Magnesium in PDB 5x9g: Crystal Structure of the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp

The structure of Crystal Structure of the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp, PDB code: 5x9g was solved by A.Tomita, M.Hattori, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.80 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	138.317, 106.672, 90.170, 90.00, 90.00, 90.00
R / Rfree (%)	24 / 29.8

The binding sites of Magnesium atom in the Crystal Structure of the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp (pdb code 5x9g). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp, PDB code: 5x9g:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Crystal Structure of the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp


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 Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:59.9 occ:1.00 OD2 A:ASP247 2.0 68.2 1.0 OD2 A:ASP91 2.2 53.1 1.0 CG A:ASP91 3.1 53.0 1.0 CG A:ASP247 3.1 66.2 1.0 OG1 A:THR244 3.3 70.7 1.0 OE2 A:GLU166 3.5 71.0 1.0 OD1 A:ASP91 3.5 52.8 1.0 OD1 A:ASP247 3.6 72.1 1.0 CD A:GLU166 3.8 72.5 1.0 OE1 A:GLU166 4.0 67.7 1.0 OD1 A:ASP246 4.3 77.2 1.0 CB A:ASP247 4.3 69.1 1.0 CB A:ASP91 4.3 50.8 1.0 CG A:GLU166 4.5 65.6 1.0 OD1 A:ASP92 4.6 61.6 1.0 CB A:THR244 4.6 59.4 1.0 OD2 A:ASP246 4.6 77.1 1.0 CG2 A:THR139 4.7 53.0 1.0 CG2 A:THR244 4.8 62.5 1.0 CG A:ASP246 4.9 80.1 1.0 O A:LEU137 4.9 52.1 1.0

Magnesium binding site 2 out of 8 in the Crystal Structure of the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp


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 Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:46.0 occ:1.00 OD1 A:ASP95 1.8 55.1 1.0 O A:GLY136 2.0 60.9 1.0 CG A:ASP95 2.7 54.1 1.0 OD2 A:ASP95 3.0 59.1 1.0 C A:GLY136 3.2 58.2 1.0 O A:ASP91 3.9 48.1 1.0 CA A:GLY136 4.0 56.5 1.0 CB A:ASP95 4.1 42.4 1.0 N A:LEU137 4.2 53.1 1.0 CA A:LEU137 4.4 54.7 1.0 N A:ASP95 4.4 50.9 1.0 CA A:ASP95 4.5 48.8 1.0 CD2 A:LEU137 4.7 67.0 1.0 C A:ASP91 4.8 50.9 1.0 OE1 A:GLN98 4.8 52.8 1.0 O A:GLU131 4.9 68.5 1.0

Magnesium binding site 3 out of 8 in the Crystal Structure of the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp


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 Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:36.1 occ:1.00 OD1 B:ASP95 1.8 53.0 1.0 O B:GLY136 2.1 60.2 1.0 CG B:ASP95 2.9 43.9 1.0 C B:GLY136 3.3 48.5 1.0 OD2 B:ASP95 3.3 49.0 1.0 CA B:GLY136 4.0 43.9 1.0 O B:ASP91 4.1 31.3 1.0 CB B:ASP95 4.2 30.2 1.0 OE1 B:GLN98 4.3 46.3 1.0 N B:LEU137 4.4 45.3 1.0 CA B:ASP95 4.5 30.6 1.0 N B:ASP95 4.5 32.6 1.0 CA B:LEU137 4.6 46.3 1.0 O B:GLU131 4.6 55.6 1.0 CB B:GLU131 4.8 59.0 1.0 CD2 B:LEU137 5.0 47.1 1.0 C B:ASP91 5.0 34.5 1.0

Magnesium binding site 4 out of 8 in the Crystal Structure of the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp


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 Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:49.9 occ:1.00 OD2 B:ASP91 2.3 48.9 1.0 OD2 B:ASP247 2.4 56.2 1.0 CG B:ASP91 3.1 44.9 1.0 CG B:ASP247 3.2 57.6 1.0 OE2 B:GLU166 3.2 51.1 1.0 OD1 B:ASP247 3.3 59.6 1.0 OD1 B:ASP91 3.3 49.8 1.0 CD B:GLU166 3.8 53.1 1.0 OE1 B:GLU166 3.9 53.2 1.0 OD2 B:ASP92 4.2 49.9 1.0 OD1 B:ASP92 4.2 51.5 1.0 OD2 B:ASP246 4.2 55.9 1.0 OG1 B:THR244 4.3 54.2 1.0 CG B:ASP92 4.5 49.1 1.0 CB B:ASP91 4.5 34.5 1.0 CB B:ASP247 4.6 55.1 1.0 OD1 B:ASP246 4.7 63.8 1.0 CB B:SER89 4.9 47.0 1.0 CG B:ASP246 4.9 61.2 1.0 CG B:GLU166 5.0 48.7 1.0

Magnesium binding site 5 out of 8 in the Crystal Structure of the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp


