Calcium in PDB 8bsc: Cryoem Structure of the RAD51 Nucleoprotein Filament in the Presence of Adp and CA2+

The binding sites of Calcium atom in the Cryoem Structure of the RAD51 Nucleoprotein Filament in the Presence of Adp and CA2+ (pdb code 8bsc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Cryoem Structure of the RAD51 Nucleoprotein Filament in the Presence of Adp and CA2+, PDB code: 8bsc:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Cryoem Structure of the RAD51 Nucleoprotein Filament in the Presence of Adp and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryoem Structure of the RAD51 Nucleoprotein Filament in the Presence of Adp and CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca401 b:37.9 occ:1.00 OG1 D:THR134 2.4 35.0 1.0 OE2 D:GLU163 2.4 28.8 1.0 OE1 D:GLU163 2.4 28.8 1.0 O1B D:ADP402 2.7 42.9 1.0 CD D:GLU163 2.7 28.8 1.0 CB D:THR134 3.7 35.0 1.0 OG1 D:THR165 3.9 27.5 1.0 PB D:ADP402 4.1 42.9 1.0 CG2 D:THR134 4.2 35.0 1.0 CG D:GLU163 4.2 28.8 1.0 OD1 D:ASP222 4.4 26.9 1.0 O3B D:ADP402 4.5 42.9 1.0 OD2 D:ASP222 4.6 26.9 1.0 NZ D:LYS133 4.6 34.7 1.0 CA D:THR134 4.6 35.0 1.0 N D:THR134 4.7 35.0 1.0 O2B D:ADP402 4.8 42.9 1.0 OG D:SER223 4.9 26.2 1.0 CE D:LYS133 4.9 34.7 1.0 CB D:GLU163 4.9 28.8 1.0 CG D:ASP222 4.9 26.9 1.0

Calcium binding site 2 out of 7 in the Cryoem Structure of the RAD51 Nucleoprotein Filament in the Presence of Adp and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryoem Structure of the RAD51 Nucleoprotein Filament in the Presence of Adp and CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:37.9 occ:1.00 OG1 A:THR134 2.4 35.0 1.0 OE2 A:GLU163 2.4 28.8 1.0 OE1 A:GLU163 2.4 28.8 1.0 O1B A:ADP402 2.7 42.9 1.0 CD A:GLU163 2.7 28.8 1.0 CB A:THR134 3.7 35.0 1.0 OG1 A:THR165 3.9 27.5 1.0 PB A:ADP402 4.1 42.9 1.0 CG2 A:THR134 4.2 35.0 1.0 CG A:GLU163 4.2 28.8 1.0 OD1 A:ASP222 4.4 26.9 1.0 O3B A:ADP402 4.5 42.9 1.0 OD2 A:ASP222 4.6 26.9 1.0 NZ A:LYS133 4.6 34.7 1.0 CA A:THR134 4.6 35.0 1.0 N A:THR134 4.7 35.0 1.0 O2B A:ADP402 4.8 42.9 1.0 OG A:SER223 4.9 26.2 1.0 CE A:LYS133 4.9 34.7 1.0 CB A:GLU163 4.9 28.8 1.0 CG A:ASP222 4.9 26.9 1.0

Calcium binding site 3 out of 7 in the Cryoem Structure of the RAD51 Nucleoprotein Filament in the Presence of Adp and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryoem Structure of the RAD51 Nucleoprotein Filament in the Presence of Adp and CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:37.9 occ:1.00 OG1 B:THR134 2.4 35.0 1.0 OE2 B:GLU163 2.4 28.8 1.0 OE1 B:GLU163 2.4 28.8 1.0 O1B B:ADP402 2.7 42.9 1.0 CD B:GLU163 2.7 28.8 1.0 CB B:THR134 3.7 35.0 1.0 OG1 B:THR165 3.9 27.5 1.0 PB B:ADP402 4.1 42.9 1.0 CG2 B:THR134 4.2 35.0 1.0 CG B:GLU163 4.2 28.8 1.0 OD1 B:ASP222 4.4 26.9 1.0 O3B B:ADP402 4.5 42.9 1.0 OD2 B:ASP222 4.6 26.9 1.0 NZ B:LYS133 4.6 34.7 1.0 CA B:THR134 4.6 35.0 1.0 N B:THR134 4.7 35.0 1.0 O2B B:ADP402 4.8 42.9 1.0 OG B:SER223 4.9 26.2 1.0 CE B:LYS133 4.9 34.7 1.0 CB B:GLU163 4.9 28.8 1.0 CG B:ASP222 4.9 26.9 1.0

