Magnesium in PDB 5x9h: Crystal Structure of the MG2+ Channel Mgte in Complex with Atp

The structure of Crystal Structure of the MG2+ Channel Mgte in Complex with Atp, PDB code: 5x9h 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)	50.33 / 3.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	135.330, 85.651, 156.558, 90.00, 100.02, 90.00
R / Rfree (%)	25 / 28.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the MG2+ Channel Mgte in Complex with Atp (pdb code 5x9h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the Crystal Structure of the MG2+ Channel Mgte in Complex with Atp, PDB code: 5x9h:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 13 in the Crystal Structure 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 MG2+ Channel Mgte in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:0.3 occ:1.00 OD1 A:ASP432 3.7 0.0 1.0 CA A:GLY325 4.1 0.9 1.0 OD2 A:ASP432 4.1 0.5 1.0 OD1 B:ASP432 4.2 0.7 1.0 CB A:ALA428 4.2 0.1 1.0 OD2 B:ASP432 4.3 0.4 1.0 CG A:ASP432 4.3 0.1 1.0 CB B:ALA428 4.5 0.9 1.0 CA B:GLY325 4.6 1.0 1.0 O A:ALA428 4.6 0.1 1.0 CG B:ASP432 4.7 0.7 1.0 N A:GLY325 4.7 0.6 1.0 CA A:ALA428 4.9 1.0 1.0 C A:ALA428 4.9 0.5 1.0 O A:LEU324 4.9 0.1 1.0 O A:GLY325 4.9 0.4 1.0

Magnesium binding site 2 out of 13 in the Crystal Structure 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 MG2+ Channel Mgte in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:0.8 occ:1.00 OE1 A:GLU255 3.8 0.2 1.0 OE2 A:GLU255 4.0 0.2 1.0 CD A:GLU255 4.2 0.5 1.0 OD2 A:ASP214 4.5 0.5 1.0 OD1 A:ASP214 4.5 0.0 1.0 OE1 A:GLU258 4.6 0.4 1.0 OE2 A:GLU258 4.7 0.3 1.0 CG A:ASP214 5.0 0.7 1.0 OD2 A:ASP132 5.0 0.6 1.0

Magnesium binding site 3 out of 13 in the Crystal Structure 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 MG2+ Channel Mgte in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:0.3 occ:1.00 OD1 A:ASP259 2.5 0.3 1.0 CG A:ASP259 3.3 0.5 1.0 OD2 A:ASP259 3.3 0.3 1.0 OD2 A:ASP418 3.9 0.8 1.0 OE1 A:GLU258 4.0 0.4 1.0 OE1 A:GLU216 4.0 0.2 1.0 OE2 A:GLU216 4.0 0.2 1.0 OD1 A:ASP418 4.2 0.8 1.0 CG A:GLU255 4.4 0.6 1.0 CD A:GLU216 4.4 0.5 1.0 CG A:ASP418 4.5 0.8 1.0 CB A:ASP259 4.7 0.7 1.0 CD A:GLU255 4.9 0.5 1.0

Magnesium binding site 4 out of 13 in the Crystal Structure 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 MG2+ Channel Mgte in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:0.4 occ:1.00 OD2 A:ASP247 2.7 0.0 1.0 OD2 A:ASP91 2.7 0.8 1.0 OD1 A:ASP247 3.1 0.1 1.0 CG A:ASP247 3.2 0.0 1.0 CG A:ASP91 3.5 0.3 1.0 OD2 A:ASP92 3.7 0.7 1.0 OD1 A:ASP91 3.8 0.0 1.0 OD2 A:ASP246 3.8 0.7 1.0 OE2 A:GLU166 3.8 0.1 1.0 OG1 A:THR244 3.9 0.5 1.0 OD1 A:ASP92 3.9 0.1 1.0 OD1 A:ASP246 4.0 0.9 1.0 CG A:ASP92 4.2 0.2 1.0 CG A:ASP246 4.3 0.6 1.0 CD A:GLU166 4.5 0.3 1.0 OE1 A:GLU166 4.6 0.3 1.0 CB A:ASP247 4.7 0.4 1.0 CB A:ASP91 4.8 0.1 1.0 MG A:MG508 4.8 0.4 1.0

