Magnesium in PDB 9bgj: Sgrai Mutant K242A Endonuclease Dna-Bound Dimer with MG2+ and Intact Primary Site Dna

The binding sites of Magnesium atom in the Sgrai Mutant K242A Endonuclease Dna-Bound Dimer with MG2+ and Intact Primary Site Dna (pdb code 9bgj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Sgrai Mutant K242A Endonuclease Dna-Bound Dimer with MG2+ and Intact Primary Site Dna, PDB code: 9bgj:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Sgrai Mutant K242A Endonuclease Dna-Bound Dimer with MG2+ and Intact Primary Site Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Sgrai Mutant K242A Endonuclease Dna-Bound Dimer with MG2+ and Intact Primary Site Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:46.4 occ:1.00 OP1 C:DC12 1.9 54.7 1.0 O A:PHE241 2.2 55.1 1.0 OD2 A:ASP188 2.6 53.5 1.0 C A:PHE241 3.0 45.8 1.0 P C:DC12 3.2 59.2 1.0 CG A:ASP188 3.5 56.2 1.0 N A:ALA242 3.7 43.6 1.0 OP2 C:DC12 3.8 56.9 1.0 CA A:ALA242 3.8 50.7 1.0 N A:PHE241 3.8 44.7 1.0 CA A:PHE241 3.9 43.4 1.0 O5' C:DC12 4.0 55.5 1.0 OD1 A:ASP188 4.1 60.9 1.0 CB A:ALA242 4.1 58.4 1.0 O3' C:DA11 4.4 61.1 1.0 C5' C:DC12 4.4 48.6 1.0 CB A:PHE241 4.5 50.0 1.0 C A:ALA240 4.5 48.4 1.0 CB A:ASP188 4.5 55.9 1.0 OP2 C:DC13 4.6 51.2 1.0 OP1 C:DC13 4.6 54.3 1.0 O3' C:DC12 4.7 48.8 1.0 P C:DC13 4.8 56.4 1.0

Magnesium binding site 2 out of 2 in the Sgrai Mutant K242A Endonuclease Dna-Bound Dimer with MG2+ and Intact Primary Site Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Sgrai Mutant K242A Endonuclease Dna-Bound Dimer with MG2+ and Intact Primary Site Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:50.4 occ:1.00 OP1 D:DC12 1.9 57.6 1.0 O B:PHE241 2.1 54.7 1.0 OD2 B:ASP188 2.2 60.6 1.0 C B:PHE241 3.1 46.4 1.0 P D:DC12 3.2 61.5 1.0 CG B:ASP188 3.4 58.8 1.0 OE2 B:GLU103 3.5 64.8 1.0 OP2 D:DC12 3.7 60.0 1.0 N B:PHE241 3.9 43.8 1.0 N B:ALA242 3.9 42.1 1.0 OD1 B:ASP188 3.9 60.1 1.0 CA B:ALA242 4.0 46.7 1.0 CA B:PHE241 4.0 43.0 1.0 O5' D:DC12 4.0 58.5 1.0 CB B:ALA242 4.2 55.7 1.0 O3' D:DA11 4.3 62.2 1.0 C5' D:DC12 4.4 53.4 1.0 CB B:ASP188 4.5 56.5 1.0 CD B:GLU103 4.6 69.0 1.0 OP2 D:DC13 4.6 50.5 1.0 C B:ALA240 4.6 49.3 1.0 CB B:PHE241 4.6 50.0 1.0 OP1 D:DC13 4.8 54.5 1.0 O3' D:DC12 4.8 43.7 1.0 P D:DC13 4.9 52.7 1.0

Z.Shan, A.Rivero-Gamez, D.Lyumkis, N.C.Horton. Two-Metal Ion Mechanism of Dna Cleavage By Activated, Filamentous Sgrai. J.Biol.Chem. V. 300 07576 2024.
ISSN: ESSN 1083-351X
PubMed: 39009341
DOI: 10.1016/J.JBC.2024.107576