Magnesium in PDB 9bgi: Activated Wild-Type Sgrai Endonuclease Dna-Bound Dimer with MG2+ and Cleaved Primary Site Dna

The binding sites of Magnesium atom in the Activated Wild-Type Sgrai Endonuclease Dna-Bound Dimer with MG2+ and Cleaved Primary Site Dna (pdb code 9bgi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Activated Wild-Type Sgrai Endonuclease Dna-Bound Dimer with MG2+ and Cleaved Primary Site Dna, PDB code: 9bgi:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Activated Wild-Type Sgrai Endonuclease Dna-Bound Dimer with MG2+ and Cleaved 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 Activated Wild-Type Sgrai Endonuclease Dna-Bound Dimer with MG2+ and Cleaved Primary Site Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:44.6 occ:1.00 O C:HOH105 1.9 43.6 1.0 O A:HOH519 1.9 42.3 1.0 O A:HOH527 1.9 46.7 1.0 O3' C:DA11 2.0 44.9 1.0 OP3 D:DC12 2.0 39.8 1.0 OD1 A:ASP188 2.3 39.8 1.0 CG A:ASP188 3.3 37.1 1.0 C3' C:DA11 3.3 40.6 1.0 P D:DC12 3.4 39.8 1.0 OD2 A:ASP188 3.7 36.6 1.0 MG A:MG402 3.7 37.2 1.0 OP1 D:DC12 3.7 32.9 1.0 C4' C:DA11 3.9 34.9 1.0 O A:THR186 4.0 54.3 1.0 O5' D:DC12 4.0 39.7 1.0 OE1 A:GLU103 4.3 50.5 1.0 C5' D:DC12 4.4 32.1 1.0 C2' C:DA11 4.4 33.0 1.0 OP2 D:DC12 4.4 30.5 1.0 NH1 A:ARG152 4.5 50.0 1.0 C5' C:DA11 4.5 36.9 1.0 CB A:ASP188 4.6 37.8 1.0 O A:HOH520 4.6 39.1 1.0 CA A:ASP188 4.7 38.8 1.0 O A:HOH515 4.7 32.9 1.0 N A:ASP188 4.9 36.6 1.0 OE2 A:GLU103 4.9 52.5 1.0

Magnesium binding site 2 out of 4 in the Activated Wild-Type Sgrai Endonuclease Dna-Bound Dimer with MG2+ and Cleaved 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 Activated Wild-Type Sgrai Endonuclease Dna-Bound Dimer with MG2+ and Cleaved Primary Site Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:37.2 occ:1.00 O A:HOH515 1.9 32.9 1.0 OP2 D:DC12 1.9 30.5 1.0 OD2 A:ASP188 2.0 36.6 1.0 OP3 D:DC12 2.0 39.8 1.0 P D:DC12 2.3 39.8 1.0 O A:PHE241 2.3 30.4 1.0 O5' D:DC12 2.8 39.7 1.0 CG A:ASP188 3.0 37.1 1.0 OD1 A:ASP188 3.3 39.8 1.0 C A:PHE241 3.5 25.9 1.0 MG A:MG401 3.7 44.6 1.0 OP1 D:DC12 3.7 32.9 1.0 N A:PHE241 4.0 25.8 1.0 OE1 A:GLU103 4.1 50.5 1.0 CA A:PHE241 4.2 24.3 1.0 O A:HOH520 4.2 39.1 1.0 C5' D:DC12 4.2 32.1 1.0 CB A:ASP188 4.4 37.8 1.0 CG A:LYS242 4.4 30.9 1.0 CB A:PHE241 4.5 26.9 1.0 O A:HOH519 4.5 42.3 1.0 N A:LYS242 4.6 23.0 1.0 C A:ALA240 4.7 28.4 1.0 CA A:LYS242 4.8 23.2 1.0 O3' C:DA11 4.8 44.9 1.0 O C:HOH105 4.8 43.6 1.0 OP2 D:DC13 5.0 30.3 1.0

Magnesium binding site 3 out of 4 in the Activated Wild-Type Sgrai Endonuclease Dna-Bound Dimer with MG2+ and Cleaved Primary Site Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Activated Wild-Type Sgrai Endonuclease Dna-Bound Dimer with MG2+ and Cleaved Primary Site Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:41.9 occ:1.00 O E:HOH102 1.9 41.5 1.0 O3' E:DA11 1.9 32.1 1.0 O E:HOH105 1.9 41.2 1.0 O E:HOH107 1.9 39.7 1.0 OD1 B:ASP188 1.9 39.1 1.0 OP3 F:DC12 2.1 32.9 1.0 CG B:ASP188 3.0 38.7 1.0 C3' E:DA11 3.3 28.3 1.0 OD2 B:ASP188 3.4 36.2 1.0 P F:DC12 3.5 34.9 1.0 MG B:MG402 3.5 33.4 1.0 O B:HOH504 3.7 38.5 1.0 OP1 F:DC12 3.9 32.1 1.0 C4' E:DA11 4.0 30.7 1.0 O B:THR186 4.0 50.9 1.0 O5' F:DC12 4.2 29.9 1.0 C2' E:DA11 4.3 24.4 1.0 CB B:ASP188 4.3 37.9 1.0 C5' F:DC12 4.3 23.9 1.0 OP2 F:DC12 4.4 31.9 1.0 CA B:ASP188 4.5 40.1 1.0 O B:HOH503 4.5 39.8 1.0 OE1 B:GLU103 4.6 43.2 1.0 C5' E:DA11 4.6 31.8 1.0 N B:ASP188 4.7 40.0 1.0

Magnesium binding site 4 out of 4 in the Activated Wild-Type Sgrai Endonuclease Dna-Bound Dimer with MG2+ and Cleaved Primary Site Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Activated Wild-Type Sgrai Endonuclease Dna-Bound Dimer with MG2+ and Cleaved Primary Site Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:33.4 occ:1.00 OP2 F:DC12 1.9 31.9 1.0 O B:HOH503 2.0 39.8 1.0 O B:HOH504 2.0 38.5 1.0 OD2 B:ASP188 2.0 36.2 1.0 OP3 F:DC12 2.0 32.9 1.0 O B:PHE241 2.2 28.9 1.0 P F:DC12 2.3 34.9 1.0 O5' F:DC12 2.9 29.9 1.0 CG B:ASP188 3.0 38.7 1.0 OD1 B:ASP188 3.3 39.1 1.0 C B:PHE241 3.4 27.1 1.0 MG B:MG401 3.5 41.9 1.0 OP1 F:DC12 3.7 32.1 1.0 N B:PHE241 3.8 30.1 1.0 CA B:PHE241 4.0 25.7 1.0 C5' F:DC12 4.1 23.9 1.0 CG B:LYS242 4.3 29.1 1.0 CB B:ASP188 4.3 37.9 1.0 CB B:PHE241 4.4 26.5 1.0 N B:LYS242 4.4 25.1 1.0 O E:HOH107 4.5 39.7 1.0 O E:HOH102 4.7 41.5 1.0 CA B:LYS242 4.7 23.6 1.0 O3' E:DA11 4.7 32.1 1.0 C B:ALA240 4.8 31.0 1.0 OE1 B:GLU103 4.8 43.2 1.0 OP2 F:DC13 4.8 31.5 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