Calcium binding site 4 out of 7 in the Cryoem Structure of the RAD51 Nucleoprotein Filament in the Presence of Adp and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryoem Structure of the RAD51 Nucleoprotein Filament in the Presence of Adp and CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:37.9 occ:1.00 OG1 C:THR134 2.4 35.0 1.0 OE2 C:GLU163 2.4 28.8 1.0 OE1 C:GLU163 2.4 28.8 1.0 O1B C:ADP402 2.7 42.9 1.0 CD C:GLU163 2.7 28.8 1.0 CB C:THR134 3.7 35.0 1.0 OG1 C:THR165 3.9 27.5 1.0 PB C:ADP402 4.1 42.9 1.0 CG2 C:THR134 4.2 35.0 1.0 CG C:GLU163 4.2 28.8 1.0 OD1 C:ASP222 4.4 26.9 1.0 O3B C:ADP402 4.5 42.9 1.0 OD2 C:ASP222 4.6 26.9 1.0 NZ C:LYS133 4.6 34.7 1.0 CA C:THR134 4.6 35.0 1.0 N C:THR134 4.7 35.0 1.0 O2B C:ADP402 4.8 42.9 1.0 OG C:SER223 4.9 26.2 1.0 CE C:LYS133 4.9 34.7 1.0 CB C:GLU163 4.9 28.8 1.0 CG C:ASP222 4.9 26.9 1.0

Calcium binding site 5 out of 7 in the Cryoem Structure of the RAD51 Nucleoprotein Filament in the Presence of Adp and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cryoem Structure of the RAD51 Nucleoprotein Filament in the Presence of Adp and CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca401 b:37.9 occ:1.00 OG1 E:THR134 2.4 35.0 1.0 OE2 E:GLU163 2.4 28.8 1.0 OE1 E:GLU163 2.4 28.8 1.0 O1B E:ADP402 2.7 42.9 1.0 CD E:GLU163 2.7 28.8 1.0 CB E:THR134 3.7 35.0 1.0 OG1 E:THR165 3.9 27.5 1.0 PB E:ADP402 4.1 42.9 1.0 CG2 E:THR134 4.2 35.0 1.0 CG E:GLU163 4.2 28.8 1.0 OD1 E:ASP222 4.4 26.9 1.0 O3B E:ADP402 4.5 42.9 1.0 OD2 E:ASP222 4.6 26.9 1.0 NZ E:LYS133 4.6 34.7 1.0 CA E:THR134 4.6 35.0 1.0 N E:THR134 4.7 35.0 1.0 O2B E:ADP402 4.8 42.9 1.0 OG E:SER223 4.9 26.2 1.0 CE E:LYS133 4.9 34.7 1.0 CB E:GLU163 4.9 28.8 1.0 CG E:ASP222 4.9 26.9 1.0

Calcium binding site 6 out of 7 in the Cryoem Structure of the RAD51 Nucleoprotein Filament in the Presence of Adp and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cryoem Structure of the RAD51 Nucleoprotein Filament in the Presence of Adp and CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca401 b:37.9 occ:1.00 OG1 F:THR134 2.4 35.0 1.0 OE2 F:GLU163 2.4 28.8 1.0 OE1 F:GLU163 2.4 28.8 1.0 O1B F:ADP402 2.7 42.9 1.0 CD F:GLU163 2.7 28.8 1.0 CB F:THR134 3.7 35.0 1.0 OG1 F:THR165 3.9 27.5 1.0 PB F:ADP402 4.1 42.9 1.0 CG2 F:THR134 4.2 35.0 1.0 CG F:GLU163 4.2 28.8 1.0 OD1 F:ASP222 4.4 26.9 1.0 O3B F:ADP402 4.5 42.9 1.0 OD2 F:ASP222 4.6 26.9 1.0 NZ F:LYS133 4.6 34.7 1.0 CA F:THR134 4.6 35.0 1.0 N F:THR134 4.7 35.0 1.0 O2B F:ADP402 4.8 42.9 1.0 OG F:SER223 4.9 26.2 1.0 CE F:LYS133 4.9 34.7 1.0 CB F:GLU163 4.9 28.8 1.0 CG F:ASP222 4.9 26.9 1.0

Calcium binding site 7 out of 7 in the Cryoem Structure of the RAD51 Nucleoprotein Filament in the Presence of Adp and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Cryoem Structure of the RAD51 Nucleoprotein Filament in the Presence of Adp and CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca401 b:37.9 occ:1.00 OG1 G:THR134 2.4 35.0 1.0 OE2 G:GLU163 2.4 28.8 1.0 OE1 G:GLU163 2.4 28.8 1.0 O1B G:ADP402 2.7 42.9 1.0 CD G:GLU163 2.7 28.8 1.0 CB G:THR134 3.7 35.0 1.0 OG1 G:THR165 3.9 27.5 1.0 PB G:ADP402 4.1 42.9 1.0 CG2 G:THR134 4.2 35.0 1.0 CG G:GLU163 4.2 28.8 1.0 OD1 G:ASP222 4.4 26.9 1.0 O3B G:ADP402 4.5 42.9 1.0 OD2 G:ASP222 4.6 26.9 1.0 NZ G:LYS133 4.6 34.7 1.0 CA G:THR134 4.6 35.0 1.0 N G:THR134 4.7 35.0 1.0 O2B G:ADP402 4.8 42.9 1.0 OG G:SER223 4.9 26.2 1.0 CE G:LYS133 4.9 34.7 1.0 CB G:GLU163 4.9 28.8 1.0 CG G:ASP222 4.9 26.9 1.0

R.Appleby, D.Bollschweiler, D.Y.Chirgadze, L.Joudeh, L.Pellegrini. A Metal Ion-Dependent Mechanism of RAD51 Nucleoprotein Filament Disassembly Iscience 2023.
ISSN: ESSN 2589-0042
DOI: 10.1016/J.ISCI.2023.106689