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Magnesium in PDB 9e6l: Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to RAD54PEPTIDE

Enzymatic activity of Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to RAD54PEPTIDE

All present enzymatic activity of Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to RAD54PEPTIDE:
3.6.4.12;

Magnesium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to RAD54PEPTIDE (pdb code 9e6l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to RAD54PEPTIDE, PDB code: 9e6l:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 9e6l

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Magnesium binding site 1 out of 12 in the Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to RAD54PEPTIDE


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to RAD54PEPTIDE within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:50.0
occ:1.00
 OD2 C:ASP374 2.1 114.1 1.0
O2G B:ATP501 2.2 119.2 1.0
CG C:ASP374 3.1 114.1 1.0
O C:SER354 3.4 108.0 1.0
OD1 C:ASP374 3.5 114.1 1.0
O C:THR355 3.6 101.8 1.0
PG B:ATP501 3.7 119.2 1.0
C C:THR355 4.3 101.8 1.0
O3B B:ATP501 4.3 119.2 1.0
CB C:ASP374 4.4 114.1 1.0
O1G B:ATP501 4.5 119.2 1.0
O3G B:ATP501 4.5 119.2 1.0
CA C:THR355 4.5 101.8 1.0
C C:SER354 4.6 108.0 1.0
O C:ALA351 4.7 109.2 1.0
O C:HIS352 4.7 107.2 1.0

Magnesium binding site 2 out of 12 in 9e6l

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Magnesium binding site 2 out of 12 in the Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to RAD54PEPTIDE


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to RAD54PEPTIDE within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg503

b:50.0
occ:1.00
 OG C:SER192 1.8 108.6 1.0
CB C:SER192 2.2 108.6 1.0
O2G C:ATP501 2.4 117.6 1.0
O1A C:ATP501 2.6 117.6 1.0
O2B C:ATP501 2.9 117.6 1.0
O3B C:ATP501 3.1 117.6 1.0
O2A C:ATP501 3.1 117.6 1.0
PA C:ATP501 3.2 117.6 1.0
PG C:ATP501 3.4 117.6 1.0
CA C:SER192 3.4 108.6 1.0
PB C:ATP501 3.4 117.6 1.0
N C:SER192 3.5 108.6 1.0
O3A C:ATP501 3.5 117.6 1.0
CG2 C:THR223 3.9 117.2 1.0
O3G C:ATP501 4.0 117.6 1.0
C C:SER192 4.5 108.6 1.0
O1G C:ATP501 4.6 117.6 1.0
O5' C:ATP501 4.7 117.6 1.0
C C:LYS191 4.7 104.9 1.0
N C:GLN193 4.8 107.2 1.0
O1B C:ATP501 4.9 117.6 1.0

Magnesium binding site 3 out of 12 in 9e6l

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Magnesium binding site 3 out of 12 in the Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to RAD54PEPTIDE


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to RAD54PEPTIDE within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg502

b:50.0
occ:1.00
 OD2 F:ASP374 2.1 134.6 1.0
O2G E:ATP501 2.2 141.9 1.0
CG F:ASP374 3.0 134.6 1.0
OD1 F:ASP374 3.2 134.6 1.0
PG E:ATP501 3.7 141.9 1.0
O F:THR355 3.7 122.9 1.0
O F:SER354 3.8 130.4 1.0
O3B E:ATP501 4.1 141.9 1.0
CB F:ASP374 4.3 134.6 1.0
O1G E:ATP501 4.5 141.9 1.0
C F:THR355 4.5 122.9 1.0
O3G E:ATP501 4.6 141.9 1.0
CA F:THR355 4.7 122.9 1.0
O2A E:ATP501 4.8 141.9 1.0
C F:SER354 4.9 130.4 1.0
CD F:PRO376 5.0 135.2 1.0

Magnesium binding site 4 out of 12 in 9e6l

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Magnesium binding site 4 out of 12 in the Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to RAD54PEPTIDE


