Magnesium in PDB 8ifm: Cryo-Em Structure of Tetrameric Sparta Grna-Ssdna Target Complex in State 2

The binding sites of Magnesium atom in the Cryo-Em Structure of Tetrameric Sparta Grna-Ssdna Target Complex in State 2 (pdb code 8ifm). 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 Tetrameric Sparta Grna-Ssdna Target Complex in State 2, PDB code: 8ifm:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Cryo-Em Structure of Tetrameric Sparta Grna-Ssdna Target Complex in State 2


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 Tetrameric Sparta Grna-Ssdna Target Complex in State 2 within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg601 b:62.4 occ:1.00 OP2 L:A1 2.1 74.1 1.0 OP1 L:A3 2.1 87.2 1.0 ND2 K:ASN468 2.2 43.8 1.0 OD1 K:ASN468 2.7 43.0 1.0 CG K:ASN468 2.7 42.0 1.0 P L:A1 3.1 77.2 1.0 C K:ILE507 3.2 47.9 1.0 P L:A3 3.4 86.8 1.0 O3' L:A2 3.5 73.3 1.0 O5' L:A1 3.6 77.1 1.0 CA K:ILE507 4.0 47.8 1.0 CB K:ASN468 4.1 35.1 1.0 C5' L:A3 4.1 88.5 1.0 O K:ILE507 4.1 51.0 1.0 CB K:ILE507 4.2 47.0 1.0 O5' L:A3 4.2 91.5 1.0 CE K:LYS485 4.3 59.9 1.0 OE1 K:GLN222 4.5 62.6 1.0 OP1 L:A1 4.5 71.4 1.0 OP2 L:A3 4.5 88.6 1.0 CG1 K:ILE507 4.6 43.9 1.0 C5' L:A1 4.6 75.4 1.0 O K:ASN468 4.7 38.7 1.0 NE2 K:GLN222 4.8 62.3 1.0 NZ K:LYS263 4.8 46.5 1.0 CA K:ASN468 4.9 34.3 1.0 C3' L:A2 4.9 74.1 1.0 NZ K:LYS485 5.0 60.7 1.0

Magnesium binding site 2 out of 4 in the Cryo-Em Structure of Tetrameric Sparta Grna-Ssdna Target Complex in State 2


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 Tetrameric Sparta Grna-Ssdna Target Complex in State 2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:36.8 occ:1.00 OP1 C:A3 2.0 48.8 1.0 O3' C:A2 2.2 41.9 1.0 OD1 B:ASN468 2.2 40.2 1.0 OP2 C:A1 2.5 47.9 1.0 P C:A3 2.5 43.5 1.0 CG B:ASN468 3.0 28.8 1.0 C5' C:A3 3.3 51.5 1.0 ND2 B:ASN468 3.3 35.5 1.0 O5' C:A3 3.4 53.5 1.0 C3' C:A2 3.5 48.3 1.0 O2' C:A2 3.6 37.5 1.0 O B:ASN468 3.6 45.1 1.0 P C:A1 3.8 31.0 1.0 OP2 C:A3 3.8 54.4 1.0 O5' C:A1 4.0 35.6 1.0 C2' C:A2 4.0 48.5 1.0 C4' C:A2 4.2 45.0 1.0 OE1 B:GLN222 4.3 46.7 1.0 NE2 B:GLN222 4.4 55.4 1.0 CB B:ASN468 4.4 27.1 1.0 C B:ASN468 4.5 36.7 1.0 C5' C:A1 4.6 38.0 1.0 CA B:ASN468 4.6 27.9 1.0 C B:ILE507 4.7 23.4 1.0 C4' C:A3 4.7 40.4 1.0 CD B:GLN222 4.8 45.6 1.0 OP1 C:A1 4.9 43.5 1.0 CB B:ALA259 4.9 20.7 1.0 C5' C:A2 5.0 43.2 1.0

Magnesium binding site 3 out of 4 in the Cryo-Em Structure of Tetrameric Sparta Grna-Ssdna Target Complex in State 2


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 Tetrameric Sparta Grna-Ssdna Target Complex in State 2 within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg101 b:55.0 occ:1.00 OP2 H:A1 2.0 46.9 1.0 OP1 H:A3 2.0 53.0 1.0 ND2 G:ASN468 2.1 49.3 1.0 O3' H:A2 2.4 45.8 1.0 P H:A3 2.7 37.8 1.0 CG G:ASN468 3.0 39.1 1.0 OD1 G:ASN468 3.1 45.4 1.0 P H:A1 3.2 27.4 1.0 C5' H:A3 3.4 49.6 1.0 O5' H:A1 3.4 33.2 1.0 O5' H:A3 3.5 46.4 1.0 C3' H:A2 3.7 46.5 1.0 O2' H:A2 3.8 33.5 1.0 O G:ASN468 3.9 51.5 1.0 OP2 H:A3 4.0 54.6 1.0 C2' H:A2 4.2 49.1 1.0 C G:ILE507 4.3 30.8 1.0 NE2 G:GLN222 4.3 54.5 1.0 OE1 G:GLN222 4.3 47.4 1.0 CB G:ASN468 4.4 40.3 1.0 OP1 H:A1 4.5 42.1 1.0 C4' H:A2 4.5 43.0 1.0 C5' H:A1 4.5 37.4 1.0 O G:ILE507 4.6 34.9 1.0 CD G:GLN222 4.8 46.8 1.0 C G:ASN468 4.8 44.9 1.0 CA G:ASN468 4.8 40.5 1.0 C4' H:A3 4.9 39.7 1.0

Magnesium binding site 4 out of 4 in the Cryo-Em Structure of Tetrameric Sparta Grna-Ssdna Target Complex in State 2


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 Tetrameric Sparta Grna-Ssdna Target Complex in State 2 within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg601 b:62.0 occ:1.00 OP2 P:A1 2.0 99.6 1.0 OP1 P:A3 2.1 99.5 1.0 ND2 O:ASN468 2.1 69.5 1.0 OD1 O:ASN468 2.5 68.8 1.0 CG O:ASN468 2.6 68.4 1.0 O O:ILE507 2.9 61.3 1.0 P P:A1 3.1 103.5 1.0 P P:A3 3.2 98.9 1.0 O3' P:A2 3.4 81.3 1.0 C5' P:A3 3.5 100.6 1.0 C O:ILE507 3.6 66.6 1.0 O5' P:A1 3.7 100.8 1.0 O5' P:A3 3.8 102.7 1.0 CB O:ASN468 4.1 64.5 1.0 CA O:ILE507 4.2 65.2 1.0 O O:ASN468 4.3 63.0 1.0 CB O:ILE507 4.5 64.7 1.0 OP1 P:A1 4.5 98.2 1.0 OP2 P:A3 4.5 102.5 1.0 CE O:LYS485 4.6 77.3 1.0 C5' P:A1 4.7 99.7 1.0 C3' P:A2 4.8 82.8 1.0 O2' P:A2 4.8 81.1 1.0 CA O:ASN468 4.8 64.6 1.0 C4' P:A3 5.0 101.3 1.0 OE1 O:GLN222 5.0 64.0 1.0

J.T.Zhang, X.Y.Wei, N.Cui, R.Tian, N.Jia. Target Ssdna Activates the Nadase Activity of Prokaryotic Sparta Immune System Nat.Chem.Biol. 2023.
ISSN: ESSN 1552-4469
DOI: 10.1038/S41589-023-01479-Z