Magnesium in PDB 8ifl: Cryo-Em Structure of Tetrameric Sparta Grna-Ssdna Target Complex in State 1

The binding sites of Magnesium atom in the Cryo-Em Structure of Tetrameric Sparta Grna-Ssdna Target Complex in State 1 (pdb code 8ifl). 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 1, PDB code: 8ifl:
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 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:49.5 occ:1.00 OD1 B:ASN468 2.0 45.1 1.0 C B:ILE507 2.1 64.3 1.0 OP2 C:A1 2.3 61.0 1.0 CG B:ASN468 2.7 44.2 1.0 CA B:ILE507 2.7 56.6 1.0 CB B:ILE507 2.8 64.2 1.0 OP1 C:A3 3.0 65.5 1.0 O B:ILE507 3.0 73.8 1.0 ND2 B:ASN468 3.2 53.8 1.0 P C:A1 3.5 60.2 1.0 CG2 B:ILE507 3.8 69.2 1.0 CB B:ASN468 3.8 44.1 1.0 CG1 B:ILE507 3.8 57.9 1.0 NZ B:LYS263 4.0 56.2 1.0 N B:ILE507 4.1 65.6 1.0 OP1 C:A1 4.3 55.8 1.0 CD1 B:ILE507 4.3 57.4 1.0 P C:A3 4.3 50.7 1.0 NZ B:LYS485 4.4 53.5 1.0 CA B:ASN468 4.5 36.2 1.0 O3' C:A2 4.6 32.2 1.0 O5' C:A1 4.7 54.2 1.0 O B:ASN468 4.8 50.3 1.0 O B:TYR506 4.8 57.0 1.0 CE B:LYS263 4.8 53.9 1.0 OE1 B:GLN222 4.9 56.2 1.0 C B:TYR506 5.0 55.9 1.0 CE B:LYS485 5.0 46.6 1.0

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


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg101 b:59.1 occ:1.00 OP1 H:A3 1.9 84.9 1.0 OP2 H:A1 2.0 69.8 1.0 ND2 G:ASN468 2.1 52.9 1.0 O3' H:A2 2.5 48.9 1.0 P H:A3 2.7 72.7 1.0 P H:A1 3.1 57.0 1.0 CG G:ASN468 3.1 60.0 1.0 OD1 G:ASN468 3.3 63.6 1.0 O G:ILE507 3.4 66.7 1.0 O5' H:A1 3.4 61.4 1.0 C5' H:A3 3.5 90.5 1.0 O5' H:A3 3.6 87.0 1.0 C3' H:A2 3.9 64.7 1.0 O G:ASN468 4.0 57.9 1.0 OP2 H:A3 4.0 90.2 1.0 O2' H:A2 4.1 65.8 1.0 OP1 H:A1 4.4 53.8 1.0 CB G:ASN468 4.4 55.7 1.0 NE2 G:GLN222 4.4 61.0 1.0 C2' H:A2 4.5 75.3 1.0 C4' H:A2 4.6 67.1 1.0 C G:ILE507 4.6 75.1 1.0 C5' H:A1 4.6 58.9 1.0 CA G:ASN468 4.8 47.7 1.0 C G:ASN468 4.8 59.6 1.0 OE1 G:GLN222 4.8 49.7 1.0 C4' H:A3 5.0 85.0 1.0

Magnesium binding site 3 out of 4 in the Cryo-Em Structure of Tetrameric Sparta Grna-Ssdna Target Complex in State 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg101 b:93.7 occ:1.00 O3' L:A2 2.0 109.6 1.0 OP1 L:A3 2.0 118.8 1.0 ND2 K:ASN468 2.1 88.3 1.0 P L:A3 2.4 124.1 1.0 OP2 L:A1 2.8 107.2 1.0 C5' L:A3 2.9 120.6 1.0 CG K:ASN468 2.9 87.6 1.0 O5' L:A3 3.1 120.2 1.0 OD1 K:ASN468 3.1 90.0 1.0 C3' L:A2 3.2 110.3 1.0 O2' L:A2 3.3 108.2 1.0 O K:ASN468 3.6 95.7 1.0 O5' L:A1 3.6 109.9 1.0 P L:A1 3.6 103.5 1.0 C2' L:A2 3.7 113.7 1.0 OP2 L:A3 3.8 121.1 1.0 C4' L:A2 4.1 105.2 1.0 C4' L:A3 4.3 113.7 1.0 CB K:ASN468 4.3 84.1 1.0 OE1 K:GLN222 4.4 100.1 1.0 C K:ASN468 4.5 92.1 1.0 CA K:ASN468 4.7 85.0 1.0 C5' L:A1 4.8 110.4 1.0 NE2 K:GLN222 4.8 104.9 1.0 O4' L:A3 4.9 114.9 1.0 C5' L:A2 4.9 106.7 1.0

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


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg101 b:63.2 occ:1.00 O3' P:A2 1.9 94.0 1.0 OD1 O:ASN468 2.2 71.2 1.0 OP1 P:A3 2.2 107.2 1.0 P P:A3 2.3 115.1 1.0 C5' P:A3 2.4 101.3 1.0 O2' P:A2 2.6 88.0 1.0 O5' P:A3 2.7 101.8 1.0 OP2 P:A1 2.9 92.0 1.0 C3' P:A2 2.9 94.7 1.0 CG O:ASN468 3.0 75.0 1.0 C2' P:A2 3.1 95.3 1.0 O O:ASN468 3.1 73.8 1.0 ND2 O:ASN468 3.4 78.6 1.0 C4' P:A3 3.7 101.3 1.0 OP2 P:A3 3.8 112.7 1.0 C4' P:A2 4.0 93.7 1.0 C O:ASN468 4.0 73.6 1.0 P P:A1 4.0 96.3 1.0 CB O:ASN468 4.2 68.7 1.0 O4' P:A3 4.2 105.0 1.0 O5' P:A1 4.2 98.9 1.0 CA O:ASN468 4.3 66.2 1.0 C1' P:A2 4.5 93.0 1.0 OE1 O:GLN222 4.7 74.0 1.0 O4' P:A2 4.9 92.2 1.0 C3' P:A3 4.9 100.6 1.0 O O:ILE507 5.0 74.3 1.0 CG2 O:THR255 5.0 59.2 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