Magnesium in PDB 8gyk: Cryoem Structure of the RAD51_ADP Filament

The binding sites of Magnesium atom in the Cryoem Structure of the RAD51_ADP Filament (pdb code 8gyk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Cryoem Structure of the RAD51_ADP Filament, PDB code: 8gyk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Cryoem Structure of the RAD51_ADP Filament


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryoem Structure of the RAD51_ADP Filament within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:117.0 occ:1.00 O2A A:ADP600 2.1 124.7 1.0 O2B A:ADP600 2.1 124.7 1.0 N A:THR134 2.4 114.3 1.0 O1A A:ADP600 2.4 124.7 1.0 PA A:ADP600 2.4 124.7 1.0 OG1 A:THR134 2.6 114.3 1.0 CG A:LYS133 2.7 114.5 1.0 N A:LYS133 3.0 114.5 1.0 PB A:ADP600 3.0 124.7 1.0 O3A A:ADP600 3.1 124.7 1.0 CB A:THR134 3.2 114.3 1.0 C A:LYS133 3.3 114.5 1.0 CA A:THR134 3.3 114.3 1.0 O3B A:ADP600 3.4 124.7 1.0 CA A:LYS133 3.4 114.5 1.0 CB A:LYS133 3.5 114.5 1.0 C A:GLY132 3.7 119.3 1.0 CD A:LYS133 3.9 114.5 1.0 NZ A:LYS133 3.9 114.5 1.0 O5' A:ADP600 4.0 124.7 1.0 CE A:LYS133 4.1 114.5 1.0 N A:GLY132 4.1 119.3 1.0 CA A:GLY132 4.2 119.3 1.0 N A:GLN135 4.4 116.5 1.0 C A:THR134 4.4 114.3 1.0 O1B A:ADP600 4.4 124.7 1.0 O A:LYS133 4.5 114.5 1.0 O A:GLY132 4.5 119.3 1.0 C5' A:ADP600 4.6 124.7 1.0 CG2 A:THR134 4.6 114.3 1.0 N A:THR131 4.9 120.5 1.0 C A:THR131 5.0 120.5 1.0 OG1 A:THR131 5.0 120.5 1.0

Magnesium binding site 2 out of 8 in the Cryoem Structure of the RAD51_ADP Filament


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryoem Structure of the RAD51_ADP Filament within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:74.7 occ:1.00 O3B B:ADP600 2.0 73.5 1.0 O3A B:ADP600 2.0 73.5 1.0 O2A B:ADP600 2.1 73.5 1.0 PA B:ADP600 2.4 73.5 1.0 PB B:ADP600 2.6 73.5 1.0 O5' B:ADP600 2.8 73.5 1.0 N B:GLY132 3.2 75.9 1.0 N B:THR131 3.3 74.8 1.0 N B:ARG130 3.5 76.6 1.0 O1B B:ADP600 3.6 73.5 1.0 O2B B:ADP600 3.6 73.5 1.0 N B:LYS133 3.7 69.0 1.0 C B:ARG130 3.8 76.6 1.0 CA B:ARG130 3.8 76.6 1.0 O1A B:ADP600 3.8 73.5 1.0 CA B:GLY132 3.9 75.9 1.0 OG1 B:THR131 4.0 74.8 1.0 NZ B:LYS133 4.0 69.0 1.0 CG B:LYS133 4.0 69.0 1.0 C5' B:ADP600 4.0 73.5 1.0 C B:THR131 4.1 74.8 1.0 CA B:THR131 4.2 74.8 1.0 C B:GLY132 4.3 75.9 1.0 C B:PHE129 4.3 75.7 1.0 N B:THR134 4.5 67.5 1.0 CB B:THR131 4.6 74.8 1.0 O B:ARG130 4.7 76.6 1.0 CA B:PHE129 4.7 75.7 1.0 CA B:LYS133 4.8 69.0 1.0 C4' B:ADP600 4.8 73.5 1.0 NH2 B:ARG130 4.8 76.6 1.0 CB B:LYS133 4.8 69.0 1.0 OG1 B:THR134 4.9 67.5 1.0 CG2 B:THR131 4.9 74.8 1.0 CE B:LYS133 5.0 69.0 1.0 CD B:LYS133 5.0 69.0 1.0

