Magnesium in PDB 9k6r: Cryo-Em Structure of HAGO2D669A-Sirna-Target (14-Nt, Uni-Lobed)

The binding sites of Magnesium atom in the Cryo-Em Structure of HAGO2D669A-Sirna-Target (14-Nt, Uni-Lobed) (pdb code 9k6r). 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 (14-Nt, Uni-Lobed), PDB code: 9k6r:

Magnesium binding site 1 out of 1 in the Cryo-Em Structure of HAGO2D669A-Sirna-Target (14-Nt, Uni-Lobed)


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 (14-Nt, Uni-Lobed) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:30.0 occ:1.00 ND1 A:HIS807 2.4 12.6 1.0 OD2 A:ASP597 2.8 9.2 1.0 CE1 A:HIS807 2.8 9.9 1.0 OP2 C:G5 2.9 98.8 1.0 CG A:HIS807 3.5 10.4 1.0 OP1 C:A4 3.7 106.0 1.0 NE2 A:HIS807 4.0 4.4 1.0 CG A:ASP597 4.0 11.0 1.0 CE1 A:PHE811 4.0 13.8 1.0 CB A:HIS807 4.2 6.4 1.0 P C:G5 4.3 101.0 1.0 CD2 A:HIS807 4.3 7.8 1.0 OD1 A:ASP597 4.5 14.7 1.0 CA A:HIS807 4.5 0.0 1.0 CD1 A:PHE811 4.6 11.2 1.0 OG1 A:THR599 4.6 26.8 1.0 CB A:THR599 4.6 18.7 1.0 OP1 C:G5 4.7 99.5 1.0 CZ A:PHE811 4.8 19.1 1.0 O A:HIS807 5.0 8.7 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