Magnesium in PDB 9de6: Structure of Full-Length Hiv Tar Rna

The structure of Structure of Full-Length Hiv Tar Rna, PDB code: 9de6 was solved by C.Bou-Nader, J.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.79 / 2.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.253, 41.982, 68.57, 90, 93.44, 90
R / Rfree (%)	26.4 / 28.3

The binding sites of Magnesium atom in the Structure of Full-Length Hiv Tar Rna (pdb code 9de6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Full-Length Hiv Tar Rna, PDB code: 9de6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Full-Length Hiv Tar Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Full-Length Hiv Tar Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:89.7 occ:1.00 O6 A:G53 2.5 86.5 1.0 O6 A:G52 2.7 91.8 1.0 O6 A:G54 2.9 87.8 1.0 N3 A:C5 3.0 104.1 1.0 O4 A:U8 3.2 88.0 1.0 C6 A:G52 3.3 89.3 1.0 N4 A:C7 3.5 89.8 1.0 C6 A:G53 3.5 86.7 1.0 N4 A:C5 3.5 98.3 1.0 C4 A:C5 3.6 102.9 1.0 C6 A:G54 3.7 86.2 1.0 C2 A:C5 3.8 104.6 1.0 N7 A:G53 3.9 89.8 1.0 N1 A:G52 3.9 87.9 1.0 C5 A:G53 4.0 87.8 1.0 O2 A:C5 4.1 106.5 1.0 C4 A:U8 4.1 87.2 1.0 C5 A:G52 4.1 89.7 1.0 N3 A:U8 4.1 87.7 1.0 N4 A:C9 4.4 88.3 1.0 C5 A:G54 4.4 85.9 1.0 N7 A:G52 4.5 91.4 1.0 N1 A:G54 4.5 85.9 1.0 C4 A:C7 4.6 87.7 1.0 N7 A:G54 4.6 87.4 1.0 N1 A:G53 4.7 88.5 1.0 C5 A:C5 4.8 105.4 1.0 N3 A:C7 4.9 87.0 1.0 N1 A:C5 5.0 124.8 1.0

Magnesium binding site 2 out of 2 in the Structure of Full-Length Hiv Tar Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Full-Length Hiv Tar Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:94.6 occ:1.00 O6 B:G11 2.4 95.1 1.0 O4 B:U10 2.7 90.9 1.0 O4 B:U50 2.9 95.7 1.0 N4 B:C49 3.5 95.1 1.0 C6 B:G11 3.6 96.1 1.0 C4 B:U10 3.7 91.0 1.0 N6 B:A51 3.8 93.4 1.0 C4 B:U50 3.8 96.2 1.0 N3 B:U50 4.0 95.5 1.0 O6 B:G12 4.0 97.0 1.0 C5 B:G11 4.4 95.1 1.0 N7 B:G11 4.4 94.5 1.0 C5 B:U10 4.5 90.0 1.0 N4 B:C9 4.5 86.0 1.0 N3 B:U10 4.5 91.6 1.0 N1 B:G11 4.6 97.0 1.0 C4 B:C49 4.7 96.5 1.0 C6 B:A51 4.7 94.8 1.0 C6 B:G12 4.7 96.2 1.0

C.Bou-Nader, K.A.Link, K.C.Suddala, J.R.Knutson, J.Zhang. Structures of Complete Hiv-1 Tar Rna Portray A Dynamic Platform Poised For Protein Binding and Structural Remodeling Nat Commun V. 16 2252 2025.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-025-57519-W