Ruthenium in PDB 6v3i: K2P2.1(Trek-1)I110D:Rur Bound Channel Structure

The structure of K2P2.1(Trek-1)I110D:Rur Bound Channel Structure, PDB code: 6v3i 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)	15.00 / 3.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.945, 120.303, 127.818, 90.00, 90.00, 90.00
R / Rfree (%)	27.6 / 32.8

The structure of K2P2.1(Trek-1)I110D:Rur Bound Channel Structure also contains other interesting chemical elements:

Potassium	(K)	5 atoms
Cadmium	(Cd)	3 atoms

The binding sites of Ruthenium atom in the K2P2.1(Trek-1)I110D:Rur Bound Channel Structure (pdb code 6v3i). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 3 binding sites of Ruthenium where determined in the K2P2.1(Trek-1)I110D:Rur Bound Channel Structure, PDB code: 6v3i:
Jump to Ruthenium binding site number: 1; 2; 3;

Ruthenium binding site 1 out of 3 in the K2P2.1(Trek-1)I110D:Rur Bound Channel Structure


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of K2P2.1(Trek-1)I110D:Rur Bound Channel Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru401 b:0.9 occ:1.00 RU2 A:R2R401 0.0 0.9 1.0 O06 A:R2R401 1.7 0.7 1.0 O13 A:R2R401 1.7 0.6 1.0 N05 A:R2R401 1.8 0.9 1.0 N04 A:R2R401 1.8 0.8 1.0 N03 A:R2R401 1.8 0.2 1.0 N01 A:R2R401 1.8 0.0 1.0 RU1 A:R2R401 3.1 0.5 1.0 RU3 A:R2R401 3.1 0.9 1.0 N16 A:R2R401 3.1 0.1 1.0 N19 A:R2R401 3.1 1.0 1.0 N12 A:R2R401 3.1 0.4 1.0 N10 A:R2R401 3.4 0.3 1.0 OD1 A:ASP110 3.5 0.3 1.0 N11 A:R2R401 3.6 0.7 1.0 N18 A:R2R401 3.9 0.3 1.0 N15 A:R2R401 4.0 0.5 1.0 N08 A:R2R401 4.1 0.6 1.0 CG A:ASP110 4.2 0.4 1.0 OD1 B:ASP110 4.3 0.7 1.0 OD2 A:ASP110 4.3 0.1 1.0 N17 A:R2R401 4.7 0.1 1.0 N09 A:R2R401 4.8 0.4 1.0 O B:ASP110 5.0 0.2 1.0

Ruthenium binding site 2 out of 3 in the K2P2.1(Trek-1)I110D:Rur Bound Channel Structure


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of K2P2.1(Trek-1)I110D:Rur Bound Channel Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru401 b:0.9 occ:1.00 RU3 A:R2R401 0.0 0.9 1.0 O06 A:R2R401 1.8 0.7 1.0 N11 A:R2R401 1.8 0.7 1.0 N08 A:R2R401 1.8 0.6 1.0 N09 A:R2R401 1.8 0.4 1.0 N10 A:R2R401 1.8 0.3 1.0 N12 A:R2R401 1.8 0.4 1.0 N05 A:R2R401 3.0 0.9 1.0 RU2 A:R2R401 3.1 0.9 1.0 N03 A:R2R401 3.1 0.2 1.0 N01 A:R2R401 3.9 0.0 1.0 N04 A:R2R401 4.1 0.8 1.0 OD1 A:ASP110 4.2 0.3 1.0 OD2 B:ASP110 4.5 0.5 1.0 O13 A:R2R401 4.6 0.6 1.0 O A:ASP110 4.7 0.5 1.0 OD1 B:ASP110 4.8 0.7 1.0 CG A:ASP110 4.9 0.4 1.0

Ruthenium binding site 3 out of 3 in the K2P2.1(Trek-1)I110D:Rur Bound Channel Structure


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 3 of K2P2.1(Trek-1)I110D:Rur Bound Channel Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru401 b:0.5 occ:1.00 RU1 A:R2R401 0.0 0.5 1.0 O13 A:R2R401 1.7 0.6 1.0 N18 A:R2R401 1.8 0.3 1.0 N19 A:R2R401 1.8 1.0 1.0 N15 A:R2R401 1.8 0.5 1.0 N16 A:R2R401 1.8 0.1 1.0 N17 A:R2R401 1.8 0.1 1.0 RU2 A:R2R401 3.1 0.9 1.0 N01 A:R2R401 3.1 0.0 1.0 N05 A:R2R401 3.3 0.9 1.0 N04 A:R2R401 3.6 0.8 1.0 OD2 A:ASP110 3.9 0.1 1.0 N03 A:R2R401 4.0 0.2 1.0 OD1 A:ASP110 4.5 0.3 1.0 OD1 B:ASP110 4.6 0.7 1.0 CG A:ASP110 4.6 0.4 1.0 O06 A:R2R401 4.7 0.7 1.0 O B:ASP110 4.8 0.2 1.0

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