Magnesium in PDB 8wt9: Cryo-Em Structure of the IS621 Recombinase in Complex with Bridge Rna, Donor Dna, and Target Dna in the Post-Strand Exchange State (Holliday Junction Resolution)

The binding sites of Magnesium atom in the Cryo-Em Structure of the IS621 Recombinase in Complex with Bridge Rna, Donor Dna, and Target Dna in the Post-Strand Exchange State (Holliday Junction Resolution) (pdb code 8wt9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Cryo-Em Structure of the IS621 Recombinase in Complex with Bridge Rna, Donor Dna, and Target Dna in the Post-Strand Exchange State (Holliday Junction Resolution), PDB code: 8wt9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Cryo-Em Structure of the IS621 Recombinase in Complex with Bridge Rna, Donor Dna, and Target Dna in the Post-Strand Exchange State (Holliday Junction Resolution)


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 the IS621 Recombinase in Complex with Bridge Rna, Donor Dna, and Target Dna in the Post-Strand Exchange State (Holliday Junction Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:26.6 occ:1.00 O B:HOH502 2.1 25.5 1.0 O B:HOH501 2.1 25.5 1.0 OE1 B:GLU60 2.1 27.0 1.0 OP1 H:DC18 2.1 26.1 1.0 O3' H:DC17 2.1 26.5 1.0 OD1 B:ASP11 2.1 25.5 1.0 CD B:GLU60 3.1 26.6 1.0 CG B:ASP11 3.3 23.6 1.0 C3' H:DC17 3.3 27.4 1.0 P H:DC18 3.4 26.5 1.0 OE2 B:GLU60 3.4 28.1 1.0 OD2 B:ASP105 3.8 31.5 1.0 O5' H:DC18 3.8 23.7 1.0 OD2 B:ASP11 3.8 27.3 1.0 OP2 H:DC18 4.1 25.5 1.0 C4' H:DC17 4.3 27.8 1.0 C2' H:DC17 4.4 26.5 1.0 CG B:GLU60 4.4 23.5 1.0 NZ B:LYS100 4.4 32.4 1.0 CB B:ASP11 4.5 18.9 1.0 CG2 B:THR62 4.6 32.2 1.0 CG B:ASP105 4.6 29.0 1.0 OG C:SER241 4.6 28.9 1.0 O B:THR12 4.7 20.6 1.0 N B:THR12 4.7 17.8 1.0 CA B:ASP11 4.8 17.5 1.0 CB B:ASP105 4.8 23.8 1.0 CB B:GLU60 4.8 20.9 1.0

Magnesium binding site 2 out of 2 in the Cryo-Em Structure of the IS621 Recombinase in Complex with Bridge Rna, Donor Dna, and Target Dna in the Post-Strand Exchange State (Holliday Junction Resolution)


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 the IS621 Recombinase in Complex with Bridge Rna, Donor Dna, and Target Dna in the Post-Strand Exchange State (Holliday Junction Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg101 b:41.0 occ:1.00 OP1 J:DA29 2.5 20.9 0.5 OE2 D:GLU60 2.5 33.2 1.0 OD2 D:ASP11 2.6 30.7 1.0 O3' J:DT28 2.6 22.0 0.5 OP1 J:DA29 2.8 42.8 0.5 O3' J:DT28 3.2 20.9 0.5 CG D:ASP11 3.4 29.4 1.0 P J:DA29 3.4 21.0 0.5 OD1 D:ASP11 3.7 32.6 1.0 CD D:GLU60 3.7 32.8 1.0 C3' J:DT28 3.9 22.0 0.5 C5' J:DA29 4.0 21.3 0.5 C5' J:DA29 4.1 33.7 0.5 O D:THR12 4.1 29.6 1.0 P J:DA29 4.2 43.5 0.5 O5' J:DA29 4.3 20.7 0.5 CG D:GLU60 4.4 29.2 1.0 CG2 D:THR62 4.5 36.6 1.0 CB D:ASP11 4.5 25.7 1.0 C3' J:DT28 4.5 20.5 0.5 N D:THR12 4.6 27.5 1.0 O5' J:DA29 4.6 38.3 0.5 OE1 D:GLU60 4.7 34.5 1.0 OP2 J:DA29 4.7 22.9 0.5 CG D:ASP105 4.7 44.6 1.0 CA D:ASP11 4.7 24.6 1.0 OD2 D:ASP105 4.8 45.9 1.0 OD1 D:ASP105 4.8 46.2 1.0 C4' J:DT28 4.8 21.4 0.5 C2' J:DT28 4.8 21.9 0.5 C4' J:DT28 4.9 20.1 0.5

M.Hiraizumi, M.Hiraizumi, K.Yamashita, H.Nishimasu. N/A N/A.