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Calcium in PDB 8pbc: RAD51 Filament on Ssdna Bound By the BRCA2 C-Terminus

Calcium Binding Sites:

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Calcium atom in the RAD51 Filament on Ssdna Bound By the BRCA2 C-Terminus (pdb code 8pbc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 22 binding sites of Calcium where determined in the RAD51 Filament on Ssdna Bound By the BRCA2 C-Terminus, PDB code: 8pbc:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 22 in 8pbc

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Calcium binding site 1 out of 22 in the RAD51 Filament on Ssdna Bound By the BRCA2 C-Terminus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of RAD51 Filament on Ssdna Bound By the BRCA2 C-Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:18.4
occ:1.00
 OG1 A:THR134 2.1 21.2 1.0
O2G A:ATP401 2.2 19.2 1.0
O2B A:ATP401 2.2 16.2 1.0
OE1 A:GLU163 3.4 37.5 1.0
CB A:THR134 3.5 13.5 1.0
PG A:ATP401 3.5 6.4 1.0
PB A:ATP401 3.5 7.9 1.0
O3B A:ATP401 3.6 8.4 1.0
OG1 A:THR165 3.7 24.2 1.0
CD A:GLU163 4.0 38.1 1.0
OE2 A:GLU163 4.1 35.7 1.0
O3A A:ATP401 4.1 9.9 1.0
CG2 A:THR134 4.1 14.7 1.0
OD2 A:ASP222 4.3 15.3 1.0
O1G A:ATP401 4.4 8.0 1.0
N A:THR134 4.5 9.7 1.0
O3G A:ATP401 4.5 14.1 1.0
CB A:THR165 4.5 22.1 1.0
CA A:THR134 4.5 9.9 1.0
O1A A:ATP401 4.5 14.1 1.0
OD1 A:ASP222 4.6 21.6 1.0
O1B A:ATP401 4.7 6.3 1.0
PA A:ATP401 4.8 13.0 1.0
CG2 A:THR165 4.8 17.0 1.0
CG A:ASP222 4.8 18.3 1.0

Calcium binding site 2 out of 22 in 8pbc

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Calcium binding site 2 out of 22 in the RAD51 Filament on Ssdna Bound By the BRCA2 C-Terminus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of RAD51 Filament on Ssdna Bound By the BRCA2 C-Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:14.8
occ:1.00
 O3G A:ATP401 2.2 14.1 1.0
PG A:ATP401 3.6 6.4 1.0
O2G A:ATP401 4.0 19.2 1.0
O1G A:ATP401 4.4 8.0 1.0
CB A:PHE129 4.5 4.4 1.0
O3B A:ATP401 4.6 8.4 1.0

Calcium binding site 3 out of 22 in 8pbc

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Calcium binding site 3 out of 22 in the RAD51 Filament on Ssdna Bound By the BRCA2 C-Terminus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of RAD51 Filament on Ssdna Bound By the BRCA2 C-Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:14.8
occ:1.00
 O3G B:ATP400 2.2 14.1 1.0
O A:ALA293 2.3 3.6 1.0
O A:SER296 2.4 7.1 1.0
OD1 A:ASP316 3.1 10.8 1.0
O A:HIS294 3.2 5.1 1.0
C A:HIS294 3.4 2.3 1.0
C A:ALA293 3.5 2.8 1.0
C A:SER296 3.5 6.2 1.0
PG B:ATP400 3.6 6.4 1.0
CA A:HIS294 3.6 1.2 1.0
CG A:ASP316 4.0 11.4 1.0
N A:HIS294 4.0 2.3 1.0
O2G B:ATP400 4.0 19.2 1.0
N A:SER296 4.1 3.7 1.0
N A:ALA295 4.2 2.6 1.0
OD2 A:ASP316 4.3 10.3 1.0
CA A:SER296 4.4 5.5 1.0
N A:THR297 4.4 6.0 1.0
O1G B:ATP400 4.4 8.0 1.0
CA A:THR297 4.4 8.6 1.0
C A:ALA295 4.5 2.5 1.0
CB B:PHE129 4.5 4.4 1.0
O3B B:ATP400 4.6 8.4 1.0
CA A:ALA293 4.7 1.8 1.0
O A:THR297 4.8 8.4 1.0
OG A:SER296 4.9 7.2 1.0
C A:THR297 4.9 9.7 1.0
CA A:ALA295 4.9 1.8 1.0
O A:ALA295 4.9 4.2 1.0

