Magnesium in PDB 9e6n: Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to HED1

The binding sites of Magnesium atom in the Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to HED1 (pdb code 9e6n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to HED1, PDB code: 9e6n:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to HED1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to HED1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:89.0 occ:1.00 O1G A:ATP501 2.0 94.7 1.0 OG A:SER192 2.0 92.9 1.0 O1B A:ATP501 2.1 94.7 1.0 PG A:ATP501 2.8 94.7 1.0 PB A:ATP501 2.8 94.7 1.0 O3B A:ATP501 2.9 94.7 1.0 CB A:SER192 3.0 92.9 1.0 O2G A:ATP501 3.3 94.7 1.0 O3A A:ATP501 3.4 94.7 1.0 N A:SER192 3.9 92.9 1.0 O2A A:ATP501 4.0 94.7 1.0 CA A:SER192 4.1 92.9 1.0 PA A:ATP501 4.1 94.7 1.0 OD2 A:ASP280 4.2 91.5 1.0 O3G A:ATP501 4.2 94.7 1.0 O2B A:ATP501 4.3 94.7 1.0 O1A A:ATP501 4.3 94.7 1.0 OG1 A:THR223 4.5 90.4 1.0 OD1 A:ASP280 4.6 91.5 1.0 OE1 A:GLU221 4.8 94.7 1.0 CG A:ASP280 4.9 91.5 1.0

Magnesium binding site 2 out of 6 in the Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to HED1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to HED1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:68.5 occ:1.00 OG B:SER192 2.0 70.8 1.0 O1G B:ATP501 2.0 75.7 1.0 O1B B:ATP501 2.1 75.7 1.0 PB B:ATP501 3.2 75.7 1.0 PG B:ATP501 3.2 75.7 1.0 CB B:SER192 3.3 70.8 1.0 O3B B:ATP501 3.4 75.7 1.0 O3A B:ATP501 3.9 75.7 1.0 OD2 B:ASP280 3.9 74.2 1.0 O2G B:ATP501 4.2 75.7 1.0 OD1 B:ASP280 4.2 74.2 1.0 OE1 B:GLU221 4.2 78.7 1.0 N B:SER192 4.3 70.8 1.0 O3G B:ATP501 4.3 75.7 1.0 CA B:SER192 4.3 70.8 1.0 O2B B:ATP501 4.5 75.7 1.0 CG B:ASP280 4.5 74.2 1.0 OG1 B:THR223 4.7 73.8 1.0 O2A B:ATP501 4.7 75.7 1.0 PA B:ATP501 4.8 75.7 1.0 CE B:LYS191 5.0 70.2 1.0 O1A B:ATP501 5.0 75.7 1.0

Magnesium binding site 3 out of 6 in the Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to HED1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to HED1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:70.1 occ:1.00 OG C:SER192 2.0 65.0 1.0 O2G C:ATP501 2.0 73.2 1.0 O2B C:ATP501 2.1 73.2 1.0 PG C:ATP501 3.2 73.2 1.0 O3B C:ATP501 3.3 73.2 1.0 PB C:ATP501 3.3 73.2 1.0 CB C:SER192 3.3 65.0 1.0 OD2 C:ASP280 4.0 68.2 1.0 O3G C:ATP501 4.1 73.2 1.0 OE1 C:GLU221 4.2 76.3 1.0 OG1 C:THR223 4.2 72.5 1.0 O1A C:ATP501 4.2 73.2 1.0 N C:SER192 4.2 65.0 1.0 O3A C:ATP501 4.2 73.2 1.0 CA C:SER192 4.3 65.0 1.0 O1G C:ATP501 4.3 73.2 1.0 OD1 C:ASP280 4.3 68.2 1.0 O1B C:ATP501 4.4 73.2 1.0 PA C:ATP501 4.6 73.2 1.0 CG C:ASP280 4.6 68.2 1.0 O2A C:ATP501 4.8 73.2 1.0

