Magnesium in PDB 2wpd: The Mg.Adp Inhibited State of the Yeast F1C10 Atp Synthase

All present enzymatic activity of The Mg.Adp Inhibited State of the Yeast F1C10 Atp Synthase:
3.6.3.14;

The structure of The Mg.Adp Inhibited State of the Yeast F1C10 Atp Synthase, PDB code: 2wpd was solved by A.Dautant, J.Velours, M.-F.Giraud, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.775 / 3.43
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	134.990, 173.944, 137.016, 90.00, 92.69, 90.00
R / Rfree (%)	28.63 / 29.72

The binding sites of Magnesium atom in the The Mg.Adp Inhibited State of the Yeast F1C10 Atp Synthase (pdb code 2wpd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the The Mg.Adp Inhibited State of the Yeast F1C10 Atp Synthase, PDB code: 2wpd:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the The Mg.Adp Inhibited State of the Yeast F1C10 Atp Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Mg.Adp Inhibited State of the Yeast F1C10 Atp Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:68.3 occ:1.00 OG1 A:THR178 2.4 73.3 1.0 O2B A:ATP600 2.4 68.3 1.0 O2G A:ATP600 2.7 68.3 1.0 OD2 A:ASP271 3.3 73.3 1.0 PB A:ATP600 3.6 68.3 1.0 CB A:THR178 3.6 73.3 1.0 PG A:ATP600 3.8 68.3 1.0 NE2 A:GLN210 3.8 73.3 1.0 O1B A:ATP600 4.0 68.3 1.0 O1G A:ATP600 4.0 68.3 1.0 OD1 A:ASP271 4.0 73.3 1.0 CG A:ASP271 4.1 73.3 1.0 O3B A:ATP600 4.2 68.3 1.0 O2A A:ATP600 4.3 68.3 1.0 CG2 A:THR178 4.4 73.3 1.0 CA A:THR178 4.7 73.3 1.0 N A:THR178 4.7 73.3 1.0 O3A A:ATP600 4.9 68.3 1.0 OH A:TYR205 4.9 73.3 1.0

Magnesium binding site 2 out of 5 in the The Mg.Adp Inhibited State of the Yeast F1C10 Atp Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Mg.Adp Inhibited State of the Yeast F1C10 Atp Synthase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:0.4 occ:1.00 OG1 B:THR178 2.1 0.6 1.0 O2B B:ATP600 2.3 0.4 1.0 O1G B:ATP600 2.3 0.4 1.0 O2G B:ATP600 2.4 0.4 1.0 PG B:ATP600 2.7 0.4 1.0 CB B:THR178 3.0 0.6 1.0 N B:THR178 3.1 0.6 1.0 PB B:ATP600 3.2 0.4 1.0 O3B B:ATP600 3.3 0.4 1.0 CA B:THR178 3.6 0.6 1.0 OD1 B:ASP271 3.6 0.6 1.0 CB B:LYS177 3.7 0.6 1.0 O1B B:ATP600 3.9 0.4 1.0 C B:LYS177 3.9 0.6 1.0 O3G B:ATP600 4.1 0.4 1.0 O2A B:ATP600 4.1 0.4 1.0 CE B:LYS177 4.2 0.6 1.0 CA B:LYS177 4.2 0.6 1.0 OD2 B:ASP271 4.2 0.6 1.0 CG B:ASP271 4.2 0.6 1.0 CG2 B:THR178 4.3 0.6 1.0 N B:LYS177 4.3 0.6 1.0 NZ B:LYS177 4.5 0.6 1.0 O3A B:ATP600 4.6 0.4 1.0 CG B:LYS177 4.7 0.6 1.0 CG1 B:VAL328 4.9 0.6 1.0 C B:THR178 4.9 0.6 1.0 O B:LYS177 4.9 0.6 1.0 PA B:ATP600 5.0 0.4 1.0 CD B:LYS177 5.0 0.6 1.0

