Magnesium in PDB 2yvx: Crystal Structure of Magnesium Transporter Mgte

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

Resolution Low / High (Å)	49.69 / 3.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	118.314, 134.897, 366.252, 90.00, 90.00, 90.00
R / Rfree (%)	29.4 / 34.1

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Magnesium Transporter Mgte (pdb code 2yvx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 18 binding sites of Magnesium where determined in the Crystal Structure of Magnesium Transporter Mgte, PDB code: 2yvx:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 18 in the 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 Crystal Structure of Magnesium Transporter Mgte within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg451 b:34.9 occ:1.00 OD2 B:ASP432 3.4 92.1 1.0 O B:ALA428 3.8 89.7 1.0 OD2 A:ASP432 4.0 0.9 1.0 CG B:ASP432 4.3 97.2 1.0 OD1 B:ASP432 4.3 98.1 1.0 OD1 A:ASP432 4.3 0.1 1.0 O A:ALA428 4.3 99.6 1.0 CA A:GLY325 4.5 0.1 1.0 CB B:ALA428 4.5 95.3 1.0 CG A:ASP432 4.6 0.0 1.0 CA B:GLY325 4.7 0.3 1.0 CB A:ALA428 4.8 90.8 1.0 C B:ALA428 4.8 90.8 1.0

Magnesium binding site 2 out of 18 in the 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 Crystal Structure of Magnesium Transporter Mgte within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg451 b:33.6 occ:1.00 OD1 C:ASP432 3.3 98.4 1.0 O C:ALA428 3.5 92.5 1.0 OD2 C:ASP432 3.7 92.1 1.0 CG C:ASP432 3.9 95.8 1.0 O D:ALA428 4.2 0.5 1.0 OD2 D:ASP432 4.2 98.2 1.0 CB C:ALA428 4.2 95.8 1.0 OD1 D:ASP432 4.3 0.7 1.0 CB D:ALA428 4.5 0.4 1.0 C C:ALA428 4.5 93.2 1.0 CA D:GLY325 4.5 0.3 1.0 CA C:GLY325 4.7 97.0 1.0 CG D:ASP432 4.7 0.1 1.0 CA C:ALA428 4.8 93.2 1.0

Magnesium binding site 3 out of 18 in the 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 Crystal Structure of Magnesium Transporter Mgte within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg451 b:46.9 occ:1.00 OD2 A:ASP259 2.2 61.4 1.0 OD1 A:ASP259 2.5 64.0 1.0 CG A:ASP259 2.7 67.3 1.0 OD2 A:ASP418 2.7 0.5 1.0 OE1 A:GLU258 3.3 57.5 1.0 OE1 A:GLU216 3.5 93.2 1.0 CG A:ASP418 3.9 0.1 1.0 OE2 A:GLU216 3.9 88.7 1.0 CD A:GLU216 4.0 92.3 1.0 CB A:ASP259 4.2 65.4 1.0 O A:GLU255 4.3 63.2 1.0 CD A:GLU258 4.3 55.5 1.0 OE1 A:GLU255 4.3 84.1 1.0 OD1 A:ASP418 4.4 0.6 1.0 OE2 A:GLU258 4.5 48.5 1.0 CA A:ASP259 5.0 55.4 1.0

Magnesium binding site 4 out of 18 in the 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 Crystal Structure of Magnesium Transporter Mgte within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg452 b:39.2 occ:1.00 OD2 B:ASP259 2.3 50.9 1.0 OE1 B:GLU216 2.9 0.8 1.0 CG B:ASP259 3.0 59.2 1.0 OD1 B:ASP259 3.0 56.8 1.0 OE1 B:GLU258 3.2 83.2 1.0 OD1 B:ASP418 3.3 0.8 1.0 OE2 B:GLU216 3.4 0.0 1.0 CD B:GLU216 3.5 0.4 1.0 OE1 B:GLU255 3.7 75.2 1.0 OD2 B:ASP418 3.9 0.9 1.0 CG B:ASP418 4.0 0.4 1.0 O B:GLU255 4.1 59.1 1.0 CD B:GLU258 4.4 80.3 1.0 CB B:ASP259 4.5 65.0 1.0 CD B:GLU255 4.8 72.5 1.0 CB B:GLU255 4.9 60.5 1.0 CG B:GLU216 4.9 0.5 1.0

Magnesium binding site 5 out of 18 in the 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 Crystal Structure of Magnesium Transporter Mgte within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg452 b:38.2 occ:1.00 OD2 C:ASP259 2.0 83.1 1.0 OE2 C:GLU216 2.6 0.8 1.0 CG C:ASP259 2.9 84.2 1.0 OD1 C:ASP259 3.0 75.4 1.0 OD1 C:ASP418 3.4 77.6 1.0 CD C:GLU216 3.7 0.2 1.0 OD2 C:ASP418 3.7 67.1 1.0 O C:GLU255 3.9 92.3 1.0 CG C:ASP418 4.0 79.7 1.0 OE1 C:GLU258 4.0 99.4 1.0 OE1 C:GLU216 4.2 0.5 1.0 OE1 C:GLU255 4.2 78.6 1.0 CB C:ASP259 4.4 86.8 1.0 CD C:GLU255 4.7 80.3 1.0 CB C:GLU255 4.9 82.7 1.0 C C:GLU255 4.9 91.3 1.0 CA C:ASP259 4.9 85.7 1.0 CG C:GLU216 4.9 0.8 1.0 CD C:GLU258 5.0 0.2 1.0

