Magnesium in PDB 8wt7: Cryo-Em Structure of the IS621 Recombinase in Complex with Bridge Rna, Donor Dna, and Target Dna in the Pre-Strand Exchange Locked 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 Locked State (pdb code 8wt7). 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 Locked State, PDB code: 8wt7:
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 Locked 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 Locked State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:97.7 occ:1.00 OE2 A:GLU60 1.9 97.2 1.0 O3' G:DT25 2.1 95.7 1.0 O A:HOH502 2.1 96.5 1.0 O A:HOH501 2.1 96.9 1.0 OP1 G:DA26 2.1 98.1 1.0 OD1 A:ASP11 2.1 95.8 1.0 CD A:GLU60 3.1 96.8 1.0 P G:DA26 3.2 98.9 1.0 CG A:ASP11 3.2 93.5 1.0 C3' G:DT25 3.5 94.6 1.0 O5' G:DA26 3.6 94.8 1.0 OD2 A:ASP11 3.7 96.2 1.0 OP2 G:DA26 3.7 98.4 1.0 OE1 A:GLU60 3.8 97.5 1.0 OD2 A:ASP105 4.1 103.8 1.0 CG A:GLU60 4.2 93.5 1.0 C4' G:DT25 4.2 94.7 1.0 C2' G:DT25 4.3 93.0 1.0 CB A:ASP11 4.5 90.3 1.0 NZ A:LYS100 4.5 106.2 1.0 O A:THR12 4.5 95.2 1.0 OG D:SER241 4.5 102.6 1.0 OG1 A:THR62 4.6 95.6 1.0 N A:THR12 4.7 91.9 1.0 CA A:ASP11 4.8 89.0 1.0 C5' G:DT25 4.9 94.8 1.0 CG A:ASP105 4.9 101.8 1.0 CB A:ASP105 4.9 97.0 1.0 C5' G:DA26 5.0 91.2 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 Locked 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 Locked State within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:91.3 occ:1.00 O C:HOH501 1.9 91.4 1.0 O C:HOH502 2.1 90.8 1.0 O3' I:DT20 2.1 90.9 1.0 OE1 C:GLU60 2.1 93.2 1.0 OP1 I:DT21 2.1 92.2 1.0 OD1 C:ASP11 2.1 91.4 1.0 CD C:GLU60 3.1 93.0 1.0 CG C:ASP11 3.2 90.9 1.0 P I:DT21 3.3 90.7 1.0 C3' I:DT20 3.5 90.3 1.0 OE2 C:GLU60 3.5 93.9 1.0 OD2 C:ASP11 3.7 94.6 1.0 O5' I:DT21 3.7 88.6 1.0 OP2 I:DT21 3.9 91.0 1.0 OD2 C:ASP105 4.1 101.2 1.0 C4' I:DT20 4.3 90.9 1.0 C2' I:DT20 4.4 90.0 1.0 CG C:GLU60 4.4 89.7 1.0 OG1 C:THR62 4.5 95.5 1.0 CB C:ASP11 4.5 86.2 1.0 O C:THR12 4.6 88.4 1.0 OG B:SER241 4.6 94.5 1.0 N C:THR12 4.6 86.8 1.0 NZ C:LYS100 4.7 99.1 1.0 CB C:ASP105 4.8 94.7 1.0 CA C:ASP11 4.8 85.5 1.0 CG C:ASP105 4.8 99.5 1.0 CB C:GLU60 4.8 87.0 1.0 C5' I:DT20 4.9 89.9 1.0

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