Calcium in PDB 8br2: Cryoem Structure of the Post-Synaptic RAD51 Nucleoprotein Filament in the Presence of Atp and CA2+

Calcium Binding Sites:

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>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Cryoem Structure of the Post-Synaptic RAD51 Nucleoprotein Filament in the Presence of Atp and CA2+ (pdb code 8br2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Cryoem Structure of the Post-Synaptic RAD51 Nucleoprotein Filament in the Presence of Atp and CA2+, PDB code: 8br2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in 8br2

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Calcium binding site 1 out of 12 in the Cryoem Structure of the Post-Synaptic RAD51 Nucleoprotein Filament in the Presence of Atp 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 Post-Synaptic RAD51 Nucleoprotein Filament in the Presence of Atp and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:1.5
occ:1.00
 OG1 A:THR134 2.1 16.9 1.0
O2G A:ATP403 2.2 30.6 1.0
O2B A:ATP403 2.3 25.9 1.0
OE1 A:GLU163 3.0 20.7 1.0
CB A:THR134 3.4 12.3 1.0
PG A:ATP403 3.5 14.1 1.0
PB A:ATP403 3.6 3.0 1.0
O3B A:ATP403 3.7 20.2 1.0
OG1 A:THR165 3.7 12.3 1.0
CD A:GLU163 4.0 20.9 1.0
CG2 A:THR134 4.1 9.6 1.0
O1A A:ATP403 4.1 28.3 1.0
OE2 A:GLU163 4.2 23.7 1.0
O3A A:ATP403 4.2 16.1 1.0
OD1 A:ASP222 4.3 21.8 1.0
OD2 A:ASP222 4.3 11.2 1.0
CB A:THR165 4.4 10.3 1.0
O1G A:ATP403 4.4 15.8 1.0
O3G A:ATP403 4.5 27.9 1.0
N A:THR134 4.5 7.2 1.0
CA A:THR134 4.5 6.3 1.0
CG2 A:THR165 4.5 11.9 1.0
PA A:ATP403 4.7 8.4 1.0
O1B A:ATP403 4.7 11.2 1.0
CG A:ASP222 4.7 20.2 1.0

Calcium binding site 2 out of 12 in 8br2

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Calcium binding site 2 out of 12 in the Cryoem Structure of the Post-Synaptic RAD51 Nucleoprotein Filament in the Presence of Atp 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 Post-Synaptic RAD51 Nucleoprotein Filament in the Presence of Atp and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:19.4
occ:1.00
 O3G A:ATP403 2.2 27.9 1.0
PG A:ATP403 3.6 14.1 1.0
O2G A:ATP403 4.0 30.6 1.0
O1G A:ATP403 4.4 15.8 1.0
CB A:PHE129 4.5 3.8 1.0
O3B A:ATP403 4.6 20.2 1.0

Calcium binding site 3 out of 12 in 8br2

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Calcium binding site 3 out of 12 in the Cryoem Structure of the Post-Synaptic RAD51 Nucleoprotein Filament in the Presence of Atp 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 Post-Synaptic RAD51 Nucleoprotein Filament in the Presence of Atp and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:19.4
occ:1.00
 O3G B:ATP402 2.2 27.9 1.0
O A:SER296 2.3 13.7 1.0
O A:ALA293 2.4 12.7 1.0
OD2 A:ASP316 2.6 17.5 1.0
O A:HIS294 3.0 15.4 1.0
C A:HIS294 3.4 4.0 1.0
C A:SER296 3.5 6.5 1.0
C A:ALA293 3.5 8.4 1.0
O A:HOH507 3.6 21.7 1.0
PG B:ATP402 3.6 14.1 1.0
CA A:HIS294 3.6 0.3 1.0
CG A:ASP316 3.8 19.7 1.0
O A:HOH511 4.0 17.8 1.0
O2G B:ATP402 4.0 30.6 1.0
N A:HIS294 4.1 9.6 1.0
N A:SER296 4.1 7.4 1.0
CA A:SER296 4.3 4.4 1.0
N A:ALA295 4.3 5.9 1.0
O1G B:ATP402 4.4 15.8 1.0
OD1 A:ASP316 4.4 19.7 1.0
N A:THR297 4.5 4.1 1.0
C A:ALA295 4.5 2.6 1.0
CB B:PHE129 4.5 3.8 1.0
CA A:THR297 4.6 6.2 1.0
O3B B:ATP402 4.6 20.2 1.0
O A:THR297 4.6 8.5 1.0
CB A:SER296 4.7 4.1 1.0
CA A:ALA293 4.8 0.0 1.0
C A:THR297 4.8 9.5 1.0
CB A:ASP316 5.0 7.2 1.0
O A:ALA295 5.0 7.2 1.0
CA A:ALA295 5.0 1.6 1.0

