Potassium in PDB 9gxh: Nanobody Bound to Tba G-Quadruplex

The structure of Nanobody Bound to Tba G-Quadruplex, PDB code: 9gxh was solved by S.Hadzi, M.Pevec, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.33 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	36.284, 59.331, 70.625, 90, 95.79, 90
R / Rfree (%)	15.4 / 19.9

The binding sites of Potassium atom in the Nanobody Bound to Tba G-Quadruplex (pdb code 9gxh). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Nanobody Bound to Tba G-Quadruplex, PDB code: 9gxh:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in the Nanobody Bound to Tba G-Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Nanobody Bound to Tba G-Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:K201 b:17.3 occ:1.00 N A:SER115 3.2 11.0 1.0 O A:HOH363 3.2 27.6 1.0 O A:HOH395 3.4 33.4 1.0 CA A:SER114 3.8 9.8 1.0 CB A:SER115 3.8 22.5 1.0 OG A:SER115 3.8 27.0 1.0 O A:HOH350 3.9 21.4 1.0 CB A:SER114 4.0 22.5 1.0 C A:SER114 4.0 14.3 1.0 CA A:SER115 4.1 19.8 1.0 OG A:SER114 4.3 21.3 1.0 O A:SER115 4.6 20.8 1.0 C A:SER115 4.8 26.3 1.0

Potassium binding site 2 out of 3 in the Nanobody Bound to Tba G-Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Nanobody Bound to Tba G-Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ C:K101 b:11.1 occ:1.00 O6 C:DG1 2.6 12.2 0.2 O6 C:DG15 2.6 11.8 1.0 O6 C:DG1 2.7 11.5 0.8 O6 C:DG5 2.7 12.2 1.0 O6 C:DG6 2.7 14.9 1.0 O6 C:DG10 2.8 13.7 1.0 O6 C:DG11 2.8 10.2 1.0 O6 C:DG14 2.8 10.4 1.0 O6 C:DG2 2.9 11.0 1.0 C6 C:DG5 3.5 10.4 1.0 C6 C:DG15 3.6 12.4 1.0 C6 C:DG1 3.6 12.8 0.8 C6 C:DG1 3.6 12.4 0.2 C6 C:DG14 3.6 10.9 1.0 C6 C:DG10 3.6 12.5 1.0 O C:HOH224 3.7 6.1 1.0 C6 C:DG6 3.7 17.3 1.0 C6 C:DG11 3.7 10.5 1.0 N1 C:DG15 3.8 13.8 1.0 N1 C:DG10 3.8 15.8 1.0 N1 C:DG5 3.8 10.2 1.0 N1 C:DG14 3.8 10.2 1.0 C6 C:DG2 3.9 10.7 1.0 N1 C:DG1 3.9 13.6 0.8 N1 C:DG1 3.9 13.3 0.2 N1 C:DG11 4.0 10.7 1.0 N1 C:DG6 4.0 15.3 1.0 N1 C:DG2 4.2 9.9 1.0 C7 C:DT9 4.7 15.2 1.0 C5 C:DG5 4.7 14.5 1.0 C5 C:DG14 4.8 10.5 1.0 C5 C:DG1 4.8 11.6 0.8 C5 C:DG1 4.9 12.5 0.2 C5 C:DG10 4.9 13.6 1.0 C5 C:DG15 4.9 14.7 1.0 C5 C:DG11 5.0 10.7 1.0

Potassium binding site 3 out of 3 in the Nanobody Bound to Tba G-Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Nanobody Bound to Tba G-Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ D:K101 b:6.2 occ:1.00 O6 D:DG1 2.6 7.4 0.7 O6 D:DG15 2.7 7.5 1.0 O6 D:DG10 2.7 7.3 1.0 O6 D:DG11 2.7 6.6 1.0 O6 D:DG5 2.7 5.5 1.0 O6 D:DG1 2.7 5.7 0.3 O6 D:DG6 2.8 7.5 1.0 O6 D:DG14 2.9 9.1 1.0 O6 D:DG2 3.0 6.0 1.0 C6 D:DG5 3.6 5.9 1.0 C6 D:DG10 3.6 7.0 1.0 C6 D:DG14 3.6 10.0 1.0 C6 D:DG1 3.6 7.8 0.3 C6 D:DG15 3.6 5.8 1.0 C6 D:DG1 3.6 7.5 0.7 C6 D:DG6 3.7 5.9 1.0 C6 D:DG11 3.7 8.6 1.0 O D:HOH225 3.7 5.2 1.0 N1 D:DG1 3.8 7.3 0.3 N1 D:DG14 3.8 8.5 1.0 N1 D:DG15 3.8 5.9 1.0 N1 D:DG5 3.9 6.2 1.0 N1 D:DG10 3.9 5.5 1.0 N1 D:DG6 3.9 5.7 1.0 C6 D:DG2 3.9 9.3 1.0 N1 D:DG11 4.1 8.3 1.0 N1 D:DG1 4.1 6.3 0.7 N1 D:DG2 4.2 6.2 1.0 C7 D:DT9 4.8 7.3 1.0 C5 D:DG5 4.8 6.3 1.0 C5 D:DG1 4.8 9.0 0.7 C5 D:DG10 4.8 6.4 1.0 C5 D:DG14 4.8 11.6 1.0 C5 D:DG1 4.9 8.2 0.3 C5 D:DG15 4.9 6.3 1.0 C5 D:DG11 5.0 5.1 1.0

M.Pevec, T.Medved, M.Kovacic, N.Zerjav, J.Imperl, J.Plavec, J.Lah, R.Loris, S.Hadzi. Structural Basis of G-Quadruplex Recognition By A Camelid Antibody Fragment. Nucleic Acids Res. V. 53 2025.
ISSN: ESSN 1362-4962
PubMed: 40433978
DOI: 10.1093/NAR/GKAF453