Magnesium in PDB 9d4n: The Cryo-Em Structure of the Yeast DMC1 Filament Bound to Ssdna in the Presence of Atp

The binding sites of Magnesium atom in the The Cryo-Em Structure of the Yeast DMC1 Filament Bound to Ssdna in the Presence of Atp (pdb code 9d4n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the The Cryo-Em Structure of the Yeast DMC1 Filament Bound to Ssdna in the Presence of Atp, PDB code: 9d4n:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the The Cryo-Em Structure of the Yeast DMC1 Filament Bound to Ssdna in the Presence of Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Cryo-Em Structure of the Yeast DMC1 Filament Bound to Ssdna in the Presence of Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:94.7 occ:1.00 O2B A:ATP401 1.9 96.3 1.0 OE1 A:GLU157 2.0 102.5 1.0 O1G A:ATP401 2.0 96.3 1.0 OG1 A:THR128 2.3 97.3 1.0 OE2 A:GLU157 2.6 102.5 1.0 CD A:GLU157 2.6 102.5 1.0 PG A:ATP401 3.1 96.3 1.0 PB A:ATP401 3.1 96.3 1.0 O3B A:ATP401 3.1 96.3 1.0 CB A:THR128 3.5 97.3 1.0 O3G A:ATP401 4.0 96.3 1.0 OG1 A:THR159 4.0 98.5 1.0 CG A:GLU157 4.1 102.5 1.0 O3A A:ATP401 4.1 96.3 1.0 O1B A:ATP401 4.1 96.3 1.0 O2G A:ATP401 4.2 96.3 1.0 O1A A:ATP401 4.3 96.3 1.0 N A:THR128 4.3 97.3 1.0 OD2 A:ASP216 4.4 100.7 1.0 OD1 A:ASP216 4.4 100.7 1.0 CG2 A:THR128 4.5 97.3 1.0 CA A:THR128 4.5 97.3 1.0 PA A:ATP401 4.5 96.3 1.0 O2A A:ATP401 4.6 96.3 1.0 CB A:GLU157 4.7 102.5 1.0 CG A:ASP216 4.8 100.7 1.0 CG2 A:THR159 4.9 98.5 1.0 CB A:THR159 4.9 98.5 1.0

Magnesium binding site 2 out of 6 in the The Cryo-Em Structure of the Yeast DMC1 Filament Bound to Ssdna in the Presence of Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Cryo-Em Structure of the Yeast DMC1 Filament Bound to Ssdna in the Presence of Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:74.3 occ:1.00 O1G B:ATP401 1.9 82.5 1.0 O2B B:ATP401 1.9 82.5 1.0 OG1 B:THR128 2.1 79.9 1.0 OE1 B:GLU157 2.4 84.9 1.0 PG B:ATP401 2.9 82.5 1.0 O3B B:ATP401 3.0 82.5 1.0 PB B:ATP401 3.0 82.5 1.0 CD B:GLU157 3.3 84.9 1.0 CB B:THR128 3.3 79.9 1.0 OE2 B:GLU157 3.6 84.9 1.0 O2G B:ATP401 3.9 82.5 1.0 O3A B:ATP401 4.0 82.5 1.0 O3G B:ATP401 4.1 82.5 1.0 O1B B:ATP401 4.1 82.5 1.0 N B:THR128 4.1 79.9 1.0 OG1 B:THR159 4.2 81.0 1.0 CA B:THR128 4.3 79.9 1.0 CG2 B:THR128 4.3 79.9 1.0 OD1 B:ASP216 4.4 81.5 1.0 OD2 B:ASP216 4.4 81.5 1.0 O1A B:ATP401 4.4 82.5 1.0 PA B:ATP401 4.6 82.5 1.0 CG B:GLU157 4.7 84.9 1.0 O2A B:ATP401 4.7 82.5 1.0 CG B:ASP216 4.8 81.5 1.0 CB B:LYS127 5.0 76.5 1.0

Magnesium binding site 3 out of 6 in the The Cryo-Em Structure of the Yeast DMC1 Filament Bound to Ssdna in the Presence of Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Cryo-Em Structure of the Yeast DMC1 Filament Bound to Ssdna in the Presence of Atp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:72.0 occ:1.00 O2B C:ATP401 1.9 78.2 1.0 O1G C:ATP401 2.0 78.2 1.0 OG1 C:THR128 2.1 75.0 1.0 PB C:ATP401 3.1 78.2 1.0 PG C:ATP401 3.1 78.2 1.0 O3B C:ATP401 3.2 78.2 1.0 CB C:THR128 3.3 75.0 1.0 OG1 C:THR159 4.0 75.4 1.0 O1B C:ATP401 4.1 78.2 1.0 O2G C:ATP401 4.1 78.2 1.0 O3A C:ATP401 4.1 78.2 1.0 N C:THR128 4.2 75.0 1.0 O3G C:ATP401 4.2 78.2 1.0 OD1 C:ASP216 4.3 76.5 1.0 OD2 C:ASP216 4.3 76.5 1.0 CA C:THR128 4.3 75.0 1.0 CG2 C:THR128 4.3 75.0 1.0 O1A C:ATP401 4.5 78.2 1.0 CG C:GLU157 4.5 80.3 1.0 OE1 C:GLU157 4.5 80.3 1.0 CG C:ASP216 4.7 76.5 1.0 CD C:GLU157 4.7 80.3 1.0 PA C:ATP401 4.7 78.2 1.0 CB C:GLU157 4.9 80.3 1.0 CG2 C:THR159 4.9 75.4 1.0 CB C:THR159 4.9 75.4 1.0 O2A C:ATP401 4.9 78.2 1.0

