Magnesium in PDB 9ixm: Cryo-Em Structure of Lactobacillus Casei Ddmde Bound with Dna

The binding sites of Magnesium atom in the Cryo-Em Structure of Lactobacillus Casei Ddmde Bound with Dna (pdb code 9ixm). 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 Lactobacillus Casei Ddmde Bound with Dna, PDB code: 9ixm:

Magnesium binding site 1 out of 1 in the Cryo-Em Structure of Lactobacillus Casei Ddmde Bound with Dna


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 Lactobacillus Casei Ddmde Bound with Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg101 b:65.0 occ:1.00 OP2 D:DT1 2.3 94.6 1.0 OP1 D:DA3 2.3 86.4 1.0 P D:DT1 3.6 89.6 1.0 P D:DA3 3.6 86.6 1.0 C5' D:DA3 3.7 75.2 1.0 NZ B:LYS395 3.7 72.2 1.0 OE2 B:GLU702 3.8 92.2 1.0 O5' D:DA3 3.9 75.4 1.0 OE1 B:GLN349 4.2 90.4 1.0 C5' D:DT1 4.3 93.8 1.0 O5' D:DT1 4.3 90.9 1.0 CE B:LYS395 4.4 63.7 1.0 CD B:GLU702 4.5 92.9 1.0 OP2 D:DA3 4.6 92.5 1.0 OE1 B:GLU702 4.6 97.4 1.0 O3' D:DG2 4.7 76.3 1.0 OE1 B:GLU391 4.7 96.3 1.0 OP1 D:DT1 4.8 98.7 1.0 C4' D:DA3 4.9 83.4 1.0 CD B:GLU391 4.9 95.6 1.0 NE2 B:GLN349 4.9 91.3 1.0 CD B:GLN349 5.0 81.7 1.0

P.Huang, P.Yan, L.Guo, W.Fei, Z.Li, J.Liu, J.Kong, Y.Yao, M.Lu, Y.Xiao, M.Chen. The Mechanism of Bacterial Defense System Ddmde From Lactobacillus Casei. Cell Res. V. 34 873 2024.
ISSN: ISSN 1001-0602
PubMed: 39448873
DOI: 10.1038/S41422-024-01042-Y