Magnesium binding site 3 out of 8 in the Cryoem Structure of the RAD51_ADP Filament


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryoem Structure of the RAD51_ADP Filament within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:83.4 occ:1.00 O2A C:ADP600 2.1 80.4 1.0 O2B C:ADP600 2.1 80.4 1.0 O3B C:ADP600 2.3 80.4 1.0 N C:THR134 2.4 69.0 1.0 CG C:LYS133 2.5 73.2 1.0 PB C:ADP600 2.6 80.4 1.0 OG1 C:THR134 2.7 69.0 1.0 PA C:ADP600 3.0 80.4 1.0 CB C:THR134 3.0 69.0 1.0 O3A C:ADP600 3.2 80.4 1.0 CA C:THR134 3.2 69.0 1.0 N C:LYS133 3.2 73.2 1.0 C C:LYS133 3.3 73.2 1.0 CA C:LYS133 3.5 73.2 1.0 O1A C:ADP600 3.5 80.4 1.0 CB C:LYS133 3.5 73.2 1.0 CD C:LYS133 3.7 73.2 1.0 O1B C:ADP600 4.0 80.4 1.0 C C:GLY132 4.1 79.3 1.0 NZ C:LYS133 4.3 73.2 1.0 C C:THR134 4.3 69.0 1.0 N C:GLN135 4.4 68.3 1.0 O5' C:ADP600 4.4 80.4 1.0 N C:GLY132 4.5 79.3 1.0 O C:LYS133 4.5 73.2 1.0 CG2 C:THR134 4.5 69.0 1.0 CE C:LYS133 4.5 73.2 1.0 CA C:GLY132 4.6 79.3 1.0 O C:GLY132 4.9 79.3 1.0

Magnesium binding site 4 out of 8 in the Cryoem Structure of the RAD51_ADP Filament


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryoem Structure of the RAD51_ADP Filament within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:88.3 occ:1.00 O3A D:ADP600 2.0 90.7 1.0 O3B D:ADP600 2.1 90.7 1.0 O2A D:ADP600 2.1 90.7 1.0 PA D:ADP600 2.4 90.7 1.0 PB D:ADP600 2.6 90.7 1.0 N D:GLY132 2.8 87.3 1.0 O5' D:ADP600 2.9 90.7 1.0 N D:THR131 2.9 89.0 1.0 CA D:ARG130 3.1 92.9 1.0 C D:ARG130 3.2 92.9 1.0 N D:ARG130 3.4 92.9 1.0 CA D:GLY132 3.5 87.3 1.0 O1B D:ADP600 3.6 90.7 1.0 O2B D:ADP600 3.7 90.7 1.0 C D:THR131 3.7 89.0 1.0 N D:LYS133 3.7 83.0 1.0 CA D:THR131 3.8 89.0 1.0 O1A D:ADP600 3.8 90.7 1.0 OG1 D:THR131 4.0 89.0 1.0 O D:ARG130 4.0 92.9 1.0 C D:GLY132 4.1 87.3 1.0 C5' D:ADP600 4.1 90.7 1.0 NZ D:LYS133 4.1 83.0 1.0 C D:PHE129 4.4 89.3 1.0 CG D:LYS133 4.4 83.0 1.0 CB D:THR131 4.5 89.0 1.0 CB D:ARG130 4.6 92.9 1.0 N D:THR134 4.6 79.3 1.0 C4' D:ADP600 4.8 90.7 1.0 O D:THR131 4.9 89.0 1.0 CA D:LYS133 4.9 83.0 1.0 OG1 D:THR134 4.9 79.3 1.0

Magnesium binding site 5 out of 8 in the Cryoem Structure of the RAD51_ADP Filament


