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Potassium in PDB 8qz2: Crystal Structure of Human Two Pore Domain Potassium Ion Channel Trek- 2 (K2P10.1) in Complex with An Inhibitory Nanobody (NB61)

Protein crystallography data

The structure of Crystal Structure of Human Two Pore Domain Potassium Ion Channel Trek- 2 (K2P10.1) in Complex with An Inhibitory Nanobody (NB61), PDB code: 8qz2 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) 52.10 / 3.50
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 56.538, 111.698, 289.208, 90, 90, 90
R / Rfree (%) 28 / 30.8

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 Inhibitory Nanobody (NB61) (pdb code 8qz2). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 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 Inhibitory Nanobody (NB61), PDB code: 8qz2:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 8qz2

Go back to Potassium Binding Sites List in 8qz2
Potassium binding site 1 out of 4 in the Crystal Structure of Human Two Pore Domain Potassium Ion Channel Trek- 2 (K2P10.1) in Complex with An Inhibitory Nanobody (NB61)


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 Inhibitory Nanobody (NB61) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K600

b:63.1
occ:1.00
 O B:TYR175 2.6 59.5 1.0
O A:TYR175 2.7 55.2 1.0
O B:PHE284 2.7 51.0 1.0
O A:GLY174 2.8 54.8 1.0
O A:PHE284 2.8 67.9 1.0
O A:GLY283 2.9 64.7 1.0
K B:K601 3.0 42.6 1.0
O B:GLY174 3.0 57.5 1.0
O B:GLY283 3.1 49.5 1.0
C B:TYR175 3.3 59.5 1.0
C A:TYR175 3.3 55.0 1.0
C B:PHE284 3.5 50.7 1.0
C A:PHE284 3.5 67.9 1.0
C A:GLY174 3.9 54.6 1.0
CA A:TYR175 4.0 54.6 1.0
CA A:PHE284 4.0 66.6 1.0
C A:GLY283 4.0 64.7 1.0
CA B:TYR175 4.0 58.5 1.0
N B:GLY176 4.0 60.2 1.0
CA B:PHE284 4.0 50.0 1.0
N A:GLY176 4.1 54.8 1.0
C B:GLY174 4.1 57.3 1.0
C B:GLY283 4.2 49.4 1.0
CA B:GLY176 4.2 61.6 1.0
CA A:GLY176 4.4 55.3 1.0
N B:GLY285 4.4 50.8 1.0
N A:TYR175 4.4 54.3 1.0
N A:GLY285 4.5 68.7 1.0
N A:PHE284 4.5 65.3 1.0
N B:TYR175 4.5 57.6 1.0
N B:PHE284 4.6 49.3 1.0
CA B:GLY285 4.8 51.5 1.0
CA A:GLY285 4.9 70.2 1.0

Potassium binding site 2 out of 4 in 8qz2

Go back to Potassium Binding Sites List in 8qz2
Potassium binding site 2 out of 4 in the Crystal Structure of Human Two Pore Domain Potassium Ion Channel Trek- 2 (K2P10.1) in Complex with An Inhibitory Nanobody (NB61)


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 Inhibitory Nanobody (NB61) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K601

b:42.6
occ:1.00
 O B:GLY174 2.3 57.5 1.0
O A:GLY174 2.3 54.8 1.0
O B:GLY283 2.4 49.5 1.0
O A:GLY283 2.5 64.7 1.0
O A:ILE173 2.7 54.9 1.0
O A:VAL282 2.9 62.3 1.0
K B:K600 3.0 63.1 1.0
O B:ILE173 3.0 55.5 1.0
O B:VAL282 3.0 48.9 1.0
K B:K602 3.3 24.4 1.0
C A:GLY174 3.3 54.6 1.0
C B:GLY174 3.4 57.3 1.0
C B:GLY283 3.5 49.4 1.0
C A:GLY283 3.5 64.7 1.0
C A:ILE173 3.8 54.7 1.0
CA A:GLY174 3.9 54.6 1.0
C A:VAL282 4.0 62.1 1.0
CA B:GLY174 4.1 56.6 1.0
CA A:GLY283 4.1 63.6 1.0
C B:ILE173 4.1 55.5 1.0
C B:VAL282 4.1 48.7 1.0
CA B:GLY283 4.1 49.1 1.0
N A:GLY174 4.3 54.3 1.0
N A:TYR175 4.4 54.3 1.0
N B:TYR175 4.4 57.6 1.0
N B:PHE284 4.5 49.3 1.0
N A:GLY283 4.5 62.6 1.0
N B:GLY174 4.5 55.8 1.0
N A:PHE284 4.5 65.3 1.0
N B:GLY283 4.6 48.7 1.0
CA B:TYR175 4.7 58.5 1.0
CA B:PHE284 4.7 50.0 1.0
O B:TYR175 4.7 59.5 1.0
CA A:TYR175 4.7 54.6 1.0
C B:TYR175 4.8 59.5 1.0
O B:PHE284 4.8 51.0 1.0
CA A:PHE284 4.8 66.6 1.0
C A:TYR175 4.9 55.0 1.0
O A:TYR175 4.9 55.2 1.0
C B:PHE284 5.0 50.7 1.0