Magnesium binding site 6 out of 18 in the 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 Crystal Structure of Magnesium Transporter Mgte within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg451 b:61.2 occ:1.00 OD2 D:ASP418 2.3 0.6 1.0 OD2 D:ASP259 2.6 94.0 1.0 CG D:ASP418 3.1 0.5 1.0 OD1 D:ASP259 3.1 87.0 1.0 OD1 D:ASP418 3.1 0.8 1.0 CG D:ASP259 3.2 91.8 1.0 OE1 D:GLU258 4.4 98.7 1.0 OE1 D:GLU216 4.5 0.1 1.0 OE2 D:GLU258 4.5 94.9 1.0 CB D:ASP418 4.5 0.6 1.0 CB D:ASP259 4.6 89.8 1.0 CD D:GLU258 4.8 95.0 1.0 CB D:ALA420 4.8 0.1 1.0 O D:GLU255 5.0 75.5 1.0

Magnesium binding site 7 out of 18 in the 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 Crystal Structure of Magnesium Transporter Mgte within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg452 b:36.3 occ:1.00 OD2 A:ASP247 1.8 91.0 1.0 OD2 A:ASP91 2.0 87.3 1.0 CG A:ASP247 2.6 95.2 1.0 CG A:ASP91 2.7 88.9 1.0 OE1 A:GLU166 2.8 0.6 1.0 OD1 A:ASP91 2.8 94.1 1.0 OD1 A:ASP247 2.9 84.8 1.0 OD1 A:ASP92 3.3 0.5 1.0 CD A:GLU166 3.7 0.7 1.0 OG1 A:THR244 3.8 89.6 1.0 CG2 A:THR139 4.0 81.0 1.0 CB A:ASP247 4.0 95.1 1.0 OE2 A:GLU166 4.1 0.0 1.0 CB A:ASP91 4.2 88.3 1.0 CG A:ASP92 4.5 0.6 1.0 CB A:THR244 4.7 81.9 1.0 OD1 A:ASP246 4.7 0.0 1.0 OG A:SER89 4.8 91.3 1.0 CG A:GLU166 4.9 0.2 1.0

Magnesium binding site 8 out of 18 in the 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 Crystal Structure of Magnesium Transporter Mgte within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg453 b:40.8 occ:1.00 O A:ALA223 1.9 67.5 1.0 OD1 A:ASP226 2.2 53.6 1.0 C A:ALA223 3.1 71.3 1.0 CG A:ASP226 3.2 63.9 1.0 OD2 A:ASP226 3.6 67.9 1.0 O A:ASP224 3.8 90.4 1.0 O B:ASP246 3.8 86.1 1.0 OD1 B:ASP250 4.0 93.8 1.0 N A:ASP224 4.0 74.6 1.0 CA A:ALA223 4.0 71.0 1.0 CA A:ASP224 4.2 79.4 1.0 C A:ASP224 4.3 81.9 1.0 CB A:ASP226 4.4 73.4 1.0 N A:ASP226 4.5 81.8 1.0 CA A:ASP226 4.6 79.6 1.0 CE1 B:HIS63 4.7 0.3 1.0 CB A:ALA223 4.8 70.1 1.0 CG B:ASP250 4.8 83.0 1.0 C B:ASP246 4.9 89.7 1.0

Magnesium binding site 9 out of 18 in the 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 Crystal Structure of Magnesium Transporter Mgte within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg453 b:40.8 occ:1.00 OD2 B:ASP91 2.2 90.8 1.0 CG B:ASP91 2.9 94.7 1.0 OD1 B:ASP247 3.0 79.3 1.0 OE2 B:GLU166 3.0 0.9 1.0 OD1 B:ASP91 3.0 91.6 1.0 CG B:ASP247 3.3 78.9 1.0 OD2 B:ASP247 3.4 62.2 1.0 CD B:GLU166 3.5 0.5 1.0 OG1 B:THR244 3.6 75.2 1.0 OE1 B:GLU166 3.8 0.1 1.0 CG2 B:THR139 4.3 63.2 1.0 OD2 B:ASP92 4.3 0.8 1.0 CG B:GLU166 4.4 0.1 1.0 CB B:ASP247 4.4 82.9 1.0 CB B:ASP91 4.4 96.5 1.0 CB B:THR244 4.6 76.2 1.0 CB B:THR139 4.7 65.4 1.0

Magnesium binding site 10 out of 18 in the 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 Crystal Structure of Magnesium Transporter Mgte within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg454 b:33.3 occ:1.00 O B:ALA223 1.8 71.5 1.0 OD1 B:ASP226 2.1 71.7 1.0 C B:ALA223 2.9 76.4 1.0 CG B:ASP226 3.2 70.5 1.0 OD2 A:ASP250 3.4 88.8 1.0 O A:ASP246 3.6 90.7 1.0 CA B:ALA223 3.7 76.6 1.0 OD2 B:ASP226 3.8 71.5 1.0 N B:ASP224 4.0 75.8 1.0 O B:ASP224 4.0 86.1 1.0 OD1 A:ASP250 4.1 87.2 1.0 CG A:ASP250 4.1 87.9 1.0 CA B:ASP224 4.3 78.6 1.0 CA B:ASP226 4.4 69.0 1.0 CB B:ASP226 4.4 64.9 1.0 CB B:ALA223 4.5 82.0 1.0 C B:ASP224 4.5 78.7 1.0 N B:ASP226 4.5 66.7 1.0 C A:ASP246 4.6 91.7 1.0 CB A:ASP246 4.7 0.0 1.0 N B:ALA223 4.9 70.5 1.0 CA A:ASP246 5.0 92.7 1.0

M.Hattori, Y.Tanaka, S.Fukai, R.Ishitani, O.Nureki. Crystal Structure of the Mgte Mg(2+) Transporter Nature V. 448 1072 2007.
ISSN: ISSN 0028-0836
PubMed: 17700703
DOI: 10.1038/NATURE06093