Potassium in PDB 8qz1: Crystal Structure of Human Two Pore Domain Potassium Ion Channel Trek- 2 (K2P10.1) in Complex with A Nanobody (NB58)

The structure of Crystal Structure of Human Two Pore Domain Potassium Ion Channel Trek- 2 (K2P10.1) in Complex with A Nanobody (NB58), PDB code: 8qz1 was solved by K.E.J.Rodstrom, A.C.W.Pike, A.Baronina, J.Ang, S.R.Bushell, R.Chalk, S.M.M.Mukhopadhyay, E.Pardon, C.H.Arrowsmith, A.M.Edwards, C.Bountra, N.A.Burgess-Brown, S.J.Tucker, J.Steyaert, E.P.Carpenter, Structuralgenomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.84 / 3.59
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	233.663, 233.663, 67.388, 90, 90, 120
R / Rfree (%)	25.6 / 29.8

The binding sites of Potassium atom in the Crystal Structure of Human Two Pore Domain Potassium Ion Channel Trek- 2 (K2P10.1) in Complex with A Nanobody (NB58) (pdb code 8qz1). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Crystal Structure of Human Two Pore Domain Potassium Ion Channel Trek- 2 (K2P10.1) in Complex with A Nanobody (NB58), PDB code: 8qz1:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in the Crystal Structure of Human Two Pore Domain Potassium Ion Channel Trek- 2 (K2P10.1) in Complex with A Nanobody (NB58)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Human Two Pore Domain Potassium Ion Channel Trek- 2 (K2P10.1) in Complex with A Nanobody (NB58) within 5.0Å range: probe atom residue distance (Å) B Occ A:K401 b:129.9 occ:1.00 O A:GLY283 2.2 141.8 1.0 O A:GLY174 2.2 135.6 1.0 O B:GLY283 2.2 125.2 1.0 O B:GLY174 2.5 137.2 1.0 O A:ILE173 2.8 135.0 1.0 O B:VAL282 2.9 123.1 1.0 O A:VAL282 2.9 139.8 1.0 C A:GLY283 3.1 141.5 1.0 O B:ILE173 3.2 136.2 1.0 C B:GLY283 3.2 124.9 1.0 C A:GLY174 3.2 135.2 1.0 C B:GLY174 3.6 136.8 1.0 K A:K402 3.6 134.6 1.0 CA A:GLY283 3.7 140.5 1.0 CA B:GLY283 3.8 123.9 1.0 C B:VAL282 3.9 122.8 1.0 C A:VAL282 3.9 139.4 1.0 C A:ILE173 3.9 134.9 1.0 CA A:GLY174 4.0 135.3 1.0 O A:TYR175 4.1 135.1 1.0 N A:TYR175 4.2 134.6 1.0 N B:PHE284 4.2 125.4 1.0 O B:TYR175 4.2 138.1 1.0 N A:PHE284 4.2 142.0 1.0 N A:GLY283 4.3 139.6 1.0 C B:ILE173 4.3 135.9 1.0 N B:GLY283 4.3 123.0 1.0 CA B:GLY174 4.4 136.5 1.0 CA A:TYR175 4.4 134.4 1.0 N A:GLY174 4.4 134.8 1.0 C A:TYR175 4.4 135.0 1.0 N B:TYR175 4.5 136.6 1.0 CA B:PHE284 4.6 126.2 1.0 C B:TYR175 4.6 138.0 1.0 CA A:PHE284 4.7 143.3 1.0 CA B:TYR175 4.7 137.0 1.0 N B:GLY174 4.8 136.0 1.0 C B:PHE284 5.0 127.8 1.0

