Magnesium in PDB 8wt6: Cryo-Em Structure of the IS621 Recombinase in Complex with Bridge Rna, Donor Dna, and Target Dna in the Pre-Strand Exchange State

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 Pre-Strand Exchange State (pdb code 8wt6). 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 Pre-Strand Exchange State, PDB code: 8wt6:
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 Pre-Strand Exchange State


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 Pre-Strand Exchange State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:75.1 occ:1.00 O G:HOH101 2.0 71.9 1.0 O3' G:DT25 2.0 75.6 1.0 O A:HOH501 2.1 70.7 1.0 OP1 G:DA26 2.1 76.1 1.0 OD1 A:ASP11 2.1 74.8 1.0 OE2 A:GLU60 2.1 75.7 1.0 CD A:GLU60 3.1 74.8 1.0 CG A:ASP11 3.2 74.7 1.0 P G:DA26 3.3 75.9 1.0 OE1 A:GLU60 3.3 77.9 1.0 C3' G:DT25 3.4 73.6 1.0 OD2 A:ASP11 3.7 80.3 1.0 O5' G:DA26 3.7 73.2 1.0 OP2 G:DA26 4.0 75.3 1.0 OD2 A:ASP105 4.1 89.1 1.0 C4' G:DT25 4.2 73.3 1.0 C2' G:DT25 4.3 73.9 1.0 CG A:GLU60 4.4 69.7 1.0 CB A:ASP11 4.5 68.1 1.0 O A:THR12 4.5 71.1 1.0 N A:THR12 4.6 70.0 1.0 OG D:SER241 4.6 79.5 1.0 NZ A:LYS100 4.7 87.2 1.0 OG1 A:THR62 4.7 72.7 1.0 CA A:ASP11 4.8 68.2 1.0 CB A:ASP105 4.8 78.4 1.0 CB A:GLU60 4.9 66.8 1.0 CG A:ASP105 4.9 86.8 1.0 C5' G:DT25 4.9 73.7 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 Pre-Strand Exchange State


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 Pre-Strand Exchange State within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:72.8 occ:1.00 OE1 C:GLU60 1.9 76.6 1.0 O C:HOH502 1.9 70.4 1.0 O3' I:DT20 2.1 78.7 1.0 O C:HOH501 2.1 71.4 1.0 OD1 C:ASP11 2.1 71.2 1.0 OP1 I:DT21 2.1 73.9 1.0 CD C:GLU60 3.0 78.8 1.0 CG C:ASP11 3.2 69.7 1.0 P I:DT21 3.3 66.6 1.0 C3' I:DT20 3.5 84.8 1.0 OE2 C:GLU60 3.7 79.7 1.0 O5' I:DT21 3.7 65.8 1.0 OD2 C:ASP11 3.7 76.5 1.0 OD2 C:ASP105 3.8 88.7 1.0 OP2 I:DT21 3.9 68.8 1.0 CG C:GLU60 4.2 77.5 1.0 C4' I:DT20 4.2 86.7 1.0 C2' I:DT20 4.4 85.3 1.0 CB C:ASP11 4.5 64.2 1.0 OG1 C:THR62 4.5 73.8 1.0 NZ C:LYS100 4.5 76.5 1.0 O C:THR12 4.5 70.4 1.0 CG C:ASP105 4.5 85.4 1.0 OG B:SER241 4.6 71.3 1.0 N C:THR12 4.6 67.2 1.0 CB C:ASP105 4.7 75.5 1.0 CA C:ASP11 4.8 65.2 1.0 C5' I:DT20 4.8 88.6 1.0

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