Calcium binding site 4 out of 12 in 8br2

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Calcium binding site 4 out of 12 in the Cryoem Structure of the Post-Synaptic RAD51 Nucleoprotein Filament in the Presence of Atp 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 Post-Synaptic RAD51 Nucleoprotein Filament in the Presence of Atp and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:1.5
occ:1.00
 OG1 B:THR134 2.1 16.9 1.0
O2G B:ATP402 2.2 30.6 1.0
O2B B:ATP402 2.3 25.9 1.0
OE1 B:GLU163 3.0 20.7 1.0
CB B:THR134 3.4 12.3 1.0
PG B:ATP402 3.5 14.1 1.0
PB B:ATP402 3.6 3.0 1.0
O3B B:ATP402 3.7 20.2 1.0
OG1 B:THR165 3.7 12.3 1.0
CD B:GLU163 4.0 20.9 1.0
CG2 B:THR134 4.1 9.6 1.0
O1A B:ATP402 4.1 28.3 1.0
OE2 B:GLU163 4.2 23.7 1.0
O3A B:ATP402 4.2 16.1 1.0
OD1 B:ASP222 4.3 21.8 1.0
OD2 B:ASP222 4.3 11.2 1.0
CB B:THR165 4.4 10.3 1.0
O1G B:ATP402 4.4 15.8 1.0
O3G B:ATP402 4.5 27.9 1.0
N B:THR134 4.5 7.2 1.0
CA B:THR134 4.5 6.3 1.0
O A:HOH507 4.5 21.7 1.0
CG2 B:THR165 4.5 11.9 1.0
PA B:ATP402 4.7 8.4 1.0
O1B B:ATP402 4.7 11.2 1.0
CG B:ASP222 4.7 20.2 1.0

Calcium binding site 5 out of 12 in 8br2

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Calcium binding site 5 out of 12 in the Cryoem Structure of the Post-Synaptic RAD51 Nucleoprotein Filament in the Presence of Atp 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 Post-Synaptic RAD51 Nucleoprotein Filament in the Presence of Atp and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:19.4
occ:1.00
 O B:SER296 2.2 13.7 1.0
O3G C:ATP402 2.2 27.9 1.0
O B:ALA293 2.3 12.7 1.0
OD2 B:ASP316 2.7 17.5 1.0
O B:HIS294 2.9 15.4 1.0
C B:SER296 3.3 6.5 1.0
C B:HIS294 3.4 4.0 1.0
C B:ALA293 3.5 8.4 1.0
PG C:ATP402 3.6 14.1 1.0
CA B:HIS294 3.6 0.3 1.0
O B:HOH509 3.7 21.7 1.0
CG B:ASP316 3.9 19.7 1.0
N B:SER296 3.9 7.4 1.0
O B:HOH513 3.9 17.8 1.0
N B:HIS294 4.0 9.6 1.0
O2G C:ATP402 4.0 30.6 1.0
CA B:SER296 4.1 4.4 1.0
N B:ALA295 4.2 5.9 1.0
N B:THR297 4.3 4.1 1.0
C B:ALA295 4.4 2.6 1.0
O1G C:ATP402 4.4 15.8 1.0
CA B:THR297 4.5 6.2 1.0
OD1 B:ASP316 4.5 19.7 1.0
CB B:SER296 4.5 4.1 1.0
CB C:PHE129 4.5 3.8 1.0
O B:THR297 4.6 8.5 1.0
O3B C:ATP402 4.6 20.2 1.0
CA B:ALA293 4.7 0.0 1.0
C B:THR297 4.7 9.5 1.0
O B:ALA295 4.9 7.2 1.0
CA B:ALA295 4.9 1.6 1.0
CD B:ARG299 5.0 10.0 1.0
CB B:ASP316 5.0 7.2 1.0

