Calcium in PDB 8rcd: RAD51 Nucleoprotein Filament on Abasic Single-Stranded Dna

Calcium Binding Sites:

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>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Calcium atom in the RAD51 Nucleoprotein Filament on Abasic Single-Stranded Dna (pdb code 8rcd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the RAD51 Nucleoprotein Filament on Abasic Single-Stranded Dna, PDB code: 8rcd:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 16 in 8rcd

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Calcium binding site 1 out of 16 in the RAD51 Nucleoprotein Filament on Abasic Single-Stranded Dna


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of RAD51 Nucleoprotein Filament on Abasic Single-Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:48.4
occ:1.00
O2B A:ATP401 2.2 55.1 1.0
OG1 A:THR134 2.3 54.5 1.0
O2G A:ATP401 2.3 63.1 1.0
OE1 A:GLU163 2.9 70.2 1.0
CB A:THR134 3.4 47.0 1.0
PB A:ATP401 3.5 49.8 1.0
PG A:ATP401 3.6 58.8 1.0
O3B A:ATP401 3.7 52.1 1.0
OG1 A:THR165 3.8 65.1 1.0
CD A:GLU163 3.9 70.0 1.0
OD2 A:ASP222 4.2 59.2 1.0
OE2 A:GLU163 4.2 68.4 1.0
CG2 A:THR134 4.2 47.1 1.0
O1A A:ATP401 4.3 53.1 1.0
CB A:THR165 4.3 59.9 1.0
O3A A:ATP401 4.3 48.7 1.0
CG2 A:THR165 4.3 56.1 1.0
OD1 A:ASP222 4.4 60.7 1.0
CA A:THR134 4.5 43.4 1.0
N A:THR134 4.5 43.5 1.0
O1G A:ATP401 4.5 49.2 1.0
O3G A:ATP401 4.6 59.2 1.0
O1B A:ATP401 4.6 47.7 1.0
PA A:ATP401 4.7 51.7 1.0
CG A:ASP222 4.7 57.0 1.0
O2A A:ATP401 4.8 54.4 1.0

Calcium binding site 2 out of 16 in 8rcd

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Calcium binding site 2 out of 16 in the RAD51 Nucleoprotein Filament on Abasic Single-Stranded Dna


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of RAD51 Nucleoprotein Filament on Abasic Single-Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:50.7
occ:1.00
O3G A:ATP401 2.1 59.2 1.0
PG A:ATP401 3.5 58.8 1.0
O2G A:ATP401 3.9 63.1 1.0
O1G A:ATP401 4.4 49.2 1.0
CB A:PHE129 4.4 41.5 1.0
O3B A:ATP401 4.5 52.1 1.0
CD2 A:PHE129 4.8 39.8 1.0

Calcium binding site 3 out of 16 in 8rcd

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Calcium binding site 3 out of 16 in the RAD51 Nucleoprotein Filament on Abasic Single-Stranded Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of RAD51 Nucleoprotein Filament on Abasic Single-Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:50.7
occ:1.00
O3G B:ATP400 2.1 59.2 1.0
O A:SER296 2.2 39.1 1.0
O A:ALA293 2.4 34.6 1.0
OD2 A:ASP316 2.6 51.0 1.0
O A:HIS294 3.1 37.4 1.0
C A:SER296 3.4 42.0 1.0
PG B:ATP400 3.5 58.8 1.0
C A:ALA293 3.6 32.0 1.0
C A:HIS294 3.6 30.5 1.0
CG A:ASP316 3.8 48.7 1.0
CA A:HIS294 3.8 26.5 1.0
O2G B:ATP400 3.9 63.1 1.0
N A:SER296 4.2 34.9 1.0
N A:HIS294 4.2 28.1 1.0
CA A:SER296 4.3 38.3 1.0
N A:THR297 4.4 40.8 1.0
OD1 A:ASP316 4.4 51.1 1.0
O1G B:ATP400 4.4 49.2 1.0
CB B:PHE129 4.4 41.5 1.0
CA A:THR297 4.4 42.8 1.0
O3B B:ATP400 4.5 52.1 1.0
N A:ALA295 4.6 28.8 1.0
CB A:SER296 4.6 37.4 1.0
C A:ALA295 4.7 33.0 1.0
CA A:ALA293 4.8 29.4 1.0
CD2 B:PHE129 4.8 39.8 1.0
C A:THR297 4.8 44.3 1.0
O A:THR297 4.9 46.2 1.0
CB A:ASP316 4.9 40.5 1.0