Calcium binding site 4 out of 22 in 8pbc

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Calcium binding site 4 out of 22 in the RAD51 Filament on Ssdna Bound By the BRCA2 C-Terminus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of RAD51 Filament on Ssdna Bound By the BRCA2 C-Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:18.4
occ:1.00
 OG1 B:THR134 2.1 21.2 1.0
O2G B:ATP400 2.2 19.2 1.0
O2B B:ATP400 2.2 16.2 1.0
OE1 B:GLU163 3.4 37.5 1.0
CB B:THR134 3.5 13.5 1.0
PG B:ATP400 3.5 6.4 1.0
PB B:ATP400 3.5 7.9 1.0
O3B B:ATP400 3.6 8.4 1.0
OG1 B:THR165 3.7 24.2 1.0
CD B:GLU163 4.0 38.1 1.0
OE2 B:GLU163 4.1 35.7 1.0
O3A B:ATP400 4.1 9.9 1.0
CG2 B:THR134 4.1 14.7 1.0
OD2 B:ASP222 4.3 15.3 1.0
O1G B:ATP400 4.4 8.0 1.0
N B:THR134 4.5 9.7 1.0
O3G B:ATP400 4.5 14.1 1.0
CB B:THR165 4.5 22.1 1.0
CA B:THR134 4.5 9.9 1.0
O1A B:ATP400 4.5 14.1 1.0
OD1 B:ASP222 4.6 21.6 1.0
O1B B:ATP400 4.7 6.3 1.0
PA B:ATP400 4.8 13.0 1.0
CG2 B:THR165 4.8 17.0 1.0
CG B:ASP222 4.8 18.3 1.0

Calcium binding site 5 out of 22 in 8pbc

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Calcium binding site 5 out of 22 in the RAD51 Filament on Ssdna Bound By the BRCA2 C-Terminus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of RAD51 Filament on Ssdna Bound By the BRCA2 C-Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:14.8
occ:1.00
 O B:SER296 2.1 7.1 1.0
O3G C:ATP400 2.2 14.1 1.0
O B:ALA293 2.3 3.6 1.0
OD1 B:ASP316 3.0 10.8 1.0
O B:HIS294 3.3 5.1 1.0
C B:SER296 3.3 6.2 1.0
C B:ALA293 3.4 2.8 1.0
C B:HIS294 3.5 2.3 1.0
PG C:ATP400 3.6 6.4 1.0
CA B:HIS294 3.7 1.2 1.0
CG B:ASP316 3.9 11.4 1.0
N B:SER296 3.9 3.7 1.0
O2G C:ATP400 4.0 19.2 1.0
N B:HIS294 4.0 2.3 1.0
CA B:SER296 4.2 5.5 1.0
N B:ALA295 4.2 2.6 1.0
N B:THR297 4.2 6.0 1.0
CA B:THR297 4.3 8.6 1.0
OD2 B:ASP316 4.3 10.3 1.0
C B:ALA295 4.4 2.5 1.0
O1G C:ATP400 4.4 8.0 1.0
CB C:PHE129 4.5 4.4 1.0
O3B C:ATP400 4.6 8.4 1.0
OG B:SER296 4.6 7.2 1.0
CA B:ALA293 4.6 1.8 1.0
O B:THR297 4.7 8.4 1.0
C B:THR297 4.7 9.7 1.0
CB B:SER296 4.8 6.7 1.0
O B:ALA295 4.8 4.2 1.0
CA B:ALA295 4.9 1.8 1.0