Calcium binding site 6 out of 12 in 8br2

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Calcium binding site 6 out of 12 in the Cryoem Structure of the Post-Synaptic RAD51 Nucleoprotein Filament in the Presence of Atp 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 Post-Synaptic RAD51 Nucleoprotein Filament in the Presence of Atp and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:1.5
occ:1.00
 OG1 C:THR134 2.1 16.9 1.0
O2G C:ATP402 2.2 30.6 1.0
O2B C:ATP402 2.3 25.9 1.0
OE1 C:GLU163 3.0 20.7 1.0
CB C:THR134 3.4 12.3 1.0
PG C:ATP402 3.5 14.1 1.0
PB C:ATP402 3.6 3.0 1.0
O3B C:ATP402 3.7 20.2 1.0
OG1 C:THR165 3.7 12.3 1.0
CD C:GLU163 4.0 20.9 1.0
CG2 C:THR134 4.1 9.6 1.0
O1A C:ATP402 4.1 28.3 1.0
OE2 C:GLU163 4.2 23.7 1.0
O3A C:ATP402 4.2 16.1 1.0
OD1 C:ASP222 4.3 21.8 1.0
OD2 C:ASP222 4.3 11.2 1.0
CB C:THR165 4.4 10.3 1.0
O B:HOH509 4.4 21.7 1.0
O1G C:ATP402 4.4 15.8 1.0
O3G C:ATP402 4.5 27.9 1.0
N C:THR134 4.5 7.2 1.0
CA C:THR134 4.5 6.3 1.0
CG2 C:THR165 4.5 11.9 1.0
PA C:ATP402 4.7 8.4 1.0
O1B C:ATP402 4.7 11.2 1.0
CG C:ASP222 4.7 20.2 1.0
O B:HOH513 4.9 17.8 1.0

Calcium binding site 7 out of 12 in 8br2

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Calcium binding site 7 out of 12 in the Cryoem Structure of the Post-Synaptic RAD51 Nucleoprotein Filament in the Presence of Atp 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 Post-Synaptic RAD51 Nucleoprotein Filament in the Presence of Atp and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:19.4
occ:1.00
 O C:SER296 2.1 13.7 1.0
O3G D:ATP402 2.2 27.9 1.0
O C:ALA293 2.5 12.7 1.0
OD2 C:ASP316 2.7 17.5 1.0
O C:HIS294 2.9 15.4 1.0
C C:SER296 3.3 6.5 1.0
C C:HIS294 3.4 4.0 1.0
O C:HOH507 3.6 21.7 1.0
PG D:ATP402 3.6 14.1 1.0
C C:ALA293 3.6 8.4 1.0
CA C:HIS294 3.7 0.3 1.0
O C:HOH511 3.8 17.8 1.0
CG C:ASP316 3.9 19.7 1.0
N C:SER296 4.0 7.4 1.0
O2G D:ATP402 4.0 30.6 1.0
CA C:SER296 4.1 4.4 1.0
N C:HIS294 4.2 9.6 1.0
N C:THR297 4.3 4.1 1.0
N C:ALA295 4.3 5.9 1.0
C C:ALA295 4.4 2.6 1.0
CA C:THR297 4.4 6.2 1.0
O1G D:ATP402 4.4 15.8 1.0
O C:THR297 4.5 8.5 1.0
OD1 C:ASP316 4.5 19.7 1.0
CB D:PHE129 4.5 3.8 1.0
O3B D:ATP402 4.6 20.2 1.0
CB C:SER296 4.6 4.1 1.0
C C:THR297 4.6 9.5 1.0
O C:ALA295 4.8 7.2 1.0
CA C:ALA295 4.9 1.6 1.0
CA C:ALA293 4.9 0.0 1.0

Calcium binding site 8 out of 12 in 8br2

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Calcium binding site 8 out of 12 in the Cryoem Structure of the Post-Synaptic RAD51 Nucleoprotein Filament in the Presence of Atp and CA2+


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 the Post-Synaptic RAD51 Nucleoprotein Filament in the Presence of Atp and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca401

b:1.5
occ:1.00
 OG1 D:THR134 2.1 16.9 1.0
O2G D:ATP402 2.2 30.6 1.0
O2B D:ATP402 2.3 25.9 1.0
OE1 D:GLU163 3.0 20.7 1.0
CB D:THR134 3.4 12.3 1.0
PG D:ATP402 3.5 14.1 1.0
PB D:ATP402 3.6 3.0 1.0
O3B D:ATP402 3.7 20.2 1.0
OG1 D:THR165 3.7 12.3 1.0
CD D:GLU163 4.0 20.9 1.0
CG2 D:THR134 4.1 9.6 1.0
O1A D:ATP402 4.1 28.3 1.0
OE2 D:GLU163 4.2 23.7 1.0
O3A D:ATP402 4.2 16.1 1.0
OD1 D:ASP222 4.3 21.8 1.0
OD2 D:ASP222 4.3 11.2 1.0
CB D:THR165 4.4 10.3 1.0
O1G D:ATP402 4.4 15.8 1.0
O3G D:ATP402 4.5 27.9 1.0
N D:THR134 4.5 7.2 1.0
CA D:THR134 4.5 6.3 1.0
O C:HOH507 4.5 21.7 1.0
CG2 D:THR165 4.5 11.9 1.0
PA D:ATP402 4.7 8.4 1.0
O1B D:ATP402 4.7 11.2 1.0
CG D:ASP222 4.7 20.2 1.0
O C:HOH511 4.9 17.8 1.0

