Magnesium in PDB 9d46: The Cryo-Em Structure of the Yeast RAD51 Filament Bound to Ssdna in the Presence of Atp

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

Binding sites:

The binding sites of Magnesium atom in the The Cryo-Em Structure of the Yeast RAD51 Filament Bound to Ssdna in the Presence of Atp (pdb code 9d46). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the The Cryo-Em Structure of the Yeast RAD51 Filament Bound to Ssdna in the Presence of Atp, PDB code: 9d46:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in the The Cryo-Em Structure of the Yeast RAD51 Filament Bound to Ssdna in the Presence of Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Cryo-Em Structure of the Yeast RAD51 Filament Bound to Ssdna in the Presence of Atp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:83.7 occ:1.00 O2G B:ATP501 2.1 95.7 1.0 OD2 C:ASP374 2.2 89.7 1.0 CG C:ASP374 2.7 89.7 1.0 OD1 C:ASP374 2.7 89.7 1.0 PG B:ATP501 3.3 95.7 1.0 O1G B:ATP501 3.6 95.7 1.0 O C:THR355 3.6 81.2 1.0 O3B B:ATP501 3.8 95.7 1.0 O C:SER354 3.9 84.1 1.0 CB C:ASP374 4.1 89.7 1.0 O3A B:ATP501 4.3 95.7 1.0 C C:THR355 4.5 81.2 1.0 O3G B:ATP501 4.5 95.7 1.0 N C:SER375 4.8 90.8 1.0 O C:ALA351 4.8 86.4 1.0 CG2 B:THR223 4.8 97.2 1.0 MG B:MG503 4.8 88.2 1.0 CA C:THR355 4.8 81.2 1.0 PB B:ATP501 4.8 95.7 1.0 C C:ASP374 4.9 89.7 1.0 CD C:PRO376 4.9 91.3 1.0 CB B:PHE187 4.9 92.5 1.0

Magnesium binding site 2 out of 12 in the The Cryo-Em Structure of the Yeast RAD51 Filament Bound to Ssdna in the Presence of Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Cryo-Em Structure of the Yeast RAD51 Filament Bound to Ssdna in the Presence of Atp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:85.5 occ:1.00 O2G C:ATP501 2.0 93.0 1.0 OG C:SER192 2.0 87.9 1.0 O2B C:ATP501 2.2 93.0 1.0 O3B C:ATP501 2.6 93.0 1.0 PG C:ATP501 2.8 93.0 1.0 PB C:ATP501 2.9 93.0 1.0 O3G C:ATP501 3.3 93.0 1.0 CB C:SER192 3.3 87.9 1.0 O1A C:ATP501 3.7 93.0 1.0 O3A C:ATP501 3.8 93.0 1.0 OD2 C:ASP280 3.8 90.3 1.0 OG1 C:THR223 4.0 93.5 1.0 OE1 C:GLU221 4.0 96.5 1.0 N C:SER192 4.1 87.9 1.0 O1G C:ATP501 4.2 93.0 1.0 PA C:ATP501 4.2 93.0 1.0 O1B C:ATP501 4.2 93.0 1.0 OD1 C:ASP280 4.3 90.3 1.0 CA C:SER192 4.3 87.9 1.0 CG C:ASP280 4.5 90.3 1.0 O2A C:ATP501 4.5 93.0 1.0 MG D:MG502 4.5 82.2 1.0 CB C:THR223 4.5 93.5 1.0 CG2 C:THR223 4.6 93.5 1.0 CD C:GLU221 4.9 96.5 1.0

