Magnesium in PDB 2zy9: Improved Crystal Structure of Magnesium Transporter Mgte

The structure of Improved Crystal Structure of Magnesium Transporter Mgte, PDB code: 2zy9 was solved by O.Nureki, R.Ishitani, M.Hattori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.71 / 2.94
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	135.364, 76.527, 160.037, 90.00, 102.17, 90.00
R / Rfree (%)	25.5 / 29.5

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the Improved Crystal Structure of Magnesium Transporter Mgte (pdb code 2zy9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the Improved Crystal Structure of Magnesium Transporter Mgte, PDB code: 2zy9:
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 Improved Crystal Structure of Magnesium Transporter Mgte


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Improved Crystal Structure of Magnesium Transporter Mgte within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg451 b:72.5 occ:1.00 CA B:GLY325 4.1 0.5 1.0 CB B:ALA428 4.5 89.8 1.0 OD1 A:ASP432 4.5 0.4 1.0 CA A:GLY325 4.5 99.4 1.0 OD1 B:ASP432 4.5 0.2 1.0 OD2 A:ASP432 4.6 94.7 1.0 OD2 B:ASP432 4.7 0.8 1.0 CB A:ALA428 4.8 83.2 1.0 N B:GLY325 4.8 0.5 1.0 CG A:ASP432 5.0 97.9 1.0

Magnesium binding site 2 out of 13 in the Improved Crystal Structure of Magnesium Transporter Mgte


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Improved Crystal Structure of Magnesium Transporter Mgte within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg452 b:70.1 occ:1.00 OE2 A:GLU255 4.0 83.8 1.0 OE1 A:GLU258 4.4 0.3 1.0 OE2 A:GLU258 4.6 0.6 1.0 OE1 A:GLU216 4.6 0.7 1.0 OE1 A:GLU255 4.7 90.2 1.0 CD A:GLU255 4.8 94.0 1.0 CD A:GLU258 4.9 0.7 1.0

Magnesium binding site 3 out of 13 in the Improved Crystal Structure of Magnesium Transporter Mgte


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Improved Crystal Structure of Magnesium Transporter Mgte within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg453 b:75.1 occ:1.00 OD2 A:ASP259 2.8 90.9 1.0 OD1 A:ASP418 3.3 88.3 1.0 OD2 A:ASP418 3.5 99.9 1.0 CG A:ASP259 3.7 89.1 1.0 CG A:ASP418 3.8 93.2 1.0 OD1 A:ASP259 3.9 81.0 1.0 OE1 A:GLU258 4.1 0.3 1.0 OE1 A:GLU216 4.2 0.7 1.0 OE2 A:GLU216 4.5 0.3 1.0 CB A:ALA420 4.7 0.8 1.0 CD A:GLU216 4.8 0.9 1.0

Magnesium binding site 4 out of 13 in the Improved Crystal Structure of Magnesium Transporter Mgte


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Improved Crystal Structure of Magnesium Transporter Mgte within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg454 b:60.3 occ:1.00 OD2 A:ASP247 2.5 0.6 1.0 OD2 A:ASP91 2.7 95.0 1.0 OD1 A:ASP247 3.1 0.8 1.0 CG A:ASP247 3.1 0.2 1.0 OG1 A:THR244 3.4 85.8 1.0 CG A:ASP91 3.5 94.0 1.0 OD1 A:ASP91 3.6 98.1 1.0 OD1 A:ASP92 3.6 0.8 1.0 OE1 A:GLU166 4.1 0.4 1.0 OE2 A:GLU166 4.1 0.4 1.0 OD2 A:ASP246 4.2 96.2 1.0 CD A:GLU166 4.2 0.1 1.0 OD1 A:ASP246 4.4 1.0 1.0 CB A:ASP247 4.4 99.6 1.0 CG A:ASP92 4.6 0.3 1.0 CG A:ASP246 4.8 0.6 1.0 CB A:THR244 4.8 91.0 1.0 OD2 A:ASP92 4.9 0.2 1.0 CB A:ASP91 5.0 86.7 1.0

Magnesium binding site 5 out of 13 in the Improved Crystal Structure of Magnesium Transporter Mgte


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Improved Crystal Structure of Magnesium Transporter Mgte within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg455 b:62.9 occ:1.00 O A:ALA223 2.6 62.4 1.0 OD1 A:ASP226 2.8 97.8 1.0 OD1 B:ASP250 3.6 0.3 1.0 CG A:ASP226 3.7 93.1 1.0 O A:ASP224 3.7 79.4 1.0 CE1 B:HIS63 3.8 0.1 1.0 C A:ALA223 3.8 72.1 1.0 ND1 B:HIS63 3.9 0.7 1.0 OD2 B:ASP250 3.9 0.4 1.0 OD2 A:ASP226 4.0 80.7 1.0 CG B:ASP250 4.1 0.1 1.0 O B:ASP246 4.2 94.4 1.0 C A:ASP224 4.5 83.6 1.0 CA A:ALA223 4.7 80.2 1.0 CA A:ASP224 4.7 77.5 1.0 N A:ASP224 4.7 62.6 1.0 N A:ASP226 4.8 88.6 1.0 CA A:ASP226 4.8 88.8 1.0 CB A:ASP226 4.9 94.9 1.0

