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Potassium in PDB 8qz3: Crystal Structure of Human Two Pore Domain Potassium Ion Channel Trek- 2 (K2P10.1) in Complex with An Activatory Nanobody (NB67)

Protein crystallography data

The structure of Crystal Structure of Human Two Pore Domain Potassium Ion Channel Trek- 2 (K2P10.1) in Complex with An Activatory Nanobody (NB67), PDB code: 8qz3 was solved by A.Baronina, A.C.W.Pike, K.E.J.Rodstrom, 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) 58.81 / 2.40
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.264, 102.1, 215.817, 90, 90, 90
R / Rfree (%) 27.8 / 29.1

Potassium Binding Sites:

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 An Activatory Nanobody (NB67) (pdb code 8qz3). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 5 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 An Activatory Nanobody (NB67), PDB code: 8qz3:
Jump to Potassium binding site number: 1; 2; 3; 4; 5;

Potassium binding site 1 out of 5 in 8qz3

Go back to Potassium Binding Sites List in 8qz3
Potassium binding site 1 out of 5 in the Crystal Structure of Human Two Pore Domain Potassium Ion Channel Trek- 2 (K2P10.1) in Complex with An Activatory Nanobody (NB67)


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 An Activatory Nanobody (NB67) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K401

b:55.8
occ:1.00
 O A:TYR175 2.7 29.2 1.0
O A:PHE284 3.2 32.6 1.0
O A:VAL144 3.6 47.8 1.0
O B:PHE284 3.6 31.9 1.0
K A:K402 3.7 50.8 1.0
C A:TYR175 3.9 29.3 1.0
C A:GLY176 3.9 30.2 1.0
CA A:GLY285 3.9 34.0 1.0
O A:GLY176 4.0 30.4 1.0
CA A:GLY176 4.0 30.0 1.0
O B:TYR175 4.0 36.7 1.0
CB A:VAL144 4.0 47.8 1.0
O A:HOH521 4.1 59.8 1.0
C A:PHE284 4.2 32.7 1.0
N A:ASN177 4.3 30.3 1.0
N A:GLY176 4.4 29.3 1.0
C A:GLY285 4.4 34.9 1.0
CG1 A:VAL144 4.5 48.4 1.0
C A:VAL144 4.5 47.7 1.0
N A:GLY285 4.5 33.1 1.0
O A:GLY285 4.6 35.2 1.0
CA A:VAL144 4.7 47.0 1.0
N A:VAL144 4.8 46.1 1.0
C B:PHE284 4.9 31.9 1.0
CG2 A:VAL144 4.9 48.3 1.0
CA B:GLY176 4.9 38.4 1.0
O B:GLY176 5.0 39.5 1.0

Potassium binding site 2 out of 5 in 8qz3

Go back to Potassium Binding Sites List in 8qz3
Potassium binding site 2 out of 5 in the Crystal Structure of Human Two Pore Domain Potassium Ion Channel Trek- 2 (K2P10.1) in Complex with An Activatory Nanobody (NB67)


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 An Activatory Nanobody (NB67) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K402

b:50.8
occ:1.00
 O A:TYR175 2.3 29.2 1.0
O A:GLY174 2.7 29.1 1.0
O B:PHE284 2.8 31.9 1.0
O B:TYR175 2.9 36.7 1.0
C A:TYR175 2.9 29.3 1.0
O A:PHE284 3.0 32.6 1.0
O A:GLY283 3.0 32.1 1.0
O B:GLY283 3.1 29.8 1.0
O B:GLY174 3.2 35.4 1.0
C B:PHE284 3.4 31.9 1.0
K B:K601 3.5 48.2 1.0
C A:PHE284 3.5 32.7 1.0
CA A:TYR175 3.6 29.3 1.0
C B:TYR175 3.6 36.6 1.0
K A:K401 3.7 55.8 1.0
N A:GLY176 3.7 29.3 1.0
C A:GLY174 3.7 29.0 1.0
CA B:PHE284 3.8 31.1 1.0
CA A:GLY176 4.1 30.0 1.0
CA A:PHE284 4.1 32.0 1.0
C A:GLY283 4.1 31.9 1.0
C B:GLY283 4.1 29.8 1.0
N A:TYR175 4.1 29.0 1.0
CA B:TYR175 4.3 35.8 1.0
N A:GLY285 4.3 33.1 1.0
C B:GLY174 4.3 35.3 1.0
N B:GLY285 4.4 32.5 1.0
N B:GLY176 4.4 37.2 1.0
N B:PHE284 4.5 30.2 1.0
N A:PHE284 4.6 31.7 1.0
CA A:GLY285 4.6 34.0 1.0
CA B:GLY176 4.7 38.4 1.0
N B:TYR175 4.8 35.3 1.0
CA B:GLY285 4.8 33.7 1.0
CB A:TYR175 5.0 29.4 1.0

