER120 4.7 43.7 1.0 OH A:TYR116 4.8 45.7 1.0 CD1 A:TYR116 4.8 41.4 1.0 CA A:SER120 4.8 39.9 1.0 CB B:GLU51 4.8 37.0 1.0 CZ A:TYR116 4.8 42.8 1.0 CA A:LEU121 4.8 38.6 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of the Nuclear Complex with SHE2P and the ASH1 Mrna E3-Localization Element


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Nuclear Complex with SHE2P and the ASH1 Mrna E3-Localization Element within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg101 b:57.5 occ:1.00 O F:HOH227 2.0 53.4 1.0 OP2 F:U7 2.0 73.2 1.0 O F:HOH236 2.2 63.8 1.0 C3' F:C6 3.4 46.0 1.0 P F:U7 3.4 81.1 1.0 O3' F:C6 3.6 55.4 1.0 O F:HOH204 4.0 57.0 1.0 O5' F:U7 4.3 70.5 1.0 C2' F:C6 4.3 43.4 1.0 C5' F:U7 4.4 66.8 1.0 C4' F:C6 4.4 40.4 1.0 C5' F:C6 4.5 38.7 1.0 OP1 F:U7 4.5 77.1 1.0 O2' F:C6 4.6 46.1 1.0 N2 F:G8 4.8 57.2 1.0 O5' F:C6 4.9 37.5 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of the Nuclear Complex with SHE2P and the ASH1 Mrna E3-Localization Element


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Nuclear Complex with SHE2P and the ASH1 Mrna E3-Localization Element within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg102 b:49.5 occ:1.00 O C:HOH448 2.3 36.1 1.0 OP1 F:G8 3.0 47.6 1.0 O F:HOH202 3.1 36.3 1.0 O3' F:U7 3.6 57.0 1.0 O F:HOH201 3.8 52.2 1.0 P F:G8 4.0 49.9 1.0 CD C:ARG63 4.0 32.9 1.0 O F:HOH209 4.1 39.5 1.0 O C:HOH422 4.3 34.0 1.0 OD2 C:ASP67 4.3 45.7 1.0 NZ D:LYS179 4.3 91.8 1.0 C5' F:G8 4.4 44.1 1.0 O C:HOH429 4.5 40.5 1.0 O2' F:U7 4.6 58.9 1.0 O5' F:G8 4.7 46.3 1.0 CG C:ARG63 4.9 33.7 1.0 O2 F:U7 4.9 98.5 1.0 C3' F:U7 4.9 63.2 1.0 C1' F:U7 4.9 75.5 1.0

F.T.Edelmann, A.Schlundt, R.G.Heym, A.Jenner, A.Niedner-Boblenz, M.I.Syed, J.C.Paillart, R.Stehle, R.Janowski, M.Sattler, R.P.Jansen, D.Niessing. Molecular Architecture and Dynamics of ASH1 Mrna Recognition By Its Mrna-Transport Complex. Nat. Struct. Mol. Biol. V. 24 152 2017.
ISSN: ESSN 1545-9985
PubMed: 28092367
DOI: 10.1038/NSMB.3351