Magnesium in PDB 8y82: Cryo-Em Structure of the Tetrameric Sparsa Grna-Ssdna-Nad+ Complex

The binding sites of Magnesium atom in the Cryo-Em Structure of the Tetrameric Sparsa Grna-Ssdna-Nad+ Complex (pdb code 8y82). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Cryo-Em Structure of the Tetrameric Sparsa Grna-Ssdna-Nad+ Complex, PDB code: 8y82:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Cryo-Em Structure of the Tetrameric Sparsa Grna-Ssdna-Nad+ Complex


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 Tetrameric Sparsa Grna-Ssdna-Nad+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:58.2 occ:1.00 OP1 C:U3 2.0 60.9 1.0 OP1 C:A1 2.0 63.1 1.0 ND2 B:ASN434 2.2 53.8 1.0 P C:A1 2.4 63.1 1.0 P C:U3 3.2 60.9 1.0 O B:MET473 3.2 48.0 1.0 CG B:ASN434 3.3 53.8 1.0 O3' C:U2 3.4 63.9 1.0 OP2 C:A1 3.4 63.1 1.0 C B:MET473 3.4 48.0 1.0 NZ B:LYS207 3.6 46.9 1.0 O5' C:A1 3.6 63.1 1.0 OD1 B:ASN434 3.8 53.8 1.0 C5' C:A1 3.9 63.1 1.0 O5' C:U3 4.0 60.9 1.0 NZ B:LYS170 4.3 55.4 1.0 OP2 C:U3 4.4 60.9 1.0 CB B:ASN434 4.5 53.8 1.0 NE2 B:GLN181 4.6 57.2 1.0 CE B:LYS207 4.6 46.9 1.0 CG B:GLN181 4.7 57.2 1.0 C3' C:U2 4.7 63.9 1.0 O2' C:U2 4.8 63.9 1.0 CA B:MET473 4.9 48.0 1.0

Magnesium binding site 2 out of 4 in the Cryo-Em Structure of the Tetrameric Sparsa Grna-Ssdna-Nad+ Complex


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 Tetrameric Sparsa Grna-Ssdna-Nad+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg501 b:52.4 occ:1.00 OP1 G:A1 2.0 52.0 1.0 P G:A1 2.3 52.0 1.0 OP1 G:U3 2.9 65.4 1.0 OP2 G:A1 3.1 52.0 1.0 O F:MET473 3.1 51.0 1.0 ND2 F:ASN434 3.2 57.1 1.0 OE1 F:GLN181 3.3 47.5 1.0 C F:MET473 3.4 51.0 1.0 NZ F:LYS207 3.6 51.4 1.0 O5' G:A1 3.7 52.0 1.0 O3' G:U2 3.7 61.7 1.0 NE2 F:GLN181 3.9 47.5 1.0 CD F:GLN181 4.0 47.5 1.0 P G:U3 4.0 65.4 1.0 C5' G:A1 4.2 52.0 1.0 CG F:ASN434 4.3 57.1 1.0 CB F:ALA203 4.6 58.1 1.0 OD1 F:ASN434 4.7 57.1 1.0 O5' G:U3 4.9 65.4 1.0 CA F:MET473 4.9 51.0 1.0 CE F:LYS207 5.0 51.4 1.0 O2' G:U2 5.0 61.7 1.0

Magnesium binding site 3 out of 4 in the Cryo-Em Structure of the Tetrameric Sparsa Grna-Ssdna-Nad+ Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of the Tetrameric Sparsa Grna-Ssdna-Nad+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg101 b:58.2 occ:1.00 OP1 K:U3 2.0 60.9 1.0 OP1 K:A1 2.0 63.1 1.0 ND2 J:ASN434 2.2 53.8 1.0 P K:A1 2.4 63.1 1.0 P K:U3 3.2 60.9 1.0 O J:MET473 3.2 48.0 1.0 CG J:ASN434 3.3 53.8 1.0 O3' K:U2 3.4 63.9 1.0 OP2 K:A1 3.4 63.1 1.0 C J:MET473 3.4 48.0 1.0 NZ J:LYS207 3.6 46.9 1.0 O5' K:A1 3.6 63.1 1.0 OD1 J:ASN434 3.8 53.8 1.0 C5' K:A1 3.9 63.1 1.0 O5' K:U3 4.0 60.9 1.0 NZ J:LYS170 4.3 55.4 1.0 OP2 K:U3 4.4 60.9 1.0 CB J:ASN434 4.5 53.8 1.0 NE2 J:GLN181 4.6 57.2 1.0 CE J:LYS207 4.6 46.9 1.0 CG J:GLN181 4.7 57.2 1.0 C3' K:U2 4.7 63.9 1.0 O2' K:U2 4.8 63.9 1.0 CA J:MET473 4.9 48.0 1.0

Magnesium binding site 4 out of 4 in the Cryo-Em Structure of the Tetrameric Sparsa Grna-Ssdna-Nad+ Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of the Tetrameric Sparsa Grna-Ssdna-Nad+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg501 b:52.4 occ:1.00 OP1 O:A1 2.0 52.0 1.0 P O:A1 2.3 52.0 1.0 OP1 O:U3 2.9 65.4 1.0 OP2 O:A1 3.1 52.0 1.0 O N:MET473 3.1 51.0 1.0 ND2 N:ASN434 3.2 57.1 1.0 OE1 N:GLN181 3.3 47.5 1.0 C N:MET473 3.4 51.0 1.0 NZ N:LYS207 3.6 51.4 1.0 O5' O:A1 3.7 52.0 1.0 O3' O:U2 3.7 61.7 1.0 NE2 N:GLN181 3.9 47.5 1.0 CD N:GLN181 4.0 47.5 1.0 P O:U3 4.0 65.4 1.0 C5' O:A1 4.2 52.0 1.0 CG N:ASN434 4.3 57.1 1.0 CB N:ALA203 4.6 58.1 1.0 OD1 N:ASN434 4.7 57.1 1.0 O5' O:U3 4.9 65.4 1.0 CA N:MET473 4.9 51.0 1.0 CE N:LYS207 5.0 51.4 1.0 O2' O:U2 5.0 61.7 1.0

N.Cui, J.T.Zhang, Z.Li, X.Y.Wei, J.Wang, N.Jia. Tetramerization-Dependent Activation of the SIR2-Associated Short Prokaryotic Argonaute Immune System. Nat Commun V. 15 8610 2024.
ISSN: ESSN 2041-1723
PubMed: 39366953
DOI: 10.1038/S41467-024-52910-5