Potassium binding site 3 out of 5 in 8qz3

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Potassium binding site 3 out of 5 in the Crystal Structure of Human Two Pore Domain Potassium Ion Channel Trek- 2 (K2P10.1) in Complex with An Activatory Nanobody (NB67)


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 An Activatory Nanobody (NB67) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K403

b:37.2
occ:1.00
 O A:THR172 2.5 27.1 1.0
O A:THR281 2.6 30.7 1.0
O B:THR172 2.7 33.6 1.0
O B:THR281 2.7 29.5 1.0
OG1 A:THR281 2.7 32.6 1.0
OG1 A:THR172 2.8 28.9 1.0
OG1 B:THR281 3.0 32.0 1.0
K B:K602 3.1 37.6 1.0
OG1 B:THR172 3.2 36.2 1.0
CB A:THR281 3.3 31.6 1.0
CB A:THR172 3.3 28.0 1.0
C A:THR172 3.4 26.9 1.0
CB B:THR281 3.5 30.8 1.0
C A:THR281 3.6 30.6 1.0
CB B:THR172 3.6 35.3 1.0
C B:THR281 3.7 29.3 1.0
C B:THR172 3.7 33.7 1.0
CA A:THR172 4.0 26.7 1.0
CA A:THR281 4.0 30.4 1.0
CA B:THR281 4.2 29.6 1.0
CA B:THR172 4.3 33.9 1.0
N A:ILE173 4.4 26.8 1.0
CG2 A:THR281 4.5 32.0 1.0
CG2 A:THR172 4.6 28.4 1.0
N A:VAL282 4.6 30.5 1.0
N B:VAL282 4.7 28.8 1.0
CG2 B:THR281 4.8 31.0 1.0
N B:ILE173 4.8 33.5 1.0
CA A:ILE173 4.8 27.3 1.0
CG2 B:THR172 4.9 35.7 1.0
O A:THR171 5.0 26.7 1.0

Potassium binding site 4 out of 5 in 8qz3

Go back to Potassium Binding Sites List in 8qz3
Potassium binding site 4 out of 5 in the Crystal Structure of Human Two Pore Domain Potassium Ion Channel Trek- 2 (K2P10.1) in Complex with An Activatory Nanobody (NB67)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of Human Two Pore Domain Potassium Ion Channel Trek- 2 (K2P10.1) in Complex with An Activatory Nanobody (NB67) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K601