Magnesium binding site 3 out of 12 in the The Cryo-Em Structure of the Yeast RAD51 Filament Bound to Ssdna in the Presence of Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Cryo-Em Structure of the Yeast RAD51 Filament Bound to Ssdna in the Presence of Atp within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg502 b:107.5 occ:1.00 O2G E:ATP501 2.1 113.1 1.0 OD2 F:ASP374 2.2 110.5 1.0 OD1 F:ASP374 2.4 110.5 1.0 CG F:ASP374 2.5 110.5 1.0 PG E:ATP501 3.6 113.1 1.0 O F:SER354 3.7 108.4 1.0 O F:THR355 3.7 104.9 1.0 CB F:ASP374 3.8 110.5 1.0 O3B E:ATP501 4.0 113.1 1.0 MG E:MG503 4.3 110.6 1.0 O1G E:ATP501 4.4 113.1 1.0 O3G E:ATP501 4.5 113.1 1.0 O3A E:ATP501 4.5 113.1 1.0 C F:THR355 4.5 104.9 1.0 O F:ALA351 4.5 109.0 1.0 N F:SER375 4.7 112.2 1.0 C F:ASP374 4.7 110.5 1.0 CA F:ASP374 4.8 110.5 1.0 CA F:THR355 4.9 104.9 1.0 C F:SER354 4.9 108.4 1.0 CG2 E:THR223 4.9 107.9 1.0 N E:ARG188 5.0 110.8 1.0

Magnesium binding site 4 out of 12 in the The Cryo-Em Structure of the Yeast RAD51 Filament Bound to Ssdna in the Presence of Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Cryo-Em Structure of the Yeast RAD51 Filament Bound to Ssdna in the Presence of Atp within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg503 b:125.6 occ:1.00 OG F:SER192 2.1 125.0 1.0 O2G F:ATP501 2.1 130.0 1.0 OD1 F:ASP280 2.8 118.6 1.0 OD2 F:ASP280 2.8 118.6 1.0 O2B F:ATP501 2.8 130.0 1.0 CG F:ASP280 3.1 118.6 1.0 CB F:SER192 3.5 125.0 1.0 PG F:ATP501 3.5 130.0 1.0 OE1 F:GLU221 3.7 123.7 1.0 O3B F:ATP501 3.8 130.0 1.0 PB F:ATP501 3.9 130.0 1.0 OG1 F:THR223 4.0 124.3 1.0 N F:SER192 4.0 125.0 1.0 CA F:SER192 4.1 125.0 1.0 CD F:GLU221 4.2 123.7 1.0 O1G F:ATP501 4.4 130.0 1.0 OE2 F:GLU221 4.5 123.7 1.0 OG1 F:THR324 4.5 112.8 1.0 O3G F:ATP501 4.5 130.0 1.0 CE F:LYS191 4.5 123.9 1.0 CB F:ASP280 4.6 118.6 1.0 CB F:LYS191 4.8 123.9 1.0 NZ F:LYS191 4.8 123.9 1.0 O1B F:ATP501 4.9 130.0 1.0 C F:LYS191 4.9 123.9 1.0 O3A F:ATP501 5.0 130.0 1.0 CB F:THR223 5.0 124.3 1.0

Magnesium binding site 5 out of 12 in the The Cryo-Em Structure of the Yeast RAD51 Filament Bound to Ssdna in the Presence of Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Cryo-Em Structure of the Yeast RAD51 Filament Bound to Ssdna in the Presence of Atp within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg504 b:114.8 occ:1.00 O3G F:ATP501 2.1 130.0 1.0 NH1 F:ARG188 3.2 130.0 1.0 PG F:ATP501 3.5 130.0 1.0 O3B F:ATP501 3.7 130.0 1.0 O2G F:ATP501 4.4 130.0 1.0 O1G F:ATP501 4.4 130.0 1.0 CG F:ARG188 4.5 130.0 1.0 CZ F:ARG188 4.5 130.0 1.0 O1A F:ATP501 4.7 130.0 1.0 N F:ARG188 4.8 130.0 1.0 CG2 F:THR223 4.9 124.3 1.0 CD F:ARG188 5.0 130.0 1.0

