Potassium in PDB 6v3c: K2P2.1(Trek-1)I110D:RU360 Bound Channel Structure
Protein crystallography data
The structure of K2P2.1(Trek-1)I110D:RU360 Bound Channel Structure, PDB code: 6v3c
was solved by
L.Pope,
M.Lolicato,
D.L.Minor,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
14.98 /
3.51
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
67.737,
120.708,
127.274,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
30.2 /
32.5
|
Other elements in 6v3c:
The structure of K2P2.1(Trek-1)I110D:RU360 Bound Channel Structure also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the K2P2.1(Trek-1)I110D:RU360 Bound Channel Structure
(pdb code 6v3c). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 5 binding sites of Potassium where determined in the
K2P2.1(Trek-1)I110D:RU360 Bound Channel Structure, PDB code: 6v3c:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
Potassium binding site 1 out
of 5 in 6v3c
Go back to
Potassium Binding Sites List in 6v3c
Potassium binding site 1 out
of 5 in the K2P2.1(Trek-1)I110D:RU360 Bound Channel Structure
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of K2P2.1(Trek-1)I110D:RU360 Bound Channel Structure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K403
b:0.3
occ:1.00
|
O
|
A:THR142
|
2.7
|
0.6
|
1.0
|
O
|
A:THR251
|
2.7
|
0.5
|
1.0
|
O
|
A:ILE252
|
2.8
|
0.7
|
1.0
|
O
|
B:THR142
|
2.8
|
0.1
|
1.0
|
O
|
B:THR251
|
2.9
|
0.9
|
1.0
|
O
|
A:ILE143
|
2.9
|
0.9
|
1.0
|
O
|
B:ILE252
|
2.9
|
1.0
|
1.0
|
K
|
A:K404
|
3.1
|
0.7
|
1.0
|
O
|
B:ILE143
|
3.2
|
0.6
|
1.0
|
C
|
A:ILE252
|
3.5
|
0.5
|
1.0
|
C
|
A:ILE143
|
3.6
|
0.6
|
1.0
|
C
|
A:THR251
|
3.6
|
0.1
|
1.0
|
C
|
B:ILE143
|
3.7
|
0.0
|
1.0
|
K
|
B:K403
|
3.7
|
0.7
|
1.0
|
C
|
B:ILE252
|
3.7
|
0.7
|
1.0
|
C
|
A:THR142
|
3.8
|
0.5
|
1.0
|
CA
|
A:ILE252
|
3.8
|
0.8
|
1.0
|
CA
|
A:ILE143
|
3.8
|
0.5
|
1.0
|
C
|
B:THR142
|
3.9
|
0.7
|
1.0
|
C
|
B:THR251
|
3.9
|
0.6
|
1.0
|
CA
|
B:ILE143
|
3.9
|
0.9
|
1.0
|
CA
|
B:ILE252
|
4.1
|
0.1
|
1.0
|
N
|
A:ILE252
|
4.1
|
0.9
|
1.0
|
N
|
A:ILE143
|
4.3
|
0.7
|
1.0
|
N
|
B:ILE143
|
4.4
|
0.8
|
1.0
|
N
|
B:ILE252
|
4.4
|
0.5
|
1.0
|
N
|
B:GLY144
|
4.6
|
0.6
|
1.0
|
N
|
A:GLY253
|
4.6
|
0.5
|
1.0
|
N
|
A:GLY144
|
4.7
|
0.1
|
1.0
|
CA
|
A:THR251
|
4.8
|
0.1
|
1.0
|
N
|
B:GLY253
|
4.8
|
0.1
|
1.0
|
CA
|
A:THR142
|
5.0
|
1.0
|
1.0
|
|
Potassium binding site 2 out
of 5 in 6v3c
Go back to
Potassium Binding Sites List in 6v3c
Potassium binding site 2 out
of 5 in the K2P2.1(Trek-1)I110D:RU360 Bound Channel Structure
