Magnesium in PDB 8dmb: Structure of Desulfovirgula Thermocuniculi Isrb (Dtisrb) in Complex with Omega Rna and Target Dna

The binding sites of Magnesium atom in the Structure of Desulfovirgula Thermocuniculi Isrb (Dtisrb) in Complex with Omega Rna and Target Dna (pdb code 8dmb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Desulfovirgula Thermocuniculi Isrb (Dtisrb) in Complex with Omega Rna and Target Dna, PDB code: 8dmb:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Desulfovirgula Thermocuniculi Isrb (Dtisrb) in Complex with Omega Rna and Target Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Desulfovirgula Thermocuniculi Isrb (Dtisrb) in Complex with Omega Rna and Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ W:Mg301 b:33.1 occ:1.00 OP1 W:A200 2.1 53.0 1.0 OP1 W:A199 2.2 50.0 1.0 OP2 W:A200 2.2 61.5 1.0 P W:A200 2.5 55.1 1.0 O4 W:U201 2.9 69.7 1.0 H5 W:U201 2.9 71.0 1.0 H3' W:A199 3.2 46.1 1.0 C5 W:U201 3.3 70.5 1.0 C4 W:U201 3.3 70.2 1.0 O3' W:A199 3.4 50.8 1.0 P W:A199 3.5 47.3 1.0 H5'' W:A199 3.6 44.8 1.0 C3' W:A199 3.8 48.9 1.0 H21 W:G190 3.8 55.5 1.0 O3' W:C198 3.8 31.1 1.0 O5' W:A200 3.9 59.0 1.0 H8 W:A200 4.1 56.1 1.0 C5' W:A199 4.3 44.5 1.0 O5' W:A199 4.3 41.5 1.0 H61 W:A189 4.3 63.3 1.0 C6 W:U201 4.5 72.6 1.0 N2 W:G190 4.5 53.4 1.0 N3 W:U201 4.5 70.9 1.0 C4' W:A199 4.6 45.2 1.0 OP2 W:A199 4.6 48.9 1.0 H22 W:G190 4.7 55.7 1.0 H6 W:U201 4.8 71.4 1.0 H3 W:U201 4.9 70.5 1.0 C8 W:A200 5.0 57.5 1.0

Magnesium binding site 2 out of 2 in the Structure of Desulfovirgula Thermocuniculi Isrb (Dtisrb) in Complex with Omega Rna and Target Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Desulfovirgula Thermocuniculi Isrb (Dtisrb) in Complex with Omega Rna and Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ W:Mg302 b:10.0 occ:1.00 OP1 W:U163 2.1 28.5 1.0 OP2 W:U164 2.1 30.5 1.0 P W:U164 3.5 17.2 1.0 H5'' W:U163 3.5 27.7 1.0 P W:U163 3.6 14.9 1.0 H5 W:U164 3.9 24.3 1.0 H3' W:G162 4.0 32.4 1.0 OP2 W:G162 4.1 27.1 1.0 OP1 W:U164 4.1 24.6 1.0 H3' W:U163 4.2 26.2 1.0 O3' W:U163 4.2 19.5 1.0 O5' W:U163 4.3 19.9 1.0 C5' W:U163 4.3 20.0 1.0 O3' W:G162 4.4 31.1 1.0 H6 W:U164 4.5 25.5 1.0 O5' W:G162 4.5 31.2 1.0 OP2 W:U163 4.5 25.2 1.0 O5' W:U164 4.6 22.0 1.0 P W:G162 4.6 11.9 1.0 C3' W:U163 4.6 24.0 1.0 C3' W:G162 4.7 26.8 1.0 OP1 W:G162 4.7 35.9 1.0 C5 W:U164 4.8 24.6 1.0 H8 W:G162 4.9 32.5 1.0 H5'' W:G162 4.9 33.2 1.0 N1 W:A108 5.0 42.4 1.0

S.Hirano, K.Kappel, H.Altae-Tran, G.Faure, M.E.Wilkinson, S.Kannan, F.E.Demircioglu, R.Yan, M.Shiozaki, Z.Yu, K.S.Makarova, E.V.Koonin, R.K.Macrae, F.Zhang. Structure of the Omega Nickase Isrb in Complex with Omega Rna and Target Dna. Nature V. 610 575 2022.
ISSN: ESSN 1476-4687
PubMed: 36224386
DOI: 10.1038/S41586-022-05324-6