Magnesium in PDB 8ffi: Structure of Tetramerized Mapsparta Upon Guide Rna-Mediated Target Dna Binding

The binding sites of Magnesium atom in the Structure of Tetramerized Mapsparta Upon Guide Rna-Mediated Target Dna Binding (pdb code 8ffi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Tetramerized Mapsparta Upon Guide Rna-Mediated Target Dna Binding, PDB code: 8ffi:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of Tetramerized Mapsparta Upon Guide Rna-Mediated Target Dna Binding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Tetramerized Mapsparta Upon Guide Rna-Mediated Target Dna Binding within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:34.8 occ:1.00 OD1 B:ASN468 2.4 29.9 1.0 OP1 C:A3 2.8 35.6 1.0 OP1 C:U1 2.9 35.9 1.0 OXT B:ILE507 3.2 27.7 1.0 CG B:ASN468 3.4 23.1 1.0 NZ B:LYS263 3.6 15.9 1.0 P C:U1 3.8 8.7 1.0 OE1 B:GLN222 3.8 22.8 1.0 ND2 B:ASN468 3.8 27.7 1.0 O3' C:G2 3.9 37.4 1.0 P C:A3 3.9 17.1 1.0 CE B:LYS263 3.9 20.4 1.0 C B:ILE507 4.4 30.6 1.0 CB B:ALA259 4.5 15.3 1.0 OP2 C:U1 4.5 32.1 1.0 O B:ASN468 4.5 25.2 1.0 O5' C:A3 4.5 41.4 1.0 NE2 B:GLN222 4.6 25.9 1.0 CD B:GLN222 4.6 18.5 1.0 CB B:ASN468 4.7 25.0 1.0 CA B:ASN468 4.9 15.2 1.0

Magnesium binding site 2 out of 4 in the Structure of Tetramerized Mapsparta Upon Guide Rna-Mediated Target Dna Binding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Tetramerized Mapsparta Upon Guide Rna-Mediated Target Dna Binding within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg601 b:22.7 occ:1.00 OP2 G:U1 2.0 41.0 1.0 OP1 G:A3 2.1 38.2 1.0 OD1 F:ASN468 2.5 39.1 1.0 OXT F:ILE507 2.6 45.3 1.0 CG F:ASN468 3.4 30.2 1.0 P G:U1 3.5 34.9 1.0 ND2 F:ASN468 3.5 33.2 1.0 P G:A3 3.5 26.1 1.0 NZ F:LYS263 3.6 27.6 1.0 C F:ILE507 3.8 43.6 1.0 O3' G:G2 3.8 26.4 1.0 O5' G:U1 4.2 34.4 1.0 OP1 G:U1 4.4 42.3 1.0 C5' G:U1 4.4 31.4 1.0 O5' G:A3 4.4 35.0 1.0 OP2 G:A3 4.5 26.9 1.0 CA F:ILE507 4.6 33.9 1.0 CE F:LYS263 4.6 27.9 1.0 O F:ILE507 4.6 48.0 1.0 OE1 F:GLN222 4.7 22.2 1.0 CB F:ILE507 4.7 32.4 1.0 CB F:ASN468 4.8 25.7 1.0 NE2 F:GLN222 4.8 23.8 1.0

Magnesium binding site 3 out of 4 in the Structure of Tetramerized Mapsparta Upon Guide Rna-Mediated Target Dna Binding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Tetramerized Mapsparta Upon Guide Rna-Mediated Target Dna Binding within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg601 b:23.2 occ:1.00 OP2 J:U1 2.1 33.6 1.0 OD1 L:ASN468 2.5 30.7 1.0 O L:ILE507 2.5 38.6 1.0 OP1 J:A3 2.5 39.3 1.0 CG L:ASN468 3.3 22.8 1.0 NZ L:LYS263 3.4 21.2 1.0 ND2 L:ASN468 3.5 30.4 1.0 P J:U1 3.5 31.8 1.0 C L:ILE507 3.7 36.6 1.0 P J:A3 3.8 25.7 1.0 O3' J:G2 4.0 22.8 1.0 O5' J:U1 4.1 29.6 1.0 OE1 L:GLN222 4.2 21.8 1.0 CE L:LYS263 4.4 14.0 1.0 OXT L:ILE507 4.4 45.0 1.0 C5' J:U1 4.4 22.1 1.0 OP1 J:U1 4.5 38.5 1.0 CA L:ILE507 4.6 25.5 1.0 O5' J:A3 4.7 38.8 1.0 CB L:ILE507 4.7 24.4 1.0 CB L:ASN468 4.8 16.1 1.0 NE2 L:GLN222 4.8 17.2 1.0 OP2 J:A3 4.9 44.0 1.0 CD L:GLN222 4.9 14.1 1.0

Magnesium binding site 4 out of 4 in the Structure of Tetramerized Mapsparta Upon Guide Rna-Mediated Target Dna Binding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Tetramerized Mapsparta Upon Guide Rna-Mediated Target Dna Binding within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg601 b:37.1 occ:1.00 OD1 N:ASN468 2.2 37.5 1.0 OP2 O:U1 2.2 39.9 1.0 OXT N:ILE507 2.5 30.9 1.0 OP1 O:A3 2.6 39.2 1.0 CG N:ASN468 3.2 22.4 1.0 P O:U1 3.6 24.4 1.0 ND2 N:ASN468 3.6 24.9 1.0 C N:ILE507 3.7 35.8 1.0 P O:A3 3.9 22.1 1.0 O3' O:G2 4.0 38.5 1.0 NZ N:LYS263 4.1 13.4 1.0 OE1 N:GLN222 4.1 29.8 1.0 OP1 O:U1 4.2 31.8 1.0 CE N:LYS263 4.4 11.9 1.0 CB N:ILE507 4.4 24.5 1.0 CA N:ILE507 4.4 29.1 1.0 NE2 N:GLN222 4.6 24.9 1.0 CB N:ASN468 4.6 21.9 1.0 O5' O:A3 4.6 43.8 1.0 O N:ILE507 4.6 35.6 1.0 O5' O:U1 4.7 34.5 1.0 CD N:GLN222 4.8 23.7 1.0 O N:ASN468 4.8 26.7 1.0 C5' O:U1 4.9 38.9 1.0 CA N:ASN468 5.0 20.8 1.0

Z.Shen, X.Y.Yang, S.Xia, W.Huang, D.J.Taylor, K.Nakanishi, T.M.Fu. Oligomerization-Mediated Activation of A Short Prokaryotic Argonaute. Nature 2023.
ISSN: ESSN 1476-4687
PubMed: 37494956
DOI: 10.1038/S41586-023-06456-Z