Magnesium in PDB 8spo: Tetramerized Activation of Mapsparta Bound with Nad+

The binding sites of Magnesium atom in the Tetramerized Activation of Mapsparta Bound with Nad+ (pdb code 8spo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Tetramerized Activation of Mapsparta Bound with Nad+, PDB code: 8spo:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Tetramerized Activation of Mapsparta Bound with Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tetramerized Activation of Mapsparta Bound with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:28.3 occ:1.00 OD1 B:ASN468 2.4 26.9 1.0 OP1 C:A3 2.7 38.0 1.0 OP1 C:U1 2.9 40.8 1.0 OXT B:ILE507 3.2 25.1 1.0 CG B:ASN468 3.4 23.5 1.0 NZ B:LYS263 3.6 20.9 1.0 P C:U1 3.8 17.3 1.0 OE1 B:GLN222 3.8 23.7 1.0 P C:A3 3.9 18.5 1.0 O3' C:G2 3.9 42.9 1.0 ND2 B:ASN468 3.9 26.9 1.0 CE B:LYS263 4.0 23.5 1.0 C B:ILE507 4.4 29.9 1.0 OP2 C:U1 4.5 34.7 1.0 CB B:ALA259 4.5 20.5 1.0 O5' C:A3 4.5 42.7 1.0 O B:ASN468 4.5 25.7 1.0 NE2 B:GLN222 4.6 25.4 1.0 CD B:GLN222 4.6 19.2 1.0 CB B:ASN468 4.7 26.8 1.0 CA B:ASN468 4.9 18.6 1.0

Magnesium binding site 2 out of 4 in the Tetramerized Activation of Mapsparta Bound with Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tetramerized Activation of Mapsparta Bound with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg601 b:21.7 occ:1.00 OP2 G:U1 1.9 41.7 1.0 OP1 G:A3 2.1 37.0 1.0 OXT F:ILE507 2.5 45.5 1.0 OD1 F:ASN468 2.6 36.0 1.0 P G:U1 3.4 37.9 1.0 CG F:ASN468 3.4 32.5 1.0 P G:A3 3.4 28.2 1.0 ND2 F:ASN468 3.5 35.4 1.0 NZ F:LYS263 3.7 34.7 1.0 C F:ILE507 3.8 44.4 1.0 O3' G:G2 3.8 28.9 1.0 O5' G:U1 4.0 36.6 1.0 C5' G:U1 4.2 37.1 1.0 OP1 G:U1 4.3 44.3 1.0 OP2 G:A3 4.4 26.6 1.0 O5' G:A3 4.5 35.2 1.0 CA F:ILE507 4.5 37.1 1.0 O F:ILE507 4.6 47.6 1.0 CE F:LYS263 4.7 33.0 1.0 CB F:ILE507 4.8 35.2 1.0 NE2 F:GLN222 4.8 29.7 1.0 OE1 F:GLN222 4.8 22.6 1.0 CB F:ASN468 4.9 30.6 1.0

Magnesium binding site 3 out of 4 in the Tetramerized Activation of Mapsparta Bound with Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tetramerized Activation of Mapsparta Bound with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg601 b:20.2 occ:1.00 OP2 J:U1 2.0 31.9 1.0 O L:ILE507 2.5 34.7 1.0 OP1 J:A3 2.5 32.8 1.0 OD1 L:ASN468 2.6 27.3 1.0 NZ L:LYS263 3.3 23.4 1.0 P J:U1 3.4 32.0 1.0 CG L:ASN468 3.4 21.9 1.0 ND2 L:ASN468 3.6 29.2 1.0 C L:ILE507 3.7 34.4 1.0 P J:A3 3.8 21.0 1.0 O3' J:G2 4.0 15.0 1.0 O5' J:U1 4.0 24.9 1.0 OE1 L:GLN222 4.2 23.1 1.0 C5' J:U1 4.3 21.6 1.0 CE L:LYS263 4.4 21.6 1.0 OXT L:ILE507 4.4 39.7 1.0 OP1 J:U1 4.5 36.2 1.0 CA L:ILE507 4.6 29.6 1.0 CB L:ILE507 4.7 27.9 1.0 O5' J:A3 4.8 29.3 1.0 NE2 L:GLN222 4.8 20.3 1.0 OP2 J:A3 4.8 31.1 1.0 CB L:ASN468 4.9 16.8 1.0 CD L:GLN222 4.9 17.0 1.0

Magnesium binding site 4 out of 4 in the Tetramerized Activation of Mapsparta Bound with Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tetramerized Activation of Mapsparta Bound with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg601 b:38.1 occ:1.00 OD1 N:ASN468 2.2 37.1 1.0 OP2 O:U1 2.2 35.6 1.0 OP1 O:A3 2.5 38.7 1.0 OXT N:ILE507 2.6 31.9 1.0 CG N:ASN468 3.2 22.8 1.0 P O:U1 3.6 23.6 1.0 ND2 N:ASN468 3.6 26.2 1.0 C N:ILE507 3.8 36.0 1.0 P O:A3 3.8 20.0 1.0 O3' O:G2 4.0 22.2 1.0 NZ N:LYS263 4.1 19.4 1.0 OE1 N:GLN222 4.1 26.9 1.0 OP1 O:U1 4.2 31.2 1.0 CE N:LYS263 4.4 18.6 1.0 CB N:ILE507 4.4 27.5 1.0 CA N:ILE507 4.4 29.3 1.0 CB N:ASN468 4.6 22.6 1.0 NE2 N:GLN222 4.6 25.2 1.0 O5' O:U1 4.7 29.9 1.0 O N:ILE507 4.7 36.1 1.0 O5' O:A3 4.7 40.3 1.0 CD N:GLN222 4.8 25.2 1.0 O N:ASN468 4.8 27.9 1.0 C5' O:U1 4.9 34.4 1.0 OP2 O:A3 4.9 39.6 1.0 CA N:ASN468 4.9 24.3 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