Magnesium in PDB 9njr: The Cryo-Em Structure of the Yeast DMC1-Ssdna Nucleoprotein Filament Adp Bound State

The binding sites of Magnesium atom in the The Cryo-Em Structure of the Yeast DMC1-Ssdna Nucleoprotein Filament Adp Bound State (pdb code 9njr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the The Cryo-Em Structure of the Yeast DMC1-Ssdna Nucleoprotein Filament Adp Bound State, PDB code: 9njr:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the The Cryo-Em Structure of the Yeast DMC1-Ssdna Nucleoprotein Filament Adp Bound State


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 DMC1-Ssdna Nucleoprotein Filament Adp Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:57.1 occ:1.00 O1B A:ADP401 2.1 71.4 1.0 OG1 A:THR128 2.1 53.4 1.0 PB A:ADP401 3.3 71.4 1.0 CB A:THR128 3.5 53.4 1.0 OG1 A:THR159 3.8 48.6 1.0 O3B A:ADP401 3.8 71.4 1.0 OD2 A:ASP216 3.9 54.8 1.0 OD1 A:ASP216 4.0 54.8 1.0 O2B A:ADP401 4.1 71.4 1.0 CG2 A:THR128 4.3 53.4 1.0 N A:THR128 4.3 53.4 1.0 CG2 A:THR159 4.3 48.6 1.0 OE1 A:GLU157 4.3 51.8 1.0 CG A:ASP216 4.4 54.8 1.0 CB A:THR159 4.4 48.6 1.0 CA A:THR128 4.4 53.4 1.0 O2A A:ADP401 4.5 71.4 1.0 O3A A:ADP401 4.5 71.4 1.0 OE1 A:GLN262 4.7 75.2 1.0 CD A:GLU157 4.7 51.8 1.0 PA A:ADP401 4.8 71.4 1.0 O1A A:ADP401 5.0 71.4 1.0

Magnesium binding site 2 out of 3 in the The Cryo-Em Structure of the Yeast DMC1-Ssdna Nucleoprotein Filament Adp Bound State


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 DMC1-Ssdna Nucleoprotein Filament Adp Bound State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:52.5 occ:1.00 OG1 B:THR128 2.3 55.1 1.0 O1B B:ADP401 2.5 67.4 1.0 O2B B:ADP401 3.4 67.4 1.0 PB B:ADP401 3.5 67.4 1.0 CB B:THR128 3.6 55.1 1.0 OD1 B:ASP216 3.8 59.8 1.0 OE1 B:GLU157 4.0 54.1 1.0 N B:THR128 4.1 55.1 1.0 OD2 B:ASP216 4.3 59.8 1.0 OG1 B:THR159 4.3 48.0 1.0 CA B:THR128 4.4 55.1 1.0 O3A B:ADP401 4.5 67.4 1.0 CG B:ASP216 4.5 59.8 1.0 O2A B:ADP401 4.5 67.4 1.0 CG2 B:THR128 4.6 55.1 1.0 CG2 B:THR159 4.6 48.0 1.0 NE2 B:GLN262 4.6 71.3 1.0 O3B B:ADP401 4.6 67.4 1.0 CB B:THR159 4.7 48.0 1.0 O1A B:ADP401 4.8 67.4 1.0 PA B:ADP401 4.8 67.4 1.0 CE B:LYS127 4.8 61.1 1.0 CB B:LYS127 5.0 61.1 1.0

Magnesium binding site 3 out of 3 in the The Cryo-Em Structure of the Yeast DMC1-Ssdna Nucleoprotein Filament Adp Bound State


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 DMC1-Ssdna Nucleoprotein Filament Adp Bound State within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:48.6 occ:1.00 OG1 C:THR128 2.0 54.9 1.0 O1B C:ADP401 2.2 68.8 1.0 OE1 C:GLU157 3.1 51.7 1.0 CB C:THR128 3.3 54.9 1.0 PB C:ADP401 3.4 68.8 1.0 O3B C:ADP401 3.7 68.8 1.0 OD1 C:ASP216 3.9 55.0 1.0 N C:THR128 3.9 54.9 1.0 CD C:GLU157 4.1 51.7 1.0 CA C:THR128 4.2 54.9 1.0 O1A C:ADP401 4.3 68.8 1.0 CG2 C:THR128 4.3 54.9 1.0 O2B C:ADP401 4.3 68.8 1.0 OE2 C:GLU157 4.4 51.7 1.0 O3A C:ADP401 4.6 68.8 1.0 CG2 C:THR159 4.8 46.1 1.0 PA C:ADP401 4.9 68.8 1.0 CE2 C:PHE123 4.9 84.3 1.0 CG C:ASP216 4.9 55.0 1.0 CB C:LYS127 4.9 60.8 1.0

Y.Shin, E.C.Greene. The Cryo-Em Structure of the Yeast DMC1-Ssdna Nucleoprotein Filament Adp Bound State To Be Published.