Potassium in PDB 9de5: Structure of Full-Length Hiv Tar Rna Bound to Hiv Tat Rna-Binding Domain

The structure of Structure of Full-Length Hiv Tar Rna Bound to Hiv Tat Rna-Binding Domain, PDB code: 9de5 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)	47.09 / 2.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.872, 40.515, 120.406, 90, 94.61, 90
R / Rfree (%)	24.9 / 28.8

The binding sites of Potassium atom in the Structure of Full-Length Hiv Tar Rna Bound to Hiv Tat Rna-Binding Domain (pdb code 9de5). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Structure of Full-Length Hiv Tar Rna Bound to Hiv Tat Rna-Binding Domain, PDB code: 9de5:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in the Structure of Full-Length Hiv Tar Rna Bound to Hiv Tat Rna-Binding Domain


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure of Full-Length Hiv Tar Rna Bound to Hiv Tat Rna-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:K101 b:46.6 occ:1.00 O6 C:G52 2.9 49.2 1.0 O6 C:G53 3.0 40.5 1.0 O6 C:G54 3.1 38.9 1.0 O4 C:U8 3.3 38.5 1.0 C6 C:G52 3.5 43.9 1.0 N4 C:C7 3.5 34.3 1.0 O C:HOH202 3.7 30.9 1.0 C6 C:G54 4.0 37.0 1.0 C6 C:G53 4.0 41.7 1.0 C4 C:U8 4.1 36.9 1.0 N1 C:G52 4.2 41.0 1.0 N3 C:U8 4.2 37.7 1.0 C5 C:G52 4.2 43.2 1.0 N7 C:G53 4.2 41.9 1.0 C5 C:G53 4.5 40.7 1.0 N7 C:G52 4.6 45.9 1.0 C4 C:C7 4.6 33.5 1.0 N4 C:C9 4.7 36.4 1.0 N1 C:G54 4.8 36.3 1.0 C5 C:G54 4.8 36.1 1.0

Potassium binding site 2 out of 3 in the Structure of Full-Length Hiv Tar Rna Bound to Hiv Tat Rna-Binding Domain


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of Full-Length Hiv Tar Rna Bound to Hiv Tat Rna-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ E:K101 b:65.2 occ:1.00 O6 E:G53 3.1 57.4 1.0 O6 E:G54 3.1 54.7 1.0 O4 E:U8 3.2 54.6 1.0 O6 E:G52 3.4 60.0 1.0 N4 E:C7 3.5 54.5 1.0 C6 E:G54 4.2 53.8 1.0 C6 E:G52 4.2 59.1 1.0 C6 E:G53 4.2 58.0 1.0 C4 E:U8 4.2 55.2 1.0 N3 E:U8 4.5 53.4 1.0 C4 E:C7 4.6 52.7 1.0 N7 E:G53 4.7 58.1 1.0 N7 E:G52 4.7 66.4 1.0 C5 E:G52 4.7 60.9 1.0 N4 E:C9 4.8 57.2 1.0 C5 E:G53 4.8 57.6 1.0 N1 E:G54 4.9 52.4 1.0

Potassium binding site 3 out of 3 in the Structure of Full-Length Hiv Tar Rna Bound to Hiv Tat Rna-Binding Domain


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure of Full-Length Hiv Tar Rna Bound to Hiv Tat Rna-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:K101 b:61.9 occ:1.00 O6 D:G54 2.7 58.0 1.0 O6 D:G52 2.8 57.2 1.0 O6 D:G53 2.9 56.8 1.0 N3 D:C5 3.0 62.9 1.0 O4 D:U8 3.2 58.9 1.0 N4 D:C7 3.4 56.1 1.0 O2 D:C5 3.4 67.2 1.0 C6 D:G52 3.5 58.5 1.0 O D:HOH201 3.5 43.5 1.0 C2 D:C5 3.6 65.1 1.0 C6 D:G54 3.6 54.6 1.0 C6 D:G53 3.8 56.7 1.0 C4 D:C5 3.9 66.0 1.0 C4 D:U8 4.0 57.1 1.0 N3 D:U8 4.0 55.7 1.0 C5 D:G52 4.0 61.2 1.0 N7 D:G53 4.0 57.6 1.0 N4 D:C5 4.0 68.0 1.0 N7 D:G52 4.2 61.9 1.0 C5 D:G53 4.3 57.5 1.0 N1 D:G52 4.4 57.1 1.0 N1 D:G54 4.4 56.9 1.0 C5 D:G54 4.4 55.8 1.0 C4 D:C7 4.5 55.9 1.0 N4 D:C9 4.6 58.0 1.0 N7 D:G54 4.7 57.8 1.0 N1 D:C5 4.9 64.6 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