Magnesium in PDB 9k6t: Cryo-Em Structure of HAGO2D669A-Sirna-Target (21-Nt)

The binding sites of Magnesium atom in the Cryo-Em Structure of HAGO2D669A-Sirna-Target (21-Nt) (pdb code 9k6t). 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 HAGO2D669A-Sirna-Target (21-Nt), PDB code: 9k6t:

Magnesium binding site 1 out of 1 in the Cryo-Em Structure of HAGO2D669A-Sirna-Target (21-Nt)


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 HAGO2D669A-Sirna-Target (21-Nt) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:30.0 occ:1.00 OP1 C:G12 2.7 88.9 1.0 ND1 A:HIS807 2.7 9.0 1.0 OD2 A:ASP597 2.9 14.1 1.0 CE1 A:HIS807 3.0 14.1 1.0 OD1 A:ASP597 3.4 26.8 1.0 CG A:ASP597 3.5 22.4 1.0 P C:G12 3.9 86.7 1.0 CG A:HIS807 3.9 9.1 1.0 O5' C:G12 3.9 88.6 1.0 NE2 A:HIS807 4.2 3.9 1.0 CA A:GLY670 4.3 31.1 1.0 N A:GLY670 4.6 40.8 1.0 CB A:HIS807 4.6 9.4 1.0 CD2 A:HIS807 4.6 12.7 1.0 C5' C:G12 4.8 90.6 1.0 OP2 C:G12 4.8 96.8 1.0 O A:VAL598 4.8 27.5 1.0 CB A:ASP597 4.9 18.0 1.0 O3' C:A11 5.0 98.2 1.0

Z.Li, Q.Xu, Y.Zhang, J.Zhong, T.Zhang, J.Xue, S.Liu, H.Gao, Z.Z.Z.Zhang, J.Wu, E.Z.Shen. Mechanistic Insights Into Rna Cleavage By Human ARGONAUTE2-Sirna Complex. Cell Res. V. 35 453 2025.
ISSN: ISSN 1001-0602
PubMed: 40240484
DOI: 10.1038/S41422-025-01114-7