Calcium binding site 6 out of 22 in 8pbc

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Calcium binding site 6 out of 22 in the RAD51 Filament on Ssdna Bound By the BRCA2 C-Terminus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of RAD51 Filament on Ssdna Bound By the BRCA2 C-Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:18.4
occ:1.00
 OG1 C:THR134 2.1 21.2 1.0
O2G C:ATP400 2.2 19.2 1.0
O2B C:ATP400 2.2 16.2 1.0
OE1 C:GLU163 3.4 37.5 1.0
CB C:THR134 3.5 13.5 1.0
PG C:ATP400 3.5 6.4 1.0
PB C:ATP400 3.5 7.9 1.0
O3B C:ATP400 3.6 8.4 1.0
OG1 C:THR165 3.7 24.2 1.0
CD C:GLU163 4.0 38.1 1.0
OE2 C:GLU163 4.1 35.7 1.0
O3A C:ATP400 4.1 9.9 1.0
CG2 C:THR134 4.1 14.7 1.0
OD2 C:ASP222 4.3 15.3 1.0
O1G C:ATP400 4.4 8.0 1.0
N C:THR134 4.5 9.7 1.0
O3G C:ATP400 4.5 14.1 1.0
CB C:THR165 4.5 22.1 1.0
CA C:THR134 4.5 9.9 1.0
O1A C:ATP400 4.5 14.1 1.0
OD1 C:ASP222 4.6 21.6 1.0
O1B C:ATP400 4.7 6.3 1.0
PA C:ATP400 4.8 13.0 1.0
CG2 C:THR165 4.8 17.0 1.0
CG C:ASP222 4.8 18.3 1.0

Calcium binding site 7 out of 22 in 8pbc

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Calcium binding site 7 out of 22 in the RAD51 Filament on Ssdna Bound By the BRCA2 C-Terminus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of RAD51 Filament on Ssdna Bound By the BRCA2 C-Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:14.8
occ:1.00
 O3G D:ATP400 2.2 14.1 1.0
O C:SER296 2.2 7.1 1.0
O C:ALA293 2.2 3.6 1.0
OD1 C:ASP316 3.0 10.8 1.0
O C:HIS294 3.3 5.1 1.0
C C:SER296 3.4 6.2 1.0
C C:ALA293 3.4 2.8 1.0
C C:HIS294 3.5 2.3 1.0
PG D:ATP400 3.6 6.4 1.0
CA C:HIS294 3.7 1.2 1.0
CG C:ASP316 3.9 11.4 1.0
N C:SER296 4.0 3.7 1.0
N C:HIS294 4.0 2.3 1.0
O2G D:ATP400 4.0 19.2 1.0
N C:ALA295 4.2 2.6 1.0
CA C:SER296 4.2 5.5 1.0
OD2 C:ASP316 4.3 10.3 1.0
N C:THR297 4.3 6.0 1.0
CA C:THR297 4.4 8.6 1.0
O1G D:ATP400 4.4 8.0 1.0
C C:ALA295 4.4 2.5 1.0
CB D:PHE129 4.5 4.4 1.0
O3B D:ATP400 4.6 8.4 1.0
CA C:ALA293 4.6 1.8 1.0
OG C:SER296 4.7 7.2 1.0
O C:THR297 4.7 8.4 1.0
C C:THR297 4.8 9.7 1.0
CB C:SER296 4.8 6.7 1.0
CA C:ALA295 4.9 1.8 1.0
O C:ALA295 4.9 4.2 1.0

Calcium binding site 8 out of 22 in 8pbc

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Calcium binding site 8 out of 22 in the RAD51 Filament on Ssdna Bound By the BRCA2 C-Terminus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of RAD51 Filament on Ssdna Bound By the BRCA2 C-Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca401

b:18.4
occ:1.00
 OG1 D:THR134 2.1 21.2 1.0
O2G D:ATP400 2.2 19.2 1.0
O2B D:ATP400 2.2 16.2 1.0
OE1 D:GLU163 3.4 37.5 1.0
CB D:THR134 3.5 13.5 1.0
PG D:ATP400 3.5 6.4 1.0
PB D:ATP400 3.5 7.9 1.0
O3B D:ATP400 3.6 8.4 1.0
OG1 D:THR165 3.7 24.2 1.0
CD D:GLU163 4.0 38.1 1.0
OE2 D:GLU163 4.1 35.7 1.0
O3A D:ATP400 4.1 9.9 1.0
CG2 D:THR134 4.1 14.7 1.0
OD2 D:ASP222 4.3 15.3 1.0
O1G D:ATP400 4.4 8.0 1.0
N D:THR134 4.5 9.7 1.0
O3G D:ATP400 4.5 14.1 1.0
CB D:THR165 4.5 22.1 1.0
CA D:THR134 4.5 9.9 1.0
O1A D:ATP400 4.5 14.1 1.0
OD1 D:ASP222 4.6 21.6 1.0
O1B D:ATP400 4.7 6.3 1.0
PA D:ATP400 4.8 13.0 1.0
CG2 D:THR165 4.8 17.0 1.0
CG D:ASP222 4.8 18.3 1.0

