Calcium in PDB 9i62: Cryoem Structure of A RAD51 D-Loop

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Calcium atom in the Cryoem Structure of A RAD51 D-Loop (pdb code 9i62). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 18 binding sites of Calcium where determined in the Cryoem Structure of A RAD51 D-Loop, PDB code: 9i62:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 18 in the Cryoem Structure of A RAD51 D-Loop


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 A RAD51 D-Loop within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:203.1 occ:1.00 O3G A:ATP402 2.3 195.6 1.0 OG1 A:THR134 2.3 192.8 1.0 O2G A:ATP402 2.7 195.5 1.0 PG A:ATP402 3.0 198.7 1.0 OE1 A:GLU163 3.1 201.4 1.0 OD2 A:ASP222 3.2 186.2 1.0 OD1 A:ASP222 3.3 184.7 1.0 CG A:ASP222 3.6 184.4 1.0 O2B A:ATP402 3.6 196.0 1.0 CB A:THR134 3.7 191.2 1.0 CD A:GLU163 3.8 198.4 1.0 O3B A:ATP402 4.0 196.8 1.0 OE2 A:GLU163 4.1 195.1 1.0 O1G A:ATP402 4.2 196.7 1.0 CG2 A:THR134 4.2 190.0 1.0 OG1 A:THR165 4.2 190.7 1.0 N A:THR134 4.4 191.2 1.0 CA A:THR134 4.5 190.2 1.0 PB A:ATP402 4.5 196.4 1.0 CG2 A:THR266 4.7 175.7 1.0 CG A:GLU163 4.8 194.0 1.0 CE A:LYS133 4.9 186.3 1.0

Calcium binding site 2 out of 18 in the Cryoem Structure of A RAD51 D-Loop


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 A RAD51 D-Loop within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:166.0 occ:1.00 O1G A:ATP402 2.3 196.7 1.0 PG A:ATP402 3.6 198.7 1.0 O3B A:ATP402 3.9 196.8 1.0 CB A:PHE129 4.4 193.0 1.0 O3G A:ATP402 4.4 195.6 1.0 O2G A:ATP402 4.8 195.5 1.0 N A:ARG130 4.9 194.6 1.0 CG A:ARG130 5.0 191.9 1.0 CA A:PHE129 5.0 195.5 1.0

Calcium binding site 3 out of 18 in the Cryoem Structure of A RAD51 D-Loop


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 A RAD51 D-Loop within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:139.3 occ:1.00 O3G B:ATP402 2.2 135.8 1.0 O A:SER296 2.2 144.3 1.0 OD2 A:ASP316 2.3 142.8 1.0 O A:ALA293 2.3 140.8 1.0 O A:HIS294 3.3 137.7 1.0 C A:SER296 3.4 140.8 1.0 CG A:ASP316 3.5 144.0 1.0 C A:ALA293 3.5 140.3 1.0 PG B:ATP402 3.6 135.8 1.0 C A:HIS294 3.7 137.3 1.0 CA A:HIS294 3.8 136.4 1.0 O1G B:ATP402 4.0 134.3 1.0 OD1 A:ASP316 4.1 143.7 1.0 N A:HIS294 4.1 139.1 1.0 N A:SER296 4.2 137.3 1.0 CB B:PHE129 4.2 131.4 1.0 CA A:SER296 4.3 139.6 1.0 N A:THR297 4.4 139.5 1.0 O3B B:ATP402 4.4 126.6 1.0 CA A:THR297 4.5 139.1 1.0 O2G B:ATP402 4.6 131.6 1.0 CB A:ASP316 4.6 144.4 1.0 CB A:SER296 4.6 143.8 1.0 N A:ALA295 4.6 138.0 1.0 C A:ALA295 4.7 135.9 1.0 CA A:ALA293 4.7 142.8 1.0 C A:THR297 5.0 140.4 1.0

Calcium binding site 4 out of 18 in the Cryoem Structure of A RAD51 D-Loop


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 A RAD51 D-Loop within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:119.8 occ:1.00 OG1 B:THR134 2.2 123.1 1.0 O2G B:ATP402 2.2 131.6 1.0 O2B B:ATP402 2.3 122.1 1.0 OE1 B:GLU163 2.6 142.2 1.0 PG B:ATP402 3.5 135.8 1.0 CD B:GLU163 3.6 138.2 1.0 CB B:THR134 3.6 120.4 1.0 PB B:ATP402 3.6 118.6 1.0 O3B B:ATP402 3.7 126.6 1.0 OG1 B:THR165 3.8 129.0 1.0 OE2 B:GLU163 4.0 137.9 1.0 O3G B:ATP402 4.0 135.8 1.0 OD2 B:ASP222 4.1 121.4 1.0 OD1 B:ASP222 4.1 121.7 1.0 O1A B:ATP402 4.2 131.6 1.0 CG2 B:THR134 4.4 120.7 1.0 O3A B:ATP402 4.4 121.9 1.0 N B:THR134 4.5 117.0 1.0 CA B:THR134 4.5 116.0 1.0 CG B:ASP222 4.5 119.3 1.0 CB B:THR165 4.6 129.6 1.0 CG2 B:THR165 4.6 129.7 1.0 O1G B:ATP402 4.7 134.3 1.0 O1B B:ATP402 4.7 123.0 1.0 PA B:ATP402 4.8 127.5 1.0 CG B:GLU163 4.9 128.7 1.0

