Magnesium in PDB 5dn6: Atp Synthase From Paracoccus Denitrificans

All present enzymatic activity of Atp Synthase From Paracoccus Denitrificans:
7.1.2.2;

The structure of Atp Synthase From Paracoccus Denitrificans, PDB code: 5dn6 was solved by E.Morales-Rios, M.G.Montgomery, A.G.W.Leslie, J.E.Walker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.84 / 3.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	112.001, 187.943, 164.724, 90.00, 97.44, 90.00
R / Rfree (%)	29.5 / 32.4

The binding sites of Magnesium atom in the Atp Synthase From Paracoccus Denitrificans (pdb code 5dn6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Atp Synthase From Paracoccus Denitrificans, PDB code: 5dn6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Atp Synthase From Paracoccus Denitrificans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Atp Synthase From Paracoccus Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:78.6 occ:1.00 O2B A:ATP600 1.9 98.9 1.0 OG1 A:THR176 2.3 0.3 1.0 O1G A:ATP600 2.8 0.0 1.0 O3G A:ATP600 3.2 1.0 1.0 PB A:ATP600 3.2 0.8 1.0 PG A:ATP600 3.4 0.3 1.0 CB A:THR176 3.4 0.7 1.0 O3B A:ATP600 3.7 0.8 1.0 O2A A:ATP600 4.0 99.7 1.0 OD2 A:ASP270 4.0 0.1 1.0 O1B A:ATP600 4.1 99.9 1.0 OD1 A:ASP270 4.1 0.9 1.0 CG2 A:THR176 4.2 0.3 1.0 O3A A:ATP600 4.4 0.4 1.0 CG A:ASP270 4.5 0.1 1.0 CA A:THR176 4.6 0.3 1.0 N A:THR176 4.6 0.2 1.0 PA A:ATP600 4.7 99.0 1.0 O2G A:ATP600 4.8 0.0 1.0

Magnesium binding site 2 out of 5 in the Atp Synthase From Paracoccus Denitrificans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Atp Synthase From Paracoccus Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:72.8 occ:1.00 OG1 B:THR176 2.1 0.6 1.0 O3B B:ADP600 2.5 0.1 1.0 CB B:THR176 3.5 0.8 1.0 OD1 B:ASP270 3.5 70.8 1.0 PB B:ADP600 3.7 0.6 1.0 OE1 B:GLN209 3.7 0.8 1.0 OD2 B:ASP270 3.8 71.3 1.0 O1B B:ADP600 3.9 0.8 1.0 CG B:ASP270 4.0 71.5 1.0 CG2 B:THR176 4.3 0.5 1.0 O1A B:ADP600 4.4 0.9 1.0 N B:THR176 4.4 0.4 1.0 CD B:GLN209 4.5 0.8 1.0 CA B:THR176 4.5 1.0 1.0 O2B B:ADP600 4.6 0.4 1.0 O3A B:ADP600 4.8 0.7 1.0

Magnesium binding site 3 out of 5 in the Atp Synthase From Paracoccus Denitrificans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Atp Synthase From Paracoccus Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:48.5 occ:1.00 OG1 C:THR176 2.0 79.4 1.0 O2B C:ATP600 2.2 0.5 1.0 O2G C:ATP600 2.5 0.9 1.0 O3G C:ATP600 3.1 0.9 1.0 PG C:ATP600 3.2 0.1 1.0 CB C:THR176 3.3 80.7 1.0 PB C:ATP600 3.4 0.2 1.0 O3B C:ATP600 3.8 0.8 1.0 OD2 C:ASP270 3.8 73.7 1.0 O3A C:ATP600 3.9 0.3 1.0 OD1 C:ASP270 3.9 74.6 1.0 CG2 C:THR176 4.1 80.5 1.0 CA C:THR176 4.3 81.6 1.0 CG C:ASP270 4.3 73.6 1.0 N C:THR176 4.3 82.0 1.0 O1G C:ATP600 4.7 0.1 1.0 PA C:ATP600 4.7 0.9 1.0 O1A C:ATP600 4.7 0.1 1.0 O2A C:ATP600 4.7 0.6 1.0 O1B C:ATP600 4.7 0.1 1.0 NE2 C:GLN209 4.9 91.7 1.0

Magnesium binding site 4 out of 5 in the Atp Synthase From Paracoccus Denitrificans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Atp Synthase From Paracoccus Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:41.5 occ:1.00 O2G D:ATP600 2.0 0.0 1.0 OG1 D:THR158 2.4 0.2 1.0 PG D:ATP600 3.0 0.3 1.0 O1G D:ATP600 3.0 0.3 1.0 OE1 D:GLU183 3.4 96.1 1.0 OE1 D:GLU187 3.4 95.5 1.0 OE2 D:GLU187 3.5 95.6 1.0 OD2 D:ASP252 3.6 94.0 1.0 NH1 D:ARG184 3.6 80.3 1.0 CB D:THR158 3.6 0.6 1.0 O2B D:ATP600 3.7 0.8 1.0 OD1 D:ASP252 3.8 90.8 1.0 CD D:GLU187 3.8 96.1 1.0 CD D:GLU183 3.9 94.6 1.0 O3B D:ATP600 4.1 0.2 1.0 CG D:ASP252 4.1 90.5 1.0 O3G D:ATP600 4.1 0.8 1.0 CG2 D:THR158 4.1 0.9 1.0 CG D:GLU183 4.4 92.9 1.0 PB D:ATP600 4.6 0.8 1.0 OE2 D:GLU183 4.6 94.9 1.0 CA D:THR158 4.8 0.2 1.0 CB D:GLU183 4.9 90.0 1.0 CZ D:ARG184 4.9 81.9 1.0

Magnesium binding site 5 out of 5 in the Atp Synthase From Paracoccus Denitrificans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Atp Synthase From Paracoccus Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg601 b:36.0 occ:1.00 OG1 F:THR158 1.9 73.2 1.0 O2G F:ATP600 2.2 0.8 1.0 O3G F:ATP600 2.3 0.4 1.0 PG F:ATP600 2.7 0.3 1.0 OD2 F:ASP252 2.8 64.0 1.0 OD1 F:ASP252 3.2 65.1 1.0 CB F:THR158 3.2 75.6 1.0 CG F:ASP252 3.4 65.0 1.0 OE1 F:GLU187 3.5 93.1 1.0 O3B F:ATP600 3.5 96.7 1.0 OE2 F:GLU183 3.6 95.3 1.0 CG2 F:THR158 3.7 76.8 1.0 O2B F:ATP600 3.9 83.5 1.0 NH1 F:ARG184 4.0 83.9 1.0 OE2 F:GLU187 4.0 94.0 1.0 O1G F:ATP600 4.0 0.7 1.0 CD F:GLU183 4.1 96.1 1.0 CA F:THR158 4.2 75.3 1.0 CG F:GLU183 4.2 93.8 1.0 CD F:GLU187 4.2 94.1 1.0 N F:THR158 4.4 76.6 1.0 PB F:ATP600 4.4 84.9 1.0 CB F:GLU183 4.5 91.7 1.0 CB F:ASP252 4.9 65.1 1.0

E.Morales-Rios, M.G.Montgomery, A.G.Leslie, J.E.Walker. Structure of Atp Synthase From Paracoccus Denitrificans Determined By X-Ray Crystallography at 4.0 Angstrom Resolution. Proc.Natl.Acad.Sci.Usa V. 112 13231 2015.
ISSN: ESSN 1091-6490
PubMed: 26460036
DOI: 10.1073/PNAS.1517542112