Magnesium binding site 6 out of 13 in the Improved Crystal Structure of Magnesium Transporter Mgte


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Improved Crystal Structure of Magnesium Transporter Mgte within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg456 b:79.3 occ:1.00 OD1 A:ASP95 2.3 82.2 1.0 O A:GLY136 2.3 95.3 1.0 C A:GLY136 3.3 90.9 1.0 CG A:ASP95 3.5 91.9 1.0 CA A:GLY136 3.6 86.8 1.0 OE1 A:GLN98 3.7 97.1 1.0 OD2 A:ASP95 4.1 91.2 1.0 N A:LEU137 4.4 88.4 1.0 O A:ASP91 4.5 85.1 1.0 CA A:GLU131 4.5 88.9 1.0 N A:ASP95 4.6 0.7 1.0 CA A:ASP95 4.7 0.7 1.0 CB A:ASP95 4.7 99.2 1.0 CD A:GLN98 4.7 99.2 1.0 O A:GLU131 4.7 99.0 1.0 CB A:ALA94 4.8 0.8 1.0 CB A:GLU131 4.9 91.2 1.0 CA A:LEU137 4.9 90.5 1.0 NE2 A:GLN98 5.0 96.1 1.0

Magnesium binding site 7 out of 13 in the Improved Crystal Structure of Magnesium Transporter Mgte


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Improved Crystal Structure of Magnesium Transporter Mgte within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg451 b:90.0 occ:1.00 OD2 B:ASP226 3.0 0.6 1.0 OE2 A:GLU59 3.9 0.6 1.0 OE1 A:GLU59 4.0 0.5 1.0 CG B:ASP226 4.1 0.4 1.0 CD A:GLU59 4.4 0.2 1.0 OD1 A:ASP246 4.4 1.0 1.0 CB B:ASP226 4.6 99.1 1.0 NE2 A:HIS63 4.6 0.3 1.0 OD2 A:ASP92 4.8 0.2 1.0 OE2 A:GLU166 4.8 0.4 1.0

Magnesium binding site 8 out of 13 in the Improved Crystal Structure of Magnesium Transporter Mgte


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Improved Crystal Structure of Magnesium Transporter Mgte within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg452 b:78.6 occ:1.00 OD2 B:ASP132 4.0 95.1 1.0 OE2 B:GLU255 4.1 0.1 1.0 OE1 B:GLU255 4.3 0.7 1.0 OD1 B:ASP214 4.4 0.3 1.0 CD B:GLU255 4.7 0.5 1.0 OD2 B:ASP214 4.8 0.5 1.0 CG B:ASP132 5.0 0.1 1.0

Magnesium binding site 9 out of 13 in the Improved Crystal Structure of Magnesium Transporter Mgte


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Improved Crystal Structure of Magnesium Transporter Mgte within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg453 b:74.0 occ:1.00 OD2 B:ASP259 2.6 0.2 1.0 CG B:ASP259 3.4 0.6 1.0 OD1 B:ASP259 3.5 0.3 1.0 OD1 B:ASP418 3.8 0.7 1.0 OE1 B:GLU258 4.0 0.7 1.0 OD2 B:ASP418 4.3 0.0 1.0 CG B:ASP418 4.4 0.8 1.0 O B:GLU255 4.4 93.9 1.0 CB B:ASP259 4.9 0.6 1.0

Magnesium binding site 10 out of 13 in the Improved Crystal Structure of Magnesium Transporter Mgte


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Improved Crystal Structure of Magnesium Transporter Mgte within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg454 b:81.3 occ:1.00 OD2 B:ASP247 2.7 89.5 1.0 OD2 B:ASP91 2.8 0.4 1.0 CG B:ASP247 3.4 78.5 1.0 CG B:ASP91 3.5 0.9 1.0 OE2 B:GLU166 3.5 0.7 1.0 OD1 B:ASP91 3.6 0.9 1.0 OD1 B:ASP247 3.7 74.7 1.0 OG1 B:THR244 3.7 0.8 1.0 CD B:GLU166 3.8 0.1 1.0 OE1 B:GLU166 4.0 0.5 1.0 OD2 B:ASP246 4.1 81.8 1.0 OD1 B:ASP246 4.1 88.3 1.0 OG B:SER89 4.4 0.5 1.0 CG B:ASP246 4.5 84.7 1.0 CG B:GLU166 4.6 0.2 1.0 CB B:ASP247 4.6 62.5 1.0 CB B:THR244 4.6 0.9 1.0 CG2 B:THR139 4.8 0.7 1.0 CB B:ASP91 4.9 92.3 1.0

M.Hattori, N.Iwase, N.Furuya, Y.Tanaka, T.Tsukazaki, R.Ishitani, M.E.Maguire, K.Ito, A.Maturana, O.Nureki. Mg(2+)-Dependent Gating of Bacterial Mgte Channel Underlies Mg(2+) Homeostasis Embo J. V. 28 3602 2009.
ISSN: ISSN 0261-4189
PubMed: 19798051
DOI: 10.1038/EMBOJ.2009.288