Magnesium binding site 3 out of 5 in the The Mg.Adp Inhibited State of the Yeast F1C10 Atp Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Mg.Adp Inhibited State of the Yeast F1C10 Atp Synthase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:71.6 occ:1.00 OG1 C:THR178 2.2 63.7 1.0 O2B C:ATP600 2.3 71.6 1.0 O1G C:ATP600 2.4 71.6 1.0 O2G C:ATP600 2.6 71.6 1.0 PG C:ATP600 2.9 71.6 1.0 CB C:THR178 3.4 63.7 1.0 PB C:ATP600 3.4 71.6 1.0 OD2 C:ASP271 3.5 63.7 1.0 O3B C:ATP600 3.7 71.6 1.0 OD1 C:ASP271 4.1 63.7 1.0 O1B C:ATP600 4.1 71.6 1.0 CG2 C:THR178 4.2 63.7 1.0 NE2 C:GLN210 4.2 63.7 1.0 CG C:ASP271 4.2 63.7 1.0 O3G C:ATP600 4.3 71.6 1.0 N C:THR178 4.5 63.7 1.0 CA C:THR178 4.5 63.7 1.0 O2A C:ATP600 4.7 71.6 1.0 O3A C:ATP600 4.8 71.6 1.0

Magnesium binding site 4 out of 5 in the The Mg.Adp Inhibited State of the Yeast F1C10 Atp Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Mg.Adp Inhibited State of the Yeast F1C10 Atp Synthase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:71.6 occ:1.00 OG1 D:THR164 2.4 75.0 1.0 O2B D:ADP600 2.5 71.6 1.0 O1B D:ADP600 3.0 71.6 1.0 O2A D:ADP600 3.0 71.6 1.0 PB D:ADP600 3.2 71.6 1.0 OE1 D:GLU189 3.5 75.0 1.0 CB D:THR164 3.6 75.0 1.0 OE2 D:GLU193 3.9 75.0 1.0 PA D:ADP600 3.9 71.6 1.0 NH1 D:ARG190 3.9 75.0 1.0 O3A D:ADP600 4.0 71.6 1.0 N D:THR164 4.3 75.0 1.0 O1A D:ADP600 4.4 71.6 1.0 CA D:THR164 4.5 75.0 1.0 O3B D:ADP600 4.5 71.6 1.0 CG2 D:THR164 4.6 75.0 1.0 CD D:GLU189 4.6 75.0 1.0 OE1 D:GLU193 4.7 75.0 1.0 CD D:GLU193 4.7 75.0 1.0 OD2 D:ASP256 5.0 75.0 1.0 CZ D:ARG190 5.0 75.0 1.0

Magnesium binding site 5 out of 5 in the The Mg.Adp Inhibited State of the Yeast F1C10 Atp Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Mg.Adp Inhibited State of the Yeast F1C10 Atp Synthase within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg601 b:0.4 occ:1.00 O2B F:ADP600 2.3 0.4 1.0 OG1 F:THR164 2.4 89.4 1.0 OE1 F:GLU189 2.9 89.4 1.0 PB F:ADP600 3.4 0.4 1.0 CB F:THR164 3.6 89.4 1.0 OD1 F:ASP256 3.7 89.4 1.0 O3B F:ADP600 3.9 0.4 1.0 CD F:GLU189 3.9 89.4 1.0 O1B F:ADP600 4.0 0.4 1.0 OD2 F:ASP256 4.0 89.4 1.0 OE1 F:GLU193 4.2 89.4 1.0 NH1 F:ARG190 4.2 89.4 1.0 CG F:ASP256 4.3 89.4 1.0 N F:THR164 4.4 89.4 1.0 OE2 F:GLU189 4.5 89.4 1.0 O2A F:ADP600 4.5 0.4 1.0 OE2 F:GLU193 4.5 89.4 1.0 CA F:THR164 4.6 89.4 1.0 CG2 F:THR164 4.6 89.4 1.0 NH1 B:ARG375 4.6 0.6 1.0 O3A F:ADP600 4.7 0.4 1.0 CD F:GLU193 4.8 89.4 1.0 CE F:LYS163 5.0 89.4 1.0

A.Dautant, J.Velours, M.Giraud. Crystal Structure of the Mg.Adp-Inhibited State of the Yeast F1C10-Atp Synthase. J.Biol.Chem. V. 285 29502 2010.
ISSN: ISSN 0021-9258
PubMed: 20610387
DOI: 10.1074/JBC.M110.124529