Calcium binding site 9 out of 22 in 8pbc

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Calcium binding site 9 out of 22 in the RAD51 Filament on Ssdna Bound By the BRCA2 C-Terminus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of RAD51 Filament on Ssdna Bound By the BRCA2 C-Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca402

b:14.8
occ:1.00
 O3G E:ATP400 2.2 14.1 1.0
O D:ALA293 2.2 3.6 1.0
O D:SER296 2.3 7.1 1.0
OD1 D:ASP316 3.0 10.8 1.0
O D:HIS294 3.3 5.1 1.0
C D:ALA293 3.4 2.8 1.0
C D:SER296 3.4 6.2 1.0
C D:HIS294 3.5 2.3 1.0
PG E:ATP400 3.6 6.4 1.0
CA D:HIS294 3.7 1.2 1.0
CG D:ASP316 3.9 11.4 1.0
N D:HIS294 4.0 2.3 1.0
N D:SER296 4.0 3.7 1.0
O2G E:ATP400 4.0 19.2 1.0
N D:ALA295 4.3 2.6 1.0
OD2 D:ASP316 4.3 10.3 1.0
CA D:SER296 4.3 5.5 1.0
N D:THR297 4.3 6.0 1.0
CA D:THR297 4.4 8.6 1.0
O1G E:ATP400 4.4 8.0 1.0
C D:ALA295 4.5 2.5 1.0
CB E:PHE129 4.5 4.4 1.0
O3B E:ATP400 4.6 8.4 1.0
CA D:ALA293 4.6 1.8 1.0
OG D:SER296 4.7 7.2 1.0
O D:THR297 4.8 8.4 1.0
C D:THR297 4.8 9.7 1.0
CB D:SER296 4.9 6.7 1.0
CA D:ALA295 4.9 1.8 1.0
O D:ALA295 5.0 4.2 1.0
CB D:ASP316 5.0 7.0 1.0

Calcium binding site 10 out of 22 in 8pbc

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Calcium binding site 10 out of 22 in the RAD51 Filament on Ssdna Bound By the BRCA2 C-Terminus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of RAD51 Filament on Ssdna Bound By the BRCA2 C-Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca401

b:18.4
occ:1.00
 OG1 E:THR134 2.1 21.2 1.0
O2G E:ATP400 2.2 19.2 1.0
O2B E:ATP400 2.2 16.2 1.0
OE1 E:GLU163 3.4 37.5 1.0
CB E:THR134 3.5 13.5 1.0
PG E:ATP400 3.5 6.4 1.0
PB E:ATP400 3.5 7.9 1.0
O3B E:ATP400 3.6 8.4 1.0
OG1 E:THR165 3.7 24.2 1.0
CD E:GLU163 4.0 38.1 1.0
OE2 E:GLU163 4.1 35.7 1.0
O3A E:ATP400 4.1 9.9 1.0
CG2 E:THR134 4.1 14.7 1.0
OD2 E:ASP222 4.3 15.3 1.0
O1G E:ATP400 4.4 8.0 1.0
N E:THR134 4.5 9.7 1.0
O3G E:ATP400 4.5 14.1 1.0
CB E:THR165 4.5 22.1 1.0
CA E:THR134 4.5 9.9 1.0
O1A E:ATP400 4.5 14.1 1.0
OD1 E:ASP222 4.6 21.6 1.0
O1B E:ATP400 4.7 6.3 1.0
PA E:ATP400 4.8 13.0 1.0
CG2 E:THR165 4.8 17.0 1.0
CG E:ASP222 4.8 18.3 1.0

Reference:

R.Appleby, L.Joudeh, K.Cobbett, L.Pellegrini. Structural Basis For Stabilisation of the RAD51 Nucleoprotein Filament By BRCA2. Nat Commun V. 14 7003 2023.
ISSN: ESSN 2041-1723
PubMed: 37919288
DOI: 10.1038/S41467-023-42830-1
Page generated: Fri Jul 19 11:10:10 2024

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