Calcium binding site 5 out of 18 in the Cryoem Structure of A RAD51 D-Loop


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 A RAD51 D-Loop within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca403 b:98.3 occ:1.00 O3G C:ATP402 2.1 99.6 1.0 O B:SER296 2.2 97.6 1.0 O B:ALA293 2.4 94.5 1.0 OD2 B:ASP316 2.4 101.1 1.0 O B:HIS294 3.1 94.3 1.0 C B:SER296 3.4 92.1 1.0 C B:HIS294 3.5 91.1 1.0 C B:ALA293 3.5 90.5 1.0 CG B:ASP316 3.6 100.8 1.0 CA B:HIS294 3.6 86.6 1.0 PG C:ATP402 3.6 98.1 1.0 N B:HIS294 4.0 88.3 1.0 N B:SER296 4.1 85.8 1.0 OD1 B:ASP316 4.2 104.3 1.0 CA B:SER296 4.2 87.3 1.0 O2G C:ATP402 4.3 97.2 1.0 N B:THR297 4.3 91.5 1.0 O1G C:ATP402 4.3 96.5 1.0 CB C:PHE129 4.4 90.8 1.0 CA B:THR297 4.4 90.8 1.0 N B:ALA295 4.4 89.5 1.0 O3B C:ATP402 4.5 90.8 1.0 C B:ALA295 4.5 87.7 1.0 CB B:SER296 4.6 92.5 1.0 O B:THR297 4.7 95.9 1.0 CA B:ALA293 4.7 88.9 1.0 CB B:ASP316 4.7 96.5 1.0 C B:THR297 4.8 91.5 1.0 O B:ALA295 5.0 92.4 1.0 CB B:HIS294 5.0 83.0 1.0

Calcium binding site 6 out of 18 in the Cryoem Structure of A RAD51 D-Loop


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 A RAD51 D-Loop within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:94.0 occ:1.00 O2G C:ATP402 2.2 97.2 1.0 OG1 C:THR134 2.2 96.6 1.0 O2B C:ATP402 2.3 95.4 1.0 OE1 C:GLU163 2.7 112.0 1.0 CB C:THR134 3.5 88.9 1.0 PG C:ATP402 3.6 98.1 1.0 PB C:ATP402 3.6 88.5 1.0 O3B C:ATP402 3.7 90.8 1.0 CD C:GLU163 3.8 112.7 1.0 OG1 C:THR165 3.8 99.2 1.0 O1A C:ATP402 4.1 101.8 1.0 OE2 C:GLU163 4.1 118.8 1.0 OD1 C:ASP222 4.2 100.4 1.0 OD2 C:ASP222 4.3 100.5 1.0 O3A C:ATP402 4.3 92.3 1.0 CG2 C:THR134 4.3 91.8 1.0 O3G C:ATP402 4.3 99.6 1.0 N C:THR134 4.4 89.0 1.0 CB C:THR165 4.5 97.9 1.0 CA C:THR134 4.5 85.5 1.0 O1G C:ATP402 4.6 96.5 1.0 CG2 C:THR165 4.6 98.5 1.0 CG C:ASP222 4.7 98.7 1.0 O1B C:ATP402 4.7 90.5 1.0 PA C:ATP402 4.7 101.6 1.0

Calcium binding site 7 out of 18 in the Cryoem Structure of A RAD51 D-Loop


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 A RAD51 D-Loop within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca403 b:90.1 occ:1.00 O3G D:ATP402 2.1 91.1 1.0 O C:SER296 2.2 86.5 1.0 O C:ALA293 2.3 82.2 1.0 OD2 C:ASP316 2.4 86.6 1.0 O C:HIS294 3.1 83.2 1.0 C C:SER296 3.4 80.4 1.0 C C:ALA293 3.4 79.0 1.0 C C:HIS294 3.5 79.8 1.0 CG C:ASP316 3.6 87.2 1.0 PG D:ATP402 3.6 91.1 1.0 CA C:HIS294 3.7 73.7 1.0 N C:HIS294 4.0 75.9 1.0 N C:SER296 4.1 76.0 1.0 OD1 C:ASP316 4.2 92.5 1.0 CA C:SER296 4.2 75.9 1.0 O2G D:ATP402 4.3 92.5 1.0 CB D:PHE129 4.3 76.9 1.0 N C:THR297 4.3 78.3 1.0 O1G D:ATP402 4.3 84.0 1.0 CA C:THR297 4.4 79.1 1.0 N C:ALA295 4.5 79.3 1.0 O3B D:ATP402 4.5 82.3 1.0 C C:ALA295 4.6 76.8 1.0 O C:THR297 4.6 87.4 1.0 CB C:SER296 4.6 78.9 1.0 CA C:ALA293 4.7 77.4 1.0 C C:THR297 4.7 80.4 1.0 CB C:ASP316 4.7 80.9 1.0