Potassium binding site 2 out of 3 in the Crystal Structure of Human Two Pore Domain Potassium Ion Channel Trek- 2 (K2P10.1) in Complex with A Nanobody (NB58)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Human Two Pore Domain Potassium Ion Channel Trek- 2 (K2P10.1) in Complex with A Nanobody (NB58) within 5.0Å range: probe atom residue distance (Å) B Occ A:K402 b:134.6 occ:1.00 O A:THR281 2.4 137.8 1.0 O A:VAL282 2.6 139.8 1.0 O A:ILE173 2.6 135.0 1.0 O B:VAL282 2.6 123.1 1.0 O A:THR172 2.7 136.2 1.0 O B:THR281 2.8 122.4 1.0 O B:ILE173 2.8 136.2 1.0 O B:THR172 2.9 136.2 1.0 C A:VAL282 3.3 139.4 1.0 C B:VAL282 3.4 122.8 1.0 C A:ILE173 3.4 134.9 1.0 C A:THR281 3.5 137.5 1.0 C B:ILE173 3.6 135.9 1.0 K A:K401 3.6 129.9 1.0 K B:K401 3.6 152.1 1.0 C A:THR172 3.7 136.0 1.0 CA A:VAL282 3.8 138.4 1.0 CA A:ILE173 3.8 134.6 1.0 C B:THR281 3.8 122.2 1.0 CA B:VAL282 3.9 122.4 1.0 C B:THR172 3.9 136.2 1.0 CA B:ILE173 4.0 135.8 1.0 N A:VAL282 4.1 137.4 1.0 N A:GLY283 4.2 139.6 1.0 N A:ILE173 4.2 135.2 1.0 N B:VAL282 4.3 121.8 1.0 N B:GLY283 4.3 123.0 1.0 N B:ILE173 4.4 135.5 1.0 N A:GLY174 4.5 134.8 1.0 CA A:GLY283 4.6 140.5 1.0 N B:GLY174 4.6 136.0 1.0 CA A:THR281 4.7 136.9 1.0 CA B:GLY283 4.8 123.9 1.0 O A:GLY174 4.9 135.6 1.0 O B:GLY174 5.0 137.2 1.0 CA A:THR172 5.0 136.7 1.0 CB A:THR281 5.0 137.8 1.0 CA A:GLY174 5.0 135.3 1.0 O A:GLY283 5.0 141.8 1.0

Potassium binding site 3 out of 3 in the Crystal Structure of Human Two Pore Domain Potassium Ion Channel Trek- 2 (K2P10.1) in Complex with A Nanobody (NB58)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Human Two Pore Domain Potassium Ion Channel Trek- 2 (K2P10.1) in Complex with A Nanobody (NB58) within 5.0Å range: probe atom residue distance (Å) B Occ B:K401 b:152.1 occ:1.00 O B:THR281 2.6 122.4 1.0 O B:THR172 2.7 136.2 1.0 OG1 B:THR281 2.7 123.9 1.0 O A:THR172 2.9 136.2 1.0 OG1 B:THR172 2.9 138.4 1.0 OG1 A:THR281 2.9 138.7 1.0 OG1 A:THR172 3.0 138.9 1.0 O A:THR281 3.0 137.8 1.0 CB B:THR281 3.2 122.9 1.0 CB A:THR172 3.5 138.3 1.0 CB B:THR172 3.5 137.6 1.0 C B:THR281 3.5 122.2 1.0 CB A:THR281 3.6 137.8 1.0 K A:K402 3.6 134.6 1.0 C B:THR172 3.7 136.2 1.0 C A:THR172 3.9 136.0 1.0 C A:THR281 3.9 137.5 1.0 CA B:THR281 4.0 121.4 1.0 CA B:THR172 4.2 136.2 1.0 CA A:THR172 4.3 136.7 1.0 CA A:THR281 4.4 136.9 1.0 CG2 B:THR281 4.4 123.1 1.0 N B:VAL282 4.7 121.8 1.0 CG2 A:THR172 4.7 139.0 1.0 CG2 A:THR281 4.7 137.9 1.0 N B:ILE173 4.8 135.5 1.0 CG2 B:THR172 4.8 138.0 1.0 O B:THR171 4.8 136.8 1.0 O B:THR280 4.8 121.1 1.0 O A:THR280 5.0 137.8 1.0 N A:VAL282 5.0 137.4 1.0

K.E.J.Rodstrom, A.Cloake, J.Sormann, A.Baronina, K.H.M.Smith, A.C.W.Pike, J.Ang, P.Proks, M.Schewe, I.Holland-Kaye, S.R.Bushell, J.Elliott, E.Pardon, T.Baukrowitz, R.J.Owens, S.Newstead, J.Steyaert, E.P.Carpenter, S.J.Tucker. Extracellular Modulation of Trek-2 Activity with Nanobodies Provides Insight Into the Mechanisms of K2P Channel Regulation. Nat Commun V. 15 4173 2024.
ISSN: ESSN 2041-1723
PubMed: 38755204
DOI: 10.1038/S41467-024-48536-2