Magnesium in PDB 8r3z: Cryo-Em Structure of the Asgard Archaeal Argonaute HRAGO1 Bound to A Guide Rna

The binding sites of Magnesium atom in the Cryo-Em Structure of the Asgard Archaeal Argonaute HRAGO1 Bound to A Guide Rna (pdb code 8r3z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Cryo-Em Structure of the Asgard Archaeal Argonaute HRAGO1 Bound to A Guide Rna, PDB code: 8r3z:

Magnesium binding site 1 out of 1 in the Cryo-Em Structure of the Asgard Archaeal Argonaute HRAGO1 Bound to A Guide Rna


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 the Asgard Archaeal Argonaute HRAGO1 Bound to A Guide Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1000 b:140.8 occ:1.00 OP3 B:U1 1.9 286.4 1.0 OP1 B:A3 2.4 309.8 1.0 O A:LEU817 2.4 156.0 1.0 OXT A:LEU817 2.5 155.6 1.0 OP2 B:U1 2.6 287.6 1.0 OE1 A:GLN551 2.7 128.0 1.0 P B:U1 2.8 286.6 1.0 C A:LEU817 2.9 155.4 1.0 CD A:GLN551 3.3 127.4 1.0 NE2 A:GLN551 3.3 128.9 1.0 P B:A3 3.8 310.3 1.0 OP1 B:U1 3.8 284.6 1.0 O5' B:U1 3.9 287.4 1.0 C5' B:A3 4.0 309.8 1.0 C5' B:U1 4.1 288.4 1.0 O3' B:G2 4.1 297.2 1.0 OE1 A:GLN528 4.3 130.8 1.0 CA A:LEU817 4.4 154.3 1.0 O5' B:A3 4.4 310.4 1.0 CG A:GLN551 4.6 126.8 1.0 NZ A:LYS516 4.8 136.0 1.0 NE2 A:GLN528 4.9 129.9 1.0 O A:TYR816 4.9 116.2 1.0 OP2 B:A3 5.0 311.2 1.0

G.Finocchio, D.Swarts, M.Jinek. Rna-Guided Rna Silencing By An Asgard Archaeal Argonaute Nat Commun 2024.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-024-49452-1