Magnesium in PDB 8wt8: 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 Intermediate)

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 Intermediate) (pdb code 8wt8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was 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 Intermediate), PDB code: 8wt8:

Magnesium binding site 1 out of 1 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 Intermediate)


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 Intermediate) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg101 b:36.9 occ:0.50 OE2 A:GLU60 2.1 36.2 1.0 O3' I:DT20 2.1 34.0 0.5 OP1 I:DA21 2.1 40.9 0.5 OD1 A:ASP11 2.1 38.4 1.0 OP1 I:DA21 2.3 33.9 0.5 O3' I:DT20 2.6 31.0 0.5 P I:DA21 2.8 32.9 0.5 O5' I:DA21 3.0 40.5 0.5 P I:DA21 3.1 44.7 0.5 O5' I:DA21 3.2 31.1 0.5 CD A:GLU60 3.2 34.3 1.0 CG A:ASP11 3.3 37.1 1.0 C3' I:DT20 3.5 31.0 0.5 CG A:GLU60 3.8 30.8 1.0 OD2 A:ASP11 3.9 38.7 1.0 C3' I:DT20 3.9 29.2 0.5 O A:THR12 4.0 34.7 1.0 OG1 A:THR62 4.0 31.6 1.0 OP2 I:DA21 4.1 43.8 0.5 C4' I:DT20 4.2 30.4 0.5 OG D:SER241 4.2 48.6 0.5 OE1 A:GLU60 4.3 36.0 1.0 OP2 I:DA21 4.3 32.5 0.5 C4' I:DT20 4.3 28.7 0.5 C5' I:DA21 4.4 37.0 0.5 N A:THR12 4.4 34.0 1.0 C2' I:DT20 4.4 30.5 0.5 CB A:ASP11 4.5 34.0 1.0 C5' I:DA21 4.5 30.0 0.5 CG2 A:THR62 4.6 32.4 1.0 C2' I:DT20 4.6 28.5 0.5 C5' I:DT20 4.7 30.4 0.5 CA A:ASP11 4.7 32.8 1.0 OD2 A:ASP105 4.7 48.9 1.0 C4' I:DA21 4.8 34.5 0.5 CB A:THR62 4.9 31.7 1.0 C5' I:DT20 4.9 28.9 0.5 C A:ASP11 4.9 32.7 1.0 C A:THR12 5.0 34.4 1.0 C4' I:DA21 5.0 29.2 0.5

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