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryoem Structure of the RAD51_ADP Filament within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg601 b:80.4 occ:1.00 O1A E:ADP600 2.0 83.0 1.0 O2B E:ADP600 2.2 83.0 1.0 O2A E:ADP600 2.3 83.0 1.0 PA E:ADP600 2.4 83.0 1.0 N E:THR134 2.6 73.4 1.0 C E:GLY132 2.7 81.9 1.0 N E:GLN135 2.8 73.8 1.0 N E:LYS133 2.8 76.5 1.0 CA E:GLY132 2.8 81.9 1.0 N E:GLY132 3.0 81.9 1.0 CA E:THR134 3.2 73.4 1.0 O3A E:ADP600 3.3 83.0 1.0 O E:GLY132 3.3 81.9 1.0 PB E:ADP600 3.4 83.0 1.0 CB E:THR134 3.4 73.4 1.0 CG E:GLN135 3.4 73.8 1.0 C E:LYS133 3.4 76.5 1.0 C E:THR134 3.5 73.4 1.0 CA E:LYS133 3.7 76.5 1.0 CB E:GLN135 3.8 73.8 1.0 O5' E:ADP600 3.8 83.0 1.0 CA E:GLN135 3.8 73.8 1.0 OG1 E:THR134 3.9 73.4 1.0 O1B E:ADP600 4.2 83.0 1.0 CG E:LYS133 4.2 76.5 1.0 C E:THR131 4.2 81.5 1.0 C5' E:ADP600 4.3 83.0 1.0 NE2 E:GLN135 4.4 73.8 1.0 CD E:GLN135 4.5 73.8 1.0 O3B E:ADP600 4.5 83.0 1.0 O E:LYS133 4.5 76.5 1.0 CB E:LYS133 4.5 76.5 1.0 N E:THR131 4.6 81.5 1.0 O E:THR134 4.7 73.4 1.0 CG2 E:THR134 4.7 73.4 1.0 C E:ARG130 4.9 88.2 1.0

Magnesium binding site 6 out of 8 in the Cryoem Structure of the RAD51_ADP Filament


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryoem Structure of the RAD51_ADP Filament within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg601 b:79.7 occ:1.00 O3A F:ADP600 2.0 81.5 1.0 O3B F:ADP600 2.0 81.5 1.0 O2A F:ADP600 2.1 81.5 1.0 PA F:ADP600 2.4 81.5 1.0 PB F:ADP600 2.6 81.5 1.0 O5' F:ADP600 2.8 81.5 1.0 N F:GLY132 2.8 77.5 1.0 N F:THR131 3.0 79.4 1.0 C F:ARG130 3.3 80.3 1.0 CA F:ARG130 3.3 80.3 1.0 N F:ARG130 3.4 80.3 1.0 O1B F:ADP600 3.6 81.5 1.0 CA F:GLY132 3.6 77.5 1.0 O2B F:ADP600 3.7 81.5 1.0 C F:THR131 3.7 79.4 1.0 O1A F:ADP600 3.8 81.5 1.0 N F:LYS133 3.8 74.1 1.0 CA F:THR131 3.9 79.4 1.0 OG1 F:THR131 3.9 79.4 1.0 C5' F:ADP600 4.0 81.5 1.0 C F:GLY132 4.1 77.5 1.0 O F:ARG130 4.2 80.3 1.0 CG F:LYS133 4.2 74.1 1.0 NZ F:LYS133 4.3 74.1 1.0 C F:PHE129 4.4 81.2 1.0 CB F:THR131 4.5 79.4 1.0 N F:THR134 4.6 71.7 1.0 C4' F:ADP600 4.7 81.5 1.0 CE F:LYS133 4.8 74.1 1.0 CB F:ARG130 4.8 80.3 1.0 O F:THR131 4.8 79.4 1.0 CA F:LYS133 5.0 74.1 1.0 OG1 F:THR134 5.0 71.7 1.0 O3' F:ADP600 5.0 81.5 1.0

Magnesium binding site 7 out of 8 in the Cryoem Structure of the RAD51_ADP Filament