Calcium binding site 4 out of 16 in 8rcd

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Calcium binding site 4 out of 16 in the RAD51 Nucleoprotein Filament on Abasic Single-Stranded Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of RAD51 Nucleoprotein Filament on Abasic Single-Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:48.4
occ:1.00
O2B B:ATP400 2.2 55.1 1.0
OG1 B:THR134 2.3 54.5 1.0
O2G B:ATP400 2.3 63.1 1.0
OE1 B:GLU163 2.9 70.2 1.0
CB B:THR134 3.4 47.0 1.0
PB B:ATP400 3.5 49.8 1.0
PG B:ATP400 3.6 58.8 1.0
O3B B:ATP400 3.7 52.1 1.0
OG1 B:THR165 3.8 65.1 1.0
CD B:GLU163 3.9 70.0 1.0
OD2 B:ASP222 4.2 59.2 1.0
OE2 B:GLU163 4.2 68.4 1.0
CG2 B:THR134 4.2 47.1 1.0
O1A B:ATP400 4.3 53.1 1.0
CB B:THR165 4.3 59.9 1.0
O3A B:ATP400 4.3 48.7 1.0
CG2 B:THR165 4.3 56.1 1.0
OD1 B:ASP222 4.4 60.7 1.0
CA B:THR134 4.5 43.4 1.0
N B:THR134 4.5 43.5 1.0
O1G B:ATP400 4.5 49.2 1.0
O3G B:ATP400 4.6 59.2 1.0
O1B B:ATP400 4.6 47.7 1.0
PA B:ATP400 4.7 51.7 1.0
CG B:ASP222 4.7 57.0 1.0
O2A B:ATP400 4.8 54.4 1.0

Calcium binding site 5 out of 16 in 8rcd

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Calcium binding site 5 out of 16 in the RAD51 Nucleoprotein Filament on Abasic Single-Stranded Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of RAD51 Nucleoprotein Filament on Abasic Single-Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:50.7
occ:1.00
O B:SER296 2.1 39.1 1.0
O3G C:ATP400 2.1 59.2 1.0
O B:ALA293 2.4 34.6 1.0
OD2 B:ASP316 2.6 51.0 1.0
O B:HIS294 3.2 37.4 1.0
C B:SER296 3.3 42.0 1.0
PG C:ATP400 3.5 58.8 1.0
C B:ALA293 3.6 32.0 1.0
C B:HIS294 3.7 30.5 1.0
CG B:ASP316 3.8 48.7 1.0
CA B:HIS294 3.9 26.5 1.0
O2G C:ATP400 3.9 63.1 1.0
N B:SER296 4.1 34.9 1.0
CA B:SER296 4.1 38.3 1.0
N B:THR297 4.2 40.8 1.0
N B:HIS294 4.2 28.1 1.0
CA B:THR297 4.3 42.8 1.0
OD1 B:ASP316 4.4 51.1 1.0
O1G C:ATP400 4.4 49.2 1.0
CB C:PHE129 4.4 41.5 1.0
O3B C:ATP400 4.5 52.1 1.0
CB B:SER296 4.5 37.4 1.0
N B:ALA295 4.6 28.8 1.0
C B:ALA295 4.6 33.0 1.0
C B:THR297 4.7 44.3 1.0
CA B:ALA293 4.8 29.4 1.0
O B:THR297 4.8 46.2 1.0
CD2 C:PHE129 4.8 39.8 1.0
CB B:ASP316 4.9 40.5 1.0