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of K2P2.1(Trek-1)I110D:RU360 Bound Channel Structure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K404
b:0.7
occ:1.00
|
O
|
A:ILE252
|
2.7
|
0.7
|
1.0
|
O
|
B:GLY144
|
2.7
|
0.6
|
1.0
|
O
|
B:ILE252
|
2.7
|
1.0
|
1.0
|
O
|
A:ILE143
|
2.7
|
0.9
|
1.0
|
O
|
A:GLY253
|
2.7
|
0.9
|
1.0
|
O
|
B:GLY253
|
2.8
|
0.1
|
1.0
|
O
|
B:ILE143
|
2.8
|
0.6
|
1.0
|
O
|
A:GLY144
|
2.8
|
0.4
|
1.0
|
K
|
A:K403
|
3.1
|
0.3
|
1.0
|
K
|
B:K404
|
3.1
|
0.4
|
1.0
|
C
|
B:GLY144
|
3.5
|
0.6
|
1.0
|
C
|
A:GLY253
|
3.6
|
0.6
|
1.0
|
C
|
A:GLY144
|
3.7
|
0.1
|
1.0
|
C
|
B:GLY253
|
3.7
|
0.6
|
1.0
|
C
|
B:ILE143
|
3.9
|
0.0
|
1.0
|
C
|
A:ILE252
|
3.9
|
0.5
|
1.0
|
C
|
A:ILE143
|
3.9
|
0.6
|
1.0
|
C
|
B:ILE252
|
3.9
|
0.7
|
1.0
|
CA
|
B:GLY144
|
4.1
|
0.7
|
1.0
|
CA
|
A:GLY253
|
4.2
|
0.7
|
1.0
|
CA
|
B:GLY253
|
4.2
|
0.9
|
1.0
|
CA
|
A:GLY144
|
4.3
|
0.6
|
1.0
|
N
|
B:GLY144
|
4.4
|
0.6
|
1.0
|
N
|
B:PHE145
|
4.5
|
0.8
|
1.0
|
N
|
A:GLY253
|
4.5
|
0.5
|
1.0
|
N
|
A:GLY144
|
4.5
|
0.1
|
1.0
|
N
|
B:GLY253
|
4.5
|
0.1
|
1.0
|
N
|
A:PHE254
|
4.6
|
0.1
|
1.0
|
N
|
A:PHE145
|
4.6
|
0.5
|
1.0
|
N
|
B:PHE254
|
4.7
|
0.4
|
1.0
|
CA
|
B:PHE145
|
4.8
|
0.2
|
1.0
|
CA
|
A:PHE254
|
4.8
|
0.2
|
1.0
|
CA
|
A:PHE145
|
4.9
|
0.1
|
1.0
|
CA
|
B:PHE254
|
5.0
|
0.1
|
1.0
|
|
Potassium binding site 3 out
of 5 in 6v3c
Go back to
Potassium Binding Sites List in 6v3c
Potassium binding site 3 out
of 5 in the K2P2.1(Trek-1)I110D:RU360 Bound Channel Structure
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of K2P2.1(Trek-1)I110D:RU360 Bound Channel Structure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K405
b:0.1
occ:1.00
|
O
|
B:HOH501
|
3.3
|
0.9
|
1.0
|
O
|
A:HOH501
|
3.8
|
0.6
|
1.0
|
OG1
|
A:THR142
|
3.8
|
0.8
|
1.0
|
OG1
|
B:THR251
|
4.2
|
0.1
|
1.0
|
K
|
B:K403
|
4.4
|
0.7
|
1.0
|
OG1
|
A:THR251
|
4.6
|
0.2
|
1.0
|
CB
|
A:THR142
|
4.9
|
0.3
|
1.0
|
|
Potassium binding site 4 out
of 5 in 6v3c
Go back to
Potassium Binding Sites List in 6v3c
Potassium binding site 4 out
of 5 in the K2P2.1(Trek-1)I110D:RU360 Bound Channel Structure
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of K2P2.1(Trek-1)I110D:RU360 Bound Channel Structure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K403
b:0.7
occ:1.00
|
O
|
A:THR251
|
2.7
|
0.5
|
1.0
|
O
|
B:THR142
|
2.8
|
0.1
|
1.0
|
O
|
B:THR251
|
2.9
|
0.9
|
1.0
|
OG1
|
B:THR142
|
3.0
|
0.3
|
1.0
|
OG1
|
A:THR251
|
3.1
|
0.2
|
1.0
|
O
|
A:THR142
|
3.2
|
0.6
|
1.0
|
CB
|
A:THR251
|