Magnesium binding site 6 out of 12 in the The Cryo-Em Structure of the Yeast RAD51 Filament Bound to Ssdna in the Presence of Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Cryo-Em Structure of the Yeast RAD51 Filament Bound to Ssdna in the Presence of Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:88.1 occ:1.00 O2G A:ATP501 2.1 103.3 1.0 OD2 B:ASP374 2.2 93.8 1.0 CG B:ASP374 2.7 93.8 1.0 OD1 B:ASP374 2.8 93.8 1.0 PG A:ATP501 3.4 103.3 1.0 O B:THR355 3.6 86.6 1.0 O B:SER354 3.6 89.8 1.0 O1G A:ATP501 3.8 103.3 1.0 O3B A:ATP501 4.0 103.3 1.0 CB B:ASP374 4.1 93.8 1.0 C B:THR355 4.4 86.6 1.0 O3G A:ATP501 4.5 103.3 1.0 O3A A:ATP501 4.6 103.3 1.0 O B:ALA351 4.7 90.1 1.0 CA B:THR355 4.7 86.6 1.0 C B:SER354 4.8 89.8 1.0 N B:SER375 4.8 96.2 1.0 CG2 A:THR223 4.9 104.5 1.0 C B:ASP374 4.9 93.8 1.0 CD B:PRO376 4.9 99.5 1.0

Magnesium binding site 7 out of 12 in the The Cryo-Em Structure of the Yeast RAD51 Filament Bound to Ssdna in the Presence of Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Cryo-Em Structure of the Yeast RAD51 Filament Bound to Ssdna in the Presence of Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:88.2 occ:1.00 O1G B:ATP501 1.9 95.7 1.0 O1B B:ATP501 2.0 95.7 1.0 OG B:SER192 2.0 90.5 1.0 PB B:ATP501 2.5 95.7 1.0 O3B B:ATP501 2.7 95.7 1.0 O3A B:ATP501 2.7 95.7 1.0 PG B:ATP501 2.8 95.7 1.0 CB B:SER192 3.2 90.5 1.0 O3G B:ATP501 3.7 95.7 1.0 N B:SER192 3.7 90.5 1.0 PA B:ATP501 3.9 95.7 1.0 O2B B:ATP501 4.0 95.7 1.0 O2G B:ATP501 4.0 95.7 1.0 OD2 B:ASP280 4.0 92.4 1.0 CA B:SER192 4.1 90.5 1.0 O1A B:ATP501 4.1 95.7 1.0 O2A B:ATP501 4.2 95.7 1.0 OD1 B:ASP280 4.3 92.4 1.0 NZ B:LYS191 4.4 87.5 1.0 CE B:LYS191 4.5 87.5 1.0 OG1 B:THR223 4.5 97.2 1.0 OE1 B:GLU221 4.6 96.8 1.0 CG B:ASP280 4.6 92.4 1.0 CB B:LYS191 4.7 87.5 1.0 MG C:MG502 4.8 83.7 1.0 C B:LYS191 4.8 87.5 1.0 CB B:THR223 5.0 97.2 1.0

Magnesium binding site 8 out of 12 in the The Cryo-Em Structure of the Yeast RAD51 Filament Bound to Ssdna in the Presence of Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Cryo-Em Structure of the Yeast RAD51 Filament Bound to Ssdna in the Presence of Atp within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg502 b:88.1 occ:1.00 O2G D:ATP501 2.1 98.1 1.0 OD2 E:ASP374 2.1 95.1 1.0 CG E:ASP374 2.7 95.1 1.0 OD1 E:ASP374 2.8 95.1 1.0 PG D:ATP501 3.3 98.1 1.0 O E:SER354 3.5 92.0 1.0 O E:THR355 3.6 88.4 1.0 O1G D:ATP501 3.7 98.1 1.0 O3B D:ATP501 3.8 98.1 1.0 CB E:ASP374 4.1 95.1 1.0 C E:THR355 4.3 88.4 1.0 O E:ALA351 4.4 94.8 1.0 O3G D:ATP501 4.5 98.1 1.0 CA E:THR355 4.6 88.4 1.0 O3A D:ATP501 4.6 98.1 1.0 C E:SER354 4.6 92.0 1.0 CG2 D:THR223 4.8 96.2 1.0 N E:SER375 4.9 95.9 1.0 O E:HIS352 4.9 94.5 1.0 CD E:PRO376 4.9 95.1 1.0 C E:ASP374 4.9 95.1 1.0

