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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:

Ruthenium (Ru) 2 atoms
Cadmium (Cd) 3 atoms

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

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