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryoem Structure of the RAD51_ADP Filament within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg601 b:86.4 occ:1.00 O2A G:ADP600 2.0 84.9 1.0 O3B G:ADP600 2.0 84.9 1.0 O2B G:ADP600 2.2 84.9 1.0 N G:THR134 2.3 75.9 1.0 PB G:ADP600 2.4 84.9 1.0 CB G:THR134 2.4 75.9 1.0 OG1 G:THR134 2.5 75.9 1.0 PA G:ADP600 2.7 84.9 1.0 CA G:THR134 2.9 75.9 1.0 O3A G:ADP600 2.9 84.9 1.0 O1A G:ADP600 3.3 84.9 1.0 C G:LYS133 3.5 78.3 1.0 N G:LYS133 3.5 78.3 1.0 CG G:LYS133 3.5 78.3 1.0 N G:GLN135 3.8 75.2 1.0 C G:THR134 3.8 75.9 1.0 O1B G:ADP600 3.8 84.9 1.0 CG2 G:THR134 3.9 75.9 1.0 CA G:LYS133 3.9 78.3 1.0 C G:GLY132 4.0 83.0 1.0 O5' G:ADP600 4.2 84.9 1.0 CB G:LYS133 4.3 78.3 1.0 N G:GLY132 4.3 83.0 1.0 CA G:GLY132 4.4 83.0 1.0 O G:LYS133 4.6 78.3 1.0 CD G:LYS133 4.7 78.3 1.0 O G:GLY132 4.7 83.0 1.0 CE G:LYS133 4.7 78.3 1.0 O G:THR134 4.9 75.9 1.0

Magnesium binding site 8 out of 8 in the Cryoem Structure of the RAD51_ADP Filament


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryoem Structure of the RAD51_ADP Filament within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg601 b:90.2 occ:1.00 O3A H:ADP600 2.0 92.7 1.0 O3B H:ADP600 2.1 92.7 1.0 O2A H:ADP600 2.2 92.7 1.0 PA H:ADP600 2.4 92.7 1.0 PB H:ADP600 2.6 92.7 1.0 O5' H:ADP600 2.7 92.7 1.0 N H:GLY132 2.7 88.2 1.0 N H:THR131 2.9 91.4 1.0 C H:ARG130 3.3 94.1 1.0 CA H:ARG130 3.3 94.1 1.0 CA H:GLY132 3.4 88.2 1.0 O1B H:ADP600 3.5 92.7 1.0 N H:ARG130 3.5 94.1 1.0 C H:THR131 3.6 91.4 1.0 O2B H:ADP600 3.7 92.7 1.0 CA H:THR131 3.8 91.4 1.0 N H:LYS133 3.8 83.7 1.0 O1A H:ADP600 3.8 92.7 1.0 C5' H:ADP600 3.9 92.7 1.0 OG1 H:THR131 3.9 91.4 1.0 C H:GLY132 4.1 88.2 1.0 O H:ARG130 4.2 94.1 1.0 NZ H:LYS133 4.2 83.7 1.0 CB H:THR131 4.5 91.4 1.0 CG H:LYS133 4.5 83.7 1.0 C H:PHE129 4.5 92.3 1.0 C4' H:ADP600 4.5 92.7 1.0 N H:THR134 4.6 80.7 1.0 O H:THR131 4.7 91.4 1.0 O3' H:ADP600 4.8 92.7 1.0 CB H:ARG130 4.8 94.1 1.0 CA H:LYS133 5.0 83.7 1.0 OG1 H:THR134 5.0 80.7 1.0

S.C.Luo, M.C.Yeh, Y.H.Lien, H.Y.Yeh, H.L.Siao, I.P.Tu, P.Chi, M.C.Ho. A RAD51-Adp Double Filament Structure Unveils the Mechanism of Filament Dynamics in Homologous Recombination. Nat Commun V. 14 4993 2023.
ISSN: ESSN 2041-1723
PubMed: 37591853
DOI: 10.1038/S41467-023-40672-5