3.3
|
0.2
|
1.0
|
CB
|
B:THR251
|
3.3
|
0.2
|
1.0
|
OG1
|
B:THR251
|
3.4
|
0.1
|
1.0
|
CB
|
B:THR142
|
3.4
|
0.1
|
1.0
|
OG1
|
A:THR142
|
3.5
|
0.8
|
1.0
|
C
|
A:THR251
|
3.7
|
0.1
|
1.0
|
K
|
A:K403
|
3.7
|
0.3
|
1.0
|
C
|
B:THR142
|
3.7
|
0.7
|
1.0
|
CB
|
A:THR142
|
3.9
|
0.3
|
1.0
|
C
|
B:THR251
|
3.9
|
0.6
|
1.0
|
CA
|
A:THR251
|
4.1
|
0.1
|
1.0
|
C
|
A:THR142
|
4.2
|
0.5
|
1.0
|
CA
|
B:THR251
|
4.2
|
0.9
|
1.0
|
CA
|
B:THR142
|
4.2
|
0.5
|
1.0
|
K
|
A:K405
|
4.4
|
0.1
|
1.0
|
CG2
|
B:THR251
|
4.4
|
0.5
|
1.0
|
CG2
|
A:THR251
|
4.5
|
0.2
|
1.0
|
CG2
|
B:THR142
|
4.7
|
0.2
|
1.0
|
CA
|
A:THR142
|
4.7
|
1.0
|
1.0
|
O
|
B:THR141
|
4.8
|
0.7
|
1.0
|
N
|
B:ILE143
|
4.8
|
0.8
|
1.0
|
N
|
A:ILE252
|
4.8
|
0.9
|
1.0
|
O
|
A:THR250
|
4.9
|
0.5
|
1.0
|
|
Potassium binding site 5 out
of 5 in 6v3c
Go back to
Potassium Binding Sites List in 6v3c
Potassium binding site 5 out
of 5 in the K2P2.1(Trek-1)I110D:RU360 Bound Channel Structure
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 5 of K2P2.1(Trek-1)I110D:RU360 Bound Channel Structure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K404
b:0.4
occ:1.00
|
O
|
A:PHE145
|
2.8
|
0.8
|
1.0
|
O
|
A:GLY144
|
2.9
|
0.4
|
1.0
|
O
|
B:PHE145
|
2.9
|
0.8
|
1.0
|
O
|
B:PHE254
|
2.9
|
0.9
|
1.0
|
O
|
A:PHE254
|
2.9
|
0.5
|
1.0
|
O
|
B:GLY253
|
2.9
|
0.1
|
1.0
|
O
|
B:GLY144
|
3.0
|
0.6
|
1.0
|
O
|
A:GLY253
|
3.0
|
0.9
|
1.0
|
K
|
A:K404
|
3.1
|
0.7
|
1.0
|
C
|
A:PHE145
|
3.3
|
1.0
|
1.0
|
C
|
B:PHE145
|
3.5
|
0.5
|
1.0
|
C
|
B:PHE254
|
3.5
|
0.4
|
1.0
|
C
|
A:PHE254
|
3.5
|
0.8
|
1.0
|
CA
|
B:PHE254
|
3.9
|
0.1
|
1.0
|
CA
|
A:PHE254
|
3.9
|
0.2
|
1.0
|
CA
|
A:PHE145
|
4.0
|
0.1
|
1.0
|
C
|
A:GLY144
|
4.0
|
0.1
|
1.0
|
N
|
A:GLY146
|
4.0
|
0.9
|
1.0
|
C
|
B:GLY253
|
4.0
|
0.6
|
1.0
|
CA
|
B:PHE145
|
4.1
|
0.2
|
1.0
|
C
|
A:GLY253
|
4.1
|
0.6
|
1.0
|
C
|
B:GLY144
|
4.1
|
0.6
|
1.0
|
N
|
B:GLY146
|
4.2
|
0.7
|
1.0
|
CA
|
A:GLY146
|
4.3
|
0.5
|
1.0
|
N
|
B:GLY255
|
4.4
|
0.5
|
1.0
|
N
|
A:GLY255
|
4.4
|
0.4
|
1.0
|
N
|
B:PHE254
|
4.5
|
0.4
|
1.0
|
N
|
A:PHE145
|
4.5
|
0.5
|
1.0
|
CA
|
B:GLY146
|
4.5
|
0.6
|
1.0
|
N
|
A:PHE254
|
4.5
|
0.1
|
1.0
|
N
|
B:PHE145
|
4.6
|
0.8
|
1.0
|
CA
|
B:GLY255
|
4.9
|
0.4
|
1.0
|
CA
|
A:GLY255
|
4.9
|
0.8
|
1.0
|
|
Reference:
L.Pope,
M.Lolicato,
D.L.Minor Jr..
Polynuclear Ruthenium Amines Inhibit K2PCHANNELS Via A "Finger in the Dam" Mechanism. Cell Chem Biol 2020.
ISSN: ESSN 2451-9456
PubMed: 32059793
DOI: 10.1016/J.CHEMBIOL.2020.01.011
Page generated: Mon Aug 12 17:54:04 2024
|