Magnesium in PDB 8qlp: Cryoem Structure of the Rna/Dna Bound Sparta (Babago/Tir-Apaz) Tetrameric Complex

The binding sites of Magnesium atom in the Cryoem Structure of the Rna/Dna Bound Sparta (Babago/Tir-Apaz) Tetrameric Complex (pdb code 8qlp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Cryoem Structure of the Rna/Dna Bound Sparta (Babago/Tir-Apaz) Tetrameric Complex, PDB code: 8qlp:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Cryoem Structure of the Rna/Dna Bound Sparta (Babago/Tir-Apaz) Tetrameric Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryoem Structure of the Rna/Dna Bound Sparta (Babago/Tir-Apaz) Tetrameric Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1000 b:97.8 occ:1.00 O B:ILE507 2.0 79.6 1.0 OP1 C:A3 2.0 102.4 1.0 OP2 C:U1 2.0 96.2 1.0 OD1 B:ASN468 2.1 79.8 1.0 CG B:ASN468 2.9 79.8 1.0 P C:U1 3.1 96.2 1.0 ND2 B:ASN468 3.1 79.8 1.0 C B:ILE507 3.2 79.6 1.0 P C:A3 3.4 102.4 1.0 OP1 C:U1 3.5 96.2 1.0 O5' C:U1 3.7 96.2 1.0 O3' C:G2 3.9 92.2 1.0 OXT B:ILE507 3.9 79.6 1.0 NZ B:LYS263 4.2 64.4 1.0 CA B:ILE507 4.2 79.6 1.0 O5' C:A3 4.3 102.4 1.0 CB B:ASN468 4.3 79.8 1.0 CB B:ILE507 4.4 79.6 1.0 OP2 C:A3 4.4 102.4 1.0 OP3 C:U1 4.4 91.1 1.0 CE B:LYS263 4.5 64.4 1.0 OE1 B:GLN222 4.6 78.3 1.0 C5' C:U1 4.7 96.2 1.0 NE2 B:GLN222 4.7 78.3 1.0 O B:ASN468 4.9 79.8 1.0 CA B:ASN468 4.9 79.8 1.0 CG1 B:ILE507 5.0 79.6 1.0

Magnesium binding site 2 out of 4 in the Cryoem Structure of the Rna/Dna Bound Sparta (Babago/Tir-Apaz) Tetrameric Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryoem Structure of the Rna/Dna Bound Sparta (Babago/Tir-Apaz) Tetrameric Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg1000 b:87.0 occ:1.00 OD1 F:ASN468 2.0 78.8 1.0 O F:ILE507 2.0 71.7 1.0 OP2 G:U1 2.1 89.2 1.0 OP1 G:A3 2.1 92.2 1.0 CG F:ASN468 3.0 78.8 1.0 C F:ILE507 3.2 71.7 1.0 P G:U1 3.4 89.2 1.0 ND2 F:ASN468 3.5 78.8 1.0 P G:A3 3.5 92.2 1.0 OP1 G:U1 3.8 89.2 1.0 OXT F:ILE507 3.8 71.7 1.0 O3' G:G2 4.1 90.1 1.0 OE1 F:GLN222 4.1 69.9 1.0 NE2 F:GLN222 4.1 69.9 1.0 NZ F:LYS263 4.1 66.2 1.0 O5' G:A3 4.2 92.2 1.0 CE F:LYS263 4.3 66.2 1.0 O5' G:U1 4.3 89.2 1.0 CA F:ILE507 4.3 71.7 1.0 CB F:ASN468 4.4 78.8 1.0 OP3 G:U1 4.4 82.1 1.0 CD F:GLN222 4.5 69.9 1.0 C5' G:U1 4.6 89.2 1.0 OP2 G:A3 4.6 92.2 1.0 CB F:ILE507 4.6 71.7 1.0 CA F:ASN468 4.7 78.8 1.0 O F:ASN468 4.8 78.8 1.0 CG1 F:ILE507 4.9 71.7 1.0