Magnesium binding site 9 out of 12 in the The Cryo-Em Structure of the Yeast RAD51 Filament Bound to Ssdna in the Presence of Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of The Cryo-Em Structure of the Yeast RAD51 Filament Bound to Ssdna in the Presence of Atp within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg503 b:110.6 occ:1.00 OG E:SER192 2.1 105.7 1.0 O1G E:ATP501 2.1 113.1 1.0 O3A E:ATP501 2.3 113.1 1.0 O1B E:ATP501 2.3 113.1 1.0 PB E:ATP501 2.4 113.1 1.0 O3B E:ATP501 2.5 113.1 1.0 PG E:ATP501 2.6 113.1 1.0 CB E:SER192 3.1 105.7 1.0 O2G E:ATP501 3.1 113.1 1.0 PA E:ATP501 3.3 113.1 1.0 O2A E:ATP501 3.4 113.1 1.0 O1A E:ATP501 3.8 113.1 1.0 O2B E:ATP501 3.9 113.1 1.0 N E:SER192 4.0 105.7 1.0 O3G E:ATP501 4.0 113.1 1.0 CA E:SER192 4.1 105.7 1.0 MG F:MG502 4.3 107.5 1.0 OG1 E:THR223 4.5 107.9 1.0 OD2 E:ASP280 4.6 102.1 1.0 O5' E:ATP501 4.6 113.1 1.0 OE1 E:GLU221 4.7 107.8 1.0 NZ E:LYS191 4.7 103.8 1.0 CB E:THR223 4.8 107.9 1.0 CG2 E:THR223 4.9 107.9 1.0

Magnesium binding site 10 out of 12 in the The Cryo-Em Structure of the Yeast RAD51 Filament Bound to Ssdna in the Presence of Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of The Cryo-Em Structure of the Yeast RAD51 Filament Bound to Ssdna in the Presence of Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:97.8 occ:1.00 OG A:SER192 2.1 98.5 1.0 O1G A:ATP501 2.1 103.3 1.0 OD2 A:ASP280 2.7 102.3 1.0 OD1 A:ASP280 2.8 102.3 1.0 CG A:ASP280 3.1 102.3 1.0 O1B A:ATP501 3.3 103.3 1.0 PG A:ATP501 3.4 103.3 1.0 CB A:SER192 3.4 98.5 1.0 OE1 A:GLU221 3.7 107.0 1.0 OG1 A:THR223 3.8 104.5 1.0 O3G A:ATP501 3.9 103.3 1.0 O3B A:ATP501 4.0 103.3 1.0 PB A:ATP501 4.1 103.3 1.0 CA A:SER192 4.2 98.5 1.0 N A:SER192 4.2 98.5 1.0 CD A:GLU221 4.3 107.0 1.0 O3A A:ATP501 4.6 103.3 1.0 OG1 A:THR324 4.6 94.6 1.0 CB A:ASP280 4.6 102.3 1.0 O2G A:ATP501 4.6 103.3 1.0 OE2 A:GLU221 4.6 107.0 1.0 CB A:THR223 4.7 104.5 1.0 CE A:LYS191 4.8 97.3 1.0 CG2 A:THR223 4.9 104.5 1.0

Y.Shin, E.C.Greene. The Cryo-Em Structure of the Yeast RAD51 Filament Bound to Ssdna in the Presence of Atp To Be Published.