Calcium binding site 8 out of 18 in the Cryoem Structure of A RAD51 D-Loop


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Cryoem Structure of A RAD51 D-Loop within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca401 b:85.2 occ:1.00 OG1 D:THR134 2.2 86.5 1.0 O2G D:ATP402 2.2 92.5 1.0 O2B D:ATP402 2.3 84.5 1.0 OE1 D:GLU163 2.5 107.1 1.0 CB D:THR134 3.5 82.2 1.0 CD D:GLU163 3.5 106.4 1.0 PB D:ATP402 3.6 79.7 1.0 PG D:ATP402 3.6 91.1 1.0 OG1 D:THR165 3.7 93.7 1.0 O3B D:ATP402 3.8 82.3 1.0 OE2 D:GLU163 3.9 110.1 1.0 O1A D:ATP402 4.1 91.0 1.0 OD1 D:ASP222 4.2 91.5 1.0 CG2 D:THR134 4.2 82.6 1.0 OD2 D:ASP222 4.3 93.0 1.0 O3A D:ATP402 4.3 82.7 1.0 O3G D:ATP402 4.4 91.1 1.0 CB D:THR165 4.5 91.4 1.0 N D:THR134 4.5 80.5 1.0 CA D:THR134 4.5 78.4 1.0 O1G D:ATP402 4.6 84.0 1.0 CG2 D:THR165 4.6 90.2 1.0 CG D:ASP222 4.7 91.7 1.0 O1B D:ATP402 4.7 81.9 1.0 PA D:ATP402 4.8 87.8 1.0 CG D:GLU163 4.9 93.7 1.0

Calcium binding site 9 out of 18 in the Cryoem Structure of A RAD51 D-Loop


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Cryoem Structure of A RAD51 D-Loop within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca403 b:83.9 occ:1.00 O3G E:ATP402 2.1 87.1 1.0 O D:SER296 2.2 83.2 1.0 O D:ALA293 2.3 79.9 1.0 OD2 D:ASP316 2.5 83.9 1.0 O D:HIS294 3.2 79.9 1.0 C D:SER296 3.4 75.6 1.0 C D:ALA293 3.5 77.5 1.0 C D:HIS294 3.6 76.7 1.0 CG D:ASP316 3.6 81.9 1.0 PG E:ATP402 3.6 90.4 1.0 CA D:HIS294 3.7 73.3 1.0 N D:SER296 4.1 75.1 1.0 N D:HIS294 4.1 76.1 1.0 OD1 D:ASP316 4.2 86.3 1.0 CA D:SER296 4.2 73.1 1.0 O2G E:ATP402 4.3 92.3 1.0 N D:THR297 4.4 72.9 1.0 CB E:PHE129 4.4 73.2 1.0 O1G E:ATP402 4.4 80.5 1.0 CA D:THR297 4.4 74.4 1.0 N D:ALA295 4.5 74.0 1.0 O3B E:ATP402 4.5 81.7 1.0 C D:ALA295 4.5 74.3 1.0 CB D:SER296 4.7 74.6 1.0 O D:THR297 4.7 84.5 1.0 CA D:ALA293 4.7 72.7 1.0 C D:THR297 4.7 76.2 1.0 CB D:ASP316 4.8 76.5 1.0

Calcium binding site 10 out of 18 in the Cryoem Structure of A RAD51 D-Loop


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Cryoem Structure of A RAD51 D-Loop within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca401 b:79.5 occ:1.00 OG1 E:THR134 2.2 82.4 1.0 O2G E:ATP402 2.3 92.3 1.0 O2B E:ATP402 2.3 82.0 1.0 OE1 E:GLU163 2.9 109.8 1.0 CB E:THR134 3.6 78.6 1.0 PG E:ATP402 3.6 90.4 1.0 PB E:ATP402 3.6 79.1 1.0 O3B E:ATP402 3.8 81.7 1.0 OG1 E:THR165 3.8 94.0 1.0 CD E:GLU163 4.0 106.0 1.0 OD1 E:ASP222 4.1 90.7 1.0 O1A E:ATP402 4.3 87.3 1.0 CG2 E:THR134 4.3 77.8 1.0 O3G E:ATP402 4.4 87.1 1.0 O3A E:ATP402 4.4 77.3 1.0 OE2 E:GLU163 4.4 104.6 1.0 OD2 E:ASP222 4.5 96.0 1.0 N E:THR134 4.5 79.0 1.0 CB E:THR165 4.5 90.4 1.0 CA E:THR134 4.6 75.5 1.0 O1G E:ATP402 4.6 80.5 1.0 CG2 E:THR165 4.7 88.9 1.0 O1B E:ATP402 4.7 77.9 1.0 CG E:ASP222 4.7 91.5 1.0 PA E:ATP402 4.9 82.8 1.0

L.Joudeh, R.E.Appleby, J.D.Maman, L.Pellegrini. Structural Mechanism of Strand Exchange By the RAD51 Filament Elife 2025.
ISSN: ESSN 2050-084X
DOI: 10.7554/ELIFE.107114.1