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
|