Potassium binding site 3 out of 4 in 8qz2

Go back to Potassium Binding Sites List in 8qz2
Potassium binding site 3 out of 4 in the Crystal Structure of Human Two Pore Domain Potassium Ion Channel Trek- 2 (K2P10.1) in Complex with An Inhibitory Nanobody (NB61)


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 Inhibitory Nanobody (NB61) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K602

b:24.4
occ:1.00
 O B:ILE173 2.5 55.5 1.0
O A:THR172 2.7 54.7 1.0
O B:VAL282 2.7 48.9 1.0
O B:THR281 2.8 48.0 1.0
O A:THR281 2.8 60.0 1.0
O B:THR172 2.8 55.0 1.0
O A:ILE173 2.9 54.9 1.0
O A:VAL282 3.0 62.3 1.0
C B:ILE173 3.2 55.5 1.0
K B:K601 3.3 42.6 1.0
C B:VAL282 3.5 48.7 1.0
K B:K603 3.5 34.5 1.0
C A:ILE173 3.6 54.7 1.0
C A:VAL282 3.7 62.1 1.0
CA B:ILE173 3.8 55.0 1.0
C A:THR172 3.8 54.6 1.0
C B:THR172 3.8 55.0 1.0
C B:THR281 3.8 47.7 1.0
C A:THR281 3.9 60.0 1.0
CA B:VAL282 4.0 48.2 1.0
CA A:ILE173 4.0 54.5 1.0
CA A:VAL282 4.1 61.0 1.0
N B:GLY174 4.2 55.8 1.0
N B:ILE173 4.2 54.7 1.0
N B:GLY283 4.4 48.7 1.0
N B:VAL282 4.4 47.6 1.0
N A:ILE173 4.4 54.2 1.0
N A:VAL282 4.5 60.3 1.0
N A:GLY174 4.5 54.3 1.0
O B:GLY174 4.5 57.5 1.0
O B:GLY283 4.6 49.5 1.0
CA B:GLY174 4.6 56.6 1.0
N A:GLY283 4.7 62.6 1.0
CA B:GLY283 4.8 49.1 1.0
O A:GLY174 4.9 54.8 1.0
C B:GLY174 4.9 57.3 1.0
CA A:GLY174 5.0 54.6 1.0
CA A:THR172 5.0 54.6 1.0
O A:GLY283 5.0 64.7 1.0

Potassium binding site 4 out of 4 in 8qz2

Go back to Potassium Binding Sites List in 8qz2
Potassium binding site 4 out of 4 in the Crystal Structure of Human Two Pore Domain Potassium Ion Channel Trek- 2 (K2P10.1) in Complex with An Inhibitory Nanobody (NB61)


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 Inhibitory Nanobody (NB61) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K603

b:34.5
occ:1.00
 O B:THR172 2.4 55.0 1.0
OG1 B:THR172 2.7 57.5 1.0
O B:THR281 2.7 48.0 1.0
OG1 B:THR281 2.9 49.7 1.0
O A:THR281 3.0 60.0 1.0
OG1 A:THR281 3.0 61.6 1.0
O A:THR172 3.0 54.7 1.0
OG1 A:THR172 3.0 57.0 1.0
CB B:THR281 3.3 48.6 1.0
CB B:THR172 3.3 56.5 1.0
C B:THR172 3.4 55.0 1.0
K B:K602 3.5 24.4 1.0
C B:THR281 3.7 47.7 1.0
CB A:THR172 3.7 56.0 1.0
CB A:THR281 3.7 60.5 1.0
C A:THR281 4.0 60.0 1.0
CA B:THR172 4.0 55.0 1.0
C A:THR172 4.0 54.6 1.0
CA B:THR281 4.1 47.1 1.0
N B:ILE173 4.4 54.7 1.0
CA A:THR281 4.5 59.4 1.0
CA A:THR172 4.5 54.6 1.0
CG2 B:THR281 4.6 49.0 1.0
CG2 B:THR172 4.7 57.0 1.0
O B:THR171 4.7 54.7 1.0
CA B:ILE173 4.7 55.0 1.0
N B:VAL282 4.8 47.6 1.0
CG2 A:THR172 4.9 56.4 1.0
CG2 A:THR281 4.9 60.8 1.0
N A:VAL282 5.0 60.3 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 00:39:17 2024

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