Calcium binding site 9 out of 12 in 8br2

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Calcium binding site 9 out of 12 in the Cryoem Structure of the Post-Synaptic RAD51 Nucleoprotein Filament in the Presence of Atp and CA2+


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 the Post-Synaptic RAD51 Nucleoprotein Filament in the Presence of Atp and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca403

b:19.4
occ:1.00
 O3G E:ATP402 2.2 27.9 1.0
O D:SER296 2.2 13.7 1.0
O D:ALA293 2.4 12.7 1.0
OD2 D:ASP316 2.8 17.5 1.0
O D:HIS294 2.9 15.4 1.0
C D:HIS294 3.3 4.0 1.0
C D:SER296 3.4 6.5 1.0
C D:ALA293 3.6 8.4 1.0
PG E:ATP402 3.6 14.1 1.0
CA D:HIS294 3.6 0.3 1.0
O D:HOH508 3.6 21.7 1.0
O D:HOH512 3.8 17.8 1.0
CG D:ASP316 3.9 19.7 1.0
N D:SER296 4.0 7.4 1.0
O2G E:ATP402 4.0 30.6 1.0
N D:HIS294 4.1 9.6 1.0
CA D:SER296 4.2 4.4 1.0
N D:ALA295 4.2 5.9 1.0
N D:THR297 4.3 4.1 1.0
C D:ALA295 4.4 2.6 1.0
O1G E:ATP402 4.4 15.8 1.0
CA D:THR297 4.5 6.2 1.0
OD1 D:ASP316 4.5 19.7 1.0
CB E:PHE129 4.5 3.8 1.0
O D:THR297 4.6 8.5 1.0
O3B E:ATP402 4.6 20.2 1.0
CB D:SER296 4.6 4.1 1.0
C D:THR297 4.7 9.5 1.0
CA D:ALA293 4.8 0.0 1.0
O D:ALA295 4.8 7.2 1.0
CA D:ALA295 4.9 1.6 1.0
CB D:HIS294 5.0 3.1 1.0

Calcium binding site 10 out of 12 in 8br2

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Calcium binding site 10 out of 12 in the Cryoem Structure of the Post-Synaptic RAD51 Nucleoprotein Filament in the Presence of Atp and CA2+


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 the Post-Synaptic RAD51 Nucleoprotein Filament in the Presence of Atp and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca401

b:1.5
occ:1.00
 OG1 E:THR134 2.1 16.9 1.0
O2G E:ATP402 2.2 30.6 1.0
O2B E:ATP402 2.3 25.9 1.0
OE1 E:GLU163 3.0 20.7 1.0
CB E:THR134 3.4 12.3 1.0
PG E:ATP402 3.5 14.1 1.0
PB E:ATP402 3.6 3.0 1.0
O3B E:ATP402 3.7 20.2 1.0
OG1 E:THR165 3.7 12.3 1.0
CD E:GLU163 4.0 20.9 1.0
CG2 E:THR134 4.1 9.6 1.0
O1A E:ATP402 4.1 28.3 1.0
OE2 E:GLU163 4.2 23.7 1.0
O3A E:ATP402 4.2 16.1 1.0
OD1 E:ASP222 4.3 21.8 1.0
OD2 E:ASP222 4.3 11.2 1.0
CB E:THR165 4.4 10.3 1.0
O1G E:ATP402 4.4 15.8 1.0
O3G E:ATP402 4.5 27.9 1.0
N E:THR134 4.5 7.2 1.0
CA E:THR134 4.5 6.3 1.0
CG2 E:THR165 4.5 11.9 1.0
O D:HOH508 4.6 21.7 1.0
PA E:ATP402 4.7 8.4 1.0
O1B E:ATP402 4.7 11.2 1.0
CG E:ASP222 4.7 20.2 1.0
O D:HOH512 4.9 17.8 1.0

Reference:

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
Page generated: Wed Jul 26 13:01:29 2023

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