Calcium binding site 6 out of 16 in 8rcd

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Calcium binding site 6 out of 16 in the RAD51 Nucleoprotein Filament on Abasic Single-Stranded Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of RAD51 Nucleoprotein Filament on Abasic Single-Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:48.4
occ:1.00
O2B C:ATP400 2.2 55.1 1.0
OG1 C:THR134 2.3 54.5 1.0
O2G C:ATP400 2.3 63.1 1.0
OE1 C:GLU163 2.9 70.2 1.0
CB C:THR134 3.4 47.0 1.0
PB C:ATP400 3.5 49.8 1.0
PG C:ATP400 3.6 58.8 1.0
O3B C:ATP400 3.7 52.1 1.0
OG1 C:THR165 3.8 65.1 1.0
CD C:GLU163 3.9 70.0 1.0
OD2 C:ASP222 4.2 59.2 1.0
OE2 C:GLU163 4.2 68.4 1.0
CG2 C:THR134 4.2 47.1 1.0
O1A C:ATP400 4.3 53.1 1.0
CB C:THR165 4.3 59.9 1.0
O3A C:ATP400 4.3 48.7 1.0
CG2 C:THR165 4.3 56.1 1.0
OD1 C:ASP222 4.4 60.7 1.0
CA C:THR134 4.5 43.4 1.0
O1G C:ATP400 4.5 49.2 1.0
N C:THR134 4.5 43.5 1.0
O3G C:ATP400 4.6 59.2 1.0
O1B C:ATP400 4.6 47.7 1.0
PA C:ATP400 4.7 51.7 1.0
CG C:ASP222 4.7 57.0 1.0
O2A C:ATP400 4.8 54.4 1.0

Calcium binding site 7 out of 16 in 8rcd

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Calcium binding site 7 out of 16 in the RAD51 Nucleoprotein Filament on Abasic Single-Stranded Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of RAD51 Nucleoprotein Filament on Abasic Single-Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:50.7
occ:1.00
O3G D:ATP400 2.1 59.2 1.0
O C:SER296 2.2 39.1 1.0
O C:ALA293 2.4 34.6 1.0
OD2 C:ASP316 2.4 51.0 1.0
O C:HIS294 3.3 37.4 1.0
C C:SER296 3.5 42.0 1.0
PG D:ATP400 3.5 58.8 1.0
C C:ALA293 3.6 32.0 1.0
CG C:ASP316 3.6 48.7 1.0
C C:HIS294 3.8 30.5 1.0
CA C:HIS294 3.9 26.5 1.0
O2G D:ATP400 3.9 63.1 1.0
OD1 C:ASP316 4.2 51.1 1.0
N C:HIS294 4.2 28.1 1.0
N C:SER296 4.2 34.9 1.0
CA C:SER296 4.3 38.3 1.0
O1G D:ATP400 4.4 49.2 1.0
CB D:PHE129 4.4 41.5 1.0
N C:THR297 4.4 40.8 1.0
O3B D:ATP400 4.5 52.1 1.0
CA C:THR297 4.5 42.8 1.0
CB C:SER296 4.6 37.4 1.0
N C:ALA295 4.7 28.8 1.0
CB C:ASP316 4.7 40.5 1.0
CA C:ALA293 4.7 29.4 1.0
C C:ALA295 4.8 33.0 1.0
CD2 D:PHE129 4.8 39.8 1.0
C C:THR297 4.8 44.3 1.0
O C:THR297 4.9 46.2 1.0

Calcium binding site 8 out of 16 in 8rcd

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Calcium binding site 8 out of 16 in the RAD51 Nucleoprotein Filament on Abasic Single-Stranded Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of RAD51 Nucleoprotein Filament on Abasic Single-Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca401

b:48.4
occ:1.00
O2B D:ATP400 2.2 55.1 1.0
OG1 D:THR134 2.3 54.5 1.0
O2G D:ATP400 2.3 63.1 1.0
OE1 D:GLU163 2.9 70.2 1.0
CB D:THR134 3.4 47.0 1.0
PB D:ATP400 3.5 49.8 1.0
PG D:ATP400 3.6 58.8 1.0
O3B D:ATP400 3.7 52.1 1.0
OG1 D:THR165 3.8 65.1 1.0
CD D:GLU163 3.9 70.0 1.0
OD2 D:ASP222 4.2 59.2 1.0
OE2 D:GLU163 4.2 68.4 1.0
CG2 D:THR134 4.2 47.1 1.0
O1A D:ATP400 4.3 53.1 1.0
CB D:THR165 4.3 59.9 1.0
O3A D:ATP400 4.3 48.7 1.0
CG2 D:THR165 4.3 56.1 1.0
OD1 D:ASP222 4.4 60.7 1.0
CA D:THR134 4.5 43.4 1.0
O1G D:ATP400 4.5 49.2 1.0
N D:THR134 4.5 43.5 1.0
O3G D:ATP400 4.6 59.2 1.0
O1B D:ATP400 4.6 47.7 1.0
PA D:ATP400 4.7 51.7 1.0
CG D:ASP222 4.7 57.0 1.0
O2A D:ATP400 4.8 54.4 1.0