Magnesium binding site 3 out of 4 in the Cryoem Structure of the Rna/Dna Bound Sparta (Babago/Tir-Apaz) Tetrameric Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryoem Structure of the Rna/Dna Bound Sparta (Babago/Tir-Apaz) Tetrameric Complex within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg1000 b:97.8 occ:1.00 O J:ILE507 2.0 79.6 1.0 OP1 K:A3 2.0 102.4 1.0 OP2 K:U1 2.0 96.2 1.0 OD1 J:ASN468 2.1 79.8 1.0 CG J:ASN468 2.9 79.8 1.0 P K:U1 3.1 96.2 1.0 ND2 J:ASN468 3.1 79.8 1.0 C J:ILE507 3.2 79.6 1.0 P K:A3 3.4 102.4 1.0 OP1 K:U1 3.5 96.2 1.0 O5' K:U1 3.7 96.2 1.0 O3' K:G2 3.9 92.2 1.0 OXT J:ILE507 3.9 79.6 1.0 NZ J:LYS263 4.2 64.4 1.0 CA J:ILE507 4.2 79.6 1.0 O5' K:A3 4.3 102.4 1.0 CB J:ASN468 4.3 79.8 1.0 CB J:ILE507 4.4 79.6 1.0 OP2 K:A3 4.4 102.4 1.0 OP3 K:U1 4.4 91.1 1.0 CE J:LYS263 4.5 64.4 1.0 OE1 J:GLN222 4.6 78.3 1.0 C5' K:U1 4.7 96.2 1.0 NE2 J:GLN222 4.7 78.3 1.0 O J:ASN468 4.9 79.8 1.0 CA J:ASN468 4.9 79.8 1.0 CG1 J:ILE507 5.0 79.6 1.0

Magnesium binding site 4 out of 4 in the Cryoem Structure of the Rna/Dna Bound Sparta (Babago/Tir-Apaz) Tetrameric Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryoem Structure of the Rna/Dna Bound Sparta (Babago/Tir-Apaz) Tetrameric Complex within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg1000 b:87.0 occ:1.00 OD1 N:ASN468 2.0 78.8 1.0 O N:ILE507 2.0 71.7 1.0 OP2 O:U1 2.1 89.2 1.0 OP1 O:A3 2.1 92.2 1.0 CG N:ASN468 3.0 78.8 1.0 C N:ILE507 3.2 71.7 1.0 P O:U1 3.4 89.2 1.0 ND2 N:ASN468 3.5 78.8 1.0 P O:A3 3.5 92.2 1.0 OP1 O:U1 3.8 89.2 1.0 OXT N:ILE507 3.8 71.7 1.0 O3' O:G2 4.1 90.1 1.0 OE1 N:GLN222 4.1 69.9 1.0 NE2 N:GLN222 4.1 69.9 1.0 NZ N:LYS263 4.1 66.2 1.0 O5' O:A3 4.2 92.2 1.0 CE N:LYS263 4.3 66.2 1.0 O5' O:U1 4.3 89.2 1.0 CA N:ILE507 4.3 71.7 1.0 CB N:ASN468 4.4 78.8 1.0 OP3 O:U1 4.4 82.1 1.0 CD N:GLN222 4.5 69.9 1.0 C5' O:U1 4.6 89.2 1.0 OP2 O:A3 4.6 92.2 1.0 CB N:ILE507 4.6 71.7 1.0 CA N:ASN468 4.7 78.8 1.0 O N:ASN468 4.8 78.8 1.0 CG1 N:ILE507 4.9 71.7 1.0

G.Finocchio, B.Koopal, A.Potocnik, C.Heijstek, A.H.Westphal, M.Jinek, D.C.Swarts. Target Dna-Dependent Activation Mechanism of the Prokaryotic Immune System Sparta. Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
PubMed: 38224450
DOI: 10.1093/NAR/GKAD1248