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to RAD54PEPTIDE within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg503

b:171.6
occ:1.00
 O3B F:ATP501 2.1 169.8 1.0
O2B F:ATP501 2.1 169.8 1.0
O2G F:ATP501 2.2 169.8 1.0
PB F:ATP501 2.4 169.8 1.0
OG F:SER192 2.5 154.6 1.0
O1A F:ATP501 2.5 169.8 1.0
PG F:ATP501 2.7 169.8 1.0
O3A F:ATP501 2.7 169.8 1.0
PA F:ATP501 2.8 169.8 1.0
O2A F:ATP501 3.1 169.8 1.0
CB F:SER192 3.4 154.6 1.0
O3G F:ATP501 3.6 169.8 1.0
N F:SER192 3.8 154.6 1.0
O1B F:ATP501 3.8 169.8 1.0
O1G F:ATP501 3.9 169.8 1.0
CA F:SER192 4.2 154.6 1.0
O5' F:ATP501 4.4 169.8 1.0
N F:LYS191 4.7 155.2 1.0
CG2 F:THR223 4.8 154.0 1.0
C F:LYS191 4.9 155.2 1.0

Magnesium binding site 5 out of 12 in 9e6l

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Magnesium binding site 5 out of 12 in the Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to RAD54PEPTIDE


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to RAD54PEPTIDE within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg504

b:50.0
occ:1.00
 O3G F:ATP501 2.3 169.8 1.0
PG F:ATP501 3.6 169.8 1.0
O3B F:ATP501 3.8 169.8 1.0
CB F:PHE187 4.3 163.3 1.0
O1G F:ATP501 4.4 169.8 1.0
CD2 F:PHE187 4.4 163.3 1.0
N F:ARG188 4.6 163.9 1.0
O2G F:ATP501 4.7 169.8 1.0
CG F:PHE187 4.9 163.3 1.0

Magnesium binding site 6 out of 12 in 9e6l

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Magnesium binding site 6 out of 12 in the Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to RAD54PEPTIDE


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to RAD54PEPTIDE within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:50.0
occ:1.00
 OD2 B:ASP374 2.0 116.8 1.0
O2G A:ATP501 2.1 123.6 1.0
CG B:ASP374 3.0 116.8 1.0
O B:SER354 3.3 113.9 1.0
O B:THR355 3.4 107.9 1.0
OD1 B:ASP374 3.4 116.8 1.0
PG A:ATP501 3.6 123.6 1.0
C B:THR355 4.1 107.9 1.0
CB B:ASP374 4.2 116.8 1.0
CA B:THR355 4.3 107.9 1.0
O1G A:ATP501 4.4 123.6 1.0
O3G A:ATP501 4.4 123.6 1.0
O3B A:ATP501 4.4 123.6 1.0
C B:SER354 4.4 113.9 1.0
O B:ALA351 4.5 113.5 1.0
O B:HIS352 4.8 112.9 1.0
N B:THR355 4.9 107.9 1.0

Magnesium binding site 7 out of 12 in 9e6l

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Magnesium binding site 7 out of 12 in the Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to RAD54PEPTIDE


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to RAD54PEPTIDE within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:113.5
occ:1.00
 O3B B:ATP501 2.0 119.2 1.0
OG B:SER192 2.1 113.8 1.0
O1B B:ATP501 2.1 119.2 1.0
O1G B:ATP501 2.2 119.2 1.0
PB B:ATP501 2.4 119.2 1.0
PG B:ATP501 2.6 119.2 1.0
O3A B:ATP501 3.2 119.2 1.0
O2A B:ATP501 3.2 119.2 1.0
CB B:SER192 3.2 113.8 1.0
PA B:ATP501 3.5 119.2 1.0
O2G B:ATP501 3.6 119.2 1.0
O1A B:ATP501 3.7 119.2 1.0
O3G B:ATP501 3.7 119.2 1.0
N B:SER192 3.8 113.8 1.0
O2B B:ATP501 3.8 119.2 1.0
CA B:SER192 4.1 113.8 1.0
OD2 B:ASP280 4.6 118.2 1.0
C B:LYS191 4.9 109.9 1.0
N B:LYS191 4.9 109.9 1.0
CB B:LYS191 4.9 109.9 1.0