Calcium binding site 9 out of 16 in 8rcd

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Calcium binding site 9 out of 16 in the RAD51 Nucleoprotein Filament on Abasic Single-Stranded Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of RAD51 Nucleoprotein Filament on Abasic Single-Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca402

b:50.7
occ:1.00
O D:SER296 2.1 39.1 1.0
O3G E:ATP400 2.1 59.2 1.0
O D:ALA293 2.5 34.6 1.0
OD2 D:ASP316 2.6 51.0 1.0
O D:HIS294 3.1 37.4 1.0
C D:SER296 3.3 42.0 1.0
PG E:ATP400 3.5 58.8 1.0
C D:HIS294 3.6 30.5 1.0
C D:ALA293 3.7 32.0 1.0
CG D:ASP316 3.8 48.7 1.0
CA D:HIS294 3.9 26.5 1.0
O2G E:ATP400 3.9 63.1 1.0
N D:SER296 4.1 34.9 1.0
CA D:SER296 4.2 38.3 1.0
N D:HIS294 4.3 28.1 1.0
N D:THR297 4.3 40.8 1.0
CA D:THR297 4.4 42.8 1.0
OD1 D:ASP316 4.4 51.1 1.0
O1G E:ATP400 4.4 49.2 1.0
CB E:PHE129 4.4 41.5 1.0
O3B E:ATP400 4.5 52.1 1.0
N D:ALA295 4.6 28.8 1.0
CB D:SER296 4.6 37.4 1.0
C D:ALA295 4.6 33.0 1.0
C D:THR297 4.8 44.3 1.0
CD2 E:PHE129 4.8 39.8 1.0
O D:THR297 4.8 46.2 1.0
CA D:ALA293 4.9 29.4 1.0
CB D:ASP316 5.0 40.5 1.0

Calcium binding site 10 out of 16 in 8rcd

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Calcium binding site 10 out of 16 in the RAD51 Nucleoprotein Filament on Abasic Single-Stranded Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of RAD51 Nucleoprotein Filament on Abasic Single-Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca401

b:48.4
occ:1.00
O2B E:ATP400 2.2 55.1 1.0
OG1 E:THR134 2.3 54.5 1.0
O2G E:ATP400 2.3 63.1 1.0
OE1 E:GLU163 2.9 70.2 1.0
CB E:THR134 3.4 47.0 1.0
PB E:ATP400 3.5 49.8 1.0
PG E:ATP400 3.6 58.8 1.0
O3B E:ATP400 3.7 52.1 1.0
OG1 E:THR165 3.8 65.1 1.0
CD E:GLU163 3.9 70.0 1.0
OD2 E:ASP222 4.2 59.2 1.0
OE2 E:GLU163 4.2 68.4 1.0
CG2 E:THR134 4.2 47.1 1.0
O1A E:ATP400 4.3 53.1 1.0
CB E:THR165 4.3 59.9 1.0
O3A E:ATP400 4.3 48.7 1.0
CG2 E:THR165 4.3 56.1 1.0
OD1 E:ASP222 4.4 60.7 1.0
CA E:THR134 4.5 43.4 1.0
O1G E:ATP400 4.5 49.2 1.0
N E:THR134 4.5 43.5 1.0
O3G E:ATP400 4.6 59.2 1.0
O1B E:ATP400 4.6 47.7 1.0
PA E:ATP400 4.7 51.7 1.0
CG E:ASP222 4.7 57.0 1.0
O2A E:ATP400 4.8 54.4 1.0

Reference:

R.Appleby, L.Pellegrini. Cryoem Structure of RAD51 Nucleoprotein Filament on Abasic Single-Stranded Dna To Be Published.
Page generated: Sat Sep 28 09:02:57 2024

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