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Cadmium 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
Potassium (K) 5 atoms

Cadmium Binding Sites:

The binding sites of Cadmium 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 Cadmium atom.
In total 3 binding sites of Cadmium where determined in the K2P2.1(Trek-1)I110D:RU360 Bound Channel Structure, PDB code: 6v3c:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in 6v3c

Go back to Cadmium Binding Sites List in 6v3c
Cadmium binding site 1 out of 3 in the K2P2.1(Trek-1)I110D:RU360 Bound Channel Structure


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd 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:Cd402

b:0.2
occ:0.30
NE2 A:HIS313 2.9 0.1 1.0
OE1 A:GLU309 3.0 0.1 1.0
CD2 A:HIS313 3.6 0.2 1.0
CE1 A:HIS313 3.8 0.7 1.0
CD A:GLU309 4.0 0.8 1.0
OE2 A:GLU309 4.6 0.3 1.0
CG A:HIS313 4.7 0.8 1.0
ND1 A:HIS313 4.8 0.9 1.0
CG A:GLU309 4.9 0.2 1.0

Cadmium binding site 2 out of 3 in 6v3c

Go back to Cadmium Binding Sites List in 6v3c
Cadmium binding site 2 out of 3 in the K2P2.1(Trek-1)I110D:RU360 Bound Channel Structure


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd 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
B:Cd401

b:0.2
occ:0.50
OD2 B:ASP263 3.0 0.2 1.0
CE1 B:HIS126 3.0 0.1 1.0
NE2 B:HIS126 3.1 0.9 1.0
CG B:ASP263 4.0 0.3 1.0
OD1 B:ASP263 4.3 0.6 1.0
ND1 B:HIS126 4.3 0.1 1.0
CD2 B:HIS126 4.5 0.4 1.0

Cadmium binding site 3 out of 3 in 6v3c

Go back to Cadmium Binding Sites List in 6v3c
Cadmium binding site 3 out of 3 in the K2P2.1(Trek-1)I110D:RU360 Bound Channel Structure


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd 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
B:Cd402

b:0.1
occ:0.30
OE2 B:GLU309 2.7 0.7 1.0
CD B:GLU309 3.5 0.2 1.0
NE2 B:HIS313 3.8 0.3 1.0
CG B:GLU309 4.3 0.7 1.0
OE1 B:GLU309 4.3 0.4 1.0
CE1 B:HIS313 4.3 0.6 1.0
CD2 B:HIS313 4.8 0.4 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: Sat Dec 12 08:29:20 2020

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