Magnesium binding site 8 out of 12 in 9e6l

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Magnesium binding site 8 out of 12 in the Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to RAD54PEPTIDE


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to RAD54PEPTIDE within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg502

b:50.0
occ:1.00
 O2G D:ATP501 2.1 123.7 1.0
OD2 E:ASP374 2.1 120.3 1.0
CG E:ASP374 3.2 120.3 1.0
OD1 E:ASP374 3.6 120.3 1.0
PG D:ATP501 3.6 123.7 1.0
O E:SER354 3.8 118.0 1.0
O3B D:ATP501 4.1 123.7 1.0
O E:THR355 4.2 111.0 1.0
O3G D:ATP501 4.3 123.7 1.0
CB E:ASP374 4.5 120.3 1.0
O E:ALA351 4.5 113.5 1.0
O1G D:ATP501 4.5 123.7 1.0
CB D:PHE187 4.6 118.0 1.0
O E:HIS352 4.8 110.8 1.0
C E:THR355 4.9 111.0 1.0
C E:SER354 5.0 118.0 1.0

Magnesium binding site 9 out of 12 in 9e6l

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Magnesium binding site 9 out of 12 in the Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to RAD54PEPTIDE


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to RAD54PEPTIDE within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg503

b:140.8
occ:1.00
 O3B E:ATP501 2.1 141.9 1.0
O1G E:ATP501 2.1 141.9 1.0
O1B E:ATP501 2.2 141.9 1.0
OG E:SER192 2.2 133.0 1.0
PB E:ATP501 2.4 141.9 1.0
PG E:ATP501 2.5 141.9 1.0
O2A E:ATP501 2.6 141.9 1.0
O3A E:ATP501 2.8 141.9 1.0
PA E:ATP501 3.0 141.9 1.0
CB E:SER192 3.2 133.0 1.0
O1A E:ATP501 3.3 141.9 1.0
O2G E:ATP501 3.5 141.9 1.0
N E:SER192 3.7 133.0 1.0
O3G E:ATP501 3.7 141.9 1.0
O2B E:ATP501 3.9 141.9 1.0
CA E:SER192 4.1 133.0 1.0
O5' E:ATP501 4.5 141.9 1.0
N E:LYS191 4.7 127.4 1.0
C E:LYS191 4.8 127.4 1.0
OD2 E:ASP280 4.9 129.2 1.0
CB E:LYS191 4.9 127.4 1.0

Magnesium binding site 10 out of 12 in 9e6l

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Magnesium binding site 10 out of 12 in the Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to RAD54PEPTIDE


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to RAD54PEPTIDE within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:50.0
occ:1.00
 O3B A:ATP501 2.1 123.6 1.0
O1B A:ATP501 2.1 123.6 1.0
OG A:SER192 2.1 116.8 1.0
O1G A:ATP501 2.3 123.6 1.0
PB A:ATP501 2.5 123.6 1.0
PG A:ATP501 2.7 123.6 1.0
CB A:SER192 3.5 116.8 1.0
O3A A:ATP501 3.6 123.6 1.0
O2A A:ATP501 3.7 123.6 1.0
O2G A:ATP501 3.7 123.6 1.0
O2B A:ATP501 3.7 123.6 1.0
O3G A:ATP501 3.8 123.6 1.0
N A:SER192 4.1 116.8 1.0
PA A:ATP501 4.1 123.6 1.0
OD2 A:ASP280 4.2 125.3 1.0
CA A:SER192 4.4 116.8 1.0
O1A A:ATP501 4.6 123.6 1.0
OG1 A:THR223 4.9 127.5 1.0
OD1 A:ASP280 4.9 125.3 1.0
CE A:LYS191 5.0 114.8 1.0
CG A:ASP280 5.0 125.3 1.0

Reference:

Y.Shin, E.C.Greene. Cryo-Em Structure of Yeast RAD51 Nucleoprotein Filament Bound to RAD54PEPTIDE To Be Published.
Page generated: Sat Feb 8 22:08:13 2025

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