Magnesium binding site 4 out of 6 in the Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to HED1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to HED1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:79.1 occ:1.00 OG D:SER192 2.0 73.3 1.0 O1G D:ATP501 2.0 81.6 1.0 O1B D:ATP501 2.1 81.6 1.0 PG D:ATP501 3.2 81.6 1.0 PB D:ATP501 3.2 81.6 1.0 CB D:SER192 3.3 73.3 1.0 O3B D:ATP501 3.4 81.6 1.0 OD2 D:ASP280 3.8 73.7 1.0 OD1 D:ASP280 3.8 73.7 1.0 OE1 D:GLU221 4.0 78.6 1.0 N D:SER192 4.2 73.3 1.0 O3G D:ATP501 4.2 81.6 1.0 CG D:ASP280 4.3 73.7 1.0 O2G D:ATP501 4.3 81.6 1.0 O3A D:ATP501 4.3 81.6 1.0 CA D:SER192 4.3 73.3 1.0 O2B D:ATP501 4.3 81.6 1.0 OG1 D:THR223 4.5 77.2 1.0 O2A D:ATP501 4.6 81.6 1.0 PA D:ATP501 4.9 81.6 1.0

Magnesium binding site 5 out of 6 in the Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to HED1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to HED1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg502 b:100.2 occ:1.00 OG E:SER192 2.0 98.2 1.0 O1G E:ATP501 2.0 107.5 1.0 O1B E:ATP501 2.1 107.5 1.0 PG E:ATP501 3.2 107.5 1.0 PB E:ATP501 3.2 107.5 1.0 CB E:SER192 3.4 98.2 1.0 O3B E:ATP501 3.4 107.5 1.0 OD2 E:ASP280 3.8 93.4 1.0 O3A E:ATP501 4.1 107.5 1.0 O2G E:ATP501 4.2 107.5 1.0 OE1 E:GLU221 4.2 102.8 1.0 O2A E:ATP501 4.2 107.5 1.0 OD1 E:ASP280 4.2 93.4 1.0 CG2 E:THR223 4.3 101.8 1.0 N E:SER192 4.3 98.2 1.0 OG1 E:THR223 4.3 101.8 1.0 O3G E:ATP501 4.4 107.5 1.0 CA E:SER192 4.4 98.2 1.0 O2B E:ATP501 4.5 107.5 1.0 CG E:ASP280 4.5 93.4 1.0 PA E:ATP501 4.6 107.5 1.0 CB E:THR223 4.7 101.8 1.0 O1A E:ATP501 4.8 107.5 1.0

Magnesium binding site 6 out of 6 in the Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to HED1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to HED1 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg502 b:158.1 occ:1.00 O3B F:ATP501 2.1 159.0 1.0 O2B F:ATP501 2.2 159.0 1.0 O1A F:ATP501 2.3 159.0 1.0 O2G F:ATP501 2.4 159.0 1.0 PB F:ATP501 2.4 159.0 1.0 PA F:ATP501 2.5 159.0 1.0 O3A F:ATP501 2.5 159.0 1.0 O2A F:ATP501 2.6 159.0 1.0 OG F:SER192 2.7 152.8 1.0 PG F:ATP501 2.8 159.0 1.0 CB F:SER192 3.0 152.8 1.0 N F:SER192 3.6 152.8 1.0 O3G F:ATP501 3.6 159.0 1.0 O1B F:ATP501 3.9 159.0 1.0 CA F:SER192 3.9 152.8 1.0 O1G F:ATP501 4.0 159.0 1.0 O5' F:ATP501 4.0 159.0 1.0 N F:LYS191 4.6 152.4 1.0 C F:LYS191 4.8 152.4 1.0 C5' F:ATP501 4.9 159.0 1.0 C F:SER192 4.9 152.8 1.0 N F:GLN193 4.9 152.4 1.0 N F:GLY190 5.0 155.9 1.0

Y.Shin, E.C.Greene. Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to HED1 To Be Published.