Magnesium in PDB 8i87: Cryo-Em Structure of Tir-Apaz/Ago-Grna-Dna Complex

The binding sites of Magnesium atom in the Cryo-Em Structure of Tir-Apaz/Ago-Grna-Dna Complex (pdb code 8i87). 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 Tir-Apaz/Ago-Grna-Dna Complex, PDB code: 8i87:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Cryo-Em Structure of Tir-Apaz/Ago-Grna-Dna Complex


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 Tir-Apaz/Ago-Grna-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:28.1 occ:1.00 OD1 B:ASN468 2.1 50.3 1.0 OP1 I:A3 2.6 37.6 1.0 O B:ILE507 2.6 47.1 1.0 OP3 I:U1 3.0 56.7 1.0 CG B:ASN468 3.0 30.3 1.0 OP1 I:U1 3.2 56.0 1.0 ND2 B:ASN468 3.4 35.5 1.0 P I:U1 3.7 58.4 1.0 P I:A3 3.8 35.4 1.0 C B:ILE507 3.8 47.4 1.0 O3' I:G2 3.9 31.1 1.0 C5' I:A3 4.3 38.7 1.0 CB B:ASN468 4.4 28.3 1.0 O B:ASN468 4.5 50.4 1.0 O5' I:A3 4.6 35.1 1.0 CA B:ILE507 4.6 35.3 1.0 CB B:ILE507 4.7 27.2 1.0 OP2 I:U1 4.8 53.9 1.0 C5' I:U1 4.8 47.8 1.0 O5' I:U1 4.8 50.3 1.0 CE B:LYS263 4.8 24.8 1.0 CA B:ASN468 4.9 28.4 1.0 NE2 B:GLN222 4.9 45.1 1.0 OE1 B:GLN222 5.0 40.1 1.0 OP2 I:A3 5.0 38.8 1.0

Magnesium binding site 2 out of 4 in the Cryo-Em Structure of Tir-Apaz/Ago-Grna-Dna Complex


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 Tir-Apaz/Ago-Grna-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:14.9 occ:1.00 OD1 D:ASN468 2.2 42.4 1.0 OP1 L:U1 2.5 69.8 1.0 OP1 L:A3 2.6 57.9 1.0 CG D:ASN468 3.2 32.8 1.0 OP3 L:U1 3.6 66.4 1.0 P L:U1 3.6 50.8 1.0 ND2 D:ASN468 3.6 40.1 1.0 NZ D:LYS263 3.7 35.0 1.0 P L:A3 3.8 35.8 1.0 O3' L:G2 3.8 29.9 1.0 C D:ILE507 3.8 45.9 1.0 OP2 L:U1 4.4 70.5 1.0 OE1 D:GLN222 4.4 55.6 1.0 O D:ILE507 4.5 52.0 1.0 C5' L:A3 4.5 59.3 1.0 O D:ASN468 4.6 48.1 1.0 CB D:ASN468 4.6 39.0 1.0 CE D:LYS263 4.6 32.3 1.0 O5' L:A3 4.6 54.1 1.0 CA D:ILE507 4.7 30.3 1.0 CB D:ALA259 4.8 33.1 1.0 O5' L:U1 4.8 63.1 1.0 CB D:ILE507 4.8 32.9 1.0 CA D:ASN468 4.9 36.1 1.0 OP2 L:A3 4.9 54.4 1.0

Magnesium binding site 3 out of 4 in the Cryo-Em Structure of Tir-Apaz/Ago-Grna-Dna Complex


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 Tir-Apaz/Ago-Grna-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg601 b:22.9 occ:1.00 OD1 F:ASN468 2.0 54.7 1.0 OP1 S:U1 2.4 58.8 1.0 OP1 S:A3 2.5 45.6 1.0 O F:ILE507 2.8 57.7 1.0 CG F:ASN468 3.0 44.8 1.0 ND2 F:ASN468 3.3 46.4 1.0 P S:U1 3.7 42.4 1.0 P S:A3 3.7 48.6 1.0 O3' S:G2 3.7 56.6 1.0 OP3 S:U1 3.9 58.2 1.0 C F:ILE507 4.0 44.4 1.0 CB F:ASN468 4.4 37.6 1.0 C5' S:A3 4.4 50.8 1.0 O F:ASN468 4.4 50.2 1.0 OE1 F:GLN222 4.4 43.7 1.0 NE2 F:GLN222 4.5 37.7 1.0 O5' S:A3 4.6 56.2 1.0 OP2 S:U1 4.6 50.9 1.0 CE F:LYS263 4.6 26.9 1.0 O5' S:U1 4.8 57.6 1.0 CA F:ASN468 4.8 34.5 1.0 CA F:ILE507 4.8 29.4 1.0 CB F:ILE507 4.8 39.6 1.0 CD F:GLN222 4.9 38.2 1.0 OP2 S:A3 4.9 49.1 1.0 C5' S:U1 4.9 60.1 1.0 CB F:ALA259 4.9 23.0 1.0

Magnesium binding site 4 out of 4 in the Cryo-Em Structure of Tir-Apaz/Ago-Grna-Dna Complex


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 Tir-Apaz/Ago-Grna-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg101 b:15.3 occ:1.00 OP1 H:U1 2.1 57.5 1.0 OD1 T:ASN468 2.3 45.8 1.0 OP1 H:A3 2.5 48.3 1.0 CG T:ASN468 3.2 34.8 1.0 P H:U1 3.4 43.6 1.0 ND2 T:ASN468 3.4 35.2 1.0 NZ T:LYS263 3.5 44.5 1.0 P H:A3 3.8 20.6 1.0 OP3 H:U1 3.8 54.1 1.0 C T:ILE507 3.8 44.3 1.0 O3' H:G2 3.8 33.5 1.0 OP2 H:U1 4.2 47.9 1.0 CA T:ILE507 4.5 25.7 1.0 O5' H:U1 4.5 52.2 1.0 C5' H:A3 4.6 48.4 1.0 O T:ILE507 4.6 52.6 1.0 CB T:ASN468 4.6 27.7 1.0 OE1 T:GLN222 4.6 40.8 1.0 O5' H:A3 4.7 52.1 1.0 CB T:ILE507 4.7 32.5 1.0 C5' H:U1 4.8 55.5 1.0 O T:ASN468 4.8 38.0 1.0 OP2 H:A3 4.9 41.5 1.0 CE T:LYS263 4.9 30.4 1.0 NE2 T:GLN222 4.9 47.8 1.0

X.Wang, X.Li, G.Yu, L.Zhang, C.Zhang, Y.Wang, F.Liao, Y.Wen, H.Yin, X.Liu, Y.Wei, Z.Li, Z.Deng, H.Zhang. Structural Insights Into Mechanisms of Argonaute Protein-Associated Nadase Activation in Bacterial Immunity. Cell Res. 2023.
ISSN: ISSN 1001-0602
PubMed: 37311833
DOI: 10.1038/S41422-023-00839-7