Magnesium binding site 4 out of 6 in the The Cryo-Em Structure of the Yeast DMC1 Filament Bound to Ssdna in the Presence of Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Cryo-Em Structure of the Yeast DMC1 Filament Bound to Ssdna in the Presence of Atp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:73.7 occ:1.00 O2B D:ATP401 1.9 81.1 1.0 OE1 D:GLU157 1.9 80.3 1.0 OG1 D:THR128 2.1 75.2 1.0 O1G D:ATP401 2.2 81.1 1.0 CD D:GLU157 2.6 80.3 1.0 OE2 D:GLU157 2.6 80.3 1.0 PB D:ATP401 3.1 81.1 1.0 PG D:ATP401 3.3 81.1 1.0 CB D:THR128 3.3 75.2 1.0 O3B D:ATP401 3.3 81.1 1.0 CG D:GLU157 4.0 80.3 1.0 O1B D:ATP401 4.1 81.1 1.0 OG1 D:THR159 4.1 76.1 1.0 OD1 D:ASP216 4.2 75.0 1.0 N D:THR128 4.2 75.2 1.0 O3A D:ATP401 4.2 81.1 1.0 O3G D:ATP401 4.2 81.1 1.0 CA D:THR128 4.3 75.2 1.0 CG2 D:THR128 4.3 75.2 1.0 OD2 D:ASP216 4.3 75.0 1.0 O2G D:ATP401 4.4 81.1 1.0 O1A D:ATP401 4.5 81.1 1.0 CB D:GLU157 4.6 80.3 1.0 CG D:ASP216 4.7 75.0 1.0 PA D:ATP401 4.7 81.1 1.0 O2A D:ATP401 4.8 81.1 1.0

Magnesium binding site 5 out of 6 in the The Cryo-Em Structure of the Yeast DMC1 Filament Bound to Ssdna in the Presence of Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Cryo-Em Structure of the Yeast DMC1 Filament Bound to Ssdna in the Presence of Atp within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg402 b:84.2 occ:1.00 O2B E:ATP401 1.9 89.9 1.0 OE1 E:GLU157 1.9 88.0 1.0 O1G E:ATP401 2.0 89.9 1.0 OE2 E:GLU157 2.4 88.0 1.0 CD E:GLU157 2.5 88.0 1.0 OG1 E:THR128 2.5 84.5 1.0 PB E:ATP401 3.1 89.9 1.0 PG E:ATP401 3.1 89.9 1.0 O3B E:ATP401 3.2 89.9 1.0 CB E:THR128 3.7 84.5 1.0 CG E:GLU157 3.9 88.0 1.0 O1B E:ATP401 4.1 89.9 1.0 O3G E:ATP401 4.1 89.9 1.0 O3A E:ATP401 4.1 89.9 1.0 O2G E:ATP401 4.2 89.9 1.0 N E:THR128 4.3 84.5 1.0 OG1 E:THR159 4.3 83.7 1.0 OD1 E:ASP216 4.4 82.2 1.0 O1A E:ATP401 4.5 89.9 1.0 OD2 E:ASP216 4.6 82.2 1.0 CA E:THR128 4.6 84.5 1.0 CB E:GLU157 4.6 88.0 1.0 PA E:ATP401 4.7 89.9 1.0 CG2 E:THR128 4.7 84.5 1.0 O2A E:ATP401 4.8 89.9 1.0 CE E:LYS127 4.9 82.4 1.0 CG E:ASP216 4.9 82.2 1.0 CG2 E:THR159 5.0 83.7 1.0

Magnesium binding site 6 out of 6 in the The Cryo-Em Structure of the Yeast DMC1 Filament Bound to Ssdna in the Presence of Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Cryo-Em Structure of the Yeast DMC1 Filament Bound to Ssdna in the Presence of Atp within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:95.8 occ:1.00 O2B F:ATP401 1.9 102.1 1.0 O1G F:ATP401 2.0 102.1 1.0 OE1 F:GLU157 2.0 96.1 1.0 OG1 F:THR128 2.2 95.6 1.0 CD F:GLU157 2.7 96.1 1.0 OE2 F:GLU157 2.8 96.1 1.0 PG F:ATP401 3.1 102.1 1.0 PB F:ATP401 3.1 102.1 1.0 O3B F:ATP401 3.1 102.1 1.0 CB F:THR128 3.4 95.6 1.0 O3G F:ATP401 4.1 102.1 1.0 O3A F:ATP401 4.1 102.1 1.0 O1B F:ATP401 4.1 102.1 1.0 O2G F:ATP401 4.2 102.1 1.0 CG F:GLU157 4.2 96.1 1.0 N F:THR128 4.2 95.6 1.0 OG1 F:THR159 4.3 93.3 1.0 CA F:THR128 4.4 95.6 1.0 OD1 F:ASP216 4.4 89.7 1.0 CG2 F:THR128 4.4 95.6 1.0 O1A F:ATP401 4.4 102.1 1.0 OD2 F:ASP216 4.5 89.7 1.0 PA F:ATP401 4.6 102.1 1.0 O2A F:ATP401 4.7 102.1 1.0 CB F:GLU157 4.7 96.1 1.0 CE F:LYS127 4.9 93.8 1.0 CG F:ASP216 4.9 89.7 1.0 CG2 F:THR159 5.0 93.3 1.0

Y.Shin, E.C.Greene. The Cryo-Em Structure of the Yeast RAD51 Filament Bound to Ssdna in the Presence of Atp To Be Published.