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 Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg302 b:44.6 occ:1.00 OD2 C:ASP247 2.2 50.0 1.0 OD2 C:ASP91 2.3 48.6 1.0 CG C:ASP91 3.2 45.8 1.0 OG1 C:THR244 3.2 46.8 1.0 OE2 C:GLU166 3.2 46.7 1.0 CG C:ASP247 3.4 51.7 1.0 CD C:GLU166 3.6 47.4 1.0 OD1 C:ASP91 3.6 47.2 1.0 OE1 C:GLU166 3.7 45.5 1.0 OD1 C:ASP247 4.0 56.7 1.0 OD2 C:ASP246 4.3 48.7 1.0 OD1 C:ASP246 4.4 54.7 1.0 CB C:ASP91 4.4 38.4 1.0 CG2 C:THR139 4.5 45.4 1.0 CB C:ASP247 4.5 48.4 1.0 CB C:THR244 4.5 49.8 1.0 CG C:GLU166 4.5 49.1 1.0 OD1 C:ASP92 4.7 47.1 1.0 CG2 C:THR244 4.7 47.1 1.0 CG C:ASP246 4.8 53.9 1.0 CB C:THR139 4.9 44.5 1.0

Magnesium binding site 6 out of 8 in the Crystal Structure of the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp


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 Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg303 b:47.0 occ:1.00 O C:GLY136 2.1 54.0 1.0 OD1 C:ASP95 2.4 50.6 1.0 OD2 C:ASP95 3.1 45.7 1.0 CG C:ASP95 3.1 45.3 1.0 C C:GLY136 3.2 46.7 1.0 CD2 C:LEU137 3.7 45.6 1.0 O C:GLU131 3.9 60.2 1.0 N C:LEU137 4.0 41.6 1.0 CA C:LEU137 4.0 41.9 1.0 CA C:GLY136 4.1 44.8 1.0 CB C:ASP95 4.6 37.9 1.0 CA C:GLU131 4.6 58.0 1.0 CG C:LEU137 4.7 49.9 1.0 C C:GLU131 4.7 58.3 1.0 O C:ASP91 4.8 37.1 1.0 OE1 C:GLN98 4.9 47.7 1.0 CB C:LEU137 4.9 47.8 1.0 CB C:GLU131 5.0 55.7 1.0 C C:LEU137 5.0 38.9 1.0

Magnesium binding site 7 out of 8 in the Crystal Structure of the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg302 b:51.0 occ:1.00 OD2 D:ASP247 2.1 48.2 1.0 OD2 D:ASP91 2.3 52.4 1.0 CG D:ASP247 3.2 58.0 1.0 CG D:ASP91 3.3 50.3 1.0 OD1 D:ASP91 3.5 52.8 1.0 OE2 D:GLU166 3.6 65.0 1.0 OG1 D:THR244 3.6 58.6 1.0 OD1 D:ASP247 3.7 60.5 1.0 CD D:GLU166 3.8 60.4 1.0 OE1 D:GLU166 3.8 65.6 1.0 OD1 D:ASP92 4.1 49.0 1.0 OD2 D:ASP246 4.2 62.0 1.0 OD1 D:ASP246 4.3 58.1 1.0 CB D:ASP247 4.4 53.2 1.0 OD2 D:ASP92 4.5 61.0 1.0 CB D:ASP91 4.6 43.2 1.0 CG D:ASP246 4.6 64.1 1.0 CG D:ASP92 4.7 48.9 1.0 CG D:GLU166 4.7 55.5 1.0 CB D:THR244 4.9 48.7 1.0

Magnesium binding site 8 out of 8 in the Crystal Structure of the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the Cytosolic Domain of the MG2+ Channel Mgte in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg303 b:51.7 occ:1.00 OD1 D:ASP95 2.0 52.7 1.0 O D:GLY136 2.1 52.0 1.0 CG D:ASP95 2.9 43.0 1.0 OD2 D:ASP95 3.2 41.7 1.0 C D:GLY136 3.3 48.5 1.0 CD2 D:LEU137 4.2 51.2 1.0 CA D:GLY136 4.2 45.8 1.0 N D:LEU137 4.2 45.6 1.0 O D:GLU131 4.3 62.1 1.0 CB D:ASP95 4.3 40.8 1.0 CA D:LEU137 4.3 39.8 1.0 OE1 D:GLN98 4.4 60.2 1.0 O D:ASP91 4.5 38.8 1.0 CA D:GLU131 4.7 59.4 1.0 CA D:ASP95 4.8 48.7 1.0 CB D:GLU131 4.8 59.8 1.0 N D:ASP95 4.9 49.1 1.0 C D:GLU131 5.0 60.8 1.0

A.Tomita, M.Zhang, F.Jin, W.Zhuang, H.Takeda, T.Maruyama, M.Osawa, K.I.Hashimoto, H.Kawasaki, K.Ito, N.Dohmae, R.Ishitani, I.Shimada, Z.Yan, M.Hattori, O.Nureki. Atp-Dependent Modulation of Mgte in Mg(2+) Homeostasis Nat Commun V. 8 148 2017.
ISSN: ESSN 2041-1723
PubMed: 28747715
DOI: 10.1038/S41467-017-00082-W