Magnesium in PDB 9k6s: Cryo-Em Structure of HAGO2D669A-Sirna-Target (19-Nt)

The binding sites of Magnesium atom in the Cryo-Em Structure of HAGO2D669A-Sirna-Target (19-Nt) (pdb code 9k6s). 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 (19-Nt), PDB code: 9k6s:

Magnesium binding site 1 out of 1 in the Cryo-Em Structure of HAGO2D669A-Sirna-Target (19-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 (19-Nt) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:30.0 occ:1.00 NE2 A:HIS807 2.7 35.0 1.0 OP1 C:G12 2.9 104.7 1.0 CD2 A:HIS807 3.0 30.7 1.0 P C:G12 3.8 108.9 1.0 OD1 A:ASP597 3.9 41.0 1.0 O3' C:A11 3.9 110.4 1.0 CE1 A:HIS807 3.9 29.7 1.0 CZ A:PHE811 4.1 39.6 1.0 CE1 A:PHE811 4.1 31.7 1.0 OG1 A:THR599 4.2 37.6 1.0 OD2 A:ASP597 4.3 37.0 1.0 OP2 C:G12 4.3 107.8 1.0 CG A:HIS807 4.4 32.7 1.0 CB A:THR599 4.5 27.1 1.0 CG A:ASP597 4.5 37.7 1.0 OP1 C:A11 4.5 110.6 1.0 ND1 A:HIS807 4.8 28.1 1.0 O A:VAL598 4.8 27.4 1.0 CA A:THR599 4.8 26.5 1.0 C5' C:A11 4.8 109.5 1.0 C3' C:A11 4.9 111.4 1.0 CE2 A:PHE811 4.9 31.8 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