b:48.2
occ:1.00
 O B:GLY174 2.4 35.4 1.0
O B:ILE173 2.4 34.1 1.0
O B:GLY283 2.6 29.8 1.0
O A:VAL282 2.7 31.3 1.0
O B:VAL282 2.7 29.1 1.0
K B:K602 2.8 37.6 1.0
O A:GLY174 2.9 29.1 1.0
O A:GLY283 2.9 32.1 1.0
O A:ILE173 3.0 27.9 1.0
C B:GLY174 3.2 35.3 1.0
K A:K402 3.5 50.8 1.0
C B:ILE173 3.5 34.1 1.0
C B:GLY283 3.5 29.8 1.0
CA B:GLY174 3.7 34.8 1.0
C A:GLY283 3.8 31.9 1.0
C A:GLY174 3.8 29.0 1.0
C B:VAL282 3.8 29.1 1.0
C A:VAL282 3.9 31.2 1.0
CA B:GLY283 4.0 29.3 1.0
N B:GLY174 4.0 34.2 1.0
C A:ILE173 4.1 27.8 1.0
N B:TYR175 4.2 35.3 1.0
CA A:GLY174 4.3 28.6 1.0
N B:GLY283 4.3 28.9 1.0
CA A:GLY283 4.3 31.6 1.0
N A:GLY283 4.5 31.2 1.0
N B:PHE284 4.6 30.2 1.0
CA B:TYR175 4.6 35.8 1.0
N A:GLY174 4.6 28.0 1.0
N A:PHE284 4.7 31.7 1.0
CA B:ILE173 4.8 33.8 1.0
N A:TYR175 4.8 29.0 1.0
O B:THR172 4.8 33.6 1.0
O B:THR281 4.8 29.5 1.0
O A:THR281 4.9 30.7 1.0
C B:TYR175 5.0 36.6 1.0
CA A:PHE284 5.0 32.0 1.0
CA B:PHE284 5.0 31.1 1.0
O A:THR172 5.0 27.1 1.0

Potassium binding site 5 out of 5 in 8qz3

Go back to Potassium Binding Sites List in 8qz3
Potassium binding site 5 out of 5 in the Crystal Structure of Human Two Pore Domain Potassium Ion Channel Trek- 2 (K2P10.1) in Complex with An Activatory Nanobody (NB67)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of Human Two Pore Domain Potassium Ion Channel Trek- 2 (K2P10.1) in Complex with An Activatory Nanobody (NB67) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K602

b:37.6
occ:1.00
 O B:THR281 2.5 29.5 1.0
O A:THR172 2.6 27.1 1.0
O B:THR172 2.7 33.6 1.0
O B:ILE173 2.7 34.1 1.0
O A:THR281 2.8 30.7 1.0
O B:VAL282 2.8 29.1 1.0
O A:ILE173 2.8 27.9 1.0
K B:K601 2.8 48.2 1.0
O A:VAL282 3.0 31.3 1.0
K A:K403 3.1 37.2 1.0
C B:ILE173 3.4 34.1 1.0
C B:VAL282 3.5 29.1 1.0
C A:ILE173 3.6 27.8 1.0
C B:THR281 3.6 29.3 1.0
C A:VAL282 3.8 31.2 1.0
C A:THR172 3.8 26.9 1.0
C B:THR172 3.8 33.7 1.0
CA B:ILE173 3.9 33.8 1.0
C A:THR281 3.9 30.6 1.0
CA B:VAL282 3.9 28.9 1.0
CA A:ILE173 4.1 27.3 1.0
CA A:VAL282 4.2 30.9 1.0
N B:VAL282 4.3 28.8 1.0
N B:ILE173 4.3 33.5 1.0
N A:ILE173 4.4 26.8 1.0
N B:GLY174 4.4 34.2 1.0
N B:GLY283 4.4 28.9 1.0
N A:GLY174 4.4 28.0 1.0
N A:VAL282 4.5 30.5 1.0
N A:GLY283 4.7 31.2 1.0
O B:GLY174 4.8 35.4 1.0
O A:GLY174 4.8 29.1 1.0
CA B:THR281 4.8 29.6 1.0
O B:GLY283 4.8 29.8 1.0
CA B:GLY174 4.8 34.8 1.0
CA A:GLY174 4.8 28.6 1.0
CA B:GLY283 4.9 29.3 1.0
CA A:THR172 4.9 26.7 1.0
CB B:THR281 5.0 30.8 1.0
O A:GLY283 5.0 32.1 1.0
CA B:THR172 5.0 33.9 1.0

Reference:

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
Page generated: Tue Aug 13 00:39:48 2024

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