Magnesium binding site 5 out of 13 in the Crystal Structure 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 MG2+ Channel Mgte in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg506 b:0.5 occ:1.00 O A:ALA223 2.1 0.9 1.0 OD1 A:ASP226 2.2 0.2 1.0 OD2 B:ASP250 3.3 0.7 1.0 CG A:ASP226 3.3 0.2 1.0 C A:ALA223 3.4 0.2 1.0 OD1 B:ASP250 3.6 0.9 1.0 O A:ASP224 3.7 0.6 1.0 OD2 A:ASP226 3.8 0.7 1.0 CG B:ASP250 3.8 0.6 1.0 C A:ASP224 4.2 0.3 1.0 N A:ASP224 4.2 0.6 1.0 CA A:ASP224 4.3 0.8 1.0 CA A:ALA223 4.4 0.3 1.0 CD2 B:HIS63 4.5 0.6 1.0 NE2 B:HIS63 4.5 0.8 1.0 CB A:ASP226 4.6 0.1 1.0 CB B:ASP246 4.6 0.7 1.0 N A:ASP226 4.7 0.1 1.0 CA A:ASP226 4.7 0.8 1.0 O B:ASP246 4.8 1.0 1.0 CB A:ALA223 4.9 0.8 1.0

Magnesium binding site 6 out of 13 in the Crystal Structure 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 MG2+ Channel Mgte in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg507 b:0.5 occ:1.00 O A:GLY136 1.8 0.2 1.0 OD1 A:ASP95 1.9 0.8 1.0 CG A:ASP95 2.6 0.8 1.0 OD2 A:ASP95 2.7 0.7 1.0 C A:GLY136 3.0 0.5 1.0 CA A:GLY136 3.7 0.6 1.0 N A:LEU137 4.0 0.3 1.0 CB A:ASP95 4.1 0.5 1.0 O A:ASP91 4.2 0.9 1.0 CA A:LEU137 4.3 0.7 1.0 CD2 A:LEU137 4.5 0.8 1.0 NE2 A:GLN98 4.6 0.2 1.0 CA A:ASP95 4.6 0.2 1.0 N A:ASP95 4.8 0.9 1.0 C A:ASP91 5.0 0.3 1.0

Magnesium binding site 7 out of 13 in the Crystal Structure 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 MG2+ Channel Mgte in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg508 b:0.4 occ:1.00 OE2 A:GLU59 3.4 0.2 1.0 OD2 B:ASP226 3.4 0.1 1.0 OD2 A:ASP246 3.8 0.7 1.0 CG B:ASP226 4.3 0.8 1.0 CB B:ASP226 4.3 0.5 1.0 CD A:GLU59 4.6 0.1 1.0 MG A:MG505 4.8 0.4 1.0 NE2 A:HIS63 4.9 0.1 1.0 OE2 A:GLU166 4.9 0.1 1.0 CG A:ASP246 5.0 0.6 1.0

Magnesium binding site 8 out of 13 in the Crystal Structure 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 MG2+ Channel Mgte in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg509 b:0.3 occ:1.00 OD2 A:ASP226 3.0 0.7 1.0 OE2 B:GLU59 3.4 0.6 1.0 OE1 B:GLU59 3.6 0.7 1.0 CD B:GLU59 3.8 0.4 1.0 CG A:ASP226 3.9 0.2 1.0 OD2 B:ASP246 4.1 0.8 1.0 CB A:ASP226 4.1 0.1 1.0 CE1 B:HIS63 4.2 0.1 1.0 NE2 B:HIS63 4.2 0.8 1.0

Magnesium binding site 9 out of 13 in the Crystal Structure 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 9 of Crystal Structure of the MG2+ Channel Mgte in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:0.6 occ:1.00 O B:ALA223 2.3 0.8 1.0 OD1 B:ASP226 2.6 0.6 1.0 C B:ALA223 3.5 0.1 1.0 O B:ASP224 3.5 0.5 1.0 CG B:ASP226 3.8 0.8 1.0 O A:ASP246 4.1 0.5 1.0 OD1 A:ASP250 4.1 0.7 1.0 C B:ASP224 4.2 0.8 1.0 OD2 B:ASP226 4.2 0.1 1.0 CA B:ASP224 4.2 0.1 1.0 CG A:ASP250 4.3 0.7 1.0 N B:ASP224 4.3 0.7 1.0 OD2 A:ASP250 4.5 0.5 1.0 CA B:ALA223 4.6 0.5 1.0 N B:ASP226 4.9 0.7 1.0 CB A:ASP250 4.9 0.8 1.0

Magnesium binding site 10 out of 13 in the Crystal Structure 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 10 of Crystal Structure of the MG2+ Channel Mgte in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:0.9 occ:1.00 OE1 B:GLU255 3.9 0.5 1.0 OD2 B:ASP132 4.1 0.2 1.0 OE2 B:GLU216 4.1 0.6 1.0 OE2 B:GLU255 4.3 0.2 1.0 OD1 B:ASP214 4.4 0.4 1.0 OE1 B:GLU258 4.4 0.3 1.0 CD B:GLU255 4.4 0.7 1.0 CD B:GLU216 4.6 0.2 1.0 OE2 B:GLU258 4.7 0.9 1.0 OD2 B:ASP214 4.7 0.8 1.0 CB B:ASP132 4.8 0.6